The supernumerary chromosome of Nectria haematococca that carries pea-pathogenicity-related genes also carries a trait for pea rhizosphere competitiveness.

Fungi are found in a wide range of environments, and the ecological and host diversity of the fungus Nectria haematococca has been shown to be due in part to unique genes on different supernumerary chromosomes. These chromosomes have been called "conditionally dispensable" (CD) since they are not needed for axenic growth but are important for expanding the host range of individual isolates. From a biological perspective, the CD chromosomes can be compared to bacterial plasmids that carry unique genes that can define the habits of these microorganisms. The current study establishes that the N. haematococca PDA1-CD chromosome, which contains the genes for pea pathogenicity (PEP cluster) on pea roots, also carries a gene(s) for the utilization of homoserine, a compound found in large amounts in pea root exudates. Competition studies demonstrate that an isolate that lacks the PEP cluster but carries a portion of the CD chromosome which includes the homoserine utilization (HUT) gene(s) is more competitive in the pea rhizosphere than an isolate without the CD chromosome.

Crystal structure of the archaeal holliday junction resolvase Hjc and implications for DNA recognition.

BACKGROUND: Homologous recombination is a crucial mechanism in determining genetic diversity and repairing damaged chromosomes. Holliday junction is the universal DNA intermediate whose interaction with proteins is one of the major events in the recombinational process. Hjc is an archaeal endonuclease, which specifically resolves the junction DNA to produce two separate recombinant DNA duplexes. The atomic structure of Hjc should clarify the mechanisms of the specific recognition with Holliday junction and the catalytic reaction. RESULTS: The crystal structure of Hjc from the hyperthermophilic archaeon Pyrococcus furiosus has been determined at 2.0 A resolution. The active Hjc molecule forms a homodimer, where an extensive hydrophobic interface tightly assembles two subunits of a single compact domain. The folding of the Hjc subunit is clearly different from any other Holliday junction resolvases thus far known. Instead, it resembles those of type II restriction endonucleases, including the configurations of the active site residues, which constitute the canonical catalytic motifs. The dimeric Hjc molecule displays an extensive basic surface on one side, which contains many conserved amino acids, including those in the active site. CONCLUSIONS: The architectural similarity of Hjc to restriction endonucleases allowed us to construct a putative model of the complex with Holliday junction. This model accounts for how Hjc recognizes and resolves the junction DNA in a specific manner. Mutational and biochemical analyses highlight the importance of some loops and the amino terminal region in interaction with DNA.

Catalytic center of an archaeal type 2 ribonuclease H as revealed by X-ray crystallographic and mutational analyses.

The catalytic center of an archaeal Type 2 RNase H has been identified by a combination of X-ray crystallographic and mutational analyses. The crystal structure of the Type 2 RNase H from Thermococcus kodakaraensis KOD1 has revealed that the N-terminal major domain adopts the RNase H fold, despite the poor sequence similarity to the Type 1 RNase H. Mutational analyses showed that the catalytic reaction requires four acidic residues, which are well conserved in the Type 1 RNase H and the members of the polynucleotidyl transferase family. Thus, the Type 1 and Type 2 RNases H seem to share a common catalytic mechanism, except for the requirement of histidine as a general base in the former enzyme. Combined with the results from deletion mutant analyses, the structure suggests that the C-terminal domain of the Type 2 RNase H is involved in the interaction with the DNA/RNA hybrid.

Cytological Karyotyping of Three Cochliobolus spp. by the Germ Tube Burst Method.

ABSTRACT Cytological karyotypes with mitotic metaphase chromosomes were analyzed for Cochliobolus heterostrophus, C. carbonum, and C. sativus by the germ tube burst method (GTBM). Prior to karyotyping, procedures of GTBM suitable to Cochliobolus were established by examining several crucial conditions such as incubation period of conidia. The estimated chromosome numbers of C. heterostrophus and C. carbonum were n = 15 or 16 and n = 13 or 15 depending on the strains, respectively. In C. sativus, n = 15 was estimated. Morphological information of chromosomes including chromosome size and a threadlike-specific structure representing the nucleolar organizing region was also obtained. Our results for some standard strains are in agreement with previous estimates by pulsed field gel electrophoresis (PFGE) or PFGE coupled with restriction fragment length polymorphism genetic linkage analysis, but inconsistent with the previous estimates for other strains by conventional light microscopic cytology. Additionally, PFGE analysis of C. heterostro-phus strains indicated that chromosome number was not determinable solely by PFGE, which is hampered by comigration and clumping of DNA bands.

Estimation of the hydrophobic effect in an antigen-antibody protein-protein interface.

Antigen-antibody complexes provide useful models for analyzing the thermodynamics of protein-protein association reactions. We have employed site-directed mutagenesis, X-ray crystallography, and isothermal titration calorimetry to investigate the role of hydrophobic interactions in stabilizing the complex between the Fv fragment of the anti-hen egg white lysozyme (HEL) antibody D1.3 and HEL. Crystal structures of six FvD1.3-HEL mutant complexes in which an interface tryptophan residue (V(L)W92) has been replaced by residues with smaller side chains (alanine, serine, valine, aspartate, histidine, and phenylalanine) were determined to resolutions between 1.75 and 2.00 A. In the wild-type complex, V(L)W92 occupies a large hydrophobic pocket on the surface of HEL and constitutes an energetic "hot spot" for antigen binding. The losses in apolar buried surface area in the mutant complexes, relative to wild-type, range from 25 (V(L)F92) to 115 A(2) (V(L)A92), with no significant shifts in the positions of protein atoms at the mutation site for any of the complexes except V(L)A92, where there is a peptide flip. The affinities of the mutant Fv fragments for HEL are 10-100-fold lower than that of the original antibody. Formation of all six mutant complexes is marked by a decrease in binding enthalpy that exceeds the decrease in binding free energy, such that the loss in enthalpy is partly offset by a compensating gain in entropy. No correlation was observed between decreases in apolar, polar, or aggregate (sum of the apolar and polar) buried surface area in the V(L)92 mutant series and changes in the enthalpy of formation. Conversely, there exist linear correlations between losses of apolar buried surface and decreases in binding free energy (R(2) = 0.937) as well as increases in the solvent portion of the entropy of binding (R(2) = 0.909). The correlation between binding free energy and apolar buried surface area corresponds to 21 cal mol(-1) A(-2) (1 cal = 4.185 J) for the effective hydrophobicity at the V(L)92 mutation site. Furthermore, the slope of the line defined by the correlation between changes in binding free energy and solvent entropy approaches unity, demonstrating that the exclusion of solvent from the binding interface is the predominant energetic factor in the formation of this protein complex. Our estimate of the hydrophobic contribution to binding at site V(L)92 in the D1.3-HEL interface is consistent with values for the hydrophobic effect derived from classical hydrocarbon solubility models. We also show how residue V(L)W92 can contribute significantly less to stabilization when buried in a more polar pocket, illustrating the dependence of the hydrophobic effect on local environment at different sites in a protein-protein interface.

[A case of olfactory neuroblastoma with intracranial extension and distant metastasis].

Olfactory neuroblastoma is a rare tumor originating in the upper nasal cavity. It rarely extends intracranially. We report a clinical case of olfactory neuroblastoma with intracranial extension and distant metastasis. A 35-year-old man complained of nasal stuffiness and bleeding, headache and vomiting. Neurological examination showed anosmia and papilledema. MRI showed a huge mass that occupied the right nasal and paranasal cavities, and extended into the right frontal base. The tumor was removed totally and was histologically diagnosed as olfactory neuroblastoma. About two months after surgery, however, MRI demonstrated a rapid recurrence of the tumor in the nasal and paranasal cavities and the frontal lobe. Metastatic lesions were also seen in the right cervical lymph nodes. Chemotherapy was administered using cisplatin and etoposide. The tumor in the frontal lobe shrunk markedly but the other lesion persisted. Whole brain irradiation and local irradiation of the cervical lymph nodes were performed. The tumors became smaller but did not disappear. MRI demonstrated spinal dissemination. Irradiation of the whole spinal cord was performed. The metastatic lesions disappeared. The patient was discharged without neurological deficits, but died of pneumonia 15 months after surgery. Olfactory neuroblastoma is a slow-growing tumor and is highly radiosensitive, but it rarely extends or develops multiple distant metastases and seldom shows a short survival time, as in our case. A review of the literature documented responses in patients treated with a cisplatin-based drug combination. We recommend systemic control using cisplatin-based chemotherapy in addition to irradiation to prevent local recurrence in cases of advanced or metastatic olfactory neuroblastoma.

[Hemifacial spasm due to a compression of the facial nerve by a fusiform aneurysm of the vertebral artery: case report].

We report a rare case of symptomatic hemifacial spasm caused by a fusiform vertebral artery aneurysm and by a branch of the anterior inferior cerebellar artery compressing the facial nerve at the root exit zone (REZ). A 71-year-old female had an 11-year history of right hemifacial spasm. MRIs demonstrated an aneurysm compressing the facial nerve at the REZ. Angiography disclosed a fusiform aneurysm of the right vertebral artery at the origin of the posterior inferior cerebellar artery. After the vertebral aneurysm was clipped distal to the origin of the posterior inferior cerebellar artery, a branch of the right anterior inferior cerebellar artery was also observed compressing the facial nerve at the REZ. Both the clipped aneurysm and the branch of the anterior inferior cerebellar artery were mobilized away from the REZ of the facial nerve, and a prosthesis was inserted between the branch of the anterior inferior cerebellar artery and the brain stem to keep the aneurysm away from its original position. The patient's hemifacial spasm immediately disappeared without any neurological deficits just after the surgery. Hemifacial spasm, especially caused by an aneurysm, is quite rare. In a review of the literature, we found only 4 cases of symptomatic hemifacial spasm caused by an aneurysm of the vertebral artery. This case is the first reported case of hemifacial spasm caused by both a fusiform vertebral artery aneurysm and a branch of the anterior inferior cerebellar artery compressing the facial nerve at the REZ.

[Suprasellar primary malignant rhabdoid tumor in an adult: a case report].

Malignant rhabdoid tumor (MRT), described for the first time in 1978 in the kidney, has rarely been reported in other organs including the brain and has involved adults in only 3 cases. We described a case of MRT in a 32-year-old woman who presented with severe headache, nausea and sudden onset of visual disturbance. MRI showed a well-enhanced mass at the suprasellar region. Subtotal removal of the tumor was performed. However, tumor regrowth occurred after the operation (doubling time, 8.36 days) and spinal dissemination was detected. Therefore, chemotherapy and radiotherapy were administered focusing on the suprasellar lesion and the spinal cord. Pathologically, light micrographs showed rhabdoid cells with large, round, single or double nuclei with one prominent nucleolus and eosinophilic cytoplasmic inclusions. Electron micrographs were made of typical rhabdoid cells displaying bundles of intermediate filaments within the perikaryon. In immunohistochemical studies, EMA, vimentin, cytokeratin and SMA were positive. Pathological findings were consistent with those of MRT. Optimal treatment for this tumor has not been established. Our case may be useful in defining treatment for MRT.

Romit profile analysis for molecular replacements.

A new procedure for evaluation of molecular replacement has been examined by using an R factor calculated from the probe structure with some omitted parts (Romit). It has been demonstrated that changes in Romit from the conventional R factor for the whole structure are sensitive to the local fitness in the omitted region even for large molecules such as proteins. Their profile, plotted against residues, is effective for distinguishing the most probable one from several solutions. In addition, this profile analysis exhibits useful information for model building.

A mutational analysis of binding interactions in an antigen-antibody protein-protein complex.

Alanine scanning mutagenesis, double mutant cycles, and X-ray crystallography were used to characterize the interface between the anti-hen egg white lysozyme (HEL) antibody D1.3 and HEL. Twelve out of the 13 nonglycine contact residues on HEL, as determined by the high-resolution crystal structure of the D1.3-HEL complex, were individually truncated to alanine. Only four positions showed a DeltaDeltaG (DeltaGmutant - DeltaGwild-type) of greater than 1.0 kcal/mol, with HEL residue Gln121 proving the most critical for binding (DeltaDeltaG = 2.9 kcal/mol). These residues form a contiguous patch at the periphery of the epitope recognized by D1.3. To understand how potentially disruptive mutations in the antigen are accommodated in the D1.3-HEL interface, we determined the crystal structure to 1.5 A resolution of the complex between D1.3 and HEL mutant Asp18 --> Ala. This mutation results in a DeltaDeltaG of only 0.3 kcal/mol, despite the loss of a hydrogen bond and seven van der Waals contacts to the Asp18 side chain. The crystal structure reveals that three additional water molecules are stably incorporated in the antigen-antibody interface at the site of the mutation. These waters help fill the cavity created by the mutation and form part of a rearranged solvent network linking the two proteins. To further dissect the energetics of specific interactions in the D1.3-HEL interface, double mutant cycles were carried out to measure the coupling of 14 amino acid pairs, 10 of which are in direct contact in the crystal structure. The highest coupling energies, 2.7 and 2.0 kcal/mol, were measured between HEL residue Gln121 and D1.3 residues VLTrp92 and VLTyr32, respectively. The interaction between Gln121 and VLTrp92 consists of three van der Waals contacts, while the interaction of Gln121 with VLTyr32 is mediated by a hydrogen bond. Surprisingly, however, most cycles between interface residues in direct contact in the crystal structure showed no significant coupling. In particular, a number of hydrogen-bonded residue pairs were found to make no net contribution to complex stabilization. We attribute these results to accessibility of the mutation sites to water, such that the mutated residues exchange their interaction with each other to interact with water. This implies that the strength of the protein-protein hydrogen bonds in these particular cases is comparable to that of the protein-water hydrogen bonds they replace. Thus, the simple fact that two residues are in direct contact in a protein-protein interface cannot be taken as evidence that there necessarily exists a productive interaction between them. Rather, the majority of such contacts may be energetically neutral, as in the D1.3-HEL complex.

Three-dimensional structure of the complex between a T cell receptor beta chain and the superantigen staphylococcal enterotoxin B.

Superantigens (SAGs) are a class of immunostimulatory proteins of bacterial or viral origin that activate T cells by binding to the V beta domain of the T cell antigen receptor (TCR). The three-dimensional structure of the complex between a TCR beta chain (mouse V beta8.2) and the SAG staphylococcal enterotoxin B (SEB) at 2.4 A resolution reveals why SEB recognizes only certain V beta families, as well as why only certain SAGs bind mouse V beta8.2. Models of the TCR-SEB-peptide/MHC class II complex indicate that V alpha interacts with the MHC beta chain in the TCR-SAG-MHC complex. The extent of the interaction is variable and is largely determined by the geometry of V alpha/V beta domain association. This variability can account for the preferential expression of certain V alpha regions among T cells reactive with SEB.

The treatment of enchondromas in the hand by endoscopic curettage without bone grafting.

Nine patients with enchondromas in the hand were treated by endoscopic curettage of the tumour without bone grafting. The procedure was performed on an out-patient basis using axillary block anaesthesia. New bone formation and remodelling of the lesions were observed in all patients. There were no postoperative fractures, infections, recurrences or other complications. Functional recovery was rapid. We conclude that endoscopic curettage without bone grafting is an effective treatment of enchondroma in the hand.

Crystal structure of 3-isopropylmalate dehydrogenase from the moderate facultative thermophile, Bacillus coagulans: two strategies for thermostabilization of protein structures.

The crystal structure of 3-isopropylmalate dehydrogenase from the moderate facultative thermophile Bacillus coagulans (BcIPMDH) has been determined by the X-ray method. BcIPMDH is a dimeric enzyme composed of two identical subunits, each of which takes an open alpha/beta structure with 11 alpha-helices and 14 beta-strands. The polypeptide is folded into two domains. The first domain is composed of residues 1-101 and 257-356, and the second domain, of residues 102-256. The latter domains of the two subunits are associated with one another by a dyad axis to make the dimer, locally forming a beta-sheet and a four-helix bundle. As compared with the structure of the enzyme from the extreme thermophile Thermus thermophilus (TtIPMDH), a new short beta-sheet (residues 329-330 and 340-341) absent in TtIPMDH is formed by the insertion of 5 residues in BcIPMDH. In terms of determinants for thermostabilization, both consistent and inconsistent changes were found between the two enzymes. The regions including inconsistent changes are formed by different usages of the determinants for stabilizing the loops at different levels. Those in BcIPMDH contain some structural redundancies in length of amino acid sequence and flexibility of residues, which seem to be unnecessary for the enzymatic reaction. Such redundancies are also found in the primary structure of the enzyme of the mesophile Bacillus subtilis, but these parts are more stabilized in BcIPMDH by hydrogen bonds and salt bridges. On the other hand, TtIPMDH is stabilized by reducing such redundant parts. This contrast suggests that different strategies may be preferred for thermostabilization, depending on temperature.

Crystallization and preliminary X-ray analysis of 3-isopropylmalate dehydrogenase from the moderate facultative thermophile Bacillus coagulans.

Three crystalline forms of 3-isopropylmalate dehydrogenase from the moderate facultative thermophile Bacillus coagulans were obtained by hanging-drop vapor-diffusion methods. One of them, which had crystallized under slightly milder conditions than the others, was suitable for X-ray analysis. Its asymmetric unit contains one dimeric molecule and the solvent content is higher than in other protein crystals. The crystal structure was solved in a preliminary manner by the molecular-replacement technique.

Enzymic O-glycosylation of synthetic peptides from sequences in basic myelin protein.

Nine synthetic peptides containing sequences in the region of a threonine residue at position 98 of bovine basic myelin protein were prepared by the Merrifield solid-phase method and tested for their ability to be glycosylated with [14C]uridinediphospho-N-acetylgalactosamine and a crude detergent-solubilized preparation of uridinediphospho-N-acetylgalactosamine:mucin polypeptide N-acetylgalactosaminyltransferase obtained from porcine submaxillary glands. The tetrapeptide Thr-Pro-Pro-Pro and all larger peptides containing this sequence were glycosylated. The glycosylation was greater for peptides containing residues N-terminal to the Thr-Pro-Pro-Pro. Under the conditions used, the peptide Val-Thr-Pro-Arg-Thr-Pro-Pro-Pro was glycoslyated twice as much as bovine basic myelin protein. Thr-Pro and Thr-Pro-Pro, as well as 10 other synthetic peptides which did not contain the Thr-Pro-Pro-Pro sequence, were not glycosylated. Treatment of the glycopeptide of Phe-Lys-Asn-Leu-Val-Thr-Pro-Arg-Thr-Pro-Pro-Pro-Ser with an alpha-N-acetylgalactosaminidase released N-acetylgalactosamine from the peptide, indicating that the hexosamine was covalently bonded to the peptide in an alpha linkage.

Illicit transport: the oligopeptide permease.

The oligopeptide permease of Escherichia coli has been characterized by Payne, Gilvarg, and their colleagues. We have confirmed its existence in Salmonella typhimurium, and have isolated a series of mutants lacking the permease. We use this transport system for smuggling a histidine biosynthetic intermediate, histidinol phosphate ester, into the bacteria as its glycylglycyl derivative, Gly-Gly-histidinol phosphate. Free histidinol phosphate ester is not transported into Salmonella. Several amino-acid analogues are shown to be much more inhibitory to Salmonella when presented to the bacteria in the form of tripeptides than as the free amino acids. The implications of this work for practical purposes are discussed. The synthesis of Gly-Gly-histidinol phosphate is described.