Heat effect on the structure and activity of the recombinant glutamate dehydrogenase from a hyperthermophilic archaeon Pyrococcus horikoshii

Glutamate dehydrogenase from Pyrococcus horikoshii (Pho-GDH) was cloned and overexpressed in Escherichia coli. The cloned enzyme with His-tag was purified to homogeneity by affinity chromatography and shown to be a hexamer enzyme of 290+/-8 kDa (subunit mass 48 kDa). Its optimal pH and temperature were 7.6 and 90 degrees C, respectively. The purified enzyme has outstanding thermostability (the half-life for thermal inactivation at 100 degrees C was 4 h). The enzyme shows strict specificity for 2-oxoglutarate and L-glutamate and requires NAD(P)H and NADP as cofactors but it does not reveal activity on NAD as cofactor. K(m) values of the recombinant enzyme are comparable for both substrates: 0.2 mM for L-glutamate and 0.53 mM for 2-oxoglutarate. The enzyme was activated by heating at 80 degrees C for 1 h, which was accompanied by the formation of its active conformation. Circular dichroism and fluorescence spectra show that the active conformation is heat-inducible and time-dependent.     

Thermophilic cytochrome P450 (CYP119) from Sulfolobus solfataricus: high resolution structure and functional properties

Crystal structures of a thermostable cytochrome P450 (CYP119) and a site-directed mutant, (Phe24Leu), from the acidothermophilic archaea Sulfolobus solfataricus were determined at 1.5-2.0 A resolution. We identify important crystallographic waters in the ferric heme pocket, observe protein conformational changes upon inhibitor binding, and detect a unique distribution of surface charge not found in other P450s. An analysis of factors contributing to thermostability of CYP119 of these high resolution structures shows an apparent increase in clustering of aromatic residues and optimum stacking. The contribution of aromatic stacking was investigated further with the mutant crystal structure and differential scanning calorimetry.     

Cloning and characterization of the deoxyribonuclease sd alpha gene from Streptococcus pyogenes

The pathogenesis of Streptococcus pyogenes infection, especially toxic shock-like syndrome (TSLS), is still not fully understood; however, the exoproteins have been considered to play a role. We analyzed the culture supernatant proteins (exoproteins) from a TSLS-related isolate belonging to M3 serotype S. pyogenes by two-dimensional gel electrophoresis and characterized a single protein spot by using BLAST database. We cloned the gene of this protein and named it sdα, which was similar to the deoxyribonuclease (DNase) sdc of S. equisimilis. We showed that the recombinant protein from the sdα gene had DNase activity. By polymerase chain reaction, we found that the sdα gene was present in most clinically isolated S. pyogenes including TSLS-related isolates. We thus conclude that Sdα is a new DNase of S. pyogenes. Received: 27 August 2001 / Accepted: 19 October 2001     

Determination of the secondary structure in solution of the Escherichia coli DnaA DNA-binding domain

DnaA protein binds specifically to a group of binding sites collectively called as DnaA boxes within the bacterial replication origin to induce local unwinding of duplex DNA. The DNA-binding domain of DnaA, domain IV, comprises the C-terminal 94 amino acid residues of the protein. We overproduced and purified a protein containing only this domain plus a methionine residue. This protein was stable as a monomer and maintained DnaA box-specific binding activity. We then analyzed its solution structure by CD spectrum and heteronuclear multi-dimensional NMR experiments. We established extensive assignments of the 1H, 13C, and 15N nuclei, and revealed by obtaining combined analyses of chemical shift index and NOE connectivities that DnaA domain IV contains six alpha-helices and no beta-sheets, consistent with results of CD analysis. Mutations known to reduce DnaA box-binding activity were specifically located in or near two of the alpha-helices. These findings indicate that the DNA-binding fold of DnaA domain IV is unique among origin-binding proteins.     

Origin of the tooth-replacement pattern in therian mammals: evidence from a 110 Myr old fossil

Living placental and marsupial mammals (therians) use distinctive tooth-replacement patterns that have not yet been traced back fully to their time of divergence in the Early Cretaceous (>100 Myr ago). Slaughteria eruptens, a small 110 Myr old fossil mammal from Texas, USA, is near the base of that divergence. Using ultra-high-resolution X-ray CT analysis we demonstrate that Slaughteria preserves an unrecognized pattern of tooth replacement with simple posterior premolars replacing molariform precursors. Differing from both placentals that have a more complex posterior adult premolar, and from marsupials, in which only one premolar is replaced, Slaughteria provides the first direct evidence of a tooth-replacement pattern that is plausible for the common ancestor of all therians. By our interpretation Slaughteria has only one adult molar in place and contains two mental foramina in the jaw, thus changing characters that are critical to reconstruction of mammalian relationships and to species discrimination and interpretations of diversity for Early Cretaceous mammals.     

Analysis of T-cell receptor Vbeta gene from infiltrating T cells in insulitis and myocarditis in encephalomyocarditis virus-infected BALB/C mice

Encephalomyocarditis (EMC) virus induces insulin-dependent diabetes and myocarditis in several strains of mice. The T-cell receptor (TCR) Vbeta genes of infiltrating T cells in the pancreas and myocardium of BALB/C mice infected with EMC virus D-variant (EMC-D virus) were analyzed. Using a nested two-step polymerase chain reaction (PCR), TCR Vbeta cDNAs were cloned and sequenced. Two and four kinds of TCR Vbeta clones were obtained from T cells infiltrating into the pancreas and myocardium of BALB/C mice infected with EMC-D virus, respectively. The infiltrating lymphocytes in the diabetic mice expressed Vbeta 8.1, 8.2, and 8.3 genes predominantly. Previously, the use of Vbeta 8.2 has been reported in autoimmune diseases such as murine experimental allergic encephalomyelitis (EAE) and non-obese diabetic (NOD) mouse. This study suggests that mice infected with EMC virus are a useful animal model for autoimmune diseases such as insulin-dependent diabetes.     

The Arabidopsis TAC Position Viewer: a high‐resolution map of transformation‐competent artificial chromosome (TAC) clones aligned with the Arabidopsis thaliana Columbia‐0 genome

We present a high‐resolution map of genomic transformation‐competent artificial chromosome (TAC) clones extending over all Arabidopsis thaliana (Arabidopsis) chromosomes. The Arabidopsis genomic TAC clones have been valuable genetic tools. Previously, we constructed an Arabidopsis genomic TAC library consisting of more than 10 000 TAC clones harboring large genomic DNA fragments extending over the whole Arabidopsis genome. Here, we determined 13 577 end sequences from 6987 Arabidopsis TAC clones and mapped 5937 TAC clones to precise locations, covering approximately 90% of the Arabidopsis chromosomes. We present the large‐scale data set of TAC clones with high‐resolution mapping information as a Java application tool, the Arabidopsis TAC Position Viewer, which provides ready‐to‐go transformable genomic DNA clones corresponding to certain loci on Arabidopsis chromosomes. The TAC clone resources will accelerate genomic DNA cloning, positional walking, complementation of mutants and DNA transformation for heterologous gene expression.