Characterization of growth-supporting factors produced by Geobacillus toebii for the commensal thermophile Symbiobacterium toebii

Symbiobacterium toebii is a commensal symbiotic thermophile that cannot grow without support from a partner bacterium. We investigated the properties of Symbiobacterium growth-supporting factors (SGSFs) produced by the partner bacterium Geobacillus toebii. SGSFs occurred in both the cell-free extract (CFE) and culture supernatant of G. toebii and might comprise multifarious materials because of their different biological properties. The heavy SGSF contained in the cytosolic component exhibited heat- and proteinase-sensitive proteinaceous properties and had a molecular mass of >50 kDa. In contrast, the light SGSF contained in the extracellular component exhibited heat-stable, proteinase-resistant, nonprotein properties and had a molecular mass of <10 kDa. Under morphological examination using light microscopy, S. toebii cultured with the culture supernatant of G. toebii was filamentous, whereas S. toebii cultured with the CFE of G. toebii was rod-shaped. These results strongly suggest that the SGSFs produced by G. toebii comprise two or more types that differ in their growth-supporting mechanisms, although all support the growth of S. toebii. Upon the examination of the distribution of SGSFs in other bacteria, both cytosolic and extracellular components of Geobacillus kaustophilus, Escherichia coli, and Bacillus subtilis had detectable growth-supporting effects for S. toebii, indicating that common SGSF materials are widely present in various bacterial strains.     

Bound nucleotide controls the endonuclease activity of mismatch repair enzyme MutL

DNA mismatch repair corrects mismatched base pairs mainly caused by replication error. Recent studies revealed that human MutL endonuclease, hPMS2, plays an essential role in the repair. However, there has been little biochemical analysis of the MutL endonuclease. In particular, it is unknown for what the MutL utilizes ATP binding and hydrolyzing activity. Here we report the detailed functional analysis of Thermus thermophilus MutL (ttMutL). ttMutL exhibited an endonuclease activity that decreased on alteration of Asp-364 in ttMutL to Asn. The biochemical characteristics of ttMutL were significantly affected on ATP binding, which suppressed nonspecific DNA digestion and promoted the mismatch- and MutS-dependent DNA binding. The inactivation of the cysteinyl residues in the C-terminal domain resulted in the perturbation in ATP-dependent regulation of the endonuclease activity, although the ATP-binding motif is located in the N-terminal domain. Complementation experiments revealed that the endonuclease activity of ttMutL and its regulation by ATP binding are necessary for DNA repair in vivo.     

Activation of newt eggs in the absence of Ca2+ activity by treatment with cycloheximide or D2O

Unfertilized eggs of urodeles that exhibit physiological polyspermy are difficult to activate by ordinary egg-activating agents, such as pricking and Ca²⁺ ionophores, that easily activate monospermic anuran eggs. Therefore, we have tested the effects of other agents that cause egg activation in non-amphibian species in order to investigate the mechanism of egg activation in urodeles. We have found that cycloheximide (a protein synthesis inhibitor), D₂O (that induces microtubule polymerization) and 6-DMAP (a protein kinase inhibitor) caused activation of unfertilized eggs of the newt, Cynops pyrrhogaster . The cell cycle, arrested at meiotic metaphase II, was resumed to form the second polar body accompanied by a loss of maturation promoting factor and cytostatic factor activity. The treated eggs underwent abnormal cleavage. These results indicate that protein synthesis followed by protein phosphorylation is necessary to maintain M phase in unfertilized Cynops eggs. Unfertilized eggs failed to be activated by pricking, but were activated by the ionophore A23187, but only at a concentration 30 times higher than that required to activate Xenopus eggs. Eggs whose intracellular Ca²⁺ ions had been chelated by BAPTA could also be activated by either cycloheximide or D₂O. Cycloheximide- as well as 6-DMAP-induced egg activations were not inhibited by nocodazole, a microtubule-depolymerizing agent. These results suggest that the inhibition of synthesis and phosphorylation of short-lived proteins acts as an egg activation mechanism, downstream of the site of Ca²⁺ action and independently of microtubule polymerization.     

Production of a xylose-stimulated β-glucosidase and a cellulase-free thermostable xylanase by the thermophilic fungus Humicola brevis var. thermoidea under solid state fermentation

Humicola brevis var. thermoidea cultivated under solid state fermentation in wheat bran and water (1:2 w/v) was a good producer of β-glucosidase and xylanase. After optimization using response surface methodology the level of xylanase reached 5,791.2 ± 411.2 U g(-1), while β-glucosidase production was increased about 2.6-fold, reaching 20.7 ± 1.5 U g(-1). Cellulase levels were negligible. Biochemical characterization of H. brevis β-glucosidase and xylanase activities showed that they were stable in a wide pH range. Optimum pH for β-glucosidase and xylanase activities were 5.0 and 5.5, respectively, but the xylanase showed 80 % of maximal activity when assayed at pH 8.0. Both enzymes presented high thermal stability. The β-glucosidase maintained about 95 % of its activity after 26 h in water at 55 °C, with half-lives of 15.7 h at 60 °C and 5.1 h at 65 °C. The presence of xylose during heat treatment at 65 °C protected β-glucosidase against thermal inactivation. Xylanase maintained about 80 % of its activity after 200 h in water at 60 °C. Xylose stimulated β-glucosidase activity up to 1.7-fold, at 200 mmol L(-1). The notable features of both xylanase and β-glucosidase suggest that H. brevis crude culture extract may be useful to compose efficient enzymatic cocktails for lignocellulosic materials treatment or paper pulp biobleaching.     

Biochemical characterization of TT1383 from Thermus thermophilus identifies a novel dNTP triphosphohydrolase activity stimulated by dATP and dTTP

The HD domain motif is found in a superfamily of proteins in bacteria, archaea and eukaryotes. A few of these proteins are known to have metal-dependant phosphohydrolase activity, but the others are functionally unknown. Here we have characterized an HD domain-containing protein, TT1383, from Thermus thermophilus HB8. This protein has sequence similarity to Escherichia coli dGTP triphosphohydrolase, however, no dGTP hydrolytic activity was detected. The hydrolytic activity of the protein was determined in the presence of more than two kinds of deoxyribonucleoside triphosphates (dNTPs), which were hydrolyzed to their respective deoxyribonucleosides and triphosphates, and was found to be strictly specific for dNTPs in the following order of relative activity: dCTP > dGTP > dTTP > dATP. Interestingly, this dNTP triphosphohydrolase (dNTPase) activity requires the presence of dATP or dTTP in the dNTP mixture. dADP, dTDP, dAMP, and dTMP, which themselves were not hydrolyzed, were nonetheless able to stimulate the hydrolysis of dCTP. These results suggest the existence of binding sites specific for dATP and dTTP as positive modulators, distinct from the dNTPase catalytic site. This is, to our knowledge, the first report of a non-specific dNTPase that is activated by dNTP itself.     

A kinetic study of the gill (Na+, K+)-ATPase, and its role in ammonia excretion in the intertidal hermit crab, Clibanarius vittatus

To better comprehend the role of gill ion regulatory mechanisms, the modulation by Na(+), K(+), NH(4)(+) and ATP of (Na(+), K(+))-ATPase activity was examined in a posterior gill microsomal fraction from the hermit crab, Clibanarius vittatus. Under saturating Mg(2+), Na(+) and K(+) concentrations, two well-defined ATP hydrolyzing sites were revealed. ATP was hydrolyzed at the high-affinity sites at a maximum rate of V=19.1+/-0.8 U mg(-1) and K(0.5)=63.8+/-2.9 nmol L(-1), obeying cooperative kinetics (n(H)=1.9); at the low-affinity sites, hydrolysis obeyed Michaelis-Menten kinetics with K(M)=44.1+/-2.6 mumol L(-1) and V=123.5+/-6.1 U mg(-1). Stimulation by Na(+) (V=149.0+/-7.4 U mg(-1); K(M)=7.4+/-0.4 mmol L(-1)), Mg(2+) (V=132.0+/-5.3 U mg(-1); K(0.5)=0.36+/-0.02 mmol L(-1)), NH(4)(+) (V=245.6+/-9.8 U mg(-1); K(M)=4.5+/-0.2 mmol L(-1)) and K(+) (V=140.0+/-4.9 U mg(-1); K(M)=1.5+/-0.1 mmol L(-1)) followed a single saturation curve and, except for Mg(2+), obeyed Michaelis-Menten kinetics. Under optimal ionic conditions, but in the absence of NH(4)(+), ouabain (K(I)=117.3+/-3.5 mumol L(-1)) and orthovanadate inhibited up to 67% of the ATPase activity. The inhibition studies performed suggest the presence of F(0)F(1), V- and P-ATPases, but not Na(+)-, K(+)- or Ca(2+)-ATPases as contaminants in the gill microsomal preparation. (Na(+), K(+))-ATPase activity was synergistically modulated by NH(4)(+) and K(+). At 20 mmol L(-1) K(+), a maximum rate of V=290.8+/-14.5 U mg(-1) was seen as NH(4)(+) concentration was increased up to 50 mmol L(-1). However, at fixed NH(4)(+) concentrations, no additional stimulation was found for increasing K(+) concentrations (V=135.2+/-4.1 U mg(-1) and V=236.6+/-9.5 U mg(-1) and for 10 and 30 mmol L(-1) NH(4)(+), respectively). This is the first report to detail ionic modulation of gill (Na(+), K(+))-ATPase in C. vittatus, revealing an asymmetrical, synergistic stimulation of the enzyme by K(+) and NH(4)(+), as yet undescribed for other (Na(+), K(+))-ATPases, and should provide a better understanding of NH(4)(+) excretion in pagurid crabs.     

Distribution and modulation of the cellular receptor for transforming growth factor-beta

Scatchard analyses of the binding of transforming growth factor-beta (TGF-beta) to a wide variety of different cell types in culture revealed the universal presence of high affinity (Kd = 1-60 pM) receptors for TGF-beta on every cell type assayed, indicating a wide potential target range for TGF-beta action. There was a strong (r = +0.85) inverse relationship between the receptor affinity and the number of receptors expressed per cell, such that at low TGF-beta concentrations, essentially all cells bound a similar number of TGF-beta molecules per cell. The binding of TGF-beta to various cell types was not altered by many agents that affect the cellular response to TGF-beta, suggesting that modulation of TGF-beta binding to its receptor may not be a primary control mechanism in TGF-beta action. Similarly, in vitro transformation resulted in only relatively small changes in the cellular binding of TGF-beta, and for those cell types that exhibited ligand-induced down-regulation of the receptor, down-regulation was not extensive. Thus the strong conservation of binding observed between cell types is also seen within a given cell type under a variety of conditions, and receptor expression appears to be essentially constitutive. Finally, the biologically inactive form of TGF-beta, which constitutes greater than 98% of autocrine TGF-beta secreted by all of the twelve different cell types assayed, was shown to be unable to bind to the receptor without prior activation in vitro. It is proposed that this may prevent premature interaction of autocrine ligand and receptor in the Golgi apparatus.     

Crystal structure of TTHA0252 from Thermus thermophilus HB8, a RNA degradation protein of the metallo-beta-lactamase superfamily

In bacterial RNA metabolism, mRNA degradation is an important process for gene expression. Recently, a novel ribonuclease (RNase), belonging to the beta-CASP family within the metallo-beta-lactamase superfamily, was identified as a functional homologue of RNase E, a major component for mRNA degradation in Escherichia coli. Here, we have determined the crystal structure of TTHA0252 from Thermus thermophilus HB8, which represents the first report of the tertiary structure of a beta-CASP family protein. TTHA0252 comprises two separate domains: a metallo-beta-lactamase domain and a "clamp" domain. The active site of the enzyme is located in a cleft between the two domains, which includes two zinc ions coordinated by seven conserved residues. Although this configuration is similar to those of other beta-lactamases, TTHA0252 has one conserved His residue characteristic of the beta-CASP family as a ligand. We also detected nuclease activity of TTHA0252 against rRNAs of T. thermophilus. Our results reveal structural and functional aspects of novel RNase E-like enzymes with a beta-CASP fold.