Appendix. Sequence of the beta-subunit of oxaloacetate decarboxylase from Klebsiella pneumoniae: a correction of the C-terminal part.
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Amino Acid Sequence↗
Biomedical subjects
P Dimroth
Publications and source records attributed to P Dimroth.
The ATPases of Propionigenium modestum and Bacillus alcalophilus. Strategies for ATP synthesis under low energy conditions.
In Propionigenium modestum, ATP synthesis is coupled via delta mu Na+ to the decarboxylation of (S)-methylmalonyl-CoA. The low energy yield of this reaction implies that approx. 4 decarboxylation cycles are necessary to synthesize 1 molecule of ATP. Theoretical considerations in accord with experimental results suggest ATP synthesis in P. modestum at delta mu Na+ = -110 mV. Other anaerobic bacteria synthesize ATP at a delta mu H+ of similar size and alkaliphilic bacteria at pH 10.3 have a delta mu H+ of only -103 mV. In these cases, the H+(Na+) to ATP stoichiometry must be at least 4.
Adenosine Triphosphatases↗
Cloning, sequencing and in vivo expression of genes encoding the F0 part of the sodium-ion-dependent ATP synthase of Propionigenium modestum in Escherichia coli.
A DNA fragment containing the genes encoding subunits of the F0 part of the sodium-translocating ATPase of Propionigenium modestum was cloned in Escherichia coli and sequenced. The predicted amino acid sequences of subunits a, b and c of the P. modestum ATPase were compared with those of the corresponding subunits of proton-translocating ATPases from other bacteria and chloroplasts. Deletion mutants of E. coli, lacking different genes for ATPase subunits, were transformed with a recombinant plasmid, containing the genes for the subunits a, c, b, delta and part of alpha of the ATPase of P. modestum. Functionally reconstituted ATPase activity could be demonstrated for the transformants. The identity of the vector containing P. modestum genes was verified by restriction analysis of plasmid DNA.
Adenosine Triphosphate↗
Malonate decarboxylase of Malonomonas rubra, a novel type of biotin-containing acetyl enzyme.
Cell suspensions or crude extracts of Malonomonas rubra grown anaerobically on malonate catalyze the decarboxylation of this substrate at a rate of 1.7-2.5 mumol.min-1.mg protein-1 which is consistent with the malonate degradation rate during growth. After fractionation of the cell extract by ultracentrifugation, neither the soluble nor the particulate fraction alone catalyzed the decarboxylation of malonate, but on recombination of the two fractions 87% of the activity of the unfractionated extract was restored. The decarboxylation pathway did not involve the intermediate formation of malonyl-CoA, but decarboxylation proceeded directly with free malonate. The catalytic activity of the enzyme was completely abolished on incubation with hydroxylamine or NaSCN. Approximately 50-65% of the original decarboxylase activity was restored by incubation of the extract with ATP in the presence of acetate, and the extent of reactivation increased after incubation with dithioerythritol. Reactivation of the enzyme was also obtained by chemical acetylation with acetic anhydride. These results indicate modification of the decarboxylase by deacetylation leading to inactivation and by acetylation of the inactivated enzyme specimens leading to reactivation. It is suggested that the catalytic mechanism involves exchange of the enzyme-bound acetyl residues by malonyl residues and subsequent decarboxylation releasing CO2 and regenerating the acetyl-enzyme. The decarboxylase was inhibited by avidin but not by an avidin-biotin complex indicating that biotin is involved in catalysis. A single biotin-containing 120-kDa polypeptide was present in the extract and is a likely component of malonate decarboxylase.
Avidin↗
The sodium ion pumping oxaloacetate decarboxylase of Klebsiella pneumoniae. Metal ion content, inhibitors and proteolytic degradation studies.
Oxaloacetate decarboxylase of Klebsiella pneumoniae was shown to contain between 0.6 and 1.0 mol zinc per mol enzyme in different preparations. The decarboxylase activity was completely abolished after 15 min incubation with 1 mM Hg(NO3)2 in phosphate buffer, while the activity decreased only 20% if the incubation was performed in MES/Tris buffer. Treatment of the isolated subunits with Hg(NO3)2 indicated that the binding site for Hg2+ ions is on the alpha subunit. Other inhibitors of the decarboxylase are KSCN and diethylstilbestrol. Inactivation of the enzyme with 2% 1-butanol was significantly reduced by 100 mM NaCl. Sodium ions also protected the isolated beta + gamma subunits from a digestion with trypsin.
Carboxy-Lyases↗
The Na(+)-translocating ATPase of Propionigenium modestum.
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Adenosine Triphosphatases↗
NADH formation by Na(+)-coupled reversed electron transfer in Klebsiella pneumoniae.
Citrate is fermented by Klebsiella pneumoniae to 2 acetate, 0.5 formate and 1.2 CO2. The formation of less than 1 formate and greater than 1 CO2 per citrate can be accounted for by the oxidation of formate to CO2 in order to provide reducing equivalents for the assimilation of citrate into cell carbon. A membrane-bound electron transport chain is apparently involved in NADH synthesis by these cells. The electrons from formate oxidation to CO2 are used to reduce ubiquinone to ubiquinol by membrane-bound formate dehydrogenase and ubiquinol further delivers its electrons to NAD+, if this endergonic reaction is powered by delta mu Na+. The endogenous NADH level of K. pneumoniae cells thus increased in the presence of formate in response to a delta pNa+ greater than -100 mV. NADH formation was completely abolished in the presence of oxygen or after addition of hydroxyquinoline-N-oxide, a specific inhibitor of the Na(+)-translocating NADH:ubiquinone oxidoreductase. The increase of endogenous NADH was dependent on the delta pNa+ applied to the cells. Inverted membrane vesicles of K. pneumoniae catalysed the reduction of NAD+ to NADH with formate as electron donor after application of delta mu Na+ of about 120 mV consisting of delta pNa+ of 60 mV and delta psi of the same magnitude. Neither the delta pNa+ nor the delta psi of this size alone was sufficient to drive the endergonic reaction. Strictly anaerobic conditions were required for NADH formation and hydroxyquinoline-N-oxide completely inactivated the reaction.(ABSTRACT TRUNCATED AT 250 WORDS)
Citrates↗
Structure and function of the Na(+)-translocating ATPase of Propionigenium modestum.
The strict anaerobic bacterium Propionigenium modestum performs a Na+ cycle over the membrane to couple ATP synthesis to the decarboxylation of methyl-malonyl-CoA. The responsible ATPase has a typical F1F0 structure, the water-soluble F1 moiety being composed of five different subunits and the more firmly membrane-bound F0 part consisting of three different subunits. The F1F0 ATPase but not F1 alone was specifically activated by Na+ ions, suggesting that the Na+ binding site is located on the F0 moiety. The ATPase reconstituted into proteoliposomes catalyzed an ATP-dependent Na+ accumulation that was stimulated to the same extent by dissipating the membrane potential with valinomycin or with the uncoupler carbonylcyanide-m-chloro phenylhydrazone. The transport of Na+ is therefore a primary event, not a secondary event involving the intermediate formation of a proton gradient. The ATPase also catalyzed H+ translocation at Na+ concentrations below 1 mM. Our results indicate a common mechanism of the ATPase for Na+ and H+ (H3O+) translocation and a switch from H+ to Na+ translocation by increasing the Na+ concentration. A hybrid ATPase consisting of F1 from E. coli and F0 from P. modestum had the same specificity with respect to the translocated cations as the homologous F1F0 ATPase of P. modestum, indicating again that the Na+ (H+) binding site is located on the F0 part. Also in accord with this supposition is a diffusion potential-induced translocation of Na+ or H+ through the F0 part of the enzyme complex. The phylogenetic relationship between the Na(+)-translocating ATPase of P. modestum and other F1F0 ATPases has been clearly demonstrated by sequencing studies.
Adenosine Triphosphatases↗
The electrochemical proton potential of Bacillus alcalophilus.
Bacillus alcalophilus strain ATCC 27647 showed usual growth characteristics, when inoculated at pH 10.4. The cells entered the logarithmic phase at pH 10.3, and as growth continued, the pH dropped further to a value of 8.8 in the stationary phase. B. alcalophilus strain DSM 485 showed comparable growth only in the initial phase after the addition to fresh medium. The small initial growth period was succeeded by a long lag phase, where the pH continuously dropped. The cells resumed growth after the pH was about 10.0 and continued to grow accompanied by a further decrease of external pH. The bioenergetic parameters measured in the initial growth phase of the two strains at high pH (10.1-10.3) were nearly the same, i.e. delta pH = +97 to +110 mV, delta psi = -206 to -213 mV and delta microH+ = -109 to -103 mV. The inverted proton gradient of about 1.7-1.9 at high pH decreased, as the external pH dropped during growth. This led to an increase of the proton motive force (delta microH+), although the membrane potential (delta psi) also declined. The ATP/ADP ratio of strain DSM 485 was high (4.5-5.5) at fast growth during the initial and second growth period. The ratio declined to about 1.5 at the end of the lag phase. At the initial growth phase and at the end of the lag phase, the delta microH+ was, however, the same (approximately -106 mV) and considerably lower than in the middle of the second growth period (approximately -140 mV). Fast growth, therefore, correlates with a high ATP/ADP ratio but not necessarily with a high delta microH+. Addition of gramicidin or carbonylcyanide m-chlorophenylhydrazone stopped growth of B. alcalophilus strain DSM 485 at pH 10.3 or 9.5 and gramicidin immediately decreased the internal ATP/ADP ratio from 4.5 to 1.2 at pH 10.3.
Adenosine Diphosphate↗
The ATPase of Bacillus alcalophilus. Reconstitution of energy-transducing functions.
The purified ATPase of Bacillus alcalophilus (F1F0) was reconstituted into proteoliposomes by gradual removal of the detergent Triton X-100 with Amberlite XAD-2. The reconstitution was apparently highly asymmetric with nearly 100% of the F1 portion of the ATPase becoming oriented to the outside. Similar to results obtained with the soluble enzyme, the membrane-bound ATPase required Mg2+ and methanol for maximum activity. With Ca2+ or Mg2+ without methanol, 25% and 1%, respectively, of the maximum activity were observed. The ATPase was unable to pump Na+ ions but catalyzed the translocation of protons into the reconstituted proteoliposomes. Optimum proton translocation required the presence of Mg2+, not Ca2+, as divalent metal ion. The proton pump was inhibited by dicyclohexylcarbodiimide, venturicidin and NaN3. On incubation of the reconstituted ATPase with [14C]dicyclohexylcarbodiimide, subunit c of the enzyme complex became specifically labeled. The proteoliposomes catalyzed the Mg2(+)-dependent incorporation of [32P]phosphate into ATP by ATP/[32P]phosphate exchange. This exchange was little affected by monensin, but was completely abolished by the uncoupler carbonyl cyanide m-chlorophenylhydrazone. Protons and not Na+ are thus the coupling ions of the ATPase of B. alcalophilus.
Adenosine Triphosphate↗
On the mechanism of sodium ion translocation by methylmalonyl-CoA decarboxylase from Veillonella alcalescens.
Veillonella alcalescens during lactate degradation developed an Na+ concentration gradient with 7-8 times higher external than internal Na+ concentrations in the logarithmic growth phase. The gradient declined to a factor of 1.9 in the late stationary phase. Methylmalonyl-CoA decarboxylase reconstituted into proteoliposomes performed an active electrogenic Na+ transport, creating delta psi of 60 mV, delta pNa+ of 50 mV, and delta mu Na+ of 110 mV. In the initial phase of the transport, the decarboxylase catalyzed the uptake of 2 Na+ ions malonyl-CoA molecule decarboxylated. During further development of the electrochemical Na+ gradient, this ratio gradually declined to zero, when decarboxylation continued without further increase of the internal Na+ concentration. The rate of malonyl-CoA decarboxylation declined initially during development of the membrane potential, but remained unchanged later on. Monensin abolished the Na+ gradient and increased the malonyl-CoA decarboxylation rate 2.8-fold. On dissipating the membrane potential with valinomycin, the internal Na+ concentration reached three times higher values than in its absence, and the decarboxylation rate increased 2.8-fold. Methylmalonyl-CoA decarboxylase catalyzed an exchange of internal and external Na+ ions in addition to net Na+ accumulation. The initial rate of Na+ influx was double that of malonyl-CoA decarboxylation. In the following, both rates decreased about twofold in parallel to values which remained constant during further development of the electrochemical Na+ gradient. Thus, Na+ influx and malonyl-CoA decarboxylation follow a stoichiometry of approximately 2:1, independent of the magnitude of the electrochemical Na+ gradient and are thus highly coupled events.
Carboxy-Lyases↗
Na(+)-coupled alternative to H(+)-coupled primary transport systems in bacteria.
Protons are the most common coupling ions in bacterial energy conversions. However, while many organisms, such as the alkaliphilic Bacilli, employ H(+)-bioenergetics for electron transport phosphorylation, they use Na+ as the coupling ion for transport and flagellar movement. The Na+ gradient required for these bioenergetic functions is established by the secondary Na+/H+ antiporter. In contrast, Vibrio alginolyticus and methanogenic bacteria have primary pumps for both H+ and Na+. They use the proton gradient for ATP synthesis while other, less energy-consuming membrane reactions are powered by the Na+ gradient. In a third mode, some anaerobic bacteria possess decarboxylases acting as primary Na+ pumps. For instance, in Klebsiella pneumoniae, the Na+ gradient established by oxaloacetate decarboxylase is used for the uptake of the growth substrate citrate, and Propionigenium modestum consumes the energy of the Na+ gradient formed by methylmalonyl-CoA decarboxylase directly for ATP synthesis.
Adenosine Triphosphate↗
The ATPase of Bacillus alcalophilus. Purification and properties of the enzyme.
The ATPase of Bacillus alcalophilus was extracted from the bacterial membranes with Triton X-100 and purified by hydroxyapatite column chromatography. SDS gel-electrophoresis of the purified protein indicated the typical subunit pattern of an F1F0 structure with five F1 subunits (alpha, beta, gamma, delta, epsilon) and three F0 subunits (a,b,c). The alpha and beta subunits were antigens for an antiserum against the corresponding subunits of the ATPase of Escherichia coli. Subunit c was extracted from the bacterial membranes with chloroform/methanol. Its amino acid composition was in the range of subunits c from other ATPases. Maximal ATPase activity was observed in the presence of 2-5 mM MgCl2, an ATP/Mg2+ ratio of 2:1 and 25% methanol. In the absence of methanol, only about 1% of the maximal activity was observed. The enzyme was also activated by Ca2+ (in the absence of methanol), reaching about 30% of the maximal activity. The dependence of initial velocity versus ATP of the Ca2(+)-activated but not of the Mg2+/methanol-activated enzyme indicted cooperativity with three strongly cooperative binding sites.
Adenosine Triphosphatases↗
Sequence of subunits a and b of the sodium ion translocating adenosine triphosphate synthase of Propionigenium modestum.
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Amino Acid Sequence↗
Sequence of subunit c of the sodium ion translocating adenosine triphosphate synthase of Propionigenium modestum.
The 30 N-terminal amino acid residues of the purified ATPase c subunit of Propionigenium modestum have been determined. An oligonucleotide mixture was derived from this sequence and used as probe for cloning the corresponding gene in Escherichia coli. The nucleotide sequence of the gene has been determined and compared with those of ATPase c subunits from other bacteria and chloroplasts. Peculiar sequence similarities are found only at the C-terminus between the c subunits of the ATPases from P. modestum and from Vibrio alginolyticus, another putative Na(+)-translocating ATPase.
Adenosine Triphosphatases↗
A hybrid adenosinetriphosphatase composed of F1 of Escherichia coli and F0 of Propionigenium modestum is a functional sodium ion pump.
Analyses on immunoblots indicated strong binding of the alpha- and beta-subunits of the ATPase of Propionigenium modestum to antibodies raised against the corresponding subunits of the F1F0 ATPase of Escherichia coli. Cross-reactivities of antibodies against the other ATPase subunits were not observed. The use of Na+ or H+ as alternate coupling ions, observed previously for the P. modestum ATPase [Laubinger, W., & Dimroth, P. (1989) Biochemistry 28, 7194-7198], is not found for the F1F0 ATPase of E. coli, which is specific for protons. However, a hybrid consisting of the F1 moiety of the E. coli ATPase and F0 of that from P. modestum performed Na+ or H+ transport in a reconstituted system. As with the homologous ATPase of P. modestum, H+ pumping of the hybrid was abolished at Na+ concentrations of greater than 1 mM. The F0 sector and not F1, therefore, determines the cation specificity of these F1F0 ATPases.
Bacteria, Anaerobic↗
Solubilization and reconstitution of the Na(+)-dependent citrate carrier of Klebsiella pneumoniae.
The citrate carrier of Klebsiella pneumoniae fermenting this substrate has been solubilized from the bacterial membranes with Triton X-100. The transport function was reconstituted by incorporation of the carrier into proteoliposomes using a freeze-thaw sonication procedure. Citrate uptake into these proteoliposomes required the presence of Na+ ions on the outside; the amount of citrate accumulated increased as the external Na+ concentration increased from 0 to 100 mM. Proteoliposomes preloaded with citrate catalyzed citrate counterflow when added to external [14C] citrate. Sodium ions were required for counterflow activity. The kinetics of citrate uptake, counterflow, or efflux were not influenced by an inside negative membrane potential, and the presence of the uncoupler carbonyl cyanide p-trifluoromethoxyphenylhydrazone was without effect on citrate uptake. The data therefore suggest an electroneutral Na(+)-citrate symport mechanism for the transport of this tricarboxylic acid into K. pneumoniae.
Biological Transport↗
Mechanisms of sodium transport in bacteria.
In some bacteria, an Na+ circuit is an important link between exergonic and endergonic membrane reactions. The physiological importance of Na+ ion cycling is described in detail for three different bacteria. Klebsiella pneumoniae fermenting citrate pumps Na+ outwards by oxaloacetate decarboxylase and uses the Na+ ion gradient thus established for citrate uptake. Another possible function of the Na+ gradient may be to drive the endergonic reduction of NAD+ with ubiquinol as electron donor. In Vibrio alginolyticus, an Na+ gradient is established by the NADH: ubiquinone oxidoreductase segment of the respiratory chain; the Na+ gradient drives solute uptake, flagellar motion and possibly ATP synthesis. In Propionigenium modestum, ATP biosynthesis is entirely dependent on the Na+ ion gradient established upon decarboxylation of methylmalonyl-CoA. The three Na(+)-translocating enzymes, oxaloacetate decarboxylase of Klebsiella pneumoniae, NADH: ubiquinone oxidoreductase of Vibrio alginolyticus and ATPase (F1F0) of Propionigenium modestum have been isolated and studied with respect to structure and function. Oxaloacetate decarboxylase consists of a peripheral subunit (alpha), that catalyses the carboxyltransfer from oxaloacetate to enzyme-bound biotin. The subunits beta and gamma are firmly embedded in the membrane and catalyse the decarboxylation of the carboxybiotin enzyme, coupled to Na+ transport. A two-step mechanism has also been demonstrated for the respiratory Na+ pump. Semiquinone radicals are first formed with the electrons from NADH; subsequently, these radicals dismutate in an Na(+)-dependent reaction to quinone and quinol. The ATPase of P. modestum is closely related in its structure to the F1F0 ATPase of E. coli, but uses Na+ as the coupling ion. A specific role of protons in the ATP synthesis mechanism is therefore excluded.
Amino Acid Sequence↗