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Characterization of an S-layer glycoprotein produced in the course of S-layer variation of Bacillus stearothermophilus ATCC 12980 and sequencing and cloning of the sbsD gene encoding the protein moiety.

The cell surface of Bacillus stearothermophilus ATCC 12980 is completely covered by an oblique lattice which consists of the S-layer protein SbsC. On SDS-polyacrylamide gels, the mature S-layer protein migrates as a single band with an apparent molecular mass of 122 kDa. During cultivation of B. stearothermophilus ATCC 12980 at 67 degrees C instead of 55 degrees C, a variant developed that had a secondary cell wall polymer identical to that of the wild-type strain, but it carried an S-layer glycoprotein that could be separated on SDS-polyacrylamide gels into four bands with apparent molecular masses of 92, 118, 150 and 175 kDa. After deglycosylation, only a single protein band with a molecular mass of 92 kDa remained. The complete nucleotide sequence encoding the protein moiety of this S-layer glycoprotein, termed SbsD, was established by PCR and inverse PCR. The sbsD gene of 2,709 bp is predicted to encode a protein of 96.2 kDa with a 30-amino-acid signal peptide. Within the 807 bp encoding the signal peptide and the N-terminal sequence (amino acids 31-269), different nucleotides for sbsD and sbsC were observed in 46 positions, but 70% of these mutations were silent, thus leading to a level of identity of 95% for the N-terminal parts. The level of identity of the remaining parts of SbsD and SbsC was below 10%, indicating that the lysine-, tyrosine- and arginine-rich N-terminal region in combination with a distinct type of secondary cell wall polymer remained conserved upon S-layer variation. The sbsD sequence encoding the mature S-layer protein cloned into the pET28a vector led to stable expression in Escherichia coli HMS174(DE3). This is the first example demonstrating that S-layer variation leads to the synthesis of an S-layer glycoprotein.

Amino Acid Sequence↗

The transposable element IS4712 prevents S-layer gene (sbsA) expression in Bacillus stearothermophilus and also affects the synthesis of altered surface layer proteins.

Cell surface (S)-layer protein synthesis in Bacillus stearothermophilus PV72/p6 is blocked when cells are grown at elevated temperature. From a culture exhibiting the S-layer-negative phenotype, the S-layer deficient mutant T5 (SbsA-) was isolated. Genetic analysis of the S-layer-encoding gene (sbsA) of mutant T5 revealed an insertion element (IS4712) integrated into the upstream regulatory region of the S-layer gene, thereby blocking sbsA transcription. The insertion element consists of 1371 base pairs which are flanked by two perfect inverted terminal repeats. Sequence similarity to other transposases of the IS4 family was detected. DNA-DNA hybridizations demonstrated that multiple homologues of IS4712 were also present within the genomes of several other thermophilic bacillus isolates. Attempts to isolate SbsA+ revertants failed. Instead, cells with altered surface proteins were detected. The synthesis of the altered S-layer proteins was correlated with the presence of IS4712 along with the occurrence of deletions in the sbsA coding region. Furthermore imprecise excision of IS4712 was detected. This work demonstrated that B. stearothermophilus is able to express at least four different S-layer proteins and that blocking of sbsA transcription by the insertion element IS4712 is associated with the expression of altered surface proteins.

5' Untranslated Regions↗

Molecular evolution within the L-malate and L-lactate dehydrogenase super-family.

The NAD(P)-dependent malate (L-MalDH) and NAD-dependent lactate (L-LDH) form a large super-family that has been characterized in organisms belonging to the three domains of life. In the first part of this study, the group of [LDH-like] L-MalDH, which are malate dehydrogenases resembling lactate dehydrogenase, were analyzed and clearly defined with respect to the other enzymes. In the second part, the phylogenetic relationships of the whole super-family were presented by taking into account the [LDH-like] L-MalDH. The inferred tree unambiguously shows that two ancestral genes duplications, and not one as generally thought, are needed to explain both the distribution into two enzymatic functions and the observation of three main groups within the super-family: L-LDH, [LDH-like] L-MalDH, and dimeric L-MalDH. In addition, various cases of functional changes within each group were observed and analyzed. The direction of evolution was found to always be polarized: from enzymes with a high stringency of substrate recognition to enzymes with a broad substrate specificity. A specific phyletic distribution of the L-LDH, [LDH-like] L-MalDH, and dimeric L-MalDH over the Archaeal, Bacterial, and Eukaryal domains was observed. This was analyzed in the light of biochemical, structural, and genomic data available for the L-LDH, [LDH-like] L-MalDH, and dimeric L-MalDH. This analysis led to the elaboration of a refined evolutionary scenario of the super-family, in which the selection of L-LDH and the fate of L-MalDH during mitochrondrial genesis are presented.

Animals↗

Membrane lipid composition of Bacillus stearothermophilus as affected by lipophilic environmental pollutants: an approach to membrane toxicity assessment.

The thermophilic eubacterium Bacillus stearothermophilus is used as a model to identify membrane perturbing effects of lipophilic compounds. A parallelism has been established between the toxicity of the organochlorine insecticide DDT and its metabolite, DDE, in bacterial growth and the effects on cell functions and physical perturbations induced at the membrane (Donato et al. 1997a, Arch Environ Contam Toxicol 33:109-116; Donato et al. 1997b, Appl Environ Microbiol 63:4948-495). In the present work, the use of B. stearothermophilus as a model of screening for chemical toxicity has been implemented. Because the regulation of the lipid composition of the membrane is a common strategy in response to adverse growth conditions, we studied the effects of DDE on the lipid composition and the consequent alterations of membrane physical properties in comparison to the parental compound DDT. As expected, different adaptation responses were induced by the compounds, being DDT more effective as compared with DDE. Collected data are consistent with the stronger perturbations induced by DDT on growth and membrane functions. It is concluded that the membrane lipid composition of the bacterium is a very sensitive criterium to detect membrane-mediated toxic effects at low concentrations of lipophilic xenobiotics.

Calorimetry, Differential Scanning↗

Bacillus stearothermophilus as a model to evaluate membrane toxicity of a lipophilic environmental pollutant (DDT).

The thermophilic eubacterium Bacillus stearothermophilus has been used as a model system to identify DDT-promoted events in biological membranes putatively related with the insecticide toxicity. Two strategies have been approached: a) bacterial growth and viability were followed and the effects of DDT (2,2-bis(p-chlorophenyl)-1,1,1-trichloroethane) determined; b) biophysical studies with fluorescent probes were performed to elucidate the effects of DDT on the organization of the membrane lipid bilayer. The effects of DDT on growth and physical properties of the membrane were also determined in the presence of Ca2+ to further identify the interference of the insecticide at the membrane level and its putative contribution to cell toxicity. Growth inhibition by DDT is concentration-dependent, being attenuated or removed by the addition of 2.5-mM Ca2+ to bacterial cultures. Consistently, fluorescence polarization of 1,6-diphenyl-1,3,5-hexatriene (DPH) and its propionic acid derivative (DPH-PA) exhibited opposite effects of Ca2+ and DDT on the physical state of bacterial polar lipid dispersions. Growth and viability of bacterial cells are affected by DDT concentrations lower than those able to induce detectable bulk fluidity alterations, indicating high sensitivity of the intact bacterial system to alterations in limited membrane domains not directly probed by fluorescent probes that only report the average behavior of membrane lipid population.

DDT↗

Effects of a lipophilic environmental pollutant (DDT) on the phospholipid and fatty acid contents of Bacillus stearothermophilus.

Cultures of Bacillus stearothermophilus grown in a complex medium containing 1 microM DDT, exhibited longer lag adapting periods, decreased specific growth rates, and lower growth yield as compared to control cultures. The membrane lipid composition from cells grown in the presence of the insecticide was significantly different from that of control cells. The effects of DDT (2,2-bis(p-chlorophenyl)-1, 1,1-trichloroethane) on growth and lipid composition of bacterial cells were also determined in cultures grown in a medium supplemented with Ca2+ (membrane stabilizer) to further clarify the influence of growth conditions on bacterial responses to the toxicant. The main membrane-lipid changes induced by DDT relate to a very significant increase (74%) of the relative concentration of a phosphoglycolipid, an increase of the phosphatidylethanolamine content, with a parallel decrease of phosphatidylglycerol and an unidentified phospholipid X0. The changes of the phospholipid acyl chains relate to an increase of straight chains and a parallel decrease of branched chains. The effects of DDT-induced lipid composition alterations on membrane physical properties were monitored by fluorescence polarization studies with bacterial polar lipid dispersions. Changes in the membrane lipids upon growing the bacteria in a DDT-containing medium promoted, as expected, more ordered membranes with a shift of the phase transition temperature to higher values. Data are interpreted in the frame of an adaptation mechanism to counteract the membrane perturbation resulting from the accumulation of the insecticide molecules in the lipid bilayer.

DDT↗

Esterases from Bacillus subtilis and B. stearothermophilus share high sequence homology but differ substantially in their properties.

A novel esterase from Bacillus subtilis (BsubE) was cloned, functionally expressed in Escherichia coli and biochemically characterized. BsubE shows high homology (74% identity, >95% homology) to an esterase from the thermophilic B. stearothermophilus (BsteE). Both enzymes were efficiently expressed in E. coli, using a L-rhamnose-expression system [11,500 units/l (BsteE), 3,400 units/l (BsubE)] and were purified by Ni-nitrilotriacetic acid chromatography, yielding specific activities of 70 units/mg (BsteE) and 40 units/mg (BsubE), as determined by the hydrolysis of p-nitrophenyl acetate. Despite the high homology, both esterases revealed remarkable differences in their properties. As expected, the esterase from the thermophilic organism showed significantly higher temperature stability. Whereas BsteE showed highest activity at 65-70 degrees C, BsubE was almost inactivated at 50 degrees C. Moreover, both enzymes showed quite different substrate patterns in the hydrolysis of various esters. Whilst the B. subtilis esterase accepted esters with a branched alcohol moiety well, the B. stearothermophilus esterase was more useful in the hydrolysis of substrates with a sterically demanding carboxylic acid group. BsteE showed excellent enantioselectivity ( E>100) in the kinetic resolution of menthyl acetate and even accepted the bulky menthyl benzoate as substrate ( E=19). In contrast, BsubE converted 1-phenethylacetate with higher selectivity ( E>150 vs E=8).

Amino Acid Sequence↗

Studies on Bacillus stearothermophilus. Part III. Transformation of testosterone.

Bacillus stearothermophilus, a thermophilic bacterium isolated from the Kuwaiti desert, produced a variety of monohydroxy androstene derivatives and an oxidized product when incubated with exogenous testosterone for 24 h at 65 degrees C. The major metabolite was identified as androst-4-en-3,17-dione while minor metabolites included 6 alpha-hydroxyandrost-4-en-3,17-dione, 6 beta-hydroxyandrost-4-en-3,17-dione, 6 alpha-hydroxytestosterone, and 6 beta-hydroxytestosterone. These metabolites were purified by TLC and HPLC followed by their identification using (1)H- and (13)C-NMR and other spectroscopic data.

Biotransformation↗

Enhanced secretion of Bacillus stearothermophilus L1 lipase in Saccharomyces cerevisiae by translational fusion to cellulose-binding domain.

The secretion of Bacillus stearothermophilus L1 lipase in Saccharomyces cerevisiae was investigated by employing a fusion partner, a cellulose-binding domain (CBD) from Trichoderma harzianum endoglucanase II (THEG). The CBD was connected to the N-terminal of L1 lipase through an endogenous linker peptide from THEG. The expression cassette for the fusion protein in S. cerevisiae was constructed using the alpha-amylase signal peptide and the galactose-inducible GAL10 promoter. Secretion of CBD-linker-L1 lipase by this fusion construct was dramatically 7-fold enhanced, compared with that of the mature L1 lipase without CBD-fusion. The fusion protein was secreted into the culture medium, reaching levels of approximately 1.3 g/l in high-cell-density fed-batch cultures. Insertion of a KEX2 cleavage site into the junction between CBD-linker and L1 lipase resulted in the same level of enhanced secretion, indicating that the CBD-linker fusion probably plays a critical role in secretion from endoplasmic reticulum to Golgi apparatus. Therefore, the CBD from THEG can be used both as an affinity tag and as a secretion enhancer for the secretory production of heterologous proteins in S. cerevisiae, since in vivo breakage at the linker was almost negligible.

Amino Acid Sequence↗

Expression of Bacillus stearothermophilus LV cadmium resistance genes in Escherichia coli causes hypersensitivity to cadmium chloride.

Determination of the nucleotide sequence of a 4.5-kb chromosomal DNA fragment of Bacillus stearothermophilus LV revealed two open reading frames (ORFs) of 121 and 727 amino acids (aa) that exhibit a high degree of similarity with the cadC and cadA cadmium resistance genes of a number of microorganisms. Transfer and expression of the B. stearothermophilus LV cadA or cadC/ cadA genes in E. coli caused increased cadmium chloride susceptibility in the bacterial host. Transfer of cadC alone did not result in any detectable phenotypic change in E. coli.

Adenosine Triphosphatases↗

Overexpression, purification, and characterization of the recombinant leucine aminopeptidase II of Bacillus stearothermophilus.

For expression of Bacillus stearothermophilus NCIB 8924 leucine aminopeptidase II (LAP II) in Escherichia coli regulated by a T5 promoter, the gene was amplified by polymerase chain reaction and cloned into expression vector pQE-32 to generate pQE-LAPII. The His(6)-tagged enzyme was overexpressed in IPTG-induced E. coli M15 (pQE-LAPII) as a soluble protein and was purified to homogeneity by nickel-chelate chromatography to a specific activity of 425 U/mg protein with a final yield of 76%. The subunit molecular mass of the purified protein was estimated to be 44.5 kDa by SDS-PAGE. The temperature and pH optima for the purified protein were 60 degrees C and 8.0, respectively. Under optimal condition, the purified enzyme showed a marked preference for Leu- p-nitroanilide, followed by Arg- and Lys-derivatives. The His(6)-tagged enzyme was stimulated by Co(2+) ions, but was strongly inhibited by Cu(2+) and Hg(2+) and by the chelating agents, DTT and EDTA. The EDTA-treated enzyme could be reactivated with Co(2+) ions, indicating that it is a cobalt-dependent exopeptidase. Taking the biochemical characteristics together, we found that the recombinant LAP II exhibits no important differences from those properties described for the native enzyme.

Anilides↗

The product of the cysK gene of Bacillus stearothermophilus V mediates potassium tellurite resistance in Escherichia coli.

The nucleotide sequence of a 4,539 bp fragment of Bacillus stearothermophilus V mediating tellurite resistance in Escherichia coli was determined. Four ORFs of more than 150 amino acids encoding polypeptides of 244, 258, 308, and 421 residues were found in the restriction fragment. E. coli cells harboring a recombinant plasmid containing the Ter determinant express, when challenged with tellurite, a 32 kDa protein with an amino terminal sequence identical to the ten first residues of the 308 ORF. This ORF shows great similarity with the cysteine synthase gene (cysK) of a number of organisms. Recombinant clones carrying the active cysK gene have minimal inhibitory concentrations to K2TeO3 that were tenfold higher than those determined for the host strain or that of clones carrying ORFs 244, 258, and 421. Introduction of the B. stearothermophilus V cysK gene into a cysK strain of Salmonella typhimurium LT2 resulted in complementation of the mutation as well as transfer of tellurite resistance.

Cloning, Molecular↗

Nucleotide sequence of the gene encoding the BstLVI DNA methyltransferase: comparison with other amino-DNA methyltransferases.

The nucleotide sequence of a 2837-base pairs (bp) EcoRI-PvuI fragment of Bacillus stearothermophilus LV chromosomal DNA encoding the bstLVIM gene was determined. It revealed a large open reading frame (ORF) of 1737 bp specifying a methylase of 579 amino acid (aa) residues and Mr 66,831. This was in agreement with the size estimated for the M. BstLVI ( approximately 67 kDa) purified from Escherichia coli cells harboring a recombinant plasmid containing the bstLVIM gene and with results of transcription-translation experiments performed in vitro. Upstream the bstLVIM gene and in the opposite transcriptional orientation, there is a 81-aa ORF that showed great homology with the regulatory C proteins identified in other type II restriction and modification (R-M) systems. This 81-aa ORF precedes a truncated ORF of 86 aa which in turn may represent the structural gene for the BstLVI restriction endonuclease.

Amino Acid Sequence↗

Crystallization and preliminary X-ray diffraction analysis of E. coli arginyl-tRNA synthetase in complex form with a tRNAArg.

Amino acids are building blocks of proteins, while aminoacyl-tRNA synthetases (aaRSs) catalyze the first reaction in such building: the biosynthesis of proteins. The E. coli arginyl-tRNA synthetase (ArgRS) has been crystallized in complex form with tRNA(Arg) (B. stearothermophilus), at pH 5.6 using ammonium sulfate as a precipitating agent. Two crystal forms have been identified based on unit cell dimension. The complete data sets from both crystal forms have been collected with a primitive hexagonal space group. A data set of Form II crystals at 3.2 A and 94% completeness has been obtained, with unit cell parameters a = b = 98.0 A, c = 463.2 A, and alpha = beta = 90 degrees , gamma = 120 degrees , being different from a = b = 110.8 A, c = 377.8 A for form I. The structure determination will demonstrate the interaction of these two macromolecules to understand the special mechanism of ArgRS that requires the presence of tRNA for amino acid activation. Such complex structure also provides a wide opening for inhibitor search using bioinformatics.

Arginine-tRNA Ligase↗

High-resolution X-ray structure of the DNA-binding protein HU from the hyper-thermophilic Thermotoga maritima and the determinants of its thermostability.

The histone-like DNA-binding proteins (HU) are a convenient model for studying factors affecting thermostability because of their relatively simple, easily comparable structures, their common function, and their presence in organisms of widely differing thermostability. We report the determination of the high-resolution structure (1.53 A) at 273 K and 100 K of the HU protein from the hyper-thermophilic eubacterium Thermotoga maritima(HU Tmar, T(m)=80.5 degrees C). The structural data presented clearly show that the HU Tmar has a fold similar to its thermophilic homologue HU from Bacillus stearothermophilus (HU Bst). Based on primary structure analysis, as well as on the results of mutational analysis of HU Bst ( T(m)=61.6 degrees C) and Bacillus subtilis (HU Bsu, T(m)=39.7 degrees C), we have designed and produced several single and combined mutations to study their effect on the thermostability of the recombinant HU Tmar. Among others, the triplet mutant HU Tmar-G15E/E34D/V42I ( T(m)=35.9 degrees C) has converted the extreme thermophilic protein HU Tmar to mesophilic, like HU Bsu. In an attempt to analyze the various mutants of HU Tmar, we crystallized the point mutation HU Tmar-E34D, in which Glu34 was replaced by Asp, similar to the mesophilic HU Bsu. The mutant has T(m)=72.9 degrees C, as measured by circular dichroism, 7.6 degrees C lower than the wild type. The crystal structure of HU Tmar-E34D was determined at 100 K and refined at 1.72 A resolution. A comparison with the wild-type structures clearly shows that two hydrogen bonds have been disrupted between Glu34 from one subunit and Thr13 from the other subunit, and vice versa. Our analysis points to this as the prime cause of the destabilization compared to the wild type. The three new structures were compared, together with the X-ray structure of a similar protein, HU Bst, with the aim of relating their structural properties and different thermal stability. The presented results show that the HU Tmar protein achieves its stability by employing a dual strategy. On the one hand, we observe local hydrophobic interactions, which stabilize the secondary structure elements, and on the other hand, electrostatic interactions between side chains.

Amino Acid Sequence↗

The thermostability of DNA-binding protein HU from mesophilic, thermophilic, and extreme thermophilic bacteria.

Based on primary structure comparison between four highly homologous DNA-binding proteins (HUs) displaying differential thermostability, we have employed in vitro site-directed mutagenesis to decipher their thermostability mechanism at the molecular level. The contribution of the 11 amino acids that differ between the thermophilic HUBst from Bacillus stearothermophilus (Tm = 61.6 degrees C) and the mesophilic HUBsu from Bacillus subtilis (Tm = 39.7 degrees C) was evaluated by replacing these amino acids in HUBst with their mesophilic counterparts. Among 11 amino acids, three residues, Gly-15, Glu-34, and Val-42, which are highly conserved in the thermophilic HUs, have been found to be responsible for the thermostability of HUBst. These amino acids in combination (HUBst-G15E/E34D/V42I) reduce the thermostability of the protein (Tm = 45.1 degrees C) at the level of its mesophilic homologue HUBsu. By replacing these amino acids in HUBsu with their thermophilic counterparts, the HUBsu-E15G/D34E/142V mutant was generated with thermostability (Tm = 57.8 degrees C) at the level of thermophilic HUBst. Employing the same strategy, we generated several mutants in the extremely thermophilic HUTmar from Thermotoga maritima (Tm = 80.5 degrees C), and obtained data consistent with the previous results. The triplet mutant HUTmar-G15E/E34D/V421 (Tm = 35.9 degrees C) converted the extremely thermophilic protein HUTmar to mesophilic. The various forms of HU proteins were overproduced in Escherichia coli, highly purified, and the thermostability of the mutants confirmed by circular dichroism spectroscopy. The results presented here were elucidated on the basis of the X-ray structure of HUBst and HUTmar (our unpublished results), and their mechanism was proposed at the molecular level. The results clearly show that three individual local interactions located at the helix-turn-helix part of the protein are responsible for the stability of HU proteins by acting cooperatively in a common mechanism for thermostability.

Amino Acid Sequence↗

Fusion of Bacillus stearothermophilus leucine aminopeptidase II with the raw-starch-binding domain of Bacillus sp. strain TS-23 alpha-amylase generates a chimeric enzyme with enhanced thermostability and catalytic activity.

Bacillus stearothermophilus leucine aminopeptidase II (LAPII) was fused at its C-terminal end with the raw-starch-binding domain of Bacillus sp. strain TS-23 alpha-amylase. The chimeric enzyme (LAPsbd), with an apparent molecular mass of approximately 61 kDa, was overexpressed in IPTG-induced Escherichia coli cells and purified to homogeneity by nickel-chelate chromatography. The purified enzyme retained LAP activity and adsorbed raw starch. LAPsbd was stable at 70 degrees C for 10 min, while the activity of wild-type enzyme was completely abolished under the same environmental condition. Compared with the wild-type enzyme, the twofold increase in the catalytic efficiency for LAPsbd was due to a 218% increase in the k(cat) value.

Binding Sites↗

Histidines 345 and 378 of Bacillus stearothermophilus leucine aminopeptidase II are essential for the catalytic activity of the enzyme.

The conserved histidine residues, His-191, His-227, His-345, and His-378, in Bacillus stearothermophilus leucine aminopeptidase II (LAPII) were replaced with leucine by site-directed mutagenesis. The overexpressed wild-type and mutant enzymes have been purified by nickel-chelate chromatography and their molecular masses were approximately 44.5 kDa. Under assay conditions, no LAP activity was detected in H345L and H378L. Although the Km value for H191L increased more than 30% with respect to the wild-type LAPII, alteration in this residue did not lead to a significant change on the catalytic efficiency. The 39% decrease in Kcat/Km for H227L was partly caused by a 3.9-fold increase in Km value. Based on these results, it is suggested that His-345 and His-378 play a crucial role in the catalytic reaction of B. stearothermophilus LAPII.

Amino Acid Sequence↗