Archaeal diversity in naturally occurring and impacted environments from a tropical region

AIMS

To evaluate archaeal diversity in natural and impacted habitats from Rio de Janeiro state, Brazil, a tropical region of South America.

METHODS AND RESULTS

16S rRNA gene was amplified directly by polymerase chain reaction (PCR) from genomic DNA, extracted from Guanabara Bay (GB) water, halomarine sediment (HS), municipal landfill leachate, agricultural soil and wastewater treatment (WT) system. Five archaeal 16S rDNA clone libraries were constructed. A total of 123 clones, within the five libraries analysed, were clustered into 29 operational taxonomic units, related to cultivated (24%) and uncultivated (76%) organisms. Rarefaction analysis showed that the libraries contained different levels of diversity. PCR-denaturing gradient gel electrophoresis (DGGE) of 16S-23S intergenic spacer regions confirmed the presence of a dominant phylotype, revealed by the WT system clone library.

CONCLUSIONS

Archaeal communities of impacted environments seem to be confined to specific ecosystems with similar physicochemical properties, while communities from natural environments appear to be widely distributed. The presence of a high number of phylotypes related to uncultivated organisms suggests new archaeal lineages.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study reports, for the first time, the analysis of archaeal diversity in tropical environments from Brazil, and adds sequences from this region to the developing database of 16S rRNA clone libraries from environmental samples.

Self-association of isolated large cytoplasmic domain of plasma membrane H+ -ATPase from Saccharomyces cerevisiae: role of the phosphorylation domain in a general dimeric model for P-ATPases

Large cytoplasmic domain (LCD) plasma membrane H+ -ATPase from S. cerevisiae was expressed as two fusion polypeptides in E. coli: a DNA sequence coding for Leu353-Ileu674 (LCDh), comprising both nucleotide (N) and phosphorylation (P) domains, and a DNA sequence coding for Leu353-Thr543 (LCDDeltah, lacking the C-terminus of P domain), were inserted in expression vectors pDEST-17, yielding the respective recombinant plasmids. Overexpressed fusion polypeptides were solubilized with 6 M urea and purified on affinity columns, and urea was removed by dialysis. Their predicted secondary structure contents were confirmed by CD spectra. In addition, both recombinant polypeptides exhibited high-affinity 2',3'-O-(2,4,6-trinitrophenyl)adenosine-5'-triphosphate (TNP-ATP) binding (Kd = 1.9 microM and 2.9 microM for LCDh and LCDDeltah, respectively), suggesting that they have native-like folding. The gel filtration profile (HPLC) of purified LCDh showed two main peaks, with molecular weights of 95 kDa and 39 kDa, compatible with dimeric and monomeric forms, respectively. However, a single elution peak was observed for purified LCDDeltah, with an estimated molecular weight of 29 kDa, as expected for a monomer. Together, these data suggest that LCDh exist in monomer-dimer equilibrium, and that the C-terminus of P domain is necessary for self-association. We propose that such association is due to interaction between vicinal P domains, which may be of functional relevance for H+ -ATPase in native membranes. We discuss a general dimeric model for P-ATPases with interacting P domains, based on published crystallography and cryo-electron microscopy evidence.

Characterization of Gordonia sp. strain F.5.25.8 capable of dibenzothiophene desulfurization and carbazole utilization

A dibenzothiophene (DBT)-degrading bacterial strain able to utilize carbazole as the only source of nitrogen was identified as Gordonia sp. F.5.25.8 due to its 16S rRNA gene sequence and phenotypic characteristics. Gas chromatography (GC) and GC-mass spectroscopy analyses showed that strain F.5.25.8 transformed DBT into 2-hydroxybiphenyl (2-HBP). This strain was also able to grow using various organic sulfur or nitrogen compounds as the sole sulfur or nitrogen sources. Resting-cell studies indicated that desulfurization occurs either in cell-associated or in cell-free extracts of F.5.25.8. The biological responses of F.5.25.8 to a series of mutagens and environmental agents were also characterized. The results revealed that this strain is highly tolerant to DNA damage and also refractory to induced mutagenesis. Strain F.5.25.8 was also characterized genetically. Results showed that genes involved in desulfurization (dsz) are located in the chromosome, and PCR amplification was observed with primers dszA and dszB designed based on Rhodococcus genes. However, no amplification product was observed with the primer based on dszC.

PCR analyses of tRNA intergenic spacer, 16S-23S internal transcribed spacer, and randomly amplified polymorphic DNA reveal inter- and intraspecific relationships of Enterobacter cloacae strains

PCR analysis of tRNA intergenic spacer (tDNA-PCR) and of the 16S-23S internal transcribed spacer (ITS-PCR) and random amplified polymorphic DNA (RAPD) analysis were evaluated for their usefulness in characterization of Enterobacter cloacae strains isolated from both clinical origins and vaccine microbial contamination. tDNA-PCR presented specific and reproducible patterns for Enterobacter sakazakii ATCC 29004, Enterobacter aerogenes ATCC 13048, and Enterobacter cloacae ATCC 13047 and 23355 that presented the same profile for all 16 E. cloacae isolates, offering an alternative tool for species-level identification. ITS-PCR and RAPD analysis yielded completely different banding patterns for the 20 strains studied, except for E. cloacae strains isolated from different batches of vaccine that exhibited a unique pattern, suggesting contamination by the same strain. The combined use of tDNA-PCR and ITS-PCR in a one-step protocol allows accurate identification and typing of E. cloacae strains a few hours after the colony has been isolated.

Pressure effects on the interaction between natural inhibitor protein and mitochondrial F1-ATPase

Pressure stability of the complex formed between F1-ATPase and the inhibitor protein (IP) was studied in the membrane-bound and soluble, purified forms of beef-heart mitochondrial enzymes. A latent preparation of submitochondrial particles (SMP-MgATP) initially exhibits low hydrolytic activity. Dissociation of IP increases the activity about 10-fold. This increase occurs in parallel with an increase in sensitivity to pressure inactivation. The membrane-bound, latent IP-F1-ATPase complex is activated 2.5-fold when incubated at a pressure of 1.7 kbar, suggesting dissociation of IP. A fully active preparation of submitochondrial particles depleted of IP (AS-particles) is highly pressure labile when compared with the latent form. In the absence of IP, soluble purified F1-ATPase is also inactivated by pressure. In contrast, the soluble IP-F1-ATPase complex is very resistant to pressure, as evidenced by enzymatic and fluorescence studies. Based on the pressure-titration experiments, binding of IP stabilizes the F1-ATPase complex by 1.54 kcal per mole of complex. The substrate MgATP confers additional protection on both preparations only in the presence of IP. Glycerol appears to prevent dissociation of IP and therefore protects SMP-MgATP from pressure inactivation. Our results demonstrate that in addition to its regulatory role in catalysis, IP stabilizes the structure of the F1-ATPase complex. The pressure-induced dissociation of IP from F1-ATPase and its prevention by glycerol suggest that nonpolar in addition to electrostatic interactions are important for the binding of IP to the regulatory site.

Inhibition of succinic dehydrogenase and F0F1-ATP synthase by 4,4'-diisothiocyanatostilbene-2,2'-disulfonic acid (DIDS)

This study shows that incubation of rat liver mitochondria in the presence of the thiol/ amino reagent 4,4'-diisothiocyanatostilbene-2,2'-disulfonic acid (DIDS) is followed by inhibition of both succinate supported respiration and oxidative phosphorylation. Half-maximal inhibition of succinic dehydrogenase activity and succinate oxidation by mitochondria was attained at 55.3 and 60.8 microM DIDS, respectively. DIDS did inhibit the net ATP synthesis and ATP<=>[32P]Pi exchange reaction catalyzed by submitochondrial particles in a dose-dependent manner (Ki = 31.7 microM and Ki = 32.7 microM), respectively. The hydrolytic activities of uncoupled heart submitochondrial particles and purified F1-ATPase were also inhibited 50% by 31.9 and 20.9 microM DIDS, respectively.

Binding of adenine nucleotides to the F1-inhibitor protein complex of bovine heart submitochondrial particles

The binding of ATP radiolabeled in the adenine ring or in the gamma- or alpha-phosphate to F1-ATPase in complex with the endogenous inhibitor protein was measured in bovine heart submitochondrial particles by filtration in Sephadex centrifuge columns or by Millipore filtration techniques. These particles had 0.44 +/- 0.05 nmol of F1 mg-1 as determined by the method of Ferguson et al. [(1976) Biochem. J. 153, 347]. By incubation of the particles with 50 microM ATP, and low magnesium concentrations (less than 0.1 microM MgATP), it was possible to observe that 3.5 mol of [gamma-32P]ATP was tightly bound per mole of F1 before the completion of one catalytic cycle. With [gamma-32P]ITP, only one tight binding site was detected. Half-maximal binding of adenine nucleotides took place with about 10 microM. All the bound radioactive nucleotides were released from the enzyme after a chase with cold ATP or ADP; 1.5 sites exchanged with a rate constant of 2.8 s-1 and 2 with a rate constant of 0.45 s-1. Only one of the tightly bound adenine nucleotides was released by 1 mM ITP; the rate constant was 3.2 s-1. It was also observed that two of the bound [gamma-32P]ATP were slowly hydrolyzed after removal of medium ATP; when the same experiment was repeated with [alpha-32P]ATP, all the label remained bound to F1, suggesting that ADP remained bound after completion of ATP hydrolysis. Particles in which the natural ATPase inhibitor protein had been released bound tightly only one adenine nucleotide per enzyme.(ABSTRACT TRUNCATED AT 250 WORDS)

Coupling of ATP hydrolysis to phosphate uptake in Rhodospirillum rubrum chromatophores under the influence of Ca2+ and Mg2+

The Pi-ATP exchange and ATP hydrolytic reactions, by the F0F1 complex, were studied in Rhodospirillum rubrum chromatophores in the dark. An optimal pH between 7.0 and 8.5 was determined for the hydrolytic and exchange reactions. Under these conditions, the hydrolysis/exchange ratio was approximately 2. The kinetic analysis of the hydrolytic and exchange reactions using Mg-ATP as substrate showed a change in the hydrolysis/exchange ratio that varied between 2.0 and 2.8 as the substrate concentration was increased. With Ca-ATP, hydrolysis was not saturated up to a substrate concentration of 5.0 mM, and the hydrolysis/exchange ratios changed from 2 to 240 as the substrate concentration was increased from 0.06 to 5.0 mM. Free Mg2+ inhibited hydrolysis and phosphate uptake without altering the hydrolysis/exchange ratio. Nigericin induced an increase in the hydrolysis/exchange ratio from 2.7 to 130, whereas in the presence of valinomycin, this ratio increased from 2.7 to 21. From these results, it can be concluded that Ca-ATP hydrolysis is loosely coupled to phosphate uptake given that Pi-ATP exchange activity is extremely low, even at high rates of ATP hydrolysis.

Pre-steady-state studies of the adenosine triphosphatase activity of coupled submitochondrial particles. Regulation by ADP

ATPase activities were measured in 10 mM MgCl2, 5 mM ATP, 1 mM ADP, and 1 microM FCCP with submitochondrial particles from bovine heart that had been stimulated by delta mu H+-forming substrates and with particles whose natural inhibitor protein was partially removed by heating. The activities were not linear with time. With both particles, the rate of ATP hydrolysis in the 7-fold greater than that in the steady state. Pre-steady-state and steady-state kinetic studies showed that the decrease of ATPase activity was due to the binding of ADP in a high-affinity site of the enzyme (K0.5 of 10 microM). Inhibition of ATP hydrolysis was accompanied by the binding of approximately 1 mol of ADP/mol of particulate F1; 10 microM ADP gave half-maximal binding. ADP could be replaced by IDP, but with an affinity 50-fold lower (K0.5 of 0.5 mM). Maximal inhibition by ADP and IDP was achieved in less than 5 s. Inhibition was enhanced by uncouplers. Even in the presence of pyruvate kinase and phosphoenolpyruvate, the rates of hydrolysis were about 2.5-fold higher in the first seconds of reaction than in the steady state. This decrease of ATPase activity also correlated with the binding of nearly 1 mol of ADP/mol of F1. This inhibitory ADP remained bound to the enzyme after several thousand turnovers. Apparently, it is possible to observe maximal rates of hydrolysis only in the first few catalytic cycles of the enzyme.

Synthesis and hydrolysis of ATP by the mitochondrial ATP synthase

A brief summary of the factors that control synthesis and hydrolysis of ATP by the mitochondrial H+-ATP synthase is made. Particular emphasis is placed on the role of the natural ATPase inhibitor protein. It is clear from the existing data obtained with a number of agents that there is no correlation between variations of the rate of ATP hydrolysis and ATP synthesis as driven by respiration. The mechanism by which each condition differentially affects the two activities is not entirely known. For the case of the natural ATPase inhibitor protein, it appears that the protein controls the kinetics of the enzyme. This control seems essential for achieving maximal accumulation of ATP during electron transport in systems that contain relatively high concentrations of ATP.

Effect of the electrochemical proton gradient and anions on the ATPase activity of soybean submitochondrial particles

Submitochondrial particles from soybean (Glycine max L. cv Jupiter) hypocotyls with an ATPase activity of 0.3 to 1.0 micromole per minute per milligram were prepared by sonication with Mg-ATP. The particles catalyzed ATP synthesis with NADH and succinate; the ratios of ATP/O with these substrates were 1.0 and 0.1, respectively. As monitored by oxonol-VI, the particles built up and maintained a membrane potential that was higher with NADH than with succinate or Mg-ATP. The ATPase activity of the particles increased two to threefold by preincubation with 50 millimolar phosphate at a temperature of 38 degrees C. The increase in ATPase activity became higher (five to sixfold) when particles were preincubated with Mg-ATP plus phosphate. Under the latter conditions, collapse of DeltamuH by carbonyl cyanide p-trifluoromethoxyphenylhydrazone prevented the activation. An increase in ATPase activity of the particles was also observed with NADH and succinate, although activation was lower with succinate. With these substrates, phosphate did not increase ATPase activation. When particles were preincubated with Mg-ATP, anions that stimulate ATP hydrolysis (malate, malonate, and bicarbonate) had an activating effect similar to that of phosphate. The data suggest that the soybean mitochondrial ATPase can be activated by DeltamuH but that this activation is increased by the binding of certain anions to a conformation of the enzyme that appears during hydrolytic cycles.

Properties and regulation of the H+-ATP synthase of mitochondria

A brief survey is made of the function of the H+-ATP synthase of mitochondria with emphasis on how it is regulated. A main regulatory factor is a low molecular weight protein whose binding to the enzyme appears to be essential for optimal accumulation of ATP as driven by electron transport. The ATP synthase is also controlled by ADP that, by binding to a site in the enzyme, inhibits ATP hydrolysis. Data on the spontaneous synthesis of a tightly bound ATP are discussed. Apparently, this requires proper subunit interactions to yield a competent catalytic site.

Stability and partial reactions of soluble and membrane-bound sarcoplasmic reticulum ATPase

The Ca-ATPase of sarcoplasmic reticulum was solubilized at pH 6.5 and 30 degrees C using different nonionic detergents, Triton X-100, C12E8, Lubrol PX, or Tween 20. After full solubilization by any of these detergents, the enzyme was unstable (t1/2 = 2-3 min) in the absence of Ca2+. The soluble enzyme was stable in the presence of calcium, half-maximal protection being attained in the presence of 0.2 mM Ca2+. In the absence of Ca2+, stability was restored by addition of co-solvents dimethyl sulfoxide or glycerol. In the presence of 4 mM Ca2+, the progressive addition of nonionic detergents to a medium containing leaky vesicles promoted an increase, up to 3-fold, in the rate of ATP hydrolysis. This was not observed when ITP was used as substrate. The small amount of ADP accumulated in the medium during ATP hydrolysis was sufficient to inhibit the ATPase activity of the membrane-bound enzyme but had no effect on the soluble enzyme. Increasing concentrations of detergent promoted a progressive inhibition of the ATP----Pi exchange reaction. The ATP hydrolysis/synthesis ratio of soluble enzyme was 10 times higher than that of membranous enzyme. Addition of co-solvent restored this ratio to values similar to those obtained with membrane-bound Ca-ATPase. Soluble enzyme prepared from native sarcoplasmic reticulum vesicles was able to catalyze the net synthesis of ATP when phosphorylated by Pi in the presence of dimethyl sulfoxide and then diluted in a medium containing 10 mM CaCl2 and 2 mM ADP. This was not observed when the soluble enzyme was prepared from purified Ca-ATPase. The results suggest that some of the partial reactions of the catalytic cycle of Ca-ATPase are dependent on the hydrophobic environment found in the native membrane. This environment can be mimicked by co-solvents.