Playing the "Harp": evolution of our understanding of hrp/hrc genes

With the advent of recombinant DNA techniques, the field of molecular plant pathology witnessed dramatic shifts in the 1970s and 1980s. The new and conventional methodologies of bacterial molecular genetics put bacteria center stage. The discovery in the mid-1980s of the hrp/hrc gene cluster and the subsequent demonstration that it encodes a type III secretion system (T3SS) common to Gram negative bacterial phytopathogens, animal pathogens, and plant symbionts was a landmark in molecular plant pathology. Today, T3SS has earned a central role in our understanding of many fundamental aspects of bacterium-plant interactions and has contributed the important concept of interkingdom transfer of effector proteins determining race-cultivar specificity in plant-bacterium pathosystems. Recent developments in genomics, proteomics, and structural biology enable detailed and comprehensive insights into the functional architecture, evolutionary origin, and distribution of T3SS among bacterial pathogens and support current research efforts to discover novel antivirulence drugs.

Endonucleases induced TRAIL-insensitive apoptosis in ovarian carcinoma cells

TRAIL induced apoptosis of tumor cells is currently entering phase II clinical settings, despite the fact that not all tumor types are sensitive to TRAIL. TRAIL resistance in ovarian carcinomas can be caused by a blockade upstream of the caspase 3 signaling cascade. We explored the ability of restriction endonucleases to directly digest DNA in vivo, thereby circumventing the caspase cascade. For this purpose, we delivered enzymatically active endonucleases via the cationic amphiphilic lipid SAINT-18((R)):DOPE to both TRAIL-sensitive and insensitive ovarian carcinoma cells (OVCAR and SKOV-3, respectively). Functional nuclear localization after delivery of various endonucleases (BfiI, PvuII and NucA) was indicated by confocal microscopy and genomic cleavage analysis. For PvuII, analysis of mitochondrial damage demonstrated extensive apoptosis both in SKOV-3 and OVCAR. This study clearly demonstrates that cellular delivery of restriction endonucleases holds promise to serve as a novel therapeutic tool for the treatment of resistant ovarian carcinomas.

Coiled-coils in type III secretion systems: structural flexibility, disorder and biological implications

Recent structural studies and analyses of microbial genomes have consolidated the understanding of the structural and functional versatility of coiled-coil domains in proteins from bacterial type III secretion systems (T3SS). Such domains consist of two or more α-helices forming a bundle structure. The occurrence of coiled-coils in T3SS is considerably higher than the average predicted occurrence in prokaryotic proteomes. T3SS proteins comprising coiled-coil domains are frequently characterized by an increased structural flexibility, which may vary from localized structural disorder to the establishment of molten globule-like state. The propensity for coiled-coil formation and structural disorder are frequently essential requirements for various T3SS functions, including the establishment of protein-protein interaction networks and the polymerization of extracellular components of T3SS appendages. Possible correlations between the frequently observed N-terminal structural disorder of effectors and the T3SS secretion signal are discussed. The results for T3SS are also compared with other Gram-negative secretory systems.

Evidence for a coiled-coil interaction mode of disordered proteins from bacterial type III secretion systems

Gene clusters encoding various type III secretion system (T3SS) injectisomes, frequently code downstream of the conserved atpase gene for small hydrophilic proteins whose amino acid sequences display a propensity for intrinsic disorder and coiled-coil formation. These properties were confirmed experimentally for a member of this class, the HrpO protein from the T3SS of Pseudomonas syringae pv phaseolicola: HrpO exhibits high alpha-helical content with coiled-coil characteristics, strikingly low melting temperature, structural properties that are typical for disordered proteins, and a pronounced self-association propensity, most likely via coiled-coil interactions, resulting in heterogeneous populations of quaternary complexes. HrpO interacts in vivo with HrpE, a T3SS protein for which coiled-coil formation is also strongly predicted. Evidence from HrpO analogues from all T3SS families and the flagellum suggests that the extreme flexibility and propensity for coiled-coil interactions of this diverse class of small, intrinsically disordered proteins, whose structures may alter as they bind to their cognate folded protein targets, might be important elements in the establishment of protein-protein interaction networks required for T3SS function.

Purification, crystallization and preliminary X-ray diffraction analysis of a variant of the ColE1 Rop protein

Rop is the paradigm of a canonical four-alpha-helical bundle. Its loop region has attracted considerable interest because a single alanine-to-proline substitution (A31P) in the loop is sufficient to change the topology of this small protein. In order to further analyse the loop region as a possible folding-control element, the double mutant D30P/A31G (RopPG) was produced, purified and crystallized. The crystals belonged to space group P2(1), with unit-cell parameters a = 26.7, b = 38.8, c = 56.6 A, beta = 100.9 degrees and two molecules in the asymmetric unit. A complete data set was collected at 100 K to a resolution of 1.4 A using synchrotron radiation.

Purification, crystallization and preliminary X-ray analysis of the peptidoglycan N-acetylglucosamine deacetylase BC1960 from Bacillus cereus in the presence of its substrate (GlcNAc)6

The peptidoglycan N-acetylglucosamine (GlcNAc) deacetylase BC1960 from Bacillus cereus (EC 3.5.1.33), an enzyme consisting of 275 amino acids, was crystallized in the presence of its substrate (GlcNAc)(6). The crystals belonged to the tetragonal space group P4(1)2(1)2, with unit-cell parameters a = b = 92.7, c = 242.9 A and four molecules in the asymmetric unit. A complete data set was collected at 100 K to a resolution of 2.38 A using synchrotron radiation.

Purification, crystallization, X-ray diffraction analysis and phasing of an engineered single-chain PvuII restriction endonuclease

The restriction endonuclease PvuII from Proteus vulgaris has been converted from its wild-type homodimeric form into the enzymatically active single-chain variant scPvuII by tandemly joining the two subunits through the peptide linker Gly-Ser-Gly-Gly. scPvuII, which is suitable for the development of programmed restriction endonucleases for highly specific DNA cleavage, was purified and crystallized. The crystals diffract to a resolution of 2.35 A and belong to space group P4(2), with unit-cell parameters a = b = 101.92, c = 100.28 A and two molecules per asymmetric unit. Phasing was successfully performed by molecular replacement.

Crystal structure of the BcZBP, a zinc-binding protein from Bacillus cereus

Bacillus cereus is an opportunistic pathogenic bacterium closely related to Bacillus anthracis, the causative agent of anthrax in mammals. A significant portion of the B. cereus chromosomal genes are common to B. anthracis, including genes which in B. anthracis code for putative virulence and surface proteins. B. cereus thus provides a convenient model organism for studying proteins potentially associated with the pathogenicity of the highly infectious B. anthracis. The zinc-binding protein of B. cereus, BcZBP, is encoded from the bc1534 gene which has three homologues to B. anthracis. The protein exhibits deacetylase activity with the N-acetyl moiety of the N-acetylglucosamine and the diacetylchitobiose and triacetylchitotriose. However, neither the specific substrate of the BcZBP nor the biochemical pathway have been conclusively identified. Here, we present the crystal structure of BcZBP at 1.8 A resolution. The N-terminal part of the 234 amino acid protein adopts a Rossmann fold whereas the C-terminal part consists of two beta-strands and two alpha-helices. In the crystal, the protein forms a compact hexamer, in agreement with solution data. A zinc binding site and a potential active site have been identified in each monomer. These sites have extensive similarities to those found in two known zinc-dependent hydrolases with deacetylase activity, MshB and LpxC, despite a low degree of amino acid sequence identity. The functional implications and a possible catalytic mechanism are discussed.

Purification, crystallization and preliminary X-ray analysis of the BseCI DNA methyltransferase from Bacillus stearothermophilus in complex with its cognate DNA

The DNA methyltransferase M.BseCI from Bacillus stearothermophilus (EC 2.1.1.72), a 579-amino-acid enzyme, methylates the N6 atom of the 3' adenine in the sequence 5'-ATCGAT-3'. M.BseCI was crystallized in complex with its cognate DNA. The crystals were found to belong to the hexagonal space group P6, with unit-cell parameters a = b = 87.0, c = 156.1 A, beta = 120.0 degrees and one molecule in the asymmetric unit. Two complete data sets were collected at wavelengths of 1.1 and 2.0 A to 2.5 and 2.8 A resolution, respectively, using synchrotron radiation at 100 K.

Loopless Rop: structure and dynamics of an engineered homotetrameric variant of the repressor of primer protein

The repressor of primer (Rop) protein has become a steady source of surprises concerning the relationship between the sequences and the structures of several of its mutants and variants. Here we add another piece to the puzzle of Rop by showing that an engineered deletion mutant of the protein (corresponding to a deletion of residues 30-34 of the wild-type protein and designed to restore the heptad periodicity at the turn region) results in a complete reorganization of the bundle which is converted from a homodimer to a homotetramer. In contrast (and as previously shown), a two-residue insertion, which also restores the heptad periodicity, is essentially identical with wild-type Rop. The new deletion mutant structure is a canonical, left-handed, all-antiparallel bundle with a completely different hydrophobic core and distinct surface properties. The structure agrees and qualitatively explains the results from functional, thermodynamic, and kinetic studies which indicated that this deletion mutant is a biologically inactive hyperstable homotetramer. Additional insight into the stability and dynamics of the mutant structure has been obtained from extensive molecular dynamics simulations in explicit water and with full treatment of electrostatics.

Purification, crystallization and preliminary characterization of a putative LmbE-like deacetylase from Bacillus cereus

The Bacillus cereus BC1534 protein, a putative deacetylase from the LmbE family, has been purified to homogeneity and crystallized using the hanging-drop vapour-diffusion method. Crystals of the 26 kDa protein grown from MPD and acetate buffer belong to space group R32, with unit-cell parameters a = b = 76.7, c = 410.5 A (in the hexagonal setting). A complete native data set was collected to a resolution of 2.5 A from a single cryoprotected crystal using synchrotron radiation. As BC1534 shows significant sequence homology with an LmbE-like protein of known structure from Thermus thermophilus, molecular replacement will be used for crystal structure determination.

Conserved features of type III secretion

Type III secretion systems (TTSSs) are essential mediators of the interaction of many Gram-negative bacteria with human, animal or plant hosts. Extensive sequence and functional similarities exist between components of TTSS from bacteria as diverse as animal and plant pathogens. Recent crystal structure determinations of TTSS proteins reveal extensive structural homologies and novel structural motifs and provide a basis on which protein interaction networks start to be drawn within the TTSSs, that are consistent with and help rationalize genetic and biochemical data. Such studies, along with electron microscopy, also established common architectural design and function among the TTSSs of plant and mammalian pathogens, as well as between the TTSS injectisome and the flagellum. Recent comparative genomic analysis, bioinformatic genome mining and genome-wide functional screening have revealed an unsuspected number of newly discovered effectors, especially in plant pathogens and uncovered a wider distribution of TTSS in pathogenic, symbiotic and commensal bacteria. Functional proteomics and analysis further reveals common themes in TTSS effector functions across phylogenetic host and pathogen boundaries. Based on advances in TTSS biology, new diagnostics, crop protection and drug development applications, as well as new cell biology research tools are beginning to emerge.

Ionic strength reducers: an efficient approach to protein purification and crystallization. Application to two Rop variants

Detailed knowledge of the influence of various parameters on macromolecular solubility is essential for crystallization. The concept of so-called 'ionic strength reducers' provides insight into the changes in solubility induced by organic solvents and hydrophilic polymers in aqueous electrolytic solutions. A simple and efficient procedure is presented which exploits the properties of ionic strength reducers in the purification and crystallization of proteins. Using two designed variants of the Rop protein as model systems, superior crystals have been obtained compared with conventional techniques. This procedure is particularly useful in cases where excessive nucleation leads to the growth of a large number of tiny crystals that are useless for crystallographic analysis.

Molecular replacement with multiple different models

Classical molecular replacement methods and the newer six-dimensional searches treat molecular replacement as a succession of sub-problems of reduced dimensionality. Due to their `divide-and-conquer' approach, these methods necessarily ignore (at least during their early stages) the very knowledge that a target crystal structure may comprise, for example, more than one copy of a search model, or several models of different types. An algorithm for a stochastic multi-dimensional molecular replacement search has been described previously and shown to locate solutions successfully, even in cases as complex as a 23-dimensional 4-body search. The original description of the method only dealt with a special case of molecular replacement, namely with the problem of placingncopies of only one search model in the asymmetric unit of a target crystal structure. Here a natural generalization of this algorithm is presented to deal with the full molecular replacement problem, that is, with the problem of determining the orientations and positions of a total ofncopies ofmdifferent models (withn≥m) which are assumed to be present in the asymmetric unit of a target crystal structure. The generality of this approach is illustrated through its successful application to a 17-dimensional 3-model problem involving one DNA and two protein molecules.

Structure of HrcQB-C, a conserved component of the bacterial type III secretion systems

Type III secretion systems enable plant and animal bacterial pathogens to deliver virulence proteins into the cytosol of eukaryotic host cells, causing a broad spectrum of diseases including bacteremia, septicemia, typhoid fever, and bubonic plague in mammals, and localized lesions, systemic wilting, and blights in plants. In addition, type III secretion systems are also required for biogenesis of the bacterial flagellum. The HrcQ(B) protein, a component of the secretion apparatus of Pseudomonas syringae with homologues in all type III systems, has a variable N-terminal and a conserved C-terminal domain (HrcQ(B)-C). Here, we report the crystal structure of HrcQ(B)-C and show that this domain retains the ability of the full-length protein to interact with other type III components. A 3D analysis of sequence conservation patterns reveals two clusters of residues potentially involved in protein-protein interactions. Based on the analogies between HrcQ(B) and its flagellum homologues, we propose that HrcQ(B)-C participates in the formation of a C-ring-like assembly.

Structural and biochemical characterization of a new Mg(2+) binding site near Tyr94 in the restriction endonuclease PvuII

We have determined the crystal structure of the PvuII endonuclease in the presence of Mg(2+). According to the structural data, divalent metal ion binding in the PvuII subunits is highly asymmetric. The PvuII-Mg(2+) complex has two distinct metal ion binding sites, one in each monomer. One site is formed by the catalytic residues Asp58 and Glu68, and has extensive similarities to a catalytically important site found in all structurally examined restriction endonucleases. The other binding site is located in the other monomer, in the immediate vicinity of the hydroxyl group of Tyr94; it has no analogy to metal ion binding sites found so far in restriction endonucleases. To assign the number of metal ions involved and to better understand the role of Mg(2+) binding to Tyr94 for the function of PvuII, we have exchanged Tyr94 by Phe and characterized the metal ion dependence of DNA cleavage of wild-type PvuII and the Y94F variant. Wild-type PvuII cleaves both strands of the DNA in a concerted reaction. Mg(2+) binding, as measured by the Mg(2+) dependence of DNA cleavage, occurs with a Hill coefficient of 4, meaning that at least two metal ions are bound to each subunit in a cooperative fashion upon formation of the active complex. Quenched-flow experiments show that DNA cleavage occurs about tenfold faster if Mg(2+) is pre-incubated with enzyme or DNA than if preformed enzyme-DNA complexes are mixed with Mg(2+). These results show that Mg(2+) cannot easily enter the active center of the preformed enzyme-DNA complex, but that for fast cleavage the metal ions must already be bound to the apoenzyme and carried with the enzyme into the enzyme-DNA complex. The Y94F variant, in contrast to wild-type PvuII, does not cleave DNA in a concerted manner and metal ion binding occurs with a Hill coefficient of 1. These results indicate that removal of the Mg(2+) binding site at Tyr94 completely disrupts the cooperativity in DNA cleavage. Moreover, in quenched-flow experiments Y94F cleaves DNA about ten times more slowly than wild-type PvuII, regardless of the order of mixing. From these results we conclude that wild-type PvuII cleaves DNA in a fast and concerted reaction, because the Mg(2+) required for catalysis are already bound at the enzyme, one of them at Tyr94. We suggest that this Mg(2+) is shifted to the active center during binding of a specific DNA substrate. These results, for the first time, shed light on the pathway by which metal ions as essential cofactors enter the catalytic center of restriction endonucleases.

Cold adaptation of a psychrophilic chitinase: a mutagenesis study

The gene encoding chitinase ArChiB from the Antarctic Arthrobacter sp. TAD20 has been expressed in Escherichia coli and the recombinant enzyme purified to homogeneity. In an effort to engineer cold-adapted biocatalysts through rational redesign to operate at elevated temperatures, we performed several mutations aiming to increase the rigidity of the molecular edifice of the selected psychrophilic chitinase. The mutations were designed on the basis of a homology-based three-dimensional model of the enzyme, and included an attempt to introduce a salt bridge (mutant N198K) and replacements of selected Gly residues by either Pro (mutants G93P, G254P) or Gln (G406Q). Mutant N198K resulted in a more stable protein (DeltaTm = 0.6 degrees C). Mutant G93P exhibited a DeltaTm of 1.2 degrees C, while mutants G254P and G406Q exhibited decreased stability. We conclude that the effect of mutating Gly residues on enzyme stability is rather complex and can only be understood in the context of the structural environment. Kinetic and spectroscopic analysis of these enzyme variants revealed that the kinetic parameters kcat and Km have been significantly modified.

Structure determination of a small protein through a 23-dimensional molecular-replacement search

The crystal structure of a 4-alpha-helical bundle protein has been determined by the application of a 23-dimensional molecular-replacement search performed using a stochastic method. The search model for the calculation was a 26-residue-long polyalanine helix amounting to less than 13% of the total number of atoms in the asymmetric unit of the target crystal structure. The crystal structure determination procedure is presented in detail, with emphasis on the molecular-replacement calculations.