THE JOURNAL OF B I O ~ I C A L CHEMISTRY 0 1994 by The American Society for Biochemistry and Molecular Biology, Inc

Vol. 269, No. 14, Iesue of April 8, pp. 10713-10719, 1994 Printed in U.S.A.

High Affinity Interaction of Dipteran High Mobility Group (HMG) Proteins 1 with DNA Is Modulated by COOH-terminal Regions Flanking the HMG Box Domain*

(Received for publication, December 3, 1993, and in revised form, January 13, 1994)

Jacek R. WiBniewskiS and Ekkehard Schulze From the Third Department of Zoology-Developmental Biology, University of Gijttingen, 0-37073 Gijttingen, Germany

The cells of the dipteran insects Chironomus and Dro- sophila contain high mobility group (HMG) 1 proteins that are homologous to the HMGl protein of mammals but comprise one instead of two DNA-binding HMG boxes. Mobility shift assays have revealed that Chirono- mu8 cHMGla and cHMGlb bind double strand and four- way junction DNA in a similar way at apparent dissocia- tion constants in the range of 7.5-20 x lo-’ M. Both proteins are monomeric and highly asymmetric mol- ecules in solution. cHMGla and cHMGlb exhibit Stokes’ radii of 2.4 and 2.3 nm, respectively, and both show a frictional ratio of 1.5. Despite these similarities in their hydrodynamic properties, the binding site of cHMGla on DNA is -1.5 of the size found for the cHMGlb. Enzy- matically and chemically prepared peptides of cHMGla as well as bacterially expressed cHMGla with terminal deletions and point substitutions showed that se- quences flanking the folded domain that constitutes the HMG box are essential for the interaction of the HMG box with DNA. In particular, changes in the number of positive and negative charges, respectively, within basic and acidic domains modulated the DNA binding affinity of the cHMGla protein. The alteration of fluorescence of the Trp residues suggest that this modulation is due to interaction of the acidic domain with the positively charged HMG box.

The high mobility group proteins 1 and 2 (HMG1 and HMG2)’ are a highly abundant class of nonhistone chromo- somal proteins found in vertebrate organisms (see Bustin et al., 1990, for a review). The functions of these proteins are only poorly understood. Their abundancy and their apparent role in both replication (Bonne et al., 1982; Duguet and De Recondo, 1978) and transcription (Tremethick and Molloy, 1988; Watt and Molloy 1988; Singh and Dixon, 1990) suggest that HMGlI2 are structural proteins regulating chromatin conformation (Bustin and Soares, 1985).

The HMGlA proteins have a highly conserved tripartite structure. Two folded domains A and B (the so-called HMG boxes) are homologous to each other and are followed by a

* This work was supported by Grant Wi 1210/1-1 from the Deutsche Forschungsgesellschaft. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked “advertisement” in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

stitut-Entwicklungsbiologie, Universitat Gottingen, Humboldtallee $ To whom correspondence should be addressed: 111. Zoologisches In-

34A, D-37073 Mttingen, Germany. Tel.: 551-395444; Fax: 551-395416. The abbreviations used are: HMG1, high mobility group protein 1;

HMG2, high mobility group protein 2; HMG, high mobility group; cHMGla, Chironomus HMG protein la; cHMGlb, Chironomus HMG protein lb; HPLC, high performance liquid chromatography; PAGE, polyacrylamide gel electrophoresis; PCR, polymerase chain reaction; bp, base pairs.

highly charged carboxyl-terminal tail (Reeck et al., 1979). Re- cently, proteins with a striking homology to HMGl have been found in another group of eucaryotic organisms, the dipteran insects Chironomus and Drosophila (Wihiewski and Schulze, 1992; Wagner et al., 1992). However, instead of two, the insect molecules have only one folded domain that is followed by a highly charged COOH-terminal region of -30 amino acid resi- dues length. The HMG boxes of Chironomus cHMGla and cHMGlb exhibit 95 and 82% homology to the Drosophila HMGl (dHMG-Dl, respectively (Fig. lA).

The interaction of vertebrate HMGl/2 proteins with DNA has been extensively studied. It has been shown that these proteins bind to double- and single-stranded DNA in a se- quence-independent manner with relatively moderate affinity (K, in the range of 106-106 M-’; Shooter et al., 1974; Goodwin et al., 1975; Butler et al., 1985). The HMGlA proteins interact preferentially with negatively supercoiled DNA (Sheflin and Spaulding, 1989; Sheflin et al., 1993), AT-rich DNA (Brown and Anderson, 1986; Wihiewski and Schulze, 1992), and bind with high selectivity to four-way junction DNA (Bianchi et al., 1989, 1992). The highly charged COOH-terminal region appears to influence the interaction of the whole molecule with DNA. A peptide of bovine HMG1, that was obtained by enzymatic cleav- age and that is lacking the COOH-terminal portion of the intact protein, exhibited an increased DNA binding affinity (Carballo et al., 1983; Sheflin et al., 1993).

We are interested in elucidating the functions of HMGU2 proteins by exploiting the cytological and genetical advantages of Drosophila and Chironomus. As the determination of struc- ture and DNA-binding parameters of chromosomal proteins may essentially contribute to understanding their role in chro- matin assembly, we have studied the interaction of the two HMGl proteins of C. tentuns, cHMGla and cHMGlb, with DNA. Native and bacterially expressed cHMGl did not virtu- ally discriminate between linear and four-way junction DNA. The binding selectivity of HMGl proteins for four-way junction DNA is thus not a general property of all HMG box proteins. The folded domain of the HMGl proteins of Chironomus exhib- ited a high affhity to DNA only when the COOH terminally flanking, positively charged sequence was present. Addition of negative charges to the COOH-terminal portion of HMGl pro- teins decreased their binding affinity considerably.

EXPERIMENTAL PROCEDURES Construction of the Expression Vectors-Oligonucleotides for muta-

genesis were synthesized on a Milligene Cyclone plus DNA synthesizer. A PCR reaction (Mullis and Faloona, 1987) was used to mutagenize the ends of the coding regions of the cDNA clones pWS5.1 (cHMGla) and pWS2.3 (cHMGlb) (Wihiewski and Schulze, 1992). The bases before the start codons, before the internal Met-12 codon, and before an arti- ficially created Met codon at position 7 were changed to the sequence CAT, so that the resulting sequence CATATG could be recognized by restriction enzyme NdeI. Single substituted amino acid codons and new

10713

10714 DNA-binding Properties of Insect HMGl Proteins stop codons, which were followed by an EcoRI restriction site, were created at appropriate positions. The following oligonucleotides were used for the generation of 5'-ends of the coding regions of cHMGla (and cHMGldlO2, cHMGlaE8, cHMGlaS/98/D): GGATCCAGCATATGGC- AGAAAAACCAAAGCG; cHMGlb, GCCGACCCATATGGCAGA(A,C)A- AACCAAAGCG; 7/cHMGla, GGATCCAGCATATGCTITCCGCATACA- TGTTATGGC; lYcHMGla, GGGTGCATATGTTATGGCTTAACTCAG- CTAGAGAG;cHMGlaW/14/F,GGATCCAGCATATGGCAGAAAAACCA- AAGCGTCCTC'I"ITCCGCATACATGTTA'I"ITCTTAACTCAGC respec- tively. Oligonucleotides used for the construction of 3'-ends of the coding regions are: cHMGla and cHMGlb, GTAAAACGACGGCCAGT (-20

cHMGla, cHMGlaW/14/F), GGGAGAAlTCTTXATCTGATTCGTCTTC- sequencing primer (Boehringer Mannheim)); 7/cHMGla (and 11/

CTCCTCAT; cHMGla/lO2, GGGAGAATTCTTAGTCCTCTTCTTGC- TCTITTTGGC; cHMGlaS/98/D, GCGGAATTCTTAATCTGA?TCGTC- TTCCTCCTCATCATCCTCCGAGTCCTTCTTCTTATCCTTTTTGGC- GG; cHMGlaE8, GGGAGAATTClTATTCTTCTTCTT(C,A)'ITC~CT- TCTTCATCTGATTCGTC'ITCCTCCTCAT. PCR was performed with 40 p~ dNTP, 1 p~ of each primer, 1 unit of Taq DNA polymerase (Amer- sham, United Kingdom)/5O pl, and 1 x Taq buffer from the enzyme manufacturer. 30 cycles with 90 s a t 94 "C, 120 s at 50 "C (40 "C for -20 primer), and 90 s at 72 "C were run. The PCR products were cut with NdeI and EcoRI and ligated with the NdeI-EcoRI fragment of pET3a (Rosenberg et al., 1987) to give the expression constructs. The cloned mutagenized DNA insert was sequenced completely to verify that only the intended changes had occurred. For the induction of expression the constructs were transformed in Escherichia coli BL21(DE3) (Rosenberg et al., 1987).

Bacterial Expression of cHMGla, cHMGlb, and Mutant Proteins- Transformed E. coli BL21(DE3) cells were grown at 37 "C in LB me- dium (Sambrook et al., 1989) in the presence of 100 pg of ampicillin on a rotary shaker with 220 revolutions/min. Two ml of a 12-h-old culture were used to inoculate 200 ml of fresh LBIampicillin medium. The culture was grown to an optical density of 0.40 measured a t 600 nm. The expression of the HMG protein was then induced by adding isopro- pylthiogalactoside to a concentration of 1 m ~ . The induced culture was incubated for another 2 h with the same conditions. The cells were harvested in a centrifuge at 4 "C with 5000 x g. Cell pellets were frozen at -20 "C.

Extraction of cHMGl Proteins from Bacterial Cells-Bacterial pro- teins from 200-ml cultures were extracted with 1 ml of 5% HClO, by three thawing-freezing cycles. The cell supernatants were acidified with HCl to 0.35 M, precipitated with 6 volumes of acetone, and dried.

Purification of HMG Proteins and Peptides-The HMG proteins and their peptides were purified on a "Protein Plus" reverse-phase HPLC column (4.6 inner diameter x 250 mm, DuPont-Zorbax) using an ace- tonitrile gradient in 0.1% trifluoroacetic acidwater at a flow rate of 1.4 mVmin. The mutant protein cHMGlaE8 was rechromatographed on a MONO S column (Pharmacia) using a NaCl gradient in 50 mM HEPEW NaOH, pH 8.2. The outflow was monitored by a diode-array W-detector (SM5000, LDC Analytical) and by a fluorometer (SFM 25, Kontron Instruments) for tryptophan detection (excitation, 295 nm; emission, 345 nm). The eluted proteins were vacuum-concentrated and lyophi- lized. The homogeneity of the purified proteins and peptides was checked by means of SDS-PAGE (Laemmli, 1970). Bovine HMGl and HMG2 were extracted and purified according to Nicolas and Goodwin (1982).

Density Gradient Centrifugation and Gel Filtration-The centrifuga- tions were performed using a swing-out AH-650 (Sorvall) rotor. 3-12% sucrose gradients (4 ml) in 200 m~ NaCl, 50 m~ Tris-HC1, pH 7.8, were overlaid with 100 pl of protein samples and centrifuged at 45,000 revolutions/min a t 20 "C for 16 h. Subsequently, the 0.25-ml gradient fractions were concentrated and analyzed by means of SDS-PAGE. Gel permeation chromatography was carried out on a 55 x 1.6-cm inner diameter Sephadex 50 Fine column, equilibrated with 200 m~ NaCl, 50 m~ Tris-HC1, pH 7.8.200 p1 of samples containing 100-200 pg of protein were applied onto the top of the column and eluted at a flow rate of 6 mVh. The elution of proteins was monitored at 280 nm.

Protein Determination-The concentrations of proteins cHMGla and cHMGlb were determined spectrophotometrically a t 280 nm using ex- tinction coefficients E = 11,100 cm" M - ~ and E = 11,600 cm" "', respec- tively (Wisniewski and Schulze, 1992). The concentrations of mutant proteins were determined according to Bradford (1976) using protein cHMGla as a standard.

Cleavage of Proteins and Amino Acid Analysis-The degradation of proteins with BrCN and the amino acid analysis were performed as described previously (Wisniewski and Schulze, 1992). Cleavage of pro- tein cHMGlb with proteinase Glu-C (V8) was performed in 25 m~

ammonium carbonate buffer, pH 7.8, using a protein to enzyme ratio of 1O:l (w/w), at 25 "C for 6 h. The peptide containing the folded domain of protein cHMGla was prepared by trypsin cleavage a t 0 "C.

DNA Probes and Mobility Shift Assay-The 32P-labeled Cla-monomer of AT-rich satellite DNA of C. thummi was prepared as described pre- viously (Wisniewski and Schulze, 1992). The 33-bp DNA containing a 17-bp fragment of Cla-monomer was obtained by cutting the Cla-mon- omer with BsmI. The four-way junction c was prepared according to Bianchi (1988). The synthetic 30-, 35-, 40-, and 46-mer nucleotides were purified by HPLC, and subsequently one of the strands was labeled with T4 polynucleotide kinase. The annealing of the nucleotides was followed by electrophoretic purification of the cruciform DNA. Purified proteins and the labeled DNA were incubated together for 10 min at 20 "C in the binding buffer: 80 m~ NaCl, 1 m~ MgCl,, 0.01% bovine serum albumin, 8% glycerol, 10 m~ Tris-HC1, pH 7.9. The DNA-protein complexes were run on low ionic strength polyacrylamide gels (Chodosh et al., 1986).

Fluorescence Measurements-Fluorescence measurements were car- ried out on a Perkin-Elmer LS-50 spectrofluorometer. The emission spectra were recorded using 2.5 and 4 nm slits, for excitation and emission, respectively. The titrations with DNA were performed setting the monochromators a t 295 and 345 nm, and slits a t 5 and 10 nm, respectively.

RESULTS

Production and Purification of Bacterially Expressed Pro- teins cHMGla and cHMGlb and Their Mutants-The avail- ability of recombinant cHMGl proteins and of appropriate mu- tants of these proteins is essential for a biochemical characterization of these molecules and its interaction with DNA. In addition to the cHMGla and cHMGlb molecules, mu- tants were constructed coding for NH,-terminal deletions of 7 and 11 residues, respectively, (7JcHMGla and 11 JcHMGla), a COOH-terminal deletion of 11 residues (cHMGlaJ 1021, a COOH-terminal addition of 8 Glu residues (cHMGlaE8), and for point substitutions Ser-98 for Asp (cHMGlaSI98JD) and Phe-14 for Trp (cHMGlaWI14JF) (Fig. 1B). The crude protein extracts (Fig. 2B, lanes b and c) were purified by means of reverse-phase HPLC. Fig. 2A shows a typical chromatographic profile of recombinant cHMGl proteins extracted from E. coli. Except for the cHMGlaE8 mutant the purified proteins were homogeneous after a single chromatographic run on a C-18 column (Fig. 2B, lanes e , g, and h-k). The cHMGlaE8 fraction (Fig. 2 0 , lane m ) required another chromatographic step on an ion-exchange column (Fig. 2C). The electrophoretic analysis proved that the recombinant proteins were purified to homo- geneity. However, they exhibited higher electrophoretic mobili- ties in comparison to proteins extracted from cell cultures (Fig. 2B, lanes d-g). Probably the apparent lower molecular weights of recombinant molecules reflect the absence of post-transla- tional modifications that are characteristic for cHMGl proteins isolated from insect cells.

The peptides 13/cHMGld45 and 67/cHMGld113 were pre- pared by cleavage with BrCN as described previously (Wisniewski and Schulze, 1992) and the peptide l/cHMGla/20 by digestion with proteinase Glu-C (not shown). The large pep- tide l/cHMGla/84 was cut from cHMGla by limited trypsin digestion (Fig. 2 8 , inset 1. After 1-2 min of digestion, essentially only one large peptide was released from the protein. The pep- tide mapping and amino acid analysis revealed that this rela- tively trypsin-resistant fragment of cHMGla extends between the NH, terminus and residue 84 (not shown). This peptide containing the whole HMG box of cHMGla was purified (Fig. 2 B , lane k) and used in the binding studies.

cHMGla and cHMGlb in Solution Are Highly Asymmetric and Monomeric Molecules-Density gradient centrifugation showed that the proteins cHMGla and cHMGlb (not shown) moved in the centrifugal field with similar rate as the 12.5-kDa cytochrome c but different from the 26.5-kDa bovine HMGl and 25-kDa a-chymotrypsinogen (Fig. 3B). This indicated that cHMGla and cHMGlb are monomeric in solution. By means of

DNA-binding Properties of Insect HMGl Proteins 10715

A.

cHm;la cMlb WD HnCl B-box

B.

cHm;la 7/cHI(Cla ll/cHm;la l/cHm;la/20 13/cHm;la/45 67/cHm;la/113 cHm;la/84 cHm;la/lO2 cHm;laE8 cHm;laW/lI/F cHm;laS/%/D

1 Folded danain - 'IiKG-box'

85 161 io2 l i 3 Regulatory domains

Drosophila (Wagner et al., 1992), and rat HMGl (residues 8S-215; Bianchi et al., 1989). Dots indicate gaps introduced into the sequences to FIG. 1. Panel A, protein sequence alignment of cHMGla and cHMGlb from Chironomus (WiBniewski and Schulze, 1992), HMG-D from

maximize alignment. The numbers indicate the amino acid residues of cHMGla. The amino acid consensus sequence is written in boldface and

of the recombinant proteins and peptides used in DNA binding studies. Panel C, the postulated three-domain structure of insect HMGl proteins. underlined. The positions of the three helices in the HMGl B-domain box structure are from Weir et al. (1993). Panel B, a schematic representation

2 and - indicate the positions of charged residues present in the regulatory domains.

gel permeation chromatography on Sephadex G-50, we ob- served that cHMGla and cHMGlb exhibit Stokes' radii of 2.4 and 2.3 nm, respectively (Fig. 3A) . Using these values, we have calculated frictional ratios that are a measure of deviation from the ideal globular symmetry. From Equation 1 (Ackers, 1975):

f l f , = r,(3M X U ~ T ~ T V - " ~ , (Eq. 1)

where flfo is the frictional ratio; rs, the Stokes' radius; M, the molecular mass; 0, the partial specific volume; N , the Avogadro constant, we obtained flf, values of 1.5 for both cHMGl pro- teins when assuming a ij value of 0.75 cm3/g. These flf, values are characteristic of molecules with strong asymmetry.

Protein Fluorescence and Its Quenching upon DNA Binding-The insect HMGl proteins contain 3 Trp residues (Trp-14, Trp-42, and Trp-51) per molecule making these pro- teins suitable for fluorescence studies including determination of DNA-binding parameters. The fluorescence emission spectra of cHMGla and cHMGlb are shown in Fig. 4. When trypto- phans were selectively excited at 295 nm the maxima of the fluorescence peaks of cHMGla and cHMGlb were at 340-345 and 345-350 nm, respectively. These blue-shifted maxima rela- tive to that of free L-tryptophan (Arna = 350 nm) under the same conditions (not shown) can be ascribed to shielding of 1 or more of the Trp residues from the aqueous phase by the tertiary structure of the proteins (Eftink and Ghiron, 1976). The sub- stitution of the "p-14 by a Phe residue (mutant cHMGlaW/ 14P) sh ihd the emission maximum of cHMGla to 230 nm (Fig. 4). This blue shift of 15 nm indicates that 1 or both Trp residues remaining in cHMGlaW/14/F are in a nonaqueous environment. Difference of the spectra of cHMGla and cHMGlaW/14/F (Fig. 4) displays an emission maximum at 345-350 nm which indicates that Trp-14 present in wild type protein is located near the surface of the cHMGla molecule (Lakowicz, 1983).

Addition of DNA to cHMGla and cHMGlb caused quenching of protein fluorescence, with a observable blue shift of 10 nm in emission wavelength (Fig. 41, whereas the emission maximum of cHMGlaW/14/F did not shift upon DNA binding. This sug- gests that DNA binding may include Trp-14 of cHMGla/b or may induce a conformational change that affects the environ- ment of this fluorophore.

The deletion of the COOH-terminal stretch of mainly acidic residues of cHMGla resulted in a 1.6-fold increase of fluores- cence intensity of cHMGldlO2 in comparison to intact cHMGla (Fig. 4). This change in the quantum yield of the fluorophore(s) suggests that the COOH-terminal part of the cHMGl proteins interacts with the HMG box.

The fluorescence changes of cHMGl proteins upon its bind- ing to DNA were used for the determination of the binding stoichiometry.

DNA Binding Stoichiometry of Proteins cHMGla and cHMGlb-To estimate the number of base pairs of DNA ( n ) covered by a single molecule of protein, we titrated a fmed amount of poly(dA-dT)-poly(dA-dT) with cHMGla and cHMGlb (Fig. 5). In the titration experiments (Fig. 51, the quenching efficiency (Z) was estimated from the ratios of the slopes corresponding to all-bound and all-free ligand (Schwarz and Watanabe, 1983). The fluorescence of cHMGla and cHMGlb was quenched upon binding to DNA by 27 and 48%, respectively. Using these values the stoichiometry n was evalu- ated from Equation 2 (Watanabe, 1989):

n = Z c & , (Eq. 2)

where cp is the concentration of base pairs and co the value of intercept on the abscissa with linear extrapolation of the final line to F = 0. The sizes of the DNAstretches binding to cHMGla and cHMGlb were thus 11-13 and 6-7 bp, respectively. Similar titrations in the presence of E. coli DNA gave n values of 6-7

DNA-binding Properties of Insect HMGl Proteins

retention time.(min)

LI 1 a b r d e

.

f g h i j k

01 C JI ::

retention time.(min) m s a b c d e

fractions

cHMGla and cHMGlb and their mutants. A, the HCIO, extracts of FIG. 2. Purification and analysis of recombinant proteins

bacterial pellets were chromatographed on a reverse-phase column. The recombinant proteins were eluted as a dominant peak (shadowed). B, SDS-PAGE of the representative crude fractions and purified proteins. a , molecular weight standards (ovalbumin, M , 43,000; carbonic anhy- drase, M , 31,000; trypsin inhibitor, M , 21,500; lysozyme, M , 14,400); b and c, crude extracts of cHMGldlO2 and cHMGlb, respectively; d and f, cHMGla and cHMGlb isolated from insect cells; e, g, h-j recombinant cHMGla, cHMGlb, ll/cHMGla, 7/cHMGla, and cHMGldlO2, respec- tively; k, the enzymatically prepared folded domain of cHMGla. Inset of panel B Isolation of the peptide cHMG/84 containing the HMG box of cHMGla. The protein was digested with trypsin in 200 m~ NaCI, 20 mM Tris-HC1, pH 7.4, for different periods of time, and the products were resolved in a 15% polyacrylamide gel. The concentrations of cHMGla protein and trypsin were 1 and 0.1 mg/ml, respectively. The arrow indicates the position of the cHMGld84 peptide; R, the undigested reference protein cHMGla. C and D, purification of mutant protein cHMGlaE8. The protein fraction obtained by reverse chromatography (rn) was chromatographed on a Monos column (C). The collected frac- tions a-e were analyzed by means of SDS-PAGE (D). The fraction c contained homogenous cHMGlaE8 protein. s, molecular weight stand- ards (see panel B) .

and 4-5 bp, respectively (not shown). Despite the differences in the n values obtained with bacterial and synthetic DNA both experiments showed that the binding site of cHMGla is 1.5-2- fold longer than estimated for cHMGlb.

Fluorescence titrations a t lower, nanomolar concentrations of the proteins and DNA did not yield sufficiently precise data that could be used for reproducible determination of binding constants (not shown). Therefore, we decided to determine the binding affinity by means of mobility shift assay.

DNA Binding Affinity-The binding of cHMGla was inves- tigated using the 168- and 33-bp DNA containing the whole monomer (120 bp) and 17-bp fragment of the AT-rich C. thummi satellite DNA, respectively (Fig. 6). The gel bands were excised, and the radioactivity was determined by scintillation counting. Partial dissociation of the DNA-protein complexes during the electrophoretic separation made the measure of the bound DNA unreliable. Therefore, the protein binding was analyzed by measuring the decrease in free DNArather than the increase in complexes (Carey, 1988). The half-saturation value obtained in the titration of the short DNA is very close to because [total DNA I << [ total cHMGla I = [ free cHMGla I.

For the interaction of the short DNA with cHMGla, a value of of 18.3 nM was calculated. The Hill coefficient (Hill, 1910) close to 1 indicated that interaction of cHMGla with

A B "b - -. "-

StokAradus,(nm) wcrose.l%)

FIG. 3. cHMGla and cHMGlb molecules are highly asymmetric and monomeric molecules in solution. A, determination of the Stokes' radii of proteins cHMGla and cHMGlb by gel filtration chro- matography on Sephadex G-50. 2 0 0 4 samples containing 0.1 mg of cHMGla and cHMGlb were applied onto the top of the column equili- brated with 200 m~ NaCl, 50 m~ Tris-HCI, pH 7.8. The column outlet was monitored at 280 nm. The column was calibrated with cytochrome c ( M , 12,400; r, 1.7 nm), myoglobin ( M , 17,800) and a-chymotrypsinogen ( M , 25,000, rs 2.3 nm). B, density gradient centrifugation in 3-12% (w/v) sucrose gradient. 60-pl samples containing 30 pg of cHMGla and 30 pg of marker proteins: cytochrome c (cyt c, M , 12,400) and a-chymo- trypsinogen (a-chy, M , 25,000) (upper panel) or bovine HMGl ( M , 26,500) (lower panel) were layered onto preformed 4-ml gradients and centrifuged in an AH 650 rotor (Sorvall) a t 45,000 revolutiondmin for 16 h. The collected fractions were concentrated and electrophoresed in a 15% SDS gel.

wavelength.(nml

FIG. 4. Fluorescence emission spectra of cHMGla, cHMGlb, cHMGlaW/14/F and cHMGldlO2 in the absence (-1 or pres- ence (- - - -) of 60 p~ bp poly(dA-dT)poly(dA-dT). (.... ) A, the dif- ference spectrum of cHMGlafcHMGlaW/14/F. The buffer used in these experiments was 0.1 M NaC1, 10 mM Tris-HCI, pH 7.8, and 0.25 m~ EDTA and the protein concentration was 1.2 p f .

short DNA is noncooperative (Fig. 6, panel C), whereas the binding of cHMGla to the 168-bp DNA has a cooperative char- acter with the nH = 1.6 and a half-binding value of 7.5 m.

Protein cHMGla Does Not Discriminate between Linear and Cruciform DNA-In mobility shift experiments the binding of cHMGla to linear and cruciform DNA (Bianchi et al., 1989) was assayed. The insect cHMGla protein interacted strongly with both types of DNA (Fig. 71, whereas the bovine HMG2 protein exhibited high affinity binding only to cruciform DNA. Inter- estingly, we were unable to demonstrate this high affinity bind- ing of bovine HMGl molecules (Fig. 7, B and E; see "Discus- sion").

The Highly Charged Carboxyl-terminal Tail of HMGl Essen- tially Modulates the DNA binding-To localize the DNA-bind- ing domain of the cHMGl proteins, we have prepared a number

DNA-binding Properties of Insect HMGl Proteins

[cHMGlal, IpM)

FIG. 5. Proteins cHMGla and cHMGlb have different sizes of the binding sites on DNA. 7.2 x lo6 M (bp) of poly(dA-dT)-poly(dA- dT) were titrated with increasing amounts of cHMGla (panel A ) and cHMGlb (panel B ) in 80 m~ NaCl, 5 m~ Tris-HC1, pH 7.8. The intensity of fluorescence excited a t 295 nm was measured a t 345 nm. The straight lines obtained with proteins in the absence of DNA are represented by closed symbols. The site size is given by the molar ratio of base pairs to ligand saturation concentration, where the latter is given by the inter- cept of the saturation asymptote with the abscissa (Schwan and Wa- tanabe, 1983). A mean stoichiometry of about 13 and 7 base pairs/ cHMGla and cHMGlb molecule, respectively, were found.

A

[cHMGlal,(nM) FIG. 6. Binding of protein cHMGla to 33-bp DNA (panel A) and

1Wbp DNA (panel B) . 32P-Labeled DNAs (final concentration < 10 PM) were incubated with increasing amounts of cHMGla. Free DNA and protein complexes with DNAwere separated on 8% (33-bp DNA) and 4% (168-bp DNA) polyacrylamide gels, respectively. The bands containing free DNA were cut out from gels and were counted. C, quantification of the gel assay. Percent of the free DNA was plotted against ligand con- centration. The lines are theoretical curves calculated for the relation- ship Kd = [ free DNA J x [ free protein y[ complexes ], where Kd(. ,,) were 18.3 and 7.5 n~ for interaction of cHMGla with 33-bp DNA (open symbols) and 168-bp DNA (closed symbols). The data points were ob- tained from two gels each of two DNAs. Inset, Hill plot of the binding data, where 0, the fractional saturation of the DNA (0 = 1 - [free DNAMtotal DNA 11. The straight lines have slopes of 0.97 and 1.6 for the protein binding to 33- and 168-bp DNA, respectively.

of peptides and mutants of cHMGla (Fig. Ut) that were tested for binding to four-way junction DNA in mobility shift assays (Table I). Any of the short peptides obtained by cleavage of cHMGla with BrCN or proteinase Glu-C was unable to bind DNA even at concentrations of 1 p ~ . Similarly, NH,-terminal deletions impaired the binding of cHMGla to DNA, indicating that the highly conserved NH, terminus is essential for high afflnity interaction with DNA. The deletion of the 11 COOH- terminal mainly acidic residues resulted in an increase of DNA binding affinities to both types of DNA, whereas elongation of the COOH terminus of cHMGla by addition of 8 glutamic resi-

cHMGla HMGl HMG2 c 0

2

5 X

U L .v al c d .-

FIG. 7. cHMGla interacts equally strong with linear and four- way junction DNA. 1 nm of S2P-labeled four-way junction ( A X ) or 0.1 nM of 32P-labeled linear duplex DNA (D-F) were incubated with cHMGla (A and D), bovine HMGl ( B and E ) , or bovine HMG2 (C and F ) and electrophoresed through a 6% polyacrylamide gel. The gels were dried and autoradiographed. F , free DNA.

TABLE I Binding of cHMGla and its mutants to the four-way junction DNA The DNA binding was analyzed by means of mobility shift assay as

shown in Fig. 8. The radioactive spots were cut out from the dried gels and counted in a scintillation spectrometer.

10717

Proteidpeptide which 50% DNA was shiRed Protein conc. at

cHMGla (wild type) 7cHMGla lYcHMGla UcHMGY20 13kHMGld45 67kHMGld113 cHMGld84 cHMGldlO2 cHMGlaE8 cHMGlaW/14/F cHMGlaS/98/D

nM

15 75

150 >loo0 >loo0 >loo0

400 3

>loo0 15 75

dues reduced the DNA binding to an extent as to make it undetectable at the protein concentration used (Table I, and Fig. 8). The enzymatically isolated folded domain of cHMGla exhibited reduced affinity to DNA in comparison to the entire molecule indicating that the positively charged region (residues 85-101) significantly enhances the interaction with DNA. In- terestingly, this basic region contains a sequence motif KKSKK (residues 96-100) that is highly conserved from protozoans to human, and is a potential substrate for protein kinase C (Pear- son and Kemp, 1991). As phosphorylatioddephosphorylation of this residue would serve a mechanism regulating the binding of HMGl proteins to DNA, we produced a mutant of cHMGla protein in which Ser-98 was replaced by Asp (cHMGlaS/98/D). We observed that this single mutation, changing the charge balance within the COOH-terminal part of the cHMGla, de- creases the binding affinity by factor 5 (Table I).

DISCUSSION

In this study we describe structural features and DNA-bind- ing properties of the HMGl molecules present in Chironomus. In contrast to the well characterized HMGU2 proteins of ver- tebrates that interact preferentially with four-way junction DNA and show only moderate affinity for binding to single- stranded DNAor double-stranded DNA (K, 105-106 "'; Shooter et al., 1974; Goodwin et al., 1975; Butler et al., 19851, Chirono- nus cHMGla and cHMGlb are exhibiting a relatively high binding affinity toward linear DNA (IC,,,,, 7.5-20 x M) and

10718 DNA-binding Properties

0

MS 0 0 0 MU3OZ8g protein concentration,(nM)

FIG. 8. The modulation of the DNA binding of the HMG box by COOH-terminal regulatory domains. 1 nm of 32P-labeled four-way junction was incubated with increasing concentrations of cHMGld84 (A), cHMGldlO2 (B), cHMGla ( C ) , and cHMGlaE8 (D). The free DNA and protein-DNA complexes were resolved in a 6% polyacrylamide gel. The gels were dried and autoradiographed. F, free DNA.

" M

four-way junction DNA molecules. Thus, our data show that preferential binding of HMG boxes of HMG1/2 proteins to four- way junction DNA is not a general property of all HMG boxes.

The peptide cHMGld84 constituting the folded domain (with the complete HMG box motif) of cHMGla protein, exhib- ited only moderate DNA binding affinity. The addition of the basic region (residues 85-101) yielded molecules that bind to DNA with about 50-fold increased strength. This observation indicates that the basic region essentially participates in the interaction with DNA; however, the peptide comprising resi- dues 67-113 that contains this basic region but not the HMG box did not exhibit DNA binding.

The DNA binding affinity of the cHMGl proteins is depend- ent on the length of their negatively charged COOH-terminal tail. The deletion of the negatively charged residues enhances, whereas the addition of 8 glutamic residues inhibits the cHMGl binding to DNA. Possibly the stretch of 30 glutamic and aspartic residues present in calf HMGl protein is respon- sible for the relatively weak interaction of this protein with DNA. The increase of DNA-binding to HMG312 by deletion of its COOH-terminal fragment has been reported previously by other authors (Carballo et al., 1983; Sheflin et al., 19931, and the possible interaction between the COOH-terminal domain and the HMG box has been suggested (Cary et al., 1983; Butler et al., 1985).

On the basis of our DNA-binding data, we propose a three- domain structure of the cHMGla and cHMGlb proteins (Fig. 1C). The folded HMG box domain extends between the NH, terminus and residue 84 of cHMGl proteins. This part of the protein is involved directly in the interaction with DNA, how- ever, with only moderate strength (Fig. 7A). The second do- main, the positively charged region 85-101, strongly enhances the DNA binding, whereas the negatively charged tail of the cHMGl proteins inhibits this interaction. The charge balance between these contrary charged domains seems to be respon- sible for the resulting binding affinities of cHMGl proteins.

Strong binding of cHMGl molecules to different forms of DNAcorresponds well with the immunofluorescence decoration of polythene chromosomes with an anti-cHMGla antibody (WiBniewski and Schulze, 1992). Those experiments showed that the antibody decorated the whole chromosomes including

of Insect HMGl Proteins centromeres and puffs in a nearly uniform manner. Due to their abundancy and their size HMGl proteins could saturate un- bound DNA in chromatin. This may implicate that the HMGl molecules can be locally depleted from the DNA by competition with a regulatory protein like a transcriptional activator with a higher binding affinity toward a specific DNA sequence. The binding specificity of the transcriptional regulators is limited. For example, the lymphoid-specific transcriptional regulator (LEF-1) interacts with its specific target site 5'-CCITTGAA with only a 2040-fold higher affinity than with nonspecific DNA (Giese et al., 1991). Therefore, the exclusive binding of this regulatory protein only to its target sequence would re- quire saturation of the bulk of unrelated DNA sequences with other DNA-binding proteins such as HMG1/2.

The centrifugation experiments showed that cHMGla and cHMGlb are monomeric in solution. We were also unable to demonstrate a dimerization of these molecules by cross-linking with glutaraldehyde and by hybridization of cHMGla with cHMGlb.2 Our data agree well with the monomeric behavior of the B domain of the HMGl protein (Weir et al., 1993). The Stokes'radii obtained for the 12- and 12.9-kDa cHMGla and b, respectively, correspond to globular proteins with 25-26 kDa. This observation indicates that the cHMGl molecules are highly asymmetric and it correlates well with the recently pub- lished NMR structure (Weir et al., 1993) showing that the B- domain of bovine HMGl has a Gshaped tertiary structure. The size of the binding site of cHMGla on DNA is about a 1.5 of the size found for the interaction of protein cHMGlb. The differ- ence in the sizes does not correlate with the only slightly dif- ferent Stokes' radii of both cHMGl molecules. This may indi- cate some difference in their tertiary structures. Supportive evidence comes from the spectroscopic data which show that cHMGla and cHMGlb differ in maxima and intensities of their emission spectra as well as in the extent of the quenching upon DNA binding. These observations may implicate different bio- logical functions of cHMGla and cHMGlb.

Acknowledgments-We thank Dr. U. Grossbach for critical evalua- tion of this manuscript, Dr. K. Zechel (Max Planck Institut fiir Bio- physikaiische Chemie, Giittingen) for help in the fluorescence measure- ments, I. Streichhan for preparing the photographs, and P. Claus for critical reading of the manuscript.

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