Understanding the molecular mosaic of cardiotoxicity of light chains in plasma cell dyscrasias and cardiac light chain amyloidosis with the use of patient derived full-length light chains

Background

Cardiac light chain amyloidosis (AL-CA) is a life-threatening disease and the major determinant of prognosis in AL amyloidosis. The management of heart failure (HF) in AL is challenging and gold standard therapies for HF are poorly tolerated or ineffective. Cardiac toxicity of LCs in AL-CA is poorly understood and the comparison of cardiotoxicity of LCs derived from plasma cell dyscrasias (PCDs) such as multiple myeloma (MM) and monoclonal gammopathy of undetermined significance (MGUS), will improve our understanding of the mechanisms of cardiac damage.

Purpose

We aimed to 1) genetically identify and biotechnologically produce full-length LCs from patients with AL-CA, MM, MGUS or non-clonal LCs from healthy volunteers (HV), 2) identify LCs' cardiotoxicity and 3) investigate the underlying mechanisms of cardiotoxicity in vitro.

Methods

Bone marrow derived CD138+ cells from n=7 patients with AL-CA, n=2 patients with MM and n=2 patients with MGUS and peripheral blood mononuclear cells (PBMCs) from n=2 HV were isolated for RNA extraction and characterization of the LC gene family repertoire. At the protein level, LC expression was confirmed by immunoprecipitation in patients' serum followed by top-down proteomics. The overexpressed LC genes in each patient, encoding the full-length clonal LCs were cloned and produced in Shuffle E. coli cells. Two LCs were produced from HV based on the primary protein structure similarity with the patients' LCs. Primary adult ventricular murine cardiomyocytes (pAVMCs) were isolated and exposed at various LC concentrations for evaluation of cell death and investigation of the cardiotoxicity mechanisms via gene and protein expression. LCs folding, oligomerization and amyloidogenic potential were assessed via circular dichroism (CD), SDS page and electron microscopy respectively.

Results

We successfully identified the LCs responsible for the disease and isolated the respective proteins in all cases (7 AL-CA, 2 MM, 2 MGUS and 3 HV). Despite the similarity of the LCs in conformation as beta-sheet and oligomerization mainly as dimers, 5 out of 7 AL-CA derived LCs led to a different extent of cardiotoxicity in pAVMCs compared to the HV, MM and MGUS derived LCs which did not alter cell viability. Interestingly, these 5 LCs bared the highest amyloidogenic potency. LCs induced different molecular responses leading to cardiomyocyte death. AL-CA proteins κ-type induced apoptosis and overexpression of endoplasmic reticulum stress (ERS) markers while LCs λ-type increased unfolded protein response (UPR) markers and autophagy without inducing apoptosis. All LCs of κ-type including from MM and MGUS patients led to inteleukin-6 mediated inflammation indicating that this mechanism is independent of the observed toxicity.

Conclusions

AL-CA derived LCs induce cardiotoxicity, which correlates to their amyloidogenic potential via ERS, UPR, autophagy and apoptosis which can be considered targets for cardioprotection.

Funding Acknowledgement

Type of funding sources: Public Institution(s). Main funding source(s): Hellenic Foundation for Research and Innovation

Joint refinement as a tool for thorough comparison between NMR and X-ray data and structures of HU protein

Joint refinement, i.e., the simultaneous refinement of a structure against both nuclear magnetic resonance (NMR) spectroscopic and X-ray crystallographic data, was performed on the HU protein from Bacillus stearothermophilus (HUBst). The procedure was aimed at investigating the compatibility of the two data sets and at identifying conflicting information. Wherever important differences were found, such as peptide flips in the main-chain conformation, the data were further analyzed to find the cause. The NMR data showed some errors arising either from the manual interpretation of the spectra or from the incorrect account for spin diffusion. The most important artefact inherent to the X-ray data is the crystal packing of the molecules: the effects range from the limitation of the freedom of the flexible parts of the HUBst molecule to possibly one of the peptide flips.

Overexpression, purification, and characterization of a thermostable chitinase (Chi40) from Streptomyces thermoviolaceus OPC-520

A new procedure for the large-scale purification of the recombinant thermostable chitinase (Chi40) cloned from Streptomyces thermoviolaceus in various expression vectors in Escherichia coli is described. Chi40 was overproduced in the cytosolic and secreted forms. The cytosolic form (Chi40c) was highly overproduced and purified by metal-affinity and ion-exchange chromatography in large amounts. The protein was highly active and thermostable but not homogeneous, since a considerable proportion of the Chi40c protein was not correctly folded as determined by native polyacrylamide gel electrophoresis. The Chi40 protein secreted into the culture medium (Chi40s) was purified by hydrophobic interaction and ion-exchange chromatography and high amounts of correctly folded and active Chi40 protein could be recovered in a short time. The enzymatic activity of Chi40s on a synthetic and on its natural substrate, chitin, was studied. Thermostability measurements showed that Chi40 has a T(m) of 60.7 degrees C at neutral pH. (13)C-(15)N double-labeled recombinant Chi40s was also produced and purified from the pECHChi40-9 construct introduced into BL21trxB(DE3) cells grown in minimal medium in the presence of the paramagnetic elements [(13)C]glucose and (15)NH(4)Cl. The presented data open the possibility of an extensive structural study on Chi40s by X-ray crystallography and on enzyme-substrate interaction by NMR spectroscopy.

High resolution structural analyses of mutant chitinase A complexes with substrates provide new insight into the mechanism of catalysis

Chitinase A (ChiA) from the bacterium Serratia marcescens is a hydrolytic enzyme, which cleaves beta-1,4-glycosidic bonds of the natural biopolymer chitin to generate di-N-acetyl-chitobiose. The refined structure of ChiA at 1.55 A shows that residue Asp313, which is located near the catalytic proton donor residue Glu315, is found in two alternative conformations of equal occupancy. In addition, the structures of the cocrystallized mutant proteins D313A, E315Q, Y390F, and D391A with octa- or hexa-N-acetyl-glucosamine have been refined at high resolution and the interactions with the substrate have been characterized. The obtained results clearly show that the active site is a semiclosed tunnel. Upon binding, the enzyme bends and rotates the substrate in the vicinity of the scissile bond. Furthermore, the enzyme imposes a critical "chair" to "boat" conformational change on the sugar residue bound to the -1 subsite. According to our results, we suggest that residues Asp313 and Tyr390 along with Glu315 play a central role in the catalysis. We propose that after the protonation of the substrate glycosidic bond, Asp313 that interacts with Asp311 flips to its alternative position where it interacts with Glu315 thus forcing the substrate acetamido group of -1 sugar to rotate around the C2-N2 bond. As a result of these structural changes, the water molecule that is hydrogen-bonded to Tyr390 and the NH of the acetamido group is displaced to a position that allows the completion of hydrolysis. The presented results suggest a mechanism for ChiA that modifies the earlier proposed "substrate assisted" catalysis.

Modular structure, local flexibility and cold-activity of a novel chitobiase from a psychrophilic Antarctic bacterium

The gene archb encoding for the cell-bound chitobiase from the Antarctic Gram-positive bacterium Arthrobacter sp. TAD20 was cloned and expressed in Escherichia coli in a soluble form. The mature chitobiase ArChb possesses four functionally independent domains: a catalytic domain stabilized by Ca(2+), a galactose-binding domain and an immunoglobulin-like domain followed by a cell-wall anchorage signal, typical of cell-surface proteins from Gram-positive bacteria. Binding of saccharides was analyzed by differential scanning calorimetry, allowing to distinguish unequivocally the catalytic domain from the galactose-binding domain and to study binding specificities. The results suggest that ArChb could play a role in bacterium attachment to natural hosts. Kinetic parameters of ArChb demonstrate perfect adaptation to catalysis at low temperatures, as shown by a low activation energy associated with unusually low K(m) and high k(cat) values. Thermodependence of these parameters indicates that discrete amino acid substitutions in the catalytic center have optimized the thermodynamic properties of weak interactions involved in substrate binding at low temperatures. Microcalorimetry also reveals that heat-lability, a general trait of psychrophilic enzymes, only affects the active site domain of ArChb.

Cloning, sequences, and characterization of two chitinase genes from the Antarctic Arthrobacter sp. strain TAD20: isolation and partial characterization of the enzymes

Arthrobacter sp. strain TAD20, a chitinolytic gram-positive organism, was isolated from the sea bottom along the Antarctic ice shell. Arthrobacter sp. strain TAD20 secretes two major chitinases, ChiA and ChiB (ArChiA and ArChiB), in response to chitin induction. A single chromosomal DNA fragment containing the genes coding for both chitinases was cloned in Escherichia coli. DNA sequencing analysis of this fragment revealed two contiguous open reading frames coding for the precursors of ArChiA (881 amino acids [aa]) and ArChiB (578 aa). ArChiA and ArChiB are modular enzymes consisting of a glycosyl-hydrolase family 18 catalytic domain as well as two and one chitin-binding domains, respectively. The catalytic domain of ArChiA exhibits 55% identity with a chitodextrinase from Vibrio furnissii. The ArChiB catalytic domain exhibits 33% identity with chitinase A of Bacillus circulans. The ArChiA chitin-binding domains are homologous to the chitin-binding domain of ArChiB. ArChiA and ArChiB were purified to homogeneity from the native Arthrobacter strain and partially characterized. Thermal unfolding of ArChiA, ArChiB, and chitinase A of Serratia marcescens was studied using differential scanning calorimetry. ArChiA and ArChiB, compared to their mesophilic counterpart, exhibited increased heat lability, similar to other cold-adapted enzymes.

PCR performance of the B-type DNA polymerase from the thermophilic euryarchaeon Thermococcus aggregans improved by mutations in the Y-GG/A motif

The effect of mutations in the highly conserved Y-GG/A motif of B-type DNA polymerases was studied in the DNA polymerase from the hyperthermophilic euryarchaeon Thermococcus aggregans. This motif plays a critical role in the balance between the synthesis and degradation of the DNA chain. Five different mutations of the tyrosine at position 387 (Tyr387-->Phe, Tyr387-->Trp, Tyr387-->His, Tyr387-->Asn and Tyr387-->Ser) revealed that an aromatic ring system is crucial for the synthetic activity of the enzyme. Amino acids at this position lacking the ring system (Ser and Asn) led to a significant decrease in polymerase activity and to enhanced exonuclease activity, which resulted in improved enzyme fidelity. Exchange of tyrosine to phenylalanine, tryptophan or histidine led to phenotypes with wild-type-like fidelity but enhanced PCR performance that could be related to a higher velocity of polymerisation. With the help of a modelled structure of T.aggregans DNA polymerase, the biochemical data were interpreted proposing that the conformation of the flexible loop containing the Y-GG/A motif is an important factor for the equilibrium between DNA polymerisation and exonucleolysis.

Molecular organization of the alkali-insoluble fraction of Aspergillus fumigatus cell wall

Physical and biological properties of the fungal cell wall are determined by the composition and arrangement of the structural polysaccharides. Cell wall polymers of fungi are classically divided into two groups depending on their solubility in hot alkali. We have analyzed the alkali-insoluble fraction of the Aspergillus fumigatus cell wall, which is the fraction believed to be responsible for fungal cell wall rigidity. Using enzymatic digestions with recombinant endo-beta-1,3-glucanase and chitinase, fractionation by gel filtration, affinity chromatography with immobilized lectins, and high performance liquid chromatography, several fractions that contained specific interpolysaccharide covalent linkages were isolated. Unique features of the A. fumigatus cell wall are (i) the absence of beta-1,6-glucan and (ii) the presence of a linear beta-1, 3/1,4-glucan, never previously described in fungi. Galactomannan, chitin, and beta-1,3-glucan were also found in the alkali-insoluble fraction. The beta-1,3-glucan is a branched polymer with 4% of beta-1,6 branch points. Chitin, galactomannan, and the linear beta-1, 3/1,4-glucan were covalently linked to the nonreducing end of beta-1, 3-glucan side chains. As in Saccharomyces cerevisiae, chitin was linked via a beta-1,4 linkage to beta-1,3-glucan. The data obtained suggested that the branching of beta-1,3-glucan is an early event in the construction of the cell wall, resulting in an increase of potential acceptor sites for chitin, galactomannan, and the linear beta-1,3/1,4-glucan.

Structures of chitobiase mutants complexed with the substrate Di-N-acetyl-d-glucosamine: the catalytic role of the conserved acidic pair, aspartate 539 and glutamate 540

The catalytic domain of chitobiase (beta-N-1-4 acetylhexosaminidase) from Serratia marcescens, is an alpha/beta TIM-barrel. This enzyme belongs to family 20 of glycosyl hydrolases in which a conserved amino acid pair, aspartate-glutamate, is present (Asp539-Glu540). It was proposed that catalysis by this enzyme family is carried out by glutamate 540 acting as a proton donor and by the acetamido group of the substrate as a nucleophile. We investigated the role of Asp539 and Glu540 by site-directed mutagenesis, biochemical characterization and by structural analyses of chitobiase -substrate co-crystals. We found that both residues are essential for chitobiase activity. The mutations, however, led to subtle changes in the catalytic site. Our results support the model that Glu540 acts as the proton donor and that Asp539 acts in several different ways. Asp539 restrains the acetamido group of the substrate in a specific orientation by forming a hydrogen bond with N2 of the non-reduced (-1) sugar. In addition, this residue participates in substrate binding. It is also required for the correct positioning of Glu540 and may provide additional negative charge at the active site. Thus, these biochemical and structural studies provide a molecular explanation for the functional importance and conservation of these residues.

Structure and dynamics of the DNA binding protein HU from Bacillus stearothermophilus by NMR spectroscopy

The DNA-binding protein HU from Bacillus stearothermophilus (HUBst) is a dimer with a molecular weight of 195 kDa that is capable of bending DNA. An x-ray structure has been determined previously [Tanaka et al. 1984) Nature, vol. 310, pp. 376-381], but no structure could be established for a large part of the supposed DNA-binding beta-arms. Distance geometry and restrained molecular dynamics using nmr restraints were used to generate a set of 25 structures. These structures display a backbone rms deviation (RMSD) of 0.36 A for the well-defined region (residues 2-54 and 75-90). The structure of the core is very similar to that observed in the x-ray structure, with a pairwise RMSD of 1.06 A. The structure of the beta-hairpin arm contains a double flip-over at the prolines in the two strands of the beta-arm. Heteronuclear 15N relaxation measurements indicate that the beta-arm and the tip of the beta-arm is flexible. This explains the disorder observed in the solution and x-ray structures of the beta-arm with respect to the core of the protein. Overlayed onto itself the beta-arm is better defined, with a backbone RMSD of 1.0 A calculated for residues 54-59 and 69-74. The tip of the arm adopts a well-defined 4 : 6 beta-hairpin conformation. Changes in amide 15N and 1H chemical shifts upon titrating DNA are most pronounced for the residues in the beta-hairpin arm and for the residues in the second half of the third alpha-helix. Heteronuclear 15N relaxation data for free and complexed HUBst show that that the arms become structured upon DNA binding. Together with chemically induced nuclear polarization measurements on a mutant HUBst (M69Y; V76Y) this shows that the beta-hairpin arm is involved in direct DNA interaction.

Cloning, overproduction, purification and crystallization of the DNA binding protein HU from the hyperthermophilic eubacterium Thermotoga maritima

The humar gene encoding for the histone-like DNA-binding protein HU from the hyperthermophilic eubacterium Thermotoga maritima was efficiently overexpressed in Escherichia coli under the T7 promoter. The HU protein was purified using SP-Sepharose ion-exchange and heparin-affinity chromatography and was successfully crystallized in ammonium sulfate. The crystals were grown in the tetragonal form in space group P43 or P41 and have unit-cell dimensions a = b = 46.12, c = 77.56 A, alpha = beta = gamma = 90 degrees. The crystals diffract X-rays to 1.6 A resolution using synchrotron radiation and are suitable for determination of the HU structure at high resolution.

Serratia marcescens chitobiase is a retaining glycosidase utilizing substrate acetamido group participation

The stereochemistry of the reaction catalysed by Serratia marcescens chitobiase was determined by HPLC separation of the anomers of N-acetylglucosamine produced during the hydrolysis of p-nitrophenyl N-acetyl-beta-d-glucosaminide (PNP-GlcNAc). In the early stages of the reaction, the beta-anomer was found to prevail, whereas the alpha-anomer dominated at mutarotation equilibrium. This established that chitobiase hydrolyses glycosidic bonds with overall retention of the anomeric configuration. Chitobiase-catalysed hydrolysis of PNP-GlcNAc was competitively inhibited by a series of chito-oligosaccharides (degree of polymerization 2-5) that were selectively de-N-acetylated at their non-reducing end. The results are in accord with the participation of the acetamido group at C-2 of the substrate in the catalytic mechanism of chitobiase and related enzymes.

Cloning, sequencing, characterization, and expression of an extracellular alpha-amylase from the hyperthermophilic archaeon Pyrococcus furiosus in Escherichia coli and Bacillus subtilis

A gene encoding a highly thermostable extracellular alpha-amylase from the hyperthermophilic archaeon Pyrococcus furiosus was identified. The gene was cloned, sequenced, and expressed in Escherichia coli and Bacillus subtilis. The gene is 1383 base pairs long and encodes a protein of 461 amino acids. The open reading frame of the gene was verified by microsequencing of the recombinant purified enzyme. The deduced amino acid sequence is 25 amino acids longer at the N terminus than that determined by sequencing of the purified protein, suggesting that a leader sequence is removed during transport of the enzyme across the membrane. The recombinant alpha-amylase was biochemically characterized and shows an activity optimum at pH 4.5, whereas the optimun temperature for enzymatic activity is close to 100 degrees C. alpha-Amylase shows sequence homology to the other known alpha-amylases and belongs to family 13 of glycosyl hydrolases. This extracellular alpha-amylase is not homologous to the subcellular alpha-amylase previously isolated from the same organism.

Molecular cloning, structural analysis, and expression in Escherichia coli of a chitinase gene from Enterobacter agglomerans

The gene chiA, which codes for endochitinase, was cloned from a soilborne Enterobacter agglomerans. Its complete sequence was determined, and the deduced amino acid sequence of the enzyme designated Chia_Entag yielded an open reading frame coding for 562 amino acids of a 61-kDa precursor protein with a putative leader peptide at its N terminus. The nucleotide and polypeptide sequences of Chia_Entag showed 86.8 and 87.7% identity with the corresponding gene and enzyme, Chia_Serma, of Serratia marcescens, respectively. Homology modeling of Chia_Entag's three-dimensional structure demonstrated that most amino acid substitutions are at solvent-accessible sites. Escherichia coli JM109 carrying the E. agglomerans chiA gene produced and secreted Chia_Entag. The antifungal activity of the secreted endochitinase was demonstrated in vitro by inhibition of Fusarium oxysporum spore germination. The transformed strain inhibited Rhizoctonia solani growth on plates and the root rot disease caused by this fungus in cotton seedlings under greenhouse conditions.

Identification of candidate active site residues in lysosomal beta-hexosaminidase A

The beta-hexosaminidases (Hex) catalyze the cleavage of terminal amino sugars on a broad spectrum of glycoconjugates. The major Hex isozymes in humans, Hex A, a heterodimer of alpha and beta subunits (alphabeta), and Hex B, a homodimer of beta subunits (betabeta), have different substrate specificities. The beta subunit (HEXB gene product), hydrolyzes neutral substrates. The alpha subunit (HEXA gene product), hydrolyzes both neutral and charged substrates. Only Hex A is able to hydrolyze the most important natural substrate, the acidic glycolipid GM2 ganglioside. Mutations in the HEXA gene cause Tay-Sachs disease (TSD), a GM2 ganglioside storage disorder. We investigated the role of putative active site residues Asp-alpha258, Glu-alpha307, Glu-alpha323, and Glu-alpha462 in the alpha subunit of Hex A. A mutation at codon 258 which we described was associated with the TSD B1 phenotype, characterized by the presence of normal amounts of mature but catalytically inactive enzyme. TSD-B1 mutations are believed to involve substitutions of residues at the enzyme active site. Glu-alpha307, Glu-alpha323, and Glu-alpha462 were predicted to be active site residues by homology studies and hydrophobic cluster analysis. We used site-directed mutagenesis and expression in a novel transformed human fetal TSD neuroglial (TSD-NG) cell line (with very low levels of endogenous Hex A activity), to study the effects of mutation at candidate active site residues. Mutant HEXA cDNAs carrying conservative or isofunctional substitutions at these positions were expressed in TSD-NG cells. alphaE323D, alphaE462D, and alphaD258N cDNAs produced normally processed peptide chains with drastically reduced activity toward the alpha subunit-specific substrate 4MUGS. The alphaE307D cDNA produced a precursor peptide with significant catalytic activity. Kinetic analysis of enzymes carrying mutations at Glu-alpha323 and Asp-alpha258 (reported earlier by Bayleran, J., Hechtman, P., Kolodny, E., and Kaback, M. (1987) Am. J. Hum. Genet. 41,532-548) indicated no significant change in substrate binding properties. Our data, viewed in the context of homology studies and modeling, and studies with suicide substrates, suggest that Glu-alpha323 and Asp-alpha258 are active site residues and that Glu-alpha323 is involved in catalysis.

Bacterial chitobiase structure provides insight into catalytic mechanism and the basis of Tay-Sachs disease

Chitin, the second most abundant polysaccharide on earth, is degraded by chitinases and chitobiases. The structure of Serratia marcescens chitobiase has been refined at 1.9 A resolution. The mature protein is folded into four domains and its active site is situated at the C-terminal end of the central (beta alpha)8-barrel. Based on the structure of the complex with the substrate disaccharide chitobiose, we propose an acid-base reaction mechanism, in which only one protein carboxylate acts as catalytic acid, while the nucleophile is the polar acetamido group of the sugar in a substrate-assisted reaction. The structural data lead to the hypothesis that the reaction proceeds with retention of anomeric configuration. The structure allows us to model the catalytic domain of the homologous hexosaminidases to give a structural rationale to pathogenic mutations that underlie Tay-Sachs and Sandhoff disease.

The crystal structure of the complexes of concanavalin A with 4'-nitrophenyl-alpha-D-mannopyranoside and 4'-nitrophenyl-alpha-D-glucopyranoside

Concanavalin A (Con A) is the best-known plant lectin and has important in vitro biological activities arising from its specific saccharide-binding ability. Its exact biological role still remains unknown. The complexes of Con A with 4'-nitrophenyl-alpha-D-mannopyranoside (alpha-PNM) and 4'-nitrophenyl-alpha-D-glucopyranoside (alpha-PNG) have been crystallized in space group P2(1)2(1)2 with cell dimensions a = 135.19 A, b = 155.38 A, c = 71.25 A and a = 134.66 A, b = 155.67 A, and c = 71.42 A, respectively. X-ray diffraction intensities to 2.75 A for the alpha-PNM and to 3.0 A resolution for the alpha-PNG complex have been collected. The structures of the complexes were solved by molecular replacement and refined by simulated annealing methods to crystallographic R-factor values of 0.185/0.186 and free-R-factor values of 0.260/0.274, respectively. In both structures, the asymmetric unit contains four molecules arranged as a tetramer, with approximate 222 symmetry. A saccharide molecule is bound in the sugar-binding site near the surface of each monomer. The nonsugar (aglycon) portion of the compounds used helps to identify the exact orientation of the saccharide in the sugar-binding pocket and is involved in major interactions between tetramers. The hydrogen bonding network in the region of the binding site has been analyzed, and only minor differences with the previously reported Con A-methyl-alpha-D-mannopyranoside complex structure have been observed. Structural differences that may contribute to the slight preference of the lectin for mannosides over glucosides are discussed. Calculations indicate a negative electrostatic surface potential for the saccharide binding site of Con A, which may be important for its biological activity. It is also shown in detail how a particular class of hydrophobic ligands interact with one of the three so-called characteristic hydrophobic sites of the lectins.

N-Acetylglucosaminidase (chitobiase) from Serratia marcescens: gene sequence, and protein production and purification in Escherichia coli

The chitobiase (Chb) encoding gene (chb) from Serratia marcescens (Sm) has been cloned, sequenced and expressed in Escherichia coli (Ec). Sequencing has revealed an open reading frame encodinga protein of 885 amino acids (aa). Ec cells harbouring plasmids containing chb can produce enzymatically active Sm Chb protein which is secreted into the periplasm. An efficient purification scheme using cation-exchange chromatographyis presented. This yields about 3 mg of > 95% pure Sm Chb per litre of Ec culture. The deduced aa sequence is 27-aa longer at the N terminus than that determined by sequencing of the purified protein, suggesting that a leader sequence is removed during transport of the enzyme across the cell membrane. Comparison with the other members of the family 20 of glycosyl hydrolases revealed that Chb has a conserved central region which aligns with almost all members of this family. According to the crystal structure of Sm Chb, this region comprises the catalytic domain of Chb which has an alpha/beta barrel fold.

Solution structure of the HU protein from Bacillus stearothermophilus

The histone-like protein HU from Bacillus stearothermophilus is a dimer with a molecular mass of 19.5 kDa that is capable of bending DNA. An X-ray structure has been determined, but no structure could be established for a large part of the supposed DNA-binding beta-arms. Using distance and dihedral constraints derived from triple-resonance NMR data of a 13C/15N doubly-labelled HU protein 49 distance geometry structures were calculated, which were refined by means of restrained Molecular Dynamics. From this set a total of 25 refined structures were selected having low constraint energy and few constraint violations. The ensemble of 25 structures display a root-mea-square co-ordinate deviation of 0.36 A with respect to the average structure, calculated over the backbone heavy atoms of residues 2 to 54 and 75 to 90 (and residues 2' to 54' and 75' to 90' of the second monomer). The structure of the core is very similar to that observed in the X-ray structure, with a pairwise r.m.s.d. of 1.06 A. The structure of the beta-hairpin arm contains a double flip-over at the prolines in the two strands of the beta-arm. Strong 15N-NH heteronuclear nuclear Overhauser effects indicate that the beta-arm and especially the tip is flexible. This explains the disorder observed in the solution and X-ray structures of the beta-arm, in respect of the core of the protein. Overlayed onto itself the beta-arm is better defined, with an r.m.s.d. of 1.0 A calculated over the backbone heavy atoms of residues 54 to 59 and 69 to 74. The tip of the arm adopts a well-defined 4:6 beta-hairpin conformation similar to the iron co-ordinating beta-arms of rubredoxin.

Cloning and primary structure of the chiA gene from Aeromonas caviae

The chiA gene from Aeromonas caviae encodes an extracellular chitinase, 865 amino acids long, that shows a high degree of similarity to chitinase A of Serratia marcescens. Expression in Escherichia coli yielded an enzymatically active protein from which a leader sequence was removed, presumably during transport of the enzyme across the cell membrane.

Crystal structure of a bacterial chitinase at 2.3 A resolution

BACKGROUND

Chitinases cleave the beta-1-4-glycosidic bond between the N-acetyl-D-glucosamine units of which chitin is comprised. Chitinases are present in plants, bacteria and fungi, but whereas structures are available for two prototypic plant enzymes, no structure is available for a bacterial or fungal chitinase.

RESULTS

To redress this imbalance, the structure of native chitinase A from Serratia marcescens has been solved by multiple isomorphous replacement and refined at 2.3 A resolution, resulting in a crystallographic R-factor of 16.2%. The enzyme comprises three domains: an all beta-strand amino-terminal domain, a catalytic alpha/beta-barrel domain, and a small alpha+beta-fold domain. There are several residues with unusual geometries in the structure. Structure determination of chitinase A in complex with N,N',N",N"'-tetra-acetylo-chitotetraose, together with biochemical and sequence analysis data, enabled the positions of the active-site and catalytic residues to be proposed.

CONCLUSIONS

The reaction mechanism seems to be similar to that of lysozyme and most other glycosylhydrolases, i.e. general acid-base catalysis. The role of the amino-terminal domain could not be identified, but it has similarities to the fibronectin III domain. This domain may possibly facilitate the interaction of chitinase A with chitin.

1H, 13C, and 15N resonance assignments and secondary structure analysis of the HU protein from Bacillus stearothermophilus using two- and three-dimensional double- and triple-resonance heteronuclear magnetic resonance spectroscopy

Nearly complete 1H, 13C, and 15N resonance assignments have been obtained for the protein HU from Bacillus stearothermophilus (dimer, 19.5 kDa) using double- and triple-resonance 2D and 3D NMR experiments. This has resulted in assignments of 91% of the observable protons, 98% of all 13C, and 92% of all 15N nuclei. NOEs obtained from a 3D time-shared NOESY-(13C,15N)-HSQC spectrum, exchange data of amide protons, and chemical shifts of the 1H alpha, 1HN, 13C beta, 13C alpha, 13CO, and 15N nuclei have been used to identify the secondary structure elements. Three alpha-helices (residues 3-13, 18-37, and 83-90) and three extended strands (residues 40-45, 48-62, and 67-82) have been found in HU. The arrangement of these elements of secondary structure is very similar to the X-ray structure [Tanaka et al. (1984) Nature 310, 376-381; White et al. (1989) Proteins 5, 281-288]. The conformation of the proposed DNA-binding region of HU, i.e., an antiparallel beta-hairpin, was not observed previously in the X-ray structure. In the NMR structure long range NOEs in the beta-arm region (residues 53-76) suggest a distortion between residue Pro-72 and Ala-73 and between Pro-63 and Gln-64 with concomitant distortions in the opposite strand. The NOE data indicate further that the loop region in the DNA-binding arms of HU is arranged as a type I beta-turn from Pro-63 to Gly-66.

Evolutionary divergence and conservation of trypsin

The trypsin sequences currently available in the data banks have been collected and aligned using first the amino acid sequence homology and, subsequently, the superposed crystal structures of trypsins from the cow, the bacterium Streptomyces griseus and the fungus Fusarium oxysporum. The phylogenetic tree constructed according to this multiple alignment is consistent with a continuous evolutionary divergence of trypsin from a common ancestor of both prokaryotes and eukaryotes. Comparison of crystal structures reveals a strict conservation of secondary structure. Similarly, in the alignment of all the sequences, insertions and deletions occur only in regions corresponding to loops between the secondary structure elements in the known crystal structures. The conserved residues cluster around the active site. Almost all conserved residues can be associated with one of the basic functional features of the protein: zymogen activation, catalysis and substrate specificity. In contrast, the residues of the hydrophobic core of the protein and the calcium ion binding sites are generally not conserved. The conserved features of trypsin and the nature of the conservation are discussed in detail.

Cloning and expression of Saccharomyces cerevisiae copper-metallothionein gene in Escherichia coli and characterization of the recombinant protein

The gene sequences for intact and truncated forms of copper-binding metallothionein from Saccharomyces cerevisiae were cloned and overexpressed in Escherichia coli BL21(DE3)pLysE cells. In contrast to several other genes, the intact and truncated metallothionein genes are amplified in the polymerase chain reaction when Mg2+ is replaced by Co2+. The recombinant truncated protein binds copper in vivo and in vitro. A ratio of 8 Cu/12 cysteines was determined from atomic absorption, X-ray fluorescence and amino acid analysis. Extended X-ray absorption spectroscopy indicates that all Cu is in Cu(I) form and coordinated to three S atoms.

Crystallization of recombinant chitobiase from Serratia marcescens

We are currently investigating the biochemical and structural properties of both chitin degrading enzymes chitinase and chitobiase from Serratia marcescens. Previously we have reported the first crystallization and characterization of chitinase crystals (Vorgias et al., 1992). In this communication we present the first crystallization of chitobiase. The protein was synthesized in Escherichia coli and purified to homogeneity using cation exchange chromatography and fast protein liquid chromatography. The crystals have the shape of small prisms and the space group is P2(1) with beta = 101.0 degrees and unit cell dimensions a = 63.2 A, b = 133.2 A, c = 55.1 A. They diffract X-rays to about 2.5 A resolution and are suitable for three-dimensional structural analysis.

Crystallization of recombinant chitinase from the cloned chiA gene of Serratia marcescens

The chiA gene encoding for the chitinase enzyme from Serratia marcescens was efficiently overexpressed under the pL promoter and the enzyme was secreted into the growth medium. The chitinase was purified to homogeneity using affinity chromatography on a Phenyl-Sepharose column and the protein was successfully crystallized. The crystals are presently in the form of small needles in space group C222(1) and have unit cell dimensions a = 204(+/- 0.5) A, b = 134(+/- 0.5) A, c = 60(+/- 0.5) A. The crystals diffract X-rays to about 3 A resolution and are suitable for three-dimensional structural analysis.

The DNA-binding protein HU from mesophilic and thermophilic bacilli: gene cloning, overproduction and purification

The major histone-like bacterial protein (HU)-encoding genes (hup) from five different Bacilli have been cloned, sequenced and overexpressed in Escherichia coli. The five Bacilli selected are closely related, but have different optimum growth temperatures: greater than 70 degrees C for Bacillus caldolyticus and B. caldotenax; 60-65 degrees C for B. stearothermophilus (Bst); 37 degrees C for B. subtilis and 30 degrees C for B. globigii. The deduced amino acid (aa) sequences from the three thermophiles are identical. Those from the two mesophiles are also identical and differ from those of the thermophiles at eleven aa positions. The mesophilic proteins have an extra two aa at the C terminus. Cells harbouring plasmids containing the hup genes can produce HU. An efficient purification scheme using cation-exchange chromatography and fast protein liquid chromatography is presented. This gives approx. 30-40 mg of more than 95% pure Bst HU per litre of E. coli culture.

Overexpression and purification of the galactose operon enzymes from Escherichia coli

A convenient new procedure for the purification of galactokinase, galactose-1-phosphate uridyltransferase, and UDP-galactose 4-epimerase overexpressed in Escherichia coli is presented. The procedure is shorter than any other described in the literature and facilitates the purification of the three recombinant enzymes in considerable amounts and at high purity and specific activity. The purified gal operon enzymes were biochemically characterized by gel-filtration column chromatography and isoelectric focusing, and the Km values for their substrates were determined.

A rapid purification procedure of recombinant integration host factor from Escherichia coli

A rapid procedure for the large-scale isolation of recombinant integration host factor (IHF) protein from Escherichia coli is presented. The protein was overproduced in the E. coli K5746 strain, whose construction has already been described. The procedure consists of a mild extraction of protein and fractionation by ammonium sulfate. A single-step affinity chromatography on heparin-Sepharose provided very pure IHF protein. A Mono-S FPLC column was used to highly concentrate the pure IHF for crystallization trials. Attempts to crystallize IHF produced small stable crystals that have a large number of molecules in the asymmetric unit and to date diffract poorly. Further attempts to crystallize IHF under other conditions as well as in a complex with the putative DNA binding site are underway.

Cloning, overexpression, purification and crystallisation of ribosomal protein L9 from Bacillus stearothermophilus

The cloning, sequencing and overexpression of the gene coding for Bacillus stearothermophilus ribosomal protein L9 is described. The sequence corresponds directly to that presented for the protein itself by classical methods, differing at only a few amino acid positions. The purification and crystallisation of the corresponding L9 protein is presented. The crystals are isomorphous to those described for L9 obtained by conventional methods.

The thermostability of DNA-binding protein HU from bacilli

The primary and tertiary structures of DNA-binding protein HU from Bacillus stearothermophilus are already known. The primary structure has been previously determined for HU from the closely related B. globigii and the determinations of the sequences from B. caldolyticus and B. subtilis are described here. These bacteria have optimum growth temperatures of greater than 70 degrees C (B. caldolyticus), 65 degrees C (B. stearothermophilus), 37 degrees C (B. subtilis) and 30 degrees C (B. globigii). In vitro measurements from circular dichroic spectra described here give Tm values reflecting these growth temperatures, of 68, 64, 43 and 41 degrees C respectively. We discuss here the relative thermostability of the four proteins in terms of the amino acid differences between the sequences and the three-dimensional model of the B. stearothermophilus HU. The current model for the interaction of the protein with DNA is only discussed in terms of its relevance with regard to thermostability.

Colchicine, colcemide and cytochalasin B do not affect translocation of the glucocorticoid hormone-receptor in rat thymocytes or Ehrlich ascites cells

The involvement of intracellular cytoskeletal elements in the translocation of the dexamethasone-receptor complex from the cytoplasm to the nucleus was studied using the cytoskeleton-disrupting agents colcemide, colchicine and cytochalasin B. These compounds did not affect the translocation of the hormone-receptor complex. We conclude that microfilaments and microtubules do not play a role in the translocation of the glucocorticoid hormone-receptor complex from the cytoplasm to the nucleus.

Interaction in vitro of non-epithelial intermediate filament proteins with supercoiled plasmid DNA

Sucrose gradient analysis of reaction products obtained from non-epithelial intermediate filament (IF) subunit proteins and a mixture of supercoiled, relaxed and linearized plasmid pBR322 DNA at low ionic strength revealed that limited amounts of these polypeptides interacted exclusively with the supercoiled form of the plasmid DNA. These results were corroborated by electron-microscopic analysis of the reaction products, which showed that only circles of supercoiled pBR322 DNA were completely and smoothly covered with vimentin. IFs reconstituted from pure vimentin reacted with supercoiled pBR322 DNA only through their physical ends. The reaction of an aged preparation of vimentin with supercoiled pBR322 DNA produced large aggregates consisting of a central, axially oriented protein scaffold to which individual loops of DNA were attached at their bases in a halo-like arrangement. The electron-microscopic appearance of such complexes was very reminiscent of that of histone-depleted metaphase chromosomes. Together with the previous observations that non-epithelial IF proteins have high affinities for single-stranded DNA and core histones and that they are structurally and functionally closely related to the nuclear lamins, these results were used to advance a novel hypothesis on the biological role of IF proteins in eukaryotic cells.

Changes in the organization of non-epithelial intermediate filaments induced by triethyl lead chloride

The in vivo effect of triethyl lead chloride (TriEL) (10(-6)-10(-8) M) on the organization of non-epithelial intermediate filaments (vimentin and desmin filaments) was studied by indirect immunofluorescence microscopy employing different mammalian cell lines. The in vitro effect of TriEL on filament formation as well as on the structure of preformed filaments was investigated by electron microscopy. TriEL induces perinuclear coil formation of intermediate filaments in SV40-transformed human fibroblasts and baby hamster kidney (BHK21) cells. The rearrangements observed are not correlated with significant changes in the microtubular system as tested by double labelling of both filament systems. The effect of TriEL is reversible. Assembly of intermediate filaments in vitro is disturbed in the presence of TriEL such that only short filaments and various kinds of fragments are formed. When preformed filaments are incubated in the presence of TriEL, unravelling of fibres into protofilamentous strands is observed. Possible mechanisms of TriEL-filament interaction are discussed.

Nucleic acid-binding activities of the intermediate filament subunit proteins desmin and glial fibrillary acidic protein

In analogy to experimental results previously obtained with vimentin and neurofilament triplet proteins, the intermediate filament (IF) proteins desmin and glial fibrillary acidic protein (GFAP) were also found to have high capacities to associate with nucleic acids. Employing a collection of native and heat-denatured pro- and eukaryotic DNAs, a series of naturally occurring single-stranded (ss)RNAs and a variety of synthetic polynucleotides of the RNA and DNA type, both proteins could be shown to bind preferentially to single-stranded polynucleotides. In the case of ssDNA and synthetic polyribonucleotides, a clear dependency of the binding activity on the G-content of the nucleic acids was demonstrated. The interaction of desmin with ssDNA and tRNA was characterized by strong cooperativity. When a mixture of desmin and vimentin was offered to excess ssDNA, the cooperativity effect brought about segregation of both protein species into two distinct populations of deoxyribonucleoprotein particles with substantially different sedimentation rates; this segregation is in sharp contrast to the ability of desmin and vimentin to form heteropolymers in filament assembly. In general, desmin and GFAP were found to be similar to vimentin and neurofilament proteins in their nucleic acid-binding properties. However, there were also striking differences between individual non-epithelial IF proteins at this level.

Efficient degradation in vitro of all intermediate filament subunit proteins by the Ca2+-activated neutral thiol proteinase from Ehrlich ascites tumor cells and porcine kidney

Vimentin, desmin, glial fibrillary acidic protein, neurofilament triplet proteins, and a mixture of cytokeratins were digested with Ca2+-activated neutral thiol proteinase isolated from Ehrlich ascites tumor (EAT) cells and porcine kidney. All intermediate filament proteins were degraded by the proteinase, although with different rates and Ca2+ optima. These results are in part at variance with our previous statement that the Ca2+-activated proteinase from EAT cells is specific for vimentin and desmin.

Interaction in vitro of the neurofilament triplet proteins from porcine spinal cord with natural RNA and DNA

Neurofilaments were isolated from porcine spinal cord and separated into their subunit proteins (68 Kd NFP, 145 Kd NFP, 200 Kd NFP) by ion exchange chromatography on DEAE-cellulose in 6 M urea. The individual proteins were reacted with total rRNA from Ehrlich ascites tumor cells and the reaction products analysed by sucrose gradient centrifugation at low ionic strength and in the presence of EDTA. All three proteins interacted with rRNA with a preference for 18S rRNA. Competition experiments with native and heat-denatured calf thymus DNA showed that the affinities of the 68 Kd and 145 Kd NFPs were considerably higher for denatured DNA than for rRNA and that native DNA was only a weak competitor. The binding of the 200 Kd NFP to rRNA was unaffected by native and by denatured DNA. When denatured DNA was reacted with a mixture of the 68 Kd and 145 Kd NFPs, the two proteins interacted independently with the nucleic acid, giving rise to two different populations of deoxyribonucleoprotein particles. This segregation is the result of the cooperative interaction of the neurofilament proteins with single-stranded DNA. It could not be observed with rRNA or bacteriophage MS2 RNA. The results clearly show that the 68 Kd and 145 Kd NFPs are single-stranded RNA- and DNA-binding proteins, whereas the 200 Kd NFP seems to be only a single-stranded RNA-binding protein.

Differential effect of arginine modification with 1,2-cyclohexanedione on the capacity of vimentin and desmin to assemble into intermediate filaments and to bind to nucleic acids

When the intermediate filament proteins vimentin and desmin were reacted for a short period of time with the arginine-specific reagent 1,2-cyclohexanedione, the modification had a severe, inhibitory effect on the assembly of intermediate filaments and on the susceptibility of the basic, amino-terminal polypeptide of both proteins to degradation by the intermediate filament-specific, Ca2+-activated proteinase. However, it had only a slightly inhibitory effect on the binding of vimentin and desmin to ribosomal RNA from Ehrlich ascites tumour cells. Since the Ca2+-activated proteinase is very likely to be a trypsin-like enzyme, with a preference for arginyl and lysyl peptide bonds, the results indicate that the arginine residues of the amino-terminal polypeptide of vimentin and desmin are highly essential for filament assembly but largely dispensable for the binding of both proteins to nucleic acids. This was supported by the observation that two breakdown products of vimentin lacking a 5 X 10(3) Mr and an 8 X 10(3) Mr polypeptide from the amino terminus, respectively, did not assemble into intermediate filaments but were still capable of binding to rRNA. Both polypeptides also bound to single-stranded DNA-cellulose under non-denaturing conditions, but passed the affinity column in the presence of 6 M-urea. Thus, the binding of vimentin to nucleic acids appears to be based on two components: a non-specific electrostatic interaction mediated by the positively charged arginine residues of the amino-terminal polypeptide that is insensitive to denaturation by urea, and a specific interaction that is sensitive to denaturation by urea.

Isolation, purification and characterization of the intermediate filament protein desmin from porcine smooth muscle

Desmin was isolated from porcine stomach smooth muscle, which had been treated with 0.6 M KCl in the presence of Triton X-100, by extraction with 6 M urea and chromatographed on CM-Sepharose CL-6B at pH 5. After delipidation with chloroform-methanol, the protein was purified by affinity chromatography on arginine methylester Sepharose 4B and single-stranded DNA-cellulose, respectively. Chromatography on single-stranded DNA-cellulose removed a considerable amount of vimentin which had been extracted and enriched together with desmin. The molecular weight of the purified desmin was 55,000 as determined by polyacrylamide gradient slab gel electrophoresis in the presence of Na-dodecylsulfate. Two-dimensional polyacrylamide gel electrophoresis revealed one major polypeptide of pI 5.3 to 5.4 accompanied by two to three acidic, isoelectric variants. During incubation in the presence of 150 mM KCl, desmin assembled into 10 nm filaments. This method allows the isolation of large amounts of pure desmin in a relatively short time with only minimal denaturation of the protein.

Involvement of the N-terminal polypeptide of vimentin in the formation of intermediate filaments

The potential to form intermediate filaments of a 54 X 10(3) molecular weight (Mr) polypeptide derived from vimentin by cleavage by the intermediate filament-specific, Ca2+-activated proteinase was investigated. Under physiological conditions of assembly, the breakdown product did not form intermediate filaments. Electron microscopy revealed short, rod-like structures similar to those described by Geisler et al. for a 38 X 10(3) Mr alpha-helical core particle derived from desmin. Since the specific, Ca2+-activated proteinase degrades vimentin preferentially from its N terminus, this result suggests the involvement of the basic, N-terminal polypeptide of vimentin in the assembly of intermediate filaments. This was supported by the observation that arginine inhibits the formation of intermediate filaments from intact vimentin. Whereas lysine had very little effect on the assembly process, guanidinium hydrochloride was effective at the same concentration as arginine. On the basis of these findings, an affinity chromatography method for the identification and isolation of intermediate filament subunit proteins was developed. Beside vimentin, desmin, the 68 X 10(3) Mr neurofilament triplet protein, the glial fibrillary acidic protein and cytokeratins also bound to arginine methylester Sepharose 4B in a salt-stable manner and could be eluted with arginine. The 145 X 10(3) Mr neurofilament triplet protein exhibited reduced binding activity, whereas the 210 X 10(3) Mr subunit did not bind to the affinity matrix. Among the degradation products of vimentin produced by the specific, Ca2+-activated proteinase, only those with molecular weights higher than 40 X 10(3) bound to arginine methylester Sepharose 4B. The same applied to the high molecular weight degradation products of desmin with a protein-resistant 37 X 10(3) Mr polypeptide as the major component. The results suggest that arginine residues of the non-alpha-helical, N-terminal polypeptides of intermediate filament subunit proteins play an important role in filament assembly.

Isolation of glial fibrillary acidic protein from bovine brain white matter and its purification by affinity chromatography on single-stranded DNA-cellulose

Myelinated axons, which had been prepared from bovine brain white matter employing the flotation method, were extracted with Triton X-100 in a low ionic strength buffer containing 4 mM Mg2+. After delipidation of the detergent-resistant, residual material with chloroform-methanol, glial fibrillary acidic protein (GFAP) was solubilized with 6 M urea. It was enriched by ion exchange chromatography in the presence of 6 M urea on CM-Sepharose CL-6B at pH 5 and on DE52-cellulose at pH 7.6, respectively. The final purification was achieved by affinity chromatography on single-stranded DNA-cellulose in 6 M urea. Employing SDS-polyacrylamide gel electrophoresis, the molecular weight of the purified GFAP was determined to be 51,000. 2D-polyacrylamide gel electrophoresis revealed a major protein constituent of pI 4.7 to 4.8, accompanied by 3 acidic isoelectric variants. Upon incubation at 37 degrees C in the presence of 150 mM KCl, GFAP assembled into 10 nm-filaments.

The interaction in vitro of the intermediate filament protein vimentin with naturally occurring RNAs and DNAs

The binding of the intermediate filament protein vimentin to a variety of naturally occurring RNAs and DNAs was studied. The relative capacities of the various nucleic acids to associate with pure [3H]vimentin were determined in competition experiments with 28 S rRNA from Ehrlich ascites tumor cells. The reaction products were analyzed by sucrose gradient centrifugation at low ionic strength and in the presence of EDTA. Under these ionic conditions, vimentin reacted preferentially with single-stranded nucleic acids, particularly with those of high (G + C) content. The vimentin binding potentials of single-stranded RNAs and DNAs were largely comparable. However, when the concentrations of mono- and divalent cations were raised to physiological and higher values, only single-stranded DNA retained its vimentin binding capacity. With increasing KCl concentrations at 0 to 1 mM Mg2+, increasing amounts of vimentin were detected in complexes which sedimented considerably faster than the bulk of the DNA, suggesting cooperative binding of vimentin. The salt optimum of this cooperativity was at 200 mM KCl. Thus, the capability of vimentin to discriminate between single-stranded RNA and DNA under physiological ionic conditions points to specificity of the interaction of vimentin with nucleic acids.