High mobility group proteins 1 and 2 stimulate transcription in vitro by RNA polymerases II and III

Genomic interaction between ER and HMGB2 identifies DDX18 as a novel driver of endocrine resistance in breast cancer cells

Breast cancer resistance to endocrine therapies such as tamoxifen and aromatase inhibitors is a significant clinical problem. Steroid receptor coactivator-1 (SRC-1), a coregulatory protein of the oestrogen receptor (ER), has previously been shown to have a significant role in the progression of breast cancer. The chromatin protein high mobility group box 2 (HMGB2) was identified as an SRC-1 interacting protein in the endocrine-resistant setting. We investigated the expression of HMGB2 in a cohort of 1068 breast cancer patients and found an association with increased disease-free survival time in patients treated with endocrine therapy. However, it was also verified that HMGB2 expression could be switched on in endocrine-resistant tumours from breast cancer patients. To explore the function of this poorly characterized protein, we performed HMGB2 ChIPseq and found distinct binding patterns between the two contexts. In the resistant setting, the HMGB2, SRC-1 and ER complex are enriched at promoter regions of target genes, with bioinformatic analysis indicating a switch in binding partners between the sensitive and resistant phenotypes. Integration of binding and gene expression data reveals a concise set of target genes of this complex including the RNA helicase DDX18. Modulation of DDX18 directly affects growth of tamoxifen-resistant cells, suggesting that it may be a critical downstream effector of the HMGB2:ER complex. This study defines HMGB2 interactions with the ER complex at specific target genes in the tamoxifen-resistant setting.

Loosening of DNA/polycation complexes by synthetic polyampholyte to improve the transcription efficiency: effect of charge balance in the polyampholyte

High mobililty group proteins are amphoteric nuclear proteins that are known to unfold chromatin to stimulate transcription. To mimic their structures, we synthesized the novel polyethylene glycol (PEG) derivatives, PEG-ACs, consisting of both amino- and carboxyl-pendants in various ratios, and their loosening and transcription-improving activity on the DNA complex was examined. Fluorescence anisotropy measurement revealed that anionic PEG-ACs with more carboxyls than amines could efficiently loosen the DNA/polyethyleneimine complex. Those anionic PEG-ACs showing a loosening effect on the DNA complex evidently increased the transcription rate to >20 times higher than that of the original complex, probably owing to the facilitated approach of transcriptional factors to the DNA segments in the loosened complexes. The complexes with anionic PEG-ACs also showed improved transgene expression level on the cultured cells, indicating the effectiveness of improving transcriptional activity to attain a high extragene expression by the plasmid complex. The loosening mechanism of DNA/polycation complexes was investigated with a simplified model via Monte Carlo simulation to discern the difference in the presence of cationic polyampholytes, anionic polyampholytes, and polyanions.

Interactions between HMG proteins and the core sequence of DNaseI hypersensitive site 2 in the locus control region (LCR) of the human beta-like globin gene cluster

HMG proteins are abundant chromosomal non-histone proteins. It has been suggested that the HMG proteins may play an important role in the structure and function of chromatin. In the present study, the binding of HMG proteins (HMG1/2 and HMG14/17) to the core DNA sequence of DNaseI hypersensitive site 2 (HS2core DNA sequence, -10681-10970 bp) in the locus control region (LCR) of the human beta-like globin gene cluster has been examined by using both thein vitro nucleosome reconstitution and the gel mobility shift assays. Here we show that HMG1/2 can bind to the naked HS2core DNA sequence, however, HMG14/17 cannot. Using thein vitro nucleosome reconstitution we demonstrate that HMG14/17 can bind to the HS2core DNA sequence which is assembled into nucleosomes with the core histone octamer transferred from chicken erythrocytes. In contrast, HMG1/2 cannot bind to the nucleosomes reconstitutedin vitro with the HS2core DNA sequence. These results indicate that the binding patterns between HMG proteins and the HS2core DNA sequence which exists in different states (the naked DNA or thein vitro reconstituted nucleosomal DNA) are quite different. We speculate that HMG proteins might play a critical role in the regulation of the human beta-like globin gene's expression.

Chromosomal high mobility group (HMG) proteins of the HMGB-type occurring in the moss Physcomitrella patens

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.

Enhancement of Transcriptional Activity of DNA Complexes by Amphoteric PEG Derivative

A water-soluble PEG derivative having both amino and carboxylic acid side chains (PEG-AC) was synthesized and explored for its transcription- and transfection-enhancing activity. PEG-AC could be deposited onto the surface of DNA/polycation complexes to form a ternary complex with slightly negative surface potential. PEG-AC-coating on the plasmid/PEI complexes obviously enhanced their transcriptional activity, and 31-fold higher consumption of UTP was observed. Amphoteric PEG-AC would loosen the tightly compacted DNA/PEI complex and facilitate the approach of transcriptional factors. PEG-AC also evidently improved the transgene expression level on the cultured CHO cells.

Effects of HMGB-1 overexpression on cell-cycle progression in MCF-7 cells

High mobility group-1 (HMGB-1) enhances the DNA interactions and possesses a transcriptional activation potential for several families of sequence-specific transcriptional activators. In order to examine the effect of HMGB-1 on the cell cycle progression in MCF-7 cells, the HMGB-1 expression vector was transfected into synchronized MCF-7 cells, and the effect of HMGB-1 overexpression on the cell cycle was examined. The HMGB-1 protein level in the transfected cells increased 4.87-fold compared to the non-transfected cells. There were few changes in the cell cycle phase distribution after HMGB-1 overexpression in the MCF-7 cells. Following the estrogen treatment, the cell cycle progressed in both the HMGB-1 overexpressed MCF-7 and the mock-treated cells. However, a larger proportion of HMGB-1 overexpressing MCF-7 cells progressed to the either S or G2 phase than the mock-treated cells. The mRNA levels of the cell cycle regulators changed after being treated with estrogen in both the HMGB-1 overexpressing MCF-7 and the mock-treated cells, but the changes in the expression level of the cell cycle regulator genes were more prominent in the HMGB-1 overexpressing MCF-7 cells than in the mock-treated cells. In conclusion, HMGB-1 overexpression itself does not alter the MCF-7 cell cycle progression, but the addition of estrogen to the HMGB-1 overexpressing MCF-7 cells appears to accelerate the cell cycle progression.

HMGN dynamics and chromatin function

Recent studies indicate that most nuclear proteins, including histone H1 and HMG are highly mobile and their interaction with chromatin is transient. These findings suggest that the structure of chromatin is dynamic and the protein composition at any particular chromatin site is not fixed. Here we discuss how the dynamic behavior of the nucleosome binding HMGN proteins affects the structure and function of chromatin. The high intranuclear mobility of HMGN insures adequate supply of protein throughout the nucleus and serves to target these proteins to their binding sites. Transient interactions of the proteins with nucleosomes destabilize the higher order chromatin, enhance the access to nucleosomal DNA, and impart flexibility to the chromatin fiber. While roaming the nucleus, the HMGN proteins encounter binding partners and form metastable multiprotein complexes, which modulate their chromatin interactions. Studies with HMGN proteins underscore the important role of protein dynamics in chromatin function.

Involvement of HMGB1 and HMGB2 proteins in exogenous DNA integration reaction into the genome of HeLa S3 cells

High mobility group 1 and 2 proteins (HMGB1 and HMGB2) are abundant chromosomal proteins in eukaryotic cells. We examined the involvement of HMGB1 and HMGB2 in nonhomologous illegitimate recombination. The HMGB1 or HMGB2 expression plasmid, carrying the neo(r) gene as a selection marker, was introduced into HeLa S3 cells to obtain stably-transfected cells. The number of G418-resistant colonies was about 10 times the number of colonies of control cells transfected with plasmids not carrying the HMGB genes. The copy number of the stably-integrated neo(r) gene was higher in the cells transfected with the HMGB expression plasmids than in control cells. The exogenous DNA integration was suggested to have occurred by nonhomologous illegitimate recombination. On the contrary, the introduction of the HMGB antisense RNA expression plasmid with a reporter plasmid carrying the neo(r) gene into HeLa S3 cells decreased the number of G418-resistant colonies. These results indicate that HMGB1 and HMGB2 each have a novel function as stimulators of stable integration of plasmid DNA into the host genome and that they may be important for the process of spontaneous DNA integration in living cells.

Specificity of the stimulatory interaction between chromosomal HMGB proteins and the transcription factor Dof2 and its negative regulation by protein kinase CK2-mediated phosphorylation

The high mobility group (HMG) proteins of the HMGB family are chromatin-associated proteins that can contribute to transcriptional control by interaction with certain transcription factors. Using the transcription factor Dof2 and five different maize HMGB proteins, we have examined the specificity of the HMGB-transcription factor interaction. The HMG-box DNA binding domain of HMGB1 is sufficient for the interaction with Dof2. Although all tested HMGB proteins can interact with Dof2, the various HMGB proteins stimulate the binding of Dof2 to its DNA target site with different efficiencies. The HMGB5 protein is clearly the most potent facilitator of Dof2 DNA binding. Maximal stimulation of the DNA binding by the HMGB proteins requires association of HMGB and Dof2 prior to DNA binding. HMGB5 and Dof2 form a ternary complex with the DNA, but within the protein-DNA complex the interaction of HMGB5 and Dof2 is different from that in solution, as in contrast to the proteins in solution, they cannot be cross-linked with glutaraldehyde when bound to DNA. Phosphorylation of HMGB1 by protein kinase CK2 abolishes the interaction with Dof2 and the stimulation of Dof2 DNA binding. These findings indicate that transcription factors may recruit certain members of the HMGB family as assistant factors.

HSM2 (HMO1) gene participates in mutagenesis control in yeast Saccharomyces cerevisiae

We have previously reported about a new Saccharomyces cerevisiae mutation, hsm2-1, that results in increase of both spontaneous and UV-induced mutation frequencies but does not alter UV-sensitivity. Now HSM2 gene has been genetically and physically mapped and identified as a gene previously characterized as HMO1, a yeast homologue of human high mobility group genes HMG1/2. We found that hsm2 mutant is slightly deficient in plasmid-borne mismatch repair. We tested UV-induced mutagenesis in double mutants carrying hsm2-1 mutation and a mutation in a gene of principal damaged DNA repair pathways (rad2 and rev3) or in a mismatch repair gene (pms1 and recently characterized in our laboratory hsm3). The frequency of UV-induced mutations in hsm2 rev3 was not altered in comparison with single rev3 mutant. In contrast, the interaction of hsm2-1 with rad2 and pms1 was characterized by an increased frequency of UV-induced mutations in comparison with single rad2 and pms1 mutants. The UV-induced mutation frequency in double hsm2 hsm3 mutant was lower than in the single hsm2 and hsm3 mutants. The role of the HSM2 gene product in control of mutagenesis is discussed.

Dynamics of reporter gene stimulation by HMG box proteins

Overcoming local DNA rigidity is required to perform three-dimensional DNA-protein configuration at promoter regions. The abundant architectural nonhistone chromosomal HMG box proteins are nonsequence-specific; however, they have been established to specifically recognize distorted DNA. Using transient transfection to overexpress two different members of the HMGB-1/2 family of DNA architectural factors, we demonstrate that these proteins provide a general enhancement in reporter gene expression irrespective of the promoter being considered. Evidences are also provided indicating that stimulation may not be achieved by recruitment of the proteins by regulatory factors or as a consequence of major chromatin unfolding as previously suggested. Interestingly, the influence of the HMG box proteins under study was overridden when the promoters were either induced or stimulated by Trichostatin A (TSA) but recovered upon extended induction period. These results also support the concept that the architectural role of these proteins can contribute to the preinitiation complex assembly required for basal transcription, but to a much lesser extent to the poised promoter scaffolding characteristic of activated transcription.

Dual roles for HMGB1: DNA binding and cytokine

Effective therapies against overwhelming Gram-negative bacteremia, or sepsis, have eluded successful development. The discovery that tumor necrosis factor (TNF), a host-derived inflammatory mediator, was both necessary and sufficient to recapitulate Gram-negative sepsis raised cautious optimism for developing a targeted therapeutic. However, the rapid kinetics of the TNF response to infection defined an extremely narrow window of opportunity during which anti-TNF therapeutics could be successfully administered. HMGB1 was previously studied as a DNA-binding protein involved in DNA replication, repair, and transcription; and as a membrane-associated protein that mediates neurite outgrowth. A decade-long search has culminated in our identification of HMGB1 as a late mediator of endotoxemia. HMGB1 is released by macrophages upon exposure to endotoxin, activates many other pro-inflammatory mediators, and is lethal to otherwise healthy animals. Elevated levels of HMGB1 are observed in the serum of patients with sepsis, and the highest levels were found in those patients that died. The delayed kinetics of HMGB1 release indicate that it may be useful to target this toxic cytokine in the development of future therapies.

Mutations in the yeast Nhp6 protein can differentially affect its in vivo functions

Nhp6A and Nhp6B from S. cerevisiae are required for viability at 38 degrees C because they are involved in transcription of SNR6 by RNA polymerase III. Nhp6A also represses transcription of NHP6B by RNA polymerase II. Nhp6 belongs to the HMG1 family, defined by an 80 amino acid DNA binding domain, which includes six highly conserved residues. These amino acids were mutated in Nhp6A and their affects on Nhp6 function were assessed in vivo. Surprisingly, most of the changes allowed Nhp6A to function normally in supporting growth at 38 degrees C. However, six mutants had differential effects on in vivo function. Finally, two of the mutant proteins that did not restore Nhp6A function in vivo were shown to bind and bend DNA in vitro as well as wild type. Together, these results suggest that Nhp6 interacts with another protein(s) to carry out some of its biological functions and that this interaction might differ at promoters transcribed by RNA polymerase II versus RNA polymerase III.

Reexamination of the high mobility group-1 protein for self-association and characterization of hydrodynamic properties

Previous studies of the 25 kDa high mobility group-1 (HMG-1) protein have generated conflicting results regarding whether HMG-1 exists as a monomer or is capable of oligomerizing to (functional) tetramers. To resolve this question, sedimentation velocity analysis yielded a s20,w value of 2.59S, which is consistent with a monomeric protein. Equilibrium sedimentation data were obtained for three HMG-1 concentrations at two rotor speeds. The six sets of data were fit to both an ideal single component and monomer-dimer equilibrium model, with essentially identical fits produced for both models, with the latter indicating a low extent (7%) of dimerization. Reaction of HMG-1 with glutaraldehyde produced a small population of oligomers consistent with a low level of dimers. This supported the monomer-dimer equilibrium model. Surprisingly, gel permeation chromatography yielded an apparent molecular mass of approx. 55 kDa for both HMG-1 and HMG-2. This finding is considered anomalous and presumably due to the high negative charge density in the C terminus of HMG-1. The sedimentation data also permit one to model HMG-1 as a hydrated prolate ellipsoid with a major axis/minor axis ratio of 2. 79. The collective evidence from the sedimentation and chemical cross-linking studies strongly supports a moderately asymmetric monomer in solution and unequivocally eliminates the possibility of a highly extended shape for HMG-1 or the existence of any extensive oligomerization.

Hmo1p, a high mobility group 1/2 homolog, genetically and physically interacts with the yeast FKBP12 prolyl isomerase

The immunosuppressive drugs FK506 and rapamycin bind to the cellular protein FKBP12, and the resulting FKBP12-drug complexes inhibit signal transduction. FKBP12 is a ubiquitous, highly conserved, abundant enzyme that catalyzes a rate-limiting step in protein folding: peptidyl-prolyl cis-trans isomerization. However, FKBP12 is dispensible for viability in both yeast and mice, and therefore does not play an essential role in protein folding. The functions of FKBP12 may involve interactions with a number of partner proteins, and a few proteins that interact with FKBP12 in the absence of FK506 or rapamycin have been identified, including the ryanodine receptor, aspartokinase, and the type II TGF-beta receptor; however, none of these are conserved from yeast to humans. To identify other targets and functions of FKBP12, we have screened for mutations that are synthetically lethal with an FKBP12 mutation in yeast. We find that mutations in HMO1, which encodes a high mobility group 1/2 homolog, are synthetically lethal with mutations in the yeast FPR1 gene encoding FKBP12. Deltahmo1 and Deltafpr1 mutants share two phenotypes: an increased rate of plasmid loss and slow growth. In addition, Hmo1p and FKBP12 physically interact in FKBP12 affinity chromatography experiments, and two-hybrid experiments suggest that FKBP12 regulates Hmo1p-Hmo1p or Hmo1p-DNA interactions. Because HMG1/2 proteins are conserved from yeast to humans, our findings suggest that FKBP12-HMG1/2 interactions could represent the first conserved function of FKBP12 other than mediating FK506 and rapamycin actions.

Enhancement of cisplatin sensitivity in high mobility group 2 cDNA-transfected human lung cancer cells

To elucidate the role of high mobility group 2 protein (HMG2) in cis-diamminedichloroplatinum (II) (cisplatin, CDDP) sensitivity, we constructed a human HMG2-transfected human non-small cell lung cancer cell line, PC-14/HMG2. The HMG2 mRNA expression level was approximately twice those of parental PC-14 and mock-transfected PC-14/CMV. Gel mobility shift assay revealed a CDDP-treated DNA-protein complex in the nuclear extract of PC-14/HMG2, which was not found in the extracts of PC-14 and PC-14/CMV. This complex formation was subject to competition by CDDP-treated non-specific salmon sperm DNA, indicating that ectopic HMG2 recognizes CDDP-damaged DNA. PC-14/HMG2 showed more than 3-fold higher sensitivity to CDDP than PC-14 and PC-14/CMV. The intracellular platinum content of PC-14/HMG2 after exposure to 300 microM CDDP was 1.1 and 1.5 times that of PC-14 and PC-14/CMV, respectively. Cellular glutathione levels were not different in these cell lines. Repair of DNA interstrand cross-links determined by alkaline elution assay was decreased in PC-14/HMG2. These results suggest that HMG2 may enhance the CDDP sensitivity of cells by inhibiting repair of the DNA lesion induced by CDDP.

Four differently chromatin-associated maize HMG domain proteins modulate DNA structure and act as architectural elements in nucleoprotein complexes

In contrast to other eukaryotes which usually express two closely related HMG1-like proteins, plant cells have multiple relatively variable proteins of this type. A systematic analysis of the DNA-binding properties of four chromosomal HMG domain proteins from maize revealed that they bind linear DNA with similar affinity. HMGa, HMGc1/2 and HMGd specifically recognise diverse DNA structures such as DNA mini-circles and supercoiled DNA. They induce DNA-bending, and constrain negative superhelical turns in DNA. In the presence of DNA, the HMG domain proteins can self-associate, whereas they are monomeric in solution. The maize HMG1-like proteins have the ability to facilitate the formation of nucleoprotein structures to different extents, since they can efficiently replace a bacterial chromatin-associated protein required for the site-specific beta-mediated recombination. A variable function of the HMG1-like proteins is indicated by their differential association with maize chromatin, as judged by their 'extractability' from chromatin with spermine and ethidium bromide. Collectively, these findings suggest that the various plant chromosomal HMG domain proteins could be adapted to act in different nucleoprotein structures in vivo.

Estrogen treatment induces elevated expression of HMG1 in MCF-7 cells

The high mobility group (HMG) 1 protein is a highly conserved and ubiquitous chromosomal protein found enriched in active chromatin. In this study, we have investigated the effect of estrogen on the expression of the human high mobility group protein HMG1 gene and found that the HMG1 mRNA level in MCF-7 cells was sharply increased 2.5-fold after 30 min of estrogen treatment. Under continuous estrogen treatment, the HMG1 mRNA level decreased to a 1.5 times that of the basal level at 90 min and remained at this elevated level under estrogen treatment for up to 24 h. These results support the recent finding by Verrier et al. (C.S. Verrier, 1997, Mol. Endocrinol. 11, 1009-1019) that HMG1 promotes the binding of the estrogen receptor to the estrogen response element and further reinforce our believe that HMG1 plays a significant role in estrogen-induced gene expression.

The high mobility group protein 1 enhances binding of the estrogen receptor DNA binding domain to the estrogen response element

We have examined the ability of the high-mobility group protein 1 (HMG1) to alter binding of the estrogen receptor DNA-binding domain (DBD) to the estrogen response element (ERE). HMG1 dramatically enhanced binding of purified, bacterially expressed DBD to the consensus vitellogenin A2 ERE in a dose-dependent manner. The ability of HMG1 to stabilize the DBD-ERE complex resulted in part from a decrease in the dissociation rate of the DBD from the ERE. Antibody supershift experiments demonstrated that HMG1 was also capable of forming a ternary complex with the ERE-bound DBD in the presence of HMG1-specific antibody. HMG1 did not substantially affect DBD-ERE contacts as assessed by methylation interference assays, nor did it alter the ability of the DBD to induce distortion in ERE-containing DNA fragments. Because HMG1 dramatically enhanced estrogen receptor DBD binding to the ERE, and the DBD is the most highly conserved region among the nuclear receptor superfamily members, HMG1 may function to enhance binding of other nuclear receptors to their respective response elements and act in concert with coactivator proteins to regulate expression of hormone-responsive genes.

Basic and acidic regions flanking the HMG domain of maize HMGa modulate the interactions with DNA and the self-association of the protein

The maize HMGa protein is a typical member of the family of plant chromosomal HMG1-like proteins. The HMG domain of HMGa is flanked by a basic N-terminal domain characteristic for plant HMG1-like proteins, and is linked to the acidic C-terminal domain by a short basic region. Various derivatives of the HMGa protein were expressed in Escherichia coli and purified. The individual HMG domain can functionally complement the defect of the HU-like chromatin-associated Hbsu protein in Bacillus subtilis. The basic N-terminal domain which contacts DNA enhances the affinity of the protein for linear DNA, whereas it has little effect on the structure-specific binding to DNA minicircles. The acidic C-terminal domain reduces the affinity of HMGa for linear DNA, but does not affect to the same extent the recognition of DNA structure which is an intrinsic property of the HMG domain. The efficiency of the HMGa constructs to facilitate circularization of short DNA fragments in the presence of DNA ligase is like the binding to linear DNA altered by the basic and acidic domains flanking the HMG domain, while the supercoiling activity of HMGa is only slightly influenced by the same regions. Both the basic N-terminal and the acidic C-terminal domains contribute directly to the self-association of HMGa in the presence of DNA. Collectively, these findings suggest that the intrinsic properties of the HMG domain can be modulated within the HMGa protein by the basic and acidic domains.

Variability in Arabidopsis thaliana chromosomal high-mobility-group-1-like proteins

The vertebrate high-mobility-group (HMG) protein HMG1 is an abundant non-histone protein which is considered as an architectural element in chromatin. In the monocotyledonous plant maize, four different HMG1-like proteins (HMGa, HMGc1/2, HMGd) have been identified, whereas other eukaryotes usually express only two different proteins of this type. We have examined here the HMG1-like proteins of the dicotyledonous plant Arabidopsis thaliana. The isolation and analysis of cDNAs encoding five different so far uncharacterised HMG1-like proteins (now termed HMG alpha, HMG beta1/2, HMG gamma, HMG delta) from Arabidopsis indicates that the expression of multiple HMG1-like proteins is a general feature of (higher) plants. The Arabidopsis HMG1-like proteins contain an HMG domain as a common feature, but outside this conserved DNA-binding motif the amino acid sequences are significantly different indicating that this protein family displays a greater structural variability in plants than in other eukaryotes. The five HMG1-like proteins were expressed in Escherichia coli and purified. They bind with somewhat different affinity to linear double-stranded DNA. The recognition of DNA structure is evident from their preferential interaction with DNA minicircles relative to linear DNA. Reverse-transcribed PCR suggested that the five HMG1-like genes are simultaneously expressed in Arabidopsis leaves and suspension culture cells.

Pairing of DNA fragments containing (GGA:TCC)n repeats and promotion by high mobility group protein 1 and histone H1

Tandemly repeated DNA sequences of (GGA:TCC)n are found in tracts up to 50 base pairs long, dispersed at thousands of sites throughout the genomes of eukaryotes. Here we demonstrate the formation of complexes paired between two DNAs containing such repeats in vitro and show enhancement of the pairing by glutathione S-transferase fusion proteins of high mobility group protein 1 and histone H1. This assembly depends on incubation time at 37 degrees C and concentrations of the proteins and DNA, and the enhancement is inhibited by distamycin and actinomycin D interacting DNA through the minor groove. Structure of the DNA-DNA complex is deduced by comparison of its mobility in gel electrophoresis with those of synthetic markers of heterotetramers. Three synthetic and genomic DNA fragments containing repeats that have different arrangements exhibit different efficiencies of DNA pairing, implying that the pairing is affected by the number of repeat units and the arrangement of repeats in a sequence. Intriguingly, pairing occurs between homologous fragments but not between heterologous DNAs among the three. These results suggest that the repeat-mediated DNA pairing plays a role in organization of higher order architecture of chromatin and possibly chromosome segregation requiring sequence-specific association events of DNA molecules.

Nuclear accumulation of HMG2 protein is mediated by basic regions interspaced with a long DNA-binding sequence, and retention within the nucleus requires the acidic carboxyl terminus

High mobility group 2 (HMG2) protein is ubiquitously distributed in the nucleus of higher eukaryotic cells. Accumulation of an HMG2-beta-galactosidase fusion protein expressed in COS-7 cells suggested active transport of HMG2 protein into the nucleus after translation in the cytoplasm. Deletion analysis of the HMG2 sequence in the HMG2-beta-galactosidase fusion protein indicated that basic regions interspaced with the long DNA-binding sequence in HMG2, called the HMG1/2 box, are necessary for the nuclear accumulation of HMG2. The close configuration of basic regions at both ends of the DNA-binding sequence in the tertiary structure may function as the nuclear localization signal. This novel nuclear localization signal structure is different from typical ones such as the single or bipartite basic cluster in many nuclear proteins. A portion of the HMG2 molecule remained in the cytoplasm after translation. Interspecies heterokaryon assay demonstrated that the acidic carboxyl terminus of HMG2 was necessary for retention of the protein in the nucleus.

Characterization of a high mobility group 1/2 homolog in yeast

A 35-kDa polypeptide belonging to the high mobility group family of proteins was purified from the yeast Saccharomyces cerevisiae on the basis of its association with a DNA helicase activity. Amino acid sequence alignment suggests that this protein, Hmo1p, is related to the HMG1/2 class of chromatin-associated proteins. Consistent with this prediction, the Hmo1 protein immunolocalizes to the nucleus, binds single-stranded DNA, and unwinds DNA in the presence of eukaryotic DNA topoisomerase I. While the purified protein has no DNA helicase activity on its own, immunoprecipitation experiments confirm that Hmo1p associates with a 5' to 3' DNA helicase activity in nuclear extracts. The in vivo role of the protein was investigated by constructing an hmo1 deletion mutant. This strain has a severe growth defect, reduced plasmid stability, and chromatin that is hypersensitive to micrococcal nuclease digestion. Taken together, the data indicate that HMO1 is likely to be the homolog of HMG1/2 in higher cells and that it plays an important role in genome maintenance.

The conserved lymphokine element-0 in the IL5 promoter binds to a high mobility group-1 protein

The conserved lymphokine elements-0 (CLE0) in the IL5 promoter is essential for the expression of IL-5. Here, we report the cloning and expression of a cDNA encoding a novel CLE0-binding protein, CLEBP-1 from a mouse Th2 clone, D10.G4.1. Interestingly, it was found that the CLEBP1 cDNA sequence was almost identical to the sequences of known high mobility group-1 (HMG1) cDNAs. When expressed as a recombinant fusion protein in Escherichia coli, CLEBP-1 was shown to bind to the IL5-CLE0 element in electrophoretic mobility-shift assays (EMSA) and southwestern blot analysis. The CLEBP-1 fusion protein cross-reacts with and-HMG-1/2 in Western blot analysis. It also binds to the CLE0 elements of IL4, GMCSF and GCSF genes. CLEBP-1 and closely related HMG-1 and HMG-2 proteins may play key roles in facilitating the expression of the lymphokine genes that contain CLE0 elements.

Structural and functional homology between the 29 kD rat liver nucleoprotein and the high mobility group 1 protein

A 29 kD soluble rat liver nucleoprotein (p29) has increased binding affinity for the hormone responsive element (RE) of the rat haptoglobin (Hp) gene during the acute-phase reaction. In this work the possibility of its structural and functional homology to the high mobility group 1 (HMG1) nonhistone protein constituent of chromatin was examined. The results of two-dimensional gel electrophoresis, Southwestern and Western immunoblot analyses, showed that p29 and HMG1 are homologous protein species. On the basis of in vitro and in vivo phosphorylation/dephosphorylation experiments, we discuss the modulatory role of phosphate groups in view of the structure and function of p29.

Vaccinia virions lacking core protein VP8 are deficient in early transcription

When synthesis of the 25-kDa vaccinia virus core protein VP8 is repressed, mature virus particles of normal appearance are produced to approximately 80% of wild-type levels but these particles are over 100-fold less infectious than wild-type particles (D. Wilcock and G. L. Smith, Virology 202:294-304, 1994). Here we show that virions which lack VP8 can bind to and enter cells but the levels of steady-state RNA are greatly reduced in comparison with those for wild-type infections. In vitro assays using permeabilized virions demonstrated that VP8-deficient virions had drastically reduced rates of transcription (RNA synthesis was decreased by 80 to 96%) and that the extrusion of RNA transcripts from these virions was also decreased. Low concentrations of sodium deoxycholate extracted proteins more efficiently from VP8-deficient virions than from wild-type virions. The increased fragility of VP8-deficient virions and their slower RNA extrusion rates suggest that VP8 may be required for the correct formation of the core. Virions which lack VP8 were shown to contain a full complement of transcription enzymes, and soluble extracts from these virions were active in transcription assays using either single-stranded M13 DNA or exogenous plasmid template containing a vaccinia virus early promoter. Thus, the defect in transcription is due not to a lack of specific transcriptional enzymes within virions but rather to the inability of these enzymes to efficiently transcribe the DNA genome packaged within VP8-deficient virions. These results suggest that VP8 is required for the correct packaging of the viral DNA genome and/or for the efficient transcription of packaged virion DNA, which has a higher degree of structural complexity than plasmid templates. Possible roles for VP8 in these processes are discussed.

The nuclear matrix and the regulation of chromatin organization and function

Nuclear DNA is organized into loop domains, with the base of the loop being bound to the nuclear matrix. Loops with transcriptionally active and/or potentially active genes have a DNase I-sensitive chromatin structure, while repressed chromatin loops have a condensed configuration that is essentially invisible to the transcription machinery. Core histone acetylation and torsional stress appear to be responsible for the generation and/or maintenance of the open potentially active chromatin loops. The transcriptionally active region of the loop makes several dynamic attachments with the nuclear matrix and is associated with core histones that are dynamically acetylated. Histone acetyltransferase and deacetylase, which catalyze this rapid acetylation and deacetylation, are bound to the nuclear matrix. Several transcription factors are components of the nuclear matrix. Histone acetyltransferase, deacetylase, and transcription factors may contribute to the dynamic attachment of the active chromatin domains with the nuclear matrix at sites of ongoing transcription.

Purification of a high-mobility-group 1 sea-urchin protein and cloning of cDNAs

The isolation of the sea urchin high-mobility-group 1 (HMG1) protein, the cloning of corresponding cDNA clones and the similarity to the human homologue are described. Sea urchin HMG1 was purified as one of the nuclear embryonic proteins which associate with an upstream regulatory element (E1) of the Strongylocentrotus purpuratus (Sp) CyIIIb actin-encoding gene. Using a synthetic oligodeoxyribonucleotide (oligo) which includes the E1 cis-acting element in a DNA affinity chromatography purification, the most prominent of the binding proteins was isolated and the N terminus sequenced. cDNA clones were isolated by screening an embryonic cDNA library with a synthetic oligo derived from the amino acid (aa) sequence. Comparison of the cDNAs ORF to known proteins revealed a 50% aa identity to the mammalian HMG1 and all the structural characteristics of this group of proteins. The sea urchin protein, SpHMG1, was synthesized in bacteria, as well as translated in vitro. Binding assays carried out with the recombinant SpHMG1 protein did not produce specific in vitro complexes with E1.

Differential expression of nuclear HMG1, HMG2 proteins and H1(zero) histone in various blood cells

Changes in the levels of chromosomal high-mobility group proteins HMG1, HMG2 and histone H1 zero were investigated in blood cells of various types, proliferation activity and stage of differentiation. The relative amounts of proteins HMG1, HMG2 and histone H1 zero were evaluated densitometrically by SDS-PAGE of 5 per cent w/v perchloric acid extracts of blood cells. Concerning the HMG1 and HMG2, the main conclusions were: the expression of these HMG proteins was higher in malignant cells, namely leukemia cell lines, then in lymphocytes or granulocytes and the distribution of HMG1 and HMG2 was highly cell-specific. In comparison with lymphoid cells, the levels of HMG1/2 were higher in myeloid cells. The results revealed that in myeloid cells HMG2 prevails over HMG1. There was no direct correlation between HMG1/2 expression and proliferation activity. The levels of HMG1/2 did not depend on the transcription of chromatin either. However, there was some connection between irreversibly differentiated nonproliferating cells and a loss of HMG1/2 proteins. Reversibly differentiated leukemic cells retain their HMG1/2 levels. Similarly to HMG1/2,H1 zero showed a strong cell specificity. The level of H1 zero was different in the various blood cell types. As compared with lymphoid cells, the level of H1 zero was several-fold higher in myeloid cells, regardless of whether they were normal or malignant. Moreover, there was an accumulation of H1 zero in differentiating HL-60 cells accompanied by only a slight decline in cell proliferation; this agrees with the idea that H1 zero expression is not directly associated with the inhibition of cell growth. Rather higher expression of H1 zero is related to changes during cell differentiation.

Stimulation of transcription accompanying relaxation of chromatin structure in cells overexpressing high mobility group 1 protein

We developed murine C-127 cell lines that stationarily overexpress high mobility group (HMG) proteins 1 and 2 by transfecting them with the bovine papilloma virus plasmid carrying their respective cDNA sequences. Using these cell lines, we examined the effects of these HMG proteins on the modulation of chromatin structure that accompanied transcription. The levels of HMG1 mRNA and protein in cells overexpressing HMG1 protein were enhanced about 7- and 3-fold, respectively, in comparison with control cells, whereas those in cells overexpressing HMG2 protein were enhanced about 17- and 9-fold. The expression of reporter genes transfected into the cells was enhanced approximately 2-fold in cells overexpressing HMG1, but not HMG2, in comparison with those in control cells, irrespective of the sources of the genes and promoters. The minichromosome derived from the reporter plasmid in cells overexpressing HMG1 protein was more susceptible to micrococcal nuclease digestion than those in cells overexpressing HMG2 protein and control cells. The enhanced accessibility to micrococcal nuclease was not restricted to the expressing gene and promoter but involved the entire minichromosome, suggesting that the enhancement of gene expression resulted from changes in the condensation of the entire minichromosomal region by HMG1 protein. Minichromosomes in cells overexpressing HMG contained enhanced amounts of the respective HMG proteins and simultaneously reduced amounts of histone H1s. These results suggest that HMG1 and -2 proteins have different functions in the modulation of chromatin structure, and that HMG1 protein may sustain the structure of the respective gene to ensure that its activity as a template is expressed fully. These observations on the modulation of chromatin structure accompanying gene transcription in cells overexpressing HMG protein may provide important information on the function of these proteins.

DNA looping by Saccharomyces cerevisiae high mobility group proteins NHP6A/B. Consequences for nucleoprotein complex assembly and chromatin condensation

The formation of higher order protein.DNA structures often requires bending of DNA strands between specific sites, a process that can be facilitated by the action of nonspecific DNA-binding proteins which serve as assembly factors. A model for this activity is the formation of the invertasome, an intermediate structure created in the Hin-mediated site-specific DNA inversion reaction, which is stimulated by the prokaryotic nucleoid-associated protein HU. Previously, we have shown that the mammalian HMG1/2 proteins substitute for HU in this system and display efficient DNA wrapping activity in vitro. In the present work, we isolate the primary sources of assembly factor activity in Saccharomyces cerevisiae, as measured by the ability to stimulate invertasome formation, and show that these are the previously identified NHP6A/B proteins. NHP6A/B have comparable or greater activity in DNA binding, bending, and supercoiling with respect to HU and HMG1 and appear to form more stable protein.DNA complexes. In addition, expression of NHP6A in mutant Escherichia coli cells lacking HU and Fis restores normal morphological appearance to these cells, specifically in nucleoid condensation and segregation. From these data we predict diverse architectural roles for NHP6A/B in manipulating chromosome structure and promoting the assembly of multicomponent protein.DNA complexes.

Increased DNA-bending activity and higher affinity DNA binding of high mobility group protein HMG-1 prepared without acids

Recently, DNA ring closure assays showed that high mobility group protein HMG-1 and its close homolog HMG-2 mediate sequence-independent DNA flexion. This DNA-bending activity appears to be central to at least some of the recently elucidated functions of HMG-1/2, such as the enhancement of progesterone receptor DNA binding. Here we show that standard purification procedures utilizing perchloric and trichloroacetic acid can produce HMG-1 significantly deficient in its abilities to bind and bend double-stranded DNA, while acid-independent methods purify HMG-1 that is superior in these respects. Significant losses of DNA ring closure activity were seen upon limited 2-5-h exposures of nonacid-purified HMG-1/2 to perchloric acid and/or trichloroacetic acid. Measurements of the apparent DNA dissociation binding constant (Kd(app)) of acid-extracted preparations of HMG-1 gave a wide range of values, and only those preparations demonstrating little DNA ring closure activity had Kd values near the previously published value (approximately 10(-6) M). The highest ring closure activities and lowest Kd(app) (< 3 x 10(-9) M) were obtained for HMG-1 purified without acids. These combined results support the use of alternative, non-acid purification procedures for preserving the DNA-bending activity of HMG-1/2 and suggest that past procedures utilizing acids have led to an underestimation of the affinity of HMG-1 for DNA.

High mobility group protein, HMG-1, contains insignificant glycosyl modification

High mobility group protein-1 (HMG-1) is a ubiquitous, highly conserved, and abundant nuclear protein. Recent findings suggest that HMG-1 may serve as a DNA chaperone protein and play a role in the regulation of transcription. There is a mounting interest in elucidating the mechanism by which HMG-1 protein takes part in these activities. HMG-1 has been reported to undergo an extensive array of posttranslational modifications, including glycosylation. We extend the earlier findings on the glycosylation of HMG-1 by quantitating the amount of carbohydrate on HMG-1 from calf thymus and chicken erythrocytes isolated by 2 different purification procedures. In addition, 2 different developmental stages (embryonic and adult) were examined in the chicken erythrocytes. The glycosyl composition was quantitated using the Dionex HPAE-PAD II system. Furthermore, the presence of O-linked GlcNAc on HMG-1 was determined by the enzymatic incorporation of 3H-galactose into HMG-1 protein. Contrary to earlier reports, less than 0.5 mol of total monosaccharides (Fuc, Man, GalNH2, GlcNH2, Gal) were detected per mole of HMG-1 protein, regardless of the source of the protein or the method of isolation. In addition, less than 0.002 mol of O-linked GlcNAc per mole of HMG-1 protein was detected. Thus, insignificant amount of glycosylation was found on HMG-1 protein. Because O-linked GlcNAc modification of proteins is believed to be a reversible posttranslational event, more definitive studies will need to be conducted before ruling out that the function of HMG-1 protein is not regulated by glycosylation.

Cruciform DNA binding protein in HeLa cell extracts

We have analyzed by band-shift assays HeLa cell protein-DNA interactions on a stable cruciform DNA molecule. The stable cruciform was formed by heteroduplexing the HindIII-SphI fragment of SV40 virus DNA that contains the origin of replication with a derivative mutant containing a heterologous substitution at the central inverted repeat. We have identified a novel binding activity in HeLa cell extracts with specificity for the cruciform-containing DNA and no apparent sequence specificity. The activity is protein-dependent, void of detectable nuclease activity, and distinct from that reported for HMG1. A cruciform binding protein (CBP) with an apparent molecular weight of 66 kDa was enriched from HeLa cell extracts. In addition to the CBP, we have detected sequence-specific binding activities to sites proximal to the cruciform. Binding to one such site is increased in the cruciform-containing heteroduplex DNA by comparison to its linear homoduplex counterpart, suggesting transmission of structural effects by the stem-loops to their local environment.

HMG-X, a Xenopus gene encoding an HMG1 homolog, is abundantly expressed in the developing nervous system

We used a PCR-based subtraction cloning procedure with Concanavalin A-treated and untreated animal caps from stage 9 Xenopus embryos to search for genes the expression of which is induced during neurogenesis. One of these genes was found to encode a homolog of mammalian HMG 1 and 2, hence named HMG-X. HMG-X mRNA was maternally transmitted, up-regulated in neuroectoderm-derived tissues throughout early development, and eventually down-regulated in all adult tissues examined except ovary. Our data suggest that we have identified a gene for a member of the HMG1/2 family that could have an important role in neurogenesis.

The human testis determining factor SRY: a new member of the HMG box protein family

The product of the sex-determining gene SRY is a member of the HMG box containing protein superfamily. The HMG box is a DNA-binding domain of about 80 amino acids shared by many proteins with diverse functions. It seems that the functions of the full length protein are restricted to the HMG box but their molecular basis remains to be determined. We have summarized here the properties of this binding domain described so far in the literature and, using a synthetic peptide mimicking the DNA binding domain (SRY80), we have confirmed the existence of DNA minor groove contacts with this domain. Using intrinsic fluorescence of the tryptophane, the interaction between SRY80 and the putative target sequence AACAAAT was also quantified. In conclusion, we also consider the possible putative action of SRY to fulfill its role in sex determination.

Comparative analysis of chromosomal HMG proteins from monocotyledons and dicotyledons

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.

Abundance of an mRNA encoding a high mobility group DNA-binding protein is regulated by light and an endogenous rhythm

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.