Proton transfer: It’s a stringent process

AbstractProton transfer into and out of proteins is important, both for many enzyme reaction mechanisms and proton pumping across membranes. Recent work on several proteins has revealed stringent requirements for amino-acid side chains and subtle reorganisation of hydrogen-bond networks involving bound water molecules

Energetic problems faced by micro-organisms growing or surviving on parsimonious energy sources and at acidic pH: I. Acidithiobacillus ferrooxidans as a paradigm

AbstractThe mitochondrial paradigm for a chemiosmotic energy transduction mechanism requires frequently misunderstood modifications for application to microbes growing and surviving at acidic pH values and/or with relatively weak reductants as energy sources. Here the bioenergetics of the iron oxidiser Acidithiobacillus ferrooxidans are reviewed and analysed so as to develop the general bioenergetic principles for understanding organisms that grow under these conditions. Extension of the principles outlined herein to organisms that survive (as opposed to grow) under these conditions is to be presented in a subsequent article

Partial uncoupling, or inhibition of electron transport rate, have equivalent effects on the relationship between the rate of ATP synthesis and proton-motive force in submitochondrial particles

AbstractThe rates of electron transport and of ATP synthesis have been measured in bovine heart Mg-ATP submito-chondrial particles oxidising succinate under conditions of partial attenuation of the proton-motive force by malonate or FCCP. This paper reports evidence that the relationship between the rate of ATP synthesis and the magnitude of the proton motive force is independent of the mode by which the decrease of the proton motive force is achieved

Structural relationships between the NADH dehydrogenases of Paracoccus denitrificans and bovine heart mitochondria as revealed by immunological cross-reactivities

AbstractAn antibody raised against two subunits (Mr, 48000 and 25000) of NADH dehydrogenase from Paracoccusdenitrificans cross-reacts with one of more than 20 polypeptides that form the bovine heart mitochondrial NADH dehydrogenase. The cross-reacting subunit has Mr, 51000 and is believed to be the NADH-binding subunit of the enzyme. Antibodies raised against certain subunits of the bovine heart NADH dehydrogenase were tested for cross-reactivity withP. denitrificans cytoplasmic membranes. Of those tested, only one, an antibody specific for the 49 kDa subunit of mitochondrial NADH dehydrogenase, cross-reacted with the bacterial membranes. It recognised a polypeptide of approximate Mr, 46000. This is an indication for a previously undetected third subunit of NADH dehydrogenase from P. denitrificans. The immunological crossreactions indicate that the NADH dehydrogenases from P. denitrificans and bovine heart mitochondria are related structurally

The development and validation of a human screening model of tobacco abstinence

Introduction Given the low efficacy of smoking cessation methods, an experimental medicine model indicating smoking abstinence would be of great benefit to the development of new treatments. Hence the sensitivity of cognitive tasks and ambulatory craving measures to smoking abstinence were investigated. Methods Cognitive tasks and ambulatory ratings of craving were assessed for sensitivity to acute abstinence (experiment 1), and nicotine replacement therapy administration (NRT) (experiment 2). Results In experiment 1 go/no-go performance was improved (Mean Difference [MD] -0.99, 95% CI: −1.90 to −0.08) and craving was lower (Regression Coefficient [RC] −33.39, 95% CI: -39.96 to -26.82) in satiated compared with abstinent smokers. There was no clear evidence that N-back (MD 0.64, 95% CI: −0.42 to 2.51), delay discounting (MD 0.01, 95% CI: 0.001 to 0.005) or dot probe performance (MD 0.61, 95% CI: −0.87 to 1.54) were sensitive to acute abstinence. In experiment 2 go/no-go performance was improved (MD 1.12, 95% CI: 0.16–2.08) and craving was lower (RC −18.59, 95% CI: −24.63 to −12.55) smokers abstinent overnight receiving NRT compared with placebo. There was no clear evidence that N-back (MD −0.25, 95% CI: −1.45 to 0.94), delay discounting (MD 0.01, 95% CI: -0.002 to 0.004) or dot probe performance (MD −0.49, 95% CI: −1.61 to −0.64) were sensitive to NRT. Conclusions Findings from two experiments converge to suggest that abstinence in smokers reliably increases ambulatory craving assessments and, to a lesser extent, decreases go/no-go task performance. These findings can be utilized in the development of an experimental medicine model to test novel treatments for smoking cessation

Transcriptional and translational adaptation to aerobic nitrate anabolism in the denitrifier Paracoccus denitrificans

Transcriptional adaptation to nitrate-dependent anabolism by Paracoccus denitrificans PD1222 was studied. A total of 74 genes were induced in cells grown with nitrate as N-source compared with ammonium, including nasTSABGHC and ntrBC genes. The nasT and nasS genes were cotranscribed, although nasT was more strongly induced by nitrate than nasS. The nasABGHC genes constituted a transcriptional unit, which is preceded by a non-coding region containing hairpin structures involved in transcription termination. The nasTS and nasABGHC transcripts were detected at similar levels with nitrate or glutamate as N-source, but nasABGHC transcript was undetectable in ammonium-grown cells. The nitrite reductase NasG subunit was detected by two-dimensional polyacrylamide gel electrophoresis in cytoplasmic fractions from nitrate-grown cells, but it was not observed when either ammonium or glutamate was used as the N-source. The nasT mutant lacked both nasABGHC transcript and nicotinamide adenine dinucleotide (NADH)-dependent nitrate reductase activity. On the contrary, the nasS mutant showed similar levels of the nasABGHC transcript to the wild-type strain and displayed NasG protein and NADH–nitrate reductase activity with all N-sources tested, except with ammonium. Ammonium repression of nasABGHC was dependent on the Ntr system. The ntrBC and ntrYX genes were expressed at low levels regardless of the nitrogen source supporting growth. Mutational analysis of the ntrBCYX genes indicated that while ntrBC genes are required for nitrate assimilation, ntrYX genes can only partially restore growth on nitrate in the absence of ntrBC genes. The existence of a regulation mechanism for nitrate assimilation in P. denitrificans, by which nitrate induction operates at both transcriptional and translational levels, is proposed

A dual functional redox enzyme maturation protein for respiratory and assimilatory nitrate reductases in bacteria

Nitrate is available to microbes in many environments due to sustained use of inorganic fertilizers on agricultural soils and many bacterial and archaeal lineages have the capacity to express respiratory (Nar) and assimilatory (Nas) nitrate reductases to utilize this abundant respiratory substrate and nutrient for growth. Here we show that in the denitrifying bacterium Paracoccus denitrificans, NarJ serves as a chaperone for both the anaerobic respiratory nitrate reductase (NarG) and the assimilatory nitrate reductase (NasC), the latter of which is active during both aerobic and anaerobic nitrate assimilation. Bioinformatic analysis suggests that the potential for this previously unrecognized role for NarJ in functional maturation of other cytoplasmic molybdenum-dependent nitrate reductases may be phylogenetically widespread as many bacteria contain both Nar and Nas systems

The Paracoccus denitrificans NarK-like nitrate and nitrite transporters—probing nitrate uptake and nitrate/nitrite exchange mechanisms

Nitrate and nitrite transport across biological membranes is often facilitated by protein transporters that are members of the major facilitator superfamily. Paracoccus denitrificans contains an unusual arrangement whereby two of these transporters, NarK1 and NarK2, are fused into a single protein, NarK, which delivers nitrate to the respiratory nitrate reductase and transfers the product, nitrite, to the periplasm. Our complementation studies, using a mutant lacking the nitrate/proton symporter NasA from the assimilatory nitrate reductase pathway, support that NarK1 functions as a nitrate/proton symporter while NarK2 is a nitrate/nitrite antiporter. Through the same experimental system, we find that Escherichia coli NarK and NarU can complement deletions in both narK and nasA in P. denitrificans, suggesting that, while these proteins are most likely nitrate/nitrite antiporters, they can also act in the net uptake of nitrate. Finally, we argue that primary sequence analysis and structural modelling do not readily explain why NasA, NarK1 and NarK2, as well as other transporters from this protein family, have such different functions, ranging from net nitrate uptake to nitrate/nitrite exchange

Stabilization of Pseudomonas aeruginosa Cytochrome c551 by Systematic Amino Acid Substitutions Based on the Structure of Thermophilic Hydrogenobacter thermophilus Cytochrome c552

A heterologous overexpression system for mesophilic Pseudomonas aeruginosa holocytochrome c551 (PA c551) was established using Escherichia coli as a host organism. Amino acid residues were systematically substituted in three regions of PA c551 with the corresponding residues from thermophilic Hydrogenobacter thermophilus cytochrome c552 (HT c552), which has similar main chain folding to PA c551, but is more stable to heat. Thermodynamic properties of PA c551 with one of three single mutations (Phe-7 to Ala, Phe-34 to Tyr, or Val-78 to Ile) showed that these mutants had increased thermostability compared with that of the wild-type. Ala-7 and Ile-78 may contribute to the thermostability by tighter hydrophobic packing, which is indicated by the three dimensional structure comparison of PA c551 with HT c552. In the Phe-34 to Tyr mutant, the hydroxyl group of the Tyr residue and the guanidyl base of Arg-47 formed a hydrogen bond, which did not exist between the corresponding residues in HT c552. We also found that stability of mutant proteins to denaturation by guanidine hydrochloride correlated with that against the thermal denaturation. These results and others described here suggest that significant stabilization of PA c551 can be achieved through a few amino acid substitutions determined by molecular modeling with reference to the structure of HT c552. The higher stability of HT c552 may in part be attributed to some of these substitutions.This work was supported in part by grants from the Japanese Ministry of Education, Science and Culture