1
|
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.
Collapse
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.)
| |
Collapse
|
2
|
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.
Collapse
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
| | | | | | | |
Collapse
|
3
|
Abstract
We isolated a 918 bp long full-length rice HMGB1 cDNA, which has an open reading frame of 471 bp encoding 157 amino acids, with a central domain of high sequence similarity to the HMG-box domain of other plant HMGB1 proteins. RNA gel blot analysis indicated that rice HMGB1 gene is constitutively expressed in various tissues and organs. Southern hybridization and sequence analyses suggested that a single copy of the HMGB1 gene composed of seven exons and six introns exists in rice. We have also cloned a 1755 bp long 5' flanking region of the rice HMGB1 gene, which can be regarded as its promoter. 5' deletion analysis of this promoter indicated that positive cis-elements residing between -1400 and -1115 are important to enhance quantitative expression, whereas negative cis-elements between -1755 and -1400 and between -1115 and -351 inhibit expression.
Collapse
MESH Headings
- 5' Flanking Region/genetics
- Amino Acid Sequence
- Base Sequence
- Cloning, Molecular
- DNA, Complementary/chemistry
- DNA, Complementary/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- Exons
- Gene Expression Regulation, Plant
- Glucuronidase/genetics
- Glucuronidase/metabolism
- HMGB1 Protein/genetics
- Introns
- Molecular Sequence Data
- Oryza/genetics
- Plant Proteins/genetics
- Promoter Regions, Genetic/genetics
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Recombinant Fusion Proteins/genetics
- Recombinant Fusion Proteins/metabolism
- Sequence Alignment
- Sequence Analysis, DNA
- Sequence Homology, Amino Acid
Collapse
Affiliation(s)
- Qiang Wu
- Department of Biological Sciences, National University of Singapore, 10 Science Drive 4, Singapore 117543, Singapore
| | | | | | | |
Collapse
|
4
|
Pandey S, Tiwari SB, Tyagi W, Reddy MK, Upadhyaya KC, Sopory SK. A Ca2+/CaM-dependent kinase from pea is stress regulated and in vitro phosphorylates a protein that binds to AtCaM5 promoter. EUROPEAN JOURNAL OF BIOCHEMISTRY 2002; 269:3193-204. [PMID: 12084059 DOI: 10.1046/j.1432-1033.2002.02994.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
An immuno-homologue of maize Ca2+/calmodulin (CaM)-dependent protein kinase with a molecular mass of 72 kDa was identified in pea. The pea kinase (PsCCaMK) was upregulated in roots in response to low temperature and increased salinity. Exogenous Ca2+ application increased the kinase level and the response was faster than that obtained following stress application. Low temperature-mediated, but not salinity-mediated stress kinase increase was inhibited by the application of EGTA and W7, a CaM inhibitor. The purification of PsCCaMK using immuno-affinity chromatography resulted in coelution of the kinase with another polypeptide of molecular mass 40 kDa (p40). Western blot revealed the presence of PsCCaMK in nuclear protein extracts and was found to phosphorylate p40 in vitro. Gel mobility shift and South-Western analysis showed that p40 is a DNA-binding protein and it interacted specifically with one of the cis acting elements of the Arabidopsis CaM5 gene (AtCaM5) promoter. The binding of p40 to the specific elements in the AtCaM5 promoter was dependent of its dephosphorylated state. Our results suggest that p40 could be an upstream signal component of the stress responses.
Collapse
Affiliation(s)
- Sona Pandey
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
| | | | | | | | | | | |
Collapse
|
5
|
Fleck O, Kunz C, Rudolph C, Kohli J. The high mobility group domain protein Cmb1 of Schizosaccharomyces pombe binds to cytosines in base mismatches and opposite chemically altered guanines. J Biol Chem 1998; 273:30398-405. [PMID: 9804804 DOI: 10.1074/jbc.273.46.30398] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The mismatch-binding activity Cmb1 of Schizosaccharomyces pombe was enriched from wild type cells, and N-terminal sequencing enabled cloning of the respective gene. The deduced amino acid sequence of cmb1(+) contains a high mobility group domain, a motif that is common to a heterogeneous family of DNA-binding proteins. In crude protein extracts of a cmb1 gene-disruption strain, specific binding to C/T, C/A, and C/Delta was abolished. Weak binding to C/C revealed the presence of a second mismatch-binding activity, Cmb2. Cmb1, enriched from S. pombe and purified from Escherichia coli, bound specifically to C/C, C/T, C/A, T/T, and C/Delta but showed little or no affinity to other mismatches and small loops. Cmb1 recognizes 1,2 GpG intrastrand cross-links, produced by the chemotherapeutic drug cisplatin, when two cytosines are opposite the cross-linked guanines but not when other bases are present. Consistently, O6-methylguanine:C but not O6-methylguanine/T lesions were bound. Thus, cytosines in mismatches and opposite chemically modified guanines are the preferred target of Cmb1 recognition. cmb1 mutant cells are more sensitive to cisplatin than wild type cells, indicating a role of Cmb1 in repair of cisplatin-induced DNA damage.
Collapse
Affiliation(s)
- O Fleck
- Institute of General Microbiology, University of Bern, Baltzer-Strasse 4, CH-3012 Bern, Switzerland.
| | | | | | | |
Collapse
|
6
|
O'Neill SD, Zheng CC. Abundance of mRNAs encoding HMG1/HMG2 class high-mobility-group DNA-binding proteins are differentially regulated in cotyledons of Pharbitis nil. PLANT MOLECULAR BIOLOGY 1998; 37:235-241. [PMID: 9617797 DOI: 10.1023/a:1005948406131] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The abundance of an mRNA encoding an HMG 1/2 protein from Pharbitis nil (HMG1) has been previously shown to be regulated by light and an endogenous rhythm in cotyledons. A second Pharbitis nil HMG cDNA (HMG2) was characterized. The sequence of HMG2 was 82% and 86% identical to HMG1 at the nucleotide and amino acid level, respectively. As with HMG1, HMG2 mRNA was detected in all vegetative tissues and was most abundant in roots. However, unlike HMG1, HMG2 mRNA abundance did not increase upon transfer of cotyledons to darkness and did not exhibit regulation by an endogenous circadian rhythm when maintained in continuous darkness over a 68 h period. Similarly, while the abundance of HMG1 mRNA during a dark period that induced photoperiodically controlled flowering was dramatically affected by brief light exposure (night break), this treatment had no effect on HMG2 mRNA abundance. Collectively, these data are consistent with a role of HMG1 in contributing to the circadian-regulated and/or dark-regulated gene expression with constitutive expression of HMG2 playing a housekeeping role in the general regulation of gene expression in Pharbitis nil cotyledons.
Collapse
Affiliation(s)
- S D O'Neill
- Division of Biological Sciences, University of California at Davis, 95616, USA
| | | |
Collapse
|
7
|
Yamamoto S, Minamikawa T. Isolation and characterization of a cDNA encoding a high mobility group protein HMG-1 from Canavalia gladiata D.C. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1396:47-50. [PMID: 9524219 DOI: 10.1016/s0167-4781(97)00226-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A cDNA clone encoding a HMG-1 protein from maturing seeds of Canavalia gladiata was isolated and characterized with respect to its sequence, genomic organization and the expression pattern in seeds. The predicted polypeptide had the characteristic conserved motifs of the HMG-1/2 protein including N-terminal basic region, one HMG-box and polyacidic carboxy terminus. Southern blot analysis suggested that the HMG-1 gene is a single copy gene. Northern blot analysis indicated that the HMG-1 gene was expressed both in maturing and germinated seeds.
Collapse
Affiliation(s)
- S Yamamoto
- Department of Biology, Tokyo Metropolitan University, Japan
| | | |
Collapse
|
8
|
Grasser KD, Grimm R, Igloi GL. Purification and cDNA cloning of maize HMGd reveal a novel plant chromosomal HMG-box protein with sequence similarity to HMGa. Gene X 1997; 190:303-7. [PMID: 9197548 DOI: 10.1016/s0378-1119(97)00017-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
We have purified the chromosomal high mobility group (HMG) protein HMGd from maize suspension culture cells, determined the N-terminal amino acid (aa) sequence, and isolated the corresponding cDNA. Sequence analysis showed that the cDNA encoded a protein of 126 aa residues with a theoretical mass of 14,104 Da. The protein contains an HMG-box DNA-binding domain and a short acidic C-terminal tail. HMGd is in approx. 65% of its residues identical to maize HMGa, whereas it is only approx. 46% identical to maize HMGcl/2. The differences to the previously reported HMG proteins in aa sequence, in overall charge and in protein size indicate that we have identified a third type of plant chromosomal HMG-box protein belonging to the HMG1 protein family. Immunoblot analysis with a HMGd antiserum reveals that HMGd is expressed in all tissues tested.
Collapse
Affiliation(s)
- K D Grasser
- Institut für Biologie III, Albert-Ludwigs-Universität Freiburg, Germany.
| | | | | |
Collapse
|
9
|
Grasser KD, Grimm R, Ritt C. Maize chromosomal HMGc. Two closely related structure-specific DNA-binding proteins specify a second type of plant high mobility group box protein. J Biol Chem 1996; 271:32900-6. [PMID: 8955131 DOI: 10.1074/jbc.271.51.32900] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The chromosomal high mobility group (HMG) proteins are small and abundant non-histone proteins common to eukaryotes. We have purified the maize HMGc protein from immature kernels and characterized it by mass spectrometry and amino acid sequence analysis. HMGc could be resolved into two similar proteins by reversed phase chromatography. Cloning and characterization of the corresponding cDNAs revealed that they encode two closely related maize HMGc proteins, now termed HMGc1 and HMGc2. Their theoretical masses of 15,316 and 15,007 Da are >300 Da lower than the masses determined for the proteins purified from maize, indicating post-translational modifications of the proteins. Despite sequence similarity to maize HMGa (and previously described homologous proteins of other species) amino acid sequence alignments reveal that HMGc is in several conserved regions distinct from these proteins. Consequently, we have identified a novel type of plant protein containing an HMG box DNA binding domain and belonging to the HMG1 protein family. HMGc1 and HMGc2 were expressed in Escherichia coli, purified to homogeneity, and analyzed for their DNA binding properties. They proved to bind to DNA structure-specifically since they formed complexes with DNA minicircles at concentrations approximately 100-fold lower than the concentrations required to form complexes with linear fragments of identical sequence. Furthermore, HMGc1 and HMGc2 can constrain negative superhelical turns in plasmid DNA.
Collapse
Affiliation(s)
- K D Grasser
- Institut für Biologie III, Albert-Ludwigs-Universität Freiburg, Schänzlestrasse 1, D-79104 Freiburg, Federal Republic of Germany.
| | | | | |
Collapse
|
10
|
de Froidmont D, Lejour C, Stoeva P, Jacquemin JM. Endosperm Box Binding Proteins: cDNA Cloning of a Wheat HMG Protein. BIOTECHNOL BIOTEC EQ 1996. [DOI: 10.1080/13102818.1996.10818875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
|
11
|
Stros M, Retief JD, Dixon GH. cDNA sequence and structure of a trout HMG-2 gene. Evidence for a trout-specific 3'-untranslated region. Gene 1995; 158:181-7. [PMID: 7607539 DOI: 10.1016/0378-1119(95)00098-q] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A complete cDNA sequence (1026 bp) and a partial structure of a gene encoding the trout testis chromosomal HMG (high mobility group) 2 protein (HMG-T2) is presented. The deduced protein consists of 214 amino acids and shares over 80% similarity to the trout HMG-1 protein (HMG-T1) as well as to the mammalian or avian HMG-2 proteins. Northern blot analysis revealed two transcripts, a major one of 1.2 kb and a minor one of 1.6 kb. Southern analysis and polymerase chain reaction of trout genomic DNA indicated that the HMG-T2 gene is encoded by several introncontaining genes. The 5'-UTR (untranslated region) of the HMG-T2 is interrupted by an intron and the coding region of the HMG-T2 is divided into four exons by three relatively short introns (173, 91 and 78 bp). The exon/intron boundaries of trout HMG-2 are identical to those of human HMG-2, as reported earlier [Shirakawa and Yoshida, J. Biol. Chem. 267 (1992) 6641-6645], suggesting the evolution of the HMG-1/2 family genes from a common ancestor. Phylogenetic analysis indicated that the common ancestor of trout HMG-1/2 genes very likely diverged from the ancestor of the mammalian (or avian) HMG-1/2 genes before its separation into two distinct mammalian or (avian) HMG-1 and HMG-2 genes. Sequence comparisons of the 3'UTR of trout HMG-2 cDNA with the corresponding regions in the mammalian (or avian) HMG-2 revealed that the trout 3'-UTR was clearly distinct from the 3'-UTR of the mammalian or avian HMG-2 cDNAs which were otherwise remarkably well conserved.(ABSTRACT TRUNCATED AT 250 WORDS)
Collapse
Affiliation(s)
- M Stros
- Department of Biochemistry, University of Calgary, Alberta, Canada
| | | | | |
Collapse
|
12
|
Baxevanis AD, Landsman D. The HMG-1 box protein family: classification and functional relationships. Nucleic Acids Res 1995; 23:1604-13. [PMID: 7784217 PMCID: PMC306904 DOI: 10.1093/nar/23.9.1604] [Citation(s) in RCA: 154] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The abundant and highly-conserved nucleoproteins comprising the high mobility group-1/2 (HMG-1/2) family contains two homologous basic domains of about 75 amino acids. These basic domains, termed HMG-1 boxes, are highly structured and facilitate HMG-DNA interactions. Many proteins that regulate various cellular functions involving DNA binding and whose target DNA sequences share common structural characteristics have been identified as having an HMG-1 box; these proteins include the RNA polymerase I transcription factor UBF, the mammalian testis-determining factor SRY and the mitochondrial transcription factors ABF2 and mtTF1, among others. The sequences of 121 HMG-1 boxes have been compiled and aligned in accordance with thermodynamic results from homology model building (threading) experiments, basing the alignment on structure rather than by using traditional sequence homology methods. The classification of a representative subset of these proteins was then determined using standard least-squares distance methods. The proteins segregate into two groups, the first consisting of HMG-1/2 proteins and the second consisting of proteins containing the HMG-1 box but which are not canonical HMG proteins. The proteins in the second group further segregate based on their function, their ability to bind specific sequences of DNA, or their ability to recognize discrete non-B-DNA structures. The HMG-1 box provides an excellent example of how a specific protein motif, with slight alteration, can be used to recognize DNA in a variety of functional contexts.
Collapse
Affiliation(s)
- A D Baxevanis
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | | |
Collapse
|
13
|
|
14
|
Pwee KH, Webster CI, Gray JC. HMG protein binding to an A/T-rich positive regulatory region of the pea plastocyanin gene promoter. PLANT MOLECULAR BIOLOGY 1994; 26:1907-20. [PMID: 7858226 DOI: 10.1007/bf00019502] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Gel retardation assays using pea nuclear extracts have detected specific binding to regions of the promoter of the pea plastocyanin gene (petE). Several complexes which differ in sensitivity to competition with unlabelled promoter fragments and various DNA alternating copolymers, to heat treatment and to digestion with proteinase K have been detected. A protein factor, PCF1, forming one of these complexes was heat-stable and most sensitive to competition with poly(dAdT).poly(dAdT) compared to other alternating copolymers. DNase I footprinting assays showed that tracts of A/T-rich sequence within the -444 to -177 positive regulatory region of the petE promoter were protected in the presence of the pea nuclear extract. The factor PCF1 copurified with a high-mobility-group (HMG) protein preparation from pea chromatin. DNase I footprinting with the HMG protein preparation demonstrated that similar tracts of A/T-rich sequences within the promoter were protected. Southwestern-blot analysis of pea HMG proteins purified by gel filtration through Superose 12 detected a single DNA-binding species of 21 kDa. The properties of the factor PCF1 suggest that it is likely to be an HMG I protein.
Collapse
Affiliation(s)
- K H Pwee
- Department of Plant Sciences, University of Cambridge, UK
| | | | | |
Collapse
|
15
|
Forde BG. AT-rich elements (ATREs) in the promoter regions of nodulin and other higher plant genes: a novel class of cis-acting regulatory element? Results Probl Cell Differ 1994; 20:87-103. [PMID: 8036322 DOI: 10.1007/978-3-540-48037-2_4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- B G Forde
- Biochemistry and Physiology Department, Rothamsted Experimental Station, Institute of Arable Crops Research, Harpenden, Herts, UK
| |
Collapse
|
16
|
Habu Y, Sakata Y, Fukasawa K, Ohno T. Ubiquitous nuclear proteins bind to 5' upstream region of major Kunitz chymotrypsin inhibitor gene in winged bean. PLANT MOLECULAR BIOLOGY 1993; 23:1139-1150. [PMID: 8292779 DOI: 10.1007/bf00042348] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Winged bean Kunitz chymotrypsin inhibitor (WCI) accumulates abundantly in seeds and tuberous roots of winged bean plant. In seeds, the WCI mRNA is observed transiently during seed maturation period. The WCI is encoded by a multigene family and the major WCI (WCI-3) is encoded by two nearly identical genes (WCI-3a and WCI-3b genes), in which nucleotide sequences in the 1.1 kb 5' flanking regions are about 99% homologous to each other and the transcribed regions are completely identical. Here we report the detection of two types of nuclear proteins which bind to the multiple sites in the 5' upstream region of the WCI-3a gene. One of the proteins, band 1-forming protein, also bound to cauliflower mosaic virus 35S (CaMV35S) promoter, but another protein, band 3-forming protein, did not. DNaseI footprinting analysis showed that these proteins bound to AT-rich upstream regions in the WCI-3a gene. Addition of poly(dA-dT)-poly(dA-dT) to the binding reaction inhibited the formation of the retarded bands, while poly(dI-dC)-poly(dI-dC) did not. In various organs and throughout seed maturation period, proteins with invariable binding specificities were detected, and these binding proteins met some operational criteria for high-mobility-group (HMG) proteins. These results suggest that leguminous seed AT-binding proteins reported on several seed storage protein genes may be HMG-like proteins which are present ubiquitously in plant organs.
Collapse
Affiliation(s)
- Y Habu
- Department of Applied Bioscience, Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | | | | | | |
Collapse
|
17
|
Grasser KD, Wohlfarth T, Bäumlein H, Feix G. Comparative analysis of chromosomal HMG proteins from monocotyledons and dicotyledons. PLANT MOLECULAR BIOLOGY 1993; 23:619-625. [PMID: 8219095 DOI: 10.1007/bf00019309] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Chromosomal high-mobility-group (HMG) proteins occur ubiquitously in eukaryotes and their common structural and biochemical features indicate a critical role. In this context, we compared structural and functional aspects of HMG proteins from the monocotyledonous plant maize and the dicotyledonous plant Vicia faba. Besides biochemical similarities and immunological differences found between these proteins, the isolation and characterization of a cDNA encoding the V. faba homologue of the maize HMGa protein revealed great similarities between these two proteins, including the HMG-box DNA-binding motif and an acidic domain. Therefore, like the maize HMGa protein, the V. faba HMG protein belongs to the vertebrate HMG1 family, which consists of HMG proteins and transcription factors of various eukaryotes.
Collapse
Affiliation(s)
- K D Grasser
- Institut für Biologie III, Albert-Ludwigs-Universität Freiburg, Germany
| | | | | | | |
Collapse
|
18
|
Zheng CC, Bui AQ, O'Neill SD. Abundance of an mRNA encoding a high mobility group DNA-binding protein is regulated by light and an endogenous rhythm. PLANT MOLECULAR BIOLOGY 1993; 23:813-823. [PMID: 8251634 DOI: 10.1007/bf00021536] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A cDNA clone encoding an HMG1 protein from Pharbitis nil was characterized with regard to its sequence, genomic organization and regulation in response to photoperiodic treatments that control floral induction. The HMG1 cDNA contains an open reading frame of 432 nucleotides encoding a 144 amino acid protein of approximately 16 kDa. The predicted polypeptide has the characteristic conserved motifs of the HMG1 and HMG2 class of proteins including an N-terminal basic region, one of two HMG-box domains, and a polyacidic carboxy terminus. Within the HMG-box region, Pharbitis HMG1 deduced amino acid sequence shares 47%, 67% and 69% identity with its animal, maize, and soybean counterparts, respectively. Southern blot hybridization analysis suggests that HMG1 is a member of a multigene family. Analysis of mRNA abundance indicates that the HMG1 gene is expressed to higher levels in dark-grown tissue, such as roots, and at lower levels in light-grown tissue, such as cotyledons and stems. Following the transition to darkness, the levels of HMG1 mRNA in cotyledons were initially stable, however, after a lag time of 8 h or more, HMG1 mRNA increased in abundance to a peak level at 20 h. A second peak in mRNA levels was observed about 24 h later, indicating that the expression of the HMG1 gene is regulated by an endogenous circadian rhythm. Abundance of the HMG1 mRNA during a dark period was dramatically affected by brief light exposure (night break), a treatment which inhibits floral induction. These data indicate that the expression of HMG1 is regulated by both an endogenous rhythm and the light/dark cycle and are consistent with a role for HMG1 in maintaining patterns of circadian-regulated gene expression activated upon the transition from light to darkness.
Collapse
Affiliation(s)
- C C Zheng
- Division of Biological Sciences, University of California at Davis 95616
| | | | | |
Collapse
|
19
|
Griess EA, Rensing SA, Grasser KD, Maier UG, Feix G. Phylogenetic relationships of HMG box DNA-binding domains. J Mol Evol 1993; 37:204-10. [PMID: 8411210 DOI: 10.1007/bf02407357] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
HMG boxes were initially identified as DNA-binding domains of the human RNA polymerase I (pol I) transcription factor hUBF and the animal high-mobility-group (HMG) protein family HMG1. Since then, numerous sequences of HMG-box-containing HMG proteins and other DNA-binding proteins from several species have become available. By sequence comparisons of a selected range of HMG boxes from these proteins and the construction of phylogenetic trees we show that the HMG box is highly conserved between DNA-binding proteins of organisms from all three eukaryotic kingdoms and that HMG boxes are linked by distinct evolutionary relationships. In addition, most HMG boxes display comparable hydropathy profiles and amino acid arrangements, which could serve as nuclear targeting sequences.
Collapse
Affiliation(s)
- E A Griess
- Institut für Biologie III, Freiburg, Federal Republic of Germany
| | | | | | | | | |
Collapse
|
20
|
Abstract
The HMG box is a novel type of DNA-binding domain found in a diverse group of proteins. The HMG box superfamily comprises a.o. the High Mobility Group proteins HMG1 and HMG2, the nucleolar transcription factor UBF, the lymphoid transcription factors TCF-1 and LEF-1, the fungal mating-type genes mat-Mc and MATA1, and the mammalian sex-determining gene SRY. The superfamily dates back to at least 1,000 million years ago, as its members appear in animals, plants and yeast. Alignment of all known HMG boxes defined an unusually loose consensus sequence. We constructed phylogenetic trees connecting the members of the HMG box superfamily in order to understand their evolution. This analysis led us to distinguish two subfamilies: one comprising proteins with a single sequence-specific HMG box, the other encompassing relatively non sequence-specific DNA-binding proteins with multiple HMG boxes. By studying the extent of diversification of the superfamily, we found that the speed of evolution was very different within the various groups of HMG-box containing factors. Comparison of the evolution of the two boxes of ABF2 and of mtTF1 implied different diversification models for these two proteins. Finally, we provide a tree for the highly complex group of SRY-like ('Sox' genes), clustering at least 40 different loci that rapidly diverged in various animal lineages.
Collapse
Affiliation(s)
- V Laudet
- CNRS URA 1160, Institut Pasteur, Lille, France
| | | | | |
Collapse
|
21
|
Yamaguchi-Shinozaki K, Shinozaki K. A novel Arabidopsis DNA binding protein contains the conserved motif of HMG-box proteins. Nucleic Acids Res 1992; 20:6737. [PMID: 1480495 PMCID: PMC334597 DOI: 10.1093/nar/20.24.6737] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
|
22
|
Okamuro JK, Goldberg RB. A mutant lectin gene is rescued from an insertion element that blocks its expression. THE PLANT CELL 1992; 4:1141-6. [PMID: 1327341 PMCID: PMC160204 DOI: 10.1105/tpc.4.9.1141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2023]
Abstract
The soybean lectin gene Le1 encodes a prevalent seed protein and is highly regulated during the life cycle. The mutant lectin gene allele le1 is not transcribed detectably, contains a 3.5-kb Tgm1 insertion element within its coding region 0.6 kb 3' to the transcription start site, and leads to a lectinless phenotype. To determine whether the Tgm1 element or a secondary mutation was responsible for repressing le1 gene transcription, we eliminated the insertion element by constructing a chimeric lectin gene (le1/Le1) that contained the 5' half of the le1 gene and its promoter region and the 3' half of the wild-type Le1 gene. Transformed tobacco seed containing the le1/Le1 gene produced both lectin mRNA and protein, demonstrating that the mutant lectin gene control region is transcriptionally competent. By contrast, transformed seed containing the le1 gene produced no detectable lectin mRNA. We conclude that the absence of detectable transcription from the le1 gene is due to transcriptional inhibition by the Tgm1 insertion element and that this element acts at a distance to block transcription from an upstream promoter region.
Collapse
Affiliation(s)
- J K Okamuro
- Department of Biology, University of California, Los Angeles 90024-1606
| | | |
Collapse
|
23
|
Dalrymple BP, Peters JM. Characterization of a cDNA clone from the haemoparasite Babesia bovis encoding a protein containing an "HMG-Box". Biochem Biophys Res Commun 1992; 184:31-5. [PMID: 1567437 DOI: 10.1016/0006-291x(92)91153-h] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The complete nucleotide sequence of a Babesia bovis cDNA clone encoding a protein containing an HMG-Box has been determined. The predicted protein of 97 amino acids has a molecular weight of 11,116. It exhibits approximately 45% overall amino acid identity with the Saccharomyces cerevisiae non-histone protein 6A (NHP6A) and approximately 57% identity in the HMG-Box. The B. bovis protein has been designated NHP1. Like HNP6A, and unlike most other HMG1 homologues, NHP1 does not have a basic or an acidic carboxy-terminal domain. The amino acid sequence of HNP1 is much less similar to HMG1 homologues of another protozoan, Tetrahymena thermophila, than to the HMG1 homologues identified in S. cerevisiae, plants and vertebrates. This suggests that the T. thermophila proteins may not be true HMG1 homologues, or that they may be evolving at a much faster rate.
Collapse
Affiliation(s)
- B P Dalrymple
- Commonwealth Scientific and Industrial Research Organisation, Division of Tropical Animal Production, Indooroopilly, Queensland, Australia
| | | |
Collapse
|
24
|
New nucleotide sequence data on the EMBL File Server. Nucleic Acids Res 1991; 19:6351-64. [PMID: 1956810 PMCID: PMC329174 DOI: 10.1093/nar/19.22.6351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
|