Intact carbonic acid is a viable protonating agent for biological bases.

Carbonic acid H2CO3 (CA) is a key constituent of the universal CA/bicarbonate/CO2 buffer maintaining the pH of both blood and the oceans. Here we demonstrate the ability of intact CA to quantitatively protonate bases with biologically-relevant pKas and argue that CA has a previously unappreciated function as a major source of protons in blood plasma. We determine with high precision the temperature dependence of pKa(CA), pKa(T) = -373.604 + 16,500/T + 56.478 ln T. At physiological-like conditions pKa(CA) = 3.45 (I = 0.15 M, 37 °C), making CA stronger than lactic acid. We further demonstrate experimentally that CA decomposition to H2O and CO2 does not impair its ability to act as an ordinary carboxylic acid and to efficiently protonate physiological-like bases. The consequences of this conclusion are far reaching for human physiology and marine biology. While CA is somewhat less reactive than (H+)aq, it is more than 1 order of magnitude more abundant than (H+)aq in the blood plasma and in the oceans. In particular, CA is about 70× more abundant than (H+)aq in the blood plasma, where we argue that its overall protonation efficiency is 10 to 20× greater than that of (H+)aq, often considered to be the major protonating agent there. CA should thus function as a major source for fast in vivo acid-base reactivity in the blood plasma, possibly penetrating intact into membranes and significantly helping to compensate for (H+)aq's kinetic deficiency in sustaining the large proton fluxes that are vital for metabolic processes and rapid enzymatic reactions.

Mitogen-activated protein kinases MPK4 and MPK12 are key components mediating CO2 -induced stomatal movements.

Respiration in leaves and the continued elevation in the atmospheric CO2 concentration cause CO2 -mediated reduction in stomatal pore apertures. Several mutants have been isolated for which stomatal responses to both abscisic acid (ABA) and CO2 are simultaneously defective. However, there are only few mutations that impair the stomatal response to elevated CO2 , but not to ABA. Such mutants are invaluable in unraveling the molecular mechanisms of early CO2 signal transduction in guard cells. Recently, mutations in the mitogen-activated protein (MAP) kinase, MPK12, have been shown to partially impair CO2 -induced stomatal closure. Here, we show that mpk12 plants, in which MPK4 is stably silenced specifically in guard cells (mpk12 mpk4GC homozygous double-mutants), completely lack CO2 -induced stomatal responses and have impaired activation of guard cell S-type anion channels in response to elevated CO2 /bicarbonate. However, ABA-induced stomatal closure, S-type anion channel activation and ABA-induced marker gene expression remain intact in the mpk12 mpk4GC double-mutants. These findings suggest that MPK12 and MPK4 act very early in CO2 signaling, upstream of, or parallel to the convergence of CO2 and ABA signal transduction. The activities of MPK4 and MPK12 protein kinases were not directly modulated by CO2 /bicarbonate in vitro, suggesting that they are not direct CO2 /bicarbonate sensors. Further data indicate that MPK4 and MPK12 have distinguishable roles in Arabidopsis and that the previously suggested role of RHC1 in stomatal CO2 signaling is minor, whereas MPK4 and MPK12 act as key components of early stomatal CO2 signal transduction.

Biocalcite and Carbonic Acid Activators.

Based on evolution of biomineralizing systems and energetic considerations, there is now compelling evidence that enzymes play a driving role in the formation of the inorganic skeletons from the simplest animals, the sponges, up to humans. Focusing on skeletons based on calcium minerals, the principle enzymes involved are the carbonic anhydrase (formation of the calcium carbonate-based skeletons of many invertebrates like the calcareous sponges, as well as deposition of the calcium carbonate bioseeds during human bone formation) and the alkaline phosphatase (providing the phosphate for bone calcium phosphate-hydroxyapatite formation). These two enzymes, both being involved in human bone formation, open novel not yet exploited targets for pharmacological intervention of human bone diseases like osteoporosis, using compounds that act as activators of these enzymes. This chapter focuses on carbonic anhydrases of biomedical interest and the search for potential activators of these enzymes, was well as the interplay between carbonic anhydrase-mediated calcium carbonate bioseed synthesis and metabolism of energy-rich inorganic polyphosphates. Beyond that, the combination of the two metabolic products, calcium carbonate and calcium-polyphosphate, if applied in an amorphous form, turned out to provide the basis for a new generation of scaffold materials for bone tissue engineering and repair that are, for the first time, morphogenetically active.

Function of the loading module in CorI and of the O-methyltransferase CorH in vinyl carbamate biosynthesis of the antibiotic corallopyronin A.

Corallopyronin A is a promising in vivo active antibiotic, currently undergoing preclinical evaluation. This myxobacterial compound interferes with a newly identified drug target site, i.e., the switch region of the bacterial DNA-dependent RNA-polymerase (RNAP). Since this target site differs from that of known RNAP inhibitors such as the rifamycins, corallopyronin A shows no cross-resistance with other antibacterial agents. Corallopyronin A is a polyketide synthase- and nonribosomal peptide synthetase-derived molecule whose structure and biosynthesis is distinguished by several peculiarities, such as the unusual vinyl carbamate functionality whose formation involves carbonic acid as an unprecedented C1-starter unit. Using in vitro experiments the nature of this starter molecule was revealed to be the methyl ester of carbonic acid. Biochemical investigations showed that methylation of carbonic acid is performed by the O-methyltransferase CorH. These experiments shed light on the biosynthesis of the Eastern chain of α-pyrone antibiotics such as corallopyronin A.

A chemoreceptor that detects molecular carbon dioxide.

Animals from diverse phyla possess neurons that are activated by the product of aerobic respiration, CO2. It has long been thought that such neurons primarily detect the CO2 metabolites protons and bicarbonate. We have determined the chemical tuning of isolated CO2 chemosensory BAG neurons of the nematode Caenorhabditis elegans. We show that BAG neurons are principally tuned to detect molecular CO2, although they can be activated by acid stimuli. One component of the BAG transduction pathway, the receptor-type guanylate cyclase GCY-9, suffices to confer cellular sensitivity to both molecular CO2 and acid, indicating that it is a bifunctional chemoreceptor. We speculate that in other animals, receptors similarly capable of detecting molecular CO2 might mediate effects of CO2 on neural circuits and behavior.

Disrupting proton dynamics and energy metabolism for cancer therapy.

Intense interest in the 'Warburg effect' has been revived by the discovery that hypoxia-inducible factor 1 (HIF1) reprogrammes pyruvate oxidation to lactic acid conversion; lactic acid is the end product of fermentative glycolysis. The most aggressive and invasive cancers, which are often hypoxic, rely on exacerbated glycolysis to meet the increased demand for ATP and biosynthetic precursors and also rely on robust pH-regulating systems to combat the excessive generation of lactic and carbonic acids. In this Review, we present the key pH-regulating systems and synthesize recent advances in strategies that combine the disruption of pH control with bioenergetic mechanisms. We discuss the possibility of exploiting, in rapidly growing tumours, acute cell death by 'metabolic catastrophe'.

Computer model of unstirred layer and intracellular pH changes. Determinants of unstirred layer pH.

Transmembrane acid-base fluxes affect the intracellular pH and unstirred layer pH around a superfused biological preparation. In this paper the factors influencing the unstirred layer pH and its gradient are studied. An analytical expression of the unstirred layer pH gradient in steady state is derived as a function of simultaneous transmembrane fluxes of (weak) acids and bases with the dehydration reaction of carbonic acid in equilibrium. Also a multicompartment computer model is described consisting of the extracellular bulk compartment, different unstirred layer compartments and the intracellular compartment. With this model also transient changes and the influence of carbonic anhydrase (CA) can be studied. The analytical expression and simulations with the multicompartment model demonstrate that in steady state the unstirred layer pH and its gradient are influenced by the size and type of transmembrane flux of acids and bases, their dissociation constant and diffusion coefficient, the concentration, diffusion coefficient and type of mobile buffers and the activity and location of CA. Similar principles contribute to the amplitude of the unstirred layer pH transients. According to these models an immobile buffer does not influence the steady-state pH, but reduces the amplitude of pH transients especially when these are fast. The unstirred layer pH provides useful information about transmembrane acid-base fluxes. This paper gives more insight how the unstirred layer pH and its transients can be interpreted. Methodological issues are discussed.

A proposed role for inorganic carbon in water oxidation.

This is an article on the peroxydicarbonic acid (PODCA) hypothesis of photosynthetic water oxidation, which follows our first article in this general area (Castelfranco et al., Photosynth Res 94:235-246, 2007). In this article I have expanded on the idea of a protein-bound intermediate containing inorganic carbon in some chemically bound form. PODCA is conceived in this article as constituting a bridge between two proteins of the oxygen-evolving complex (OEC) that are essential for the evolution of O2. Presumably, these are two proteins which have been shown to possess Mn-dependent carbonic anhydrase activity (Lu et al., Plant Cell Physiol 46:1944-1953, 2005; Shitov et al., Biochemistry (Moscow) 74:509-517, 2009). One of these proteins may be the D(I) of the OEC core and the other may be the PsbO extrinsic protein. I attempt to relate briefly the PODCA hypothesis to the role of two cofactors for O2 evolution: Ca(2+) and inorganic carbon. In this scheme, inorganic carbon (HCO3 (-)) mediates the oxidation of peroxide to dioxygen, thus avoiding the homolytic cleavage of the peroxide into two free radicals. I visualize the role of Ca(2+) in the binding of PODCA to two essential photosystem II proteins. I propose that PODCA alternates between two Phases. In Phase 1, PODCA is broken down with the production of O2. In Phase 2, PODCA is regenerated.

[Metabolic characteristics of air microbial communities from sandstorm source areas of the Taklamakan desert].

The aim was to compare the characteristics and the differences in carbon catabolic diversity of air samples collected from five locations that around the edge of Taklamakan desert. The characteristics and the differences of carbon metabolic profiles were detected by using the BIOLOG micro plate (BIOLOG EcoPlate). The results showed that the average well color development (AWCD) curve of all five samples did not reach clear saturation during the incubation time (10 days), but differences among them were significant. The highest AWCD value appeared in Shache and the lowest was in Hotan, which were 0.24 and 0.1, respectively. Carbon utilization showed that all samples exhibited high level of polymer, carbohydrates, amino acids and carboxylic acid; however, amine and the phenol compound were the lowest. Principal components analysis (PCA) indicated that twenty categories of carbon significantly related to PC1 and twelve categories for PC2. Hierarchical cluster analysis showed these five areas could be divided into 2 clusters: (1) Hotan, Pishan, (2) Shache, Luntai, Ulugqat. Canonical correspondence analysis (CCA) showed that those community functional diversities were highly affected by some environmental factors, such as wind speed, altitude, humidity. Further investigation by correlation analysis revealed that the microbial communities using single carbon source were significantly affected by abiotic factors, such as the utilization of beta-methyl-D-glucoside, D-galacturonic acid and putrescine had significantly positive correlation (P < 0.05) with latitude; 2-hydroxy benzoic acid and alpha-D-lactose significantly related to wind speed (P < 0.05); and D-glucosaminic acid was positive with air pressure, but it negatively correlated with altitude (P < 0.05). In conclusion,the carbon sources provided by BIOLOG EcoPlate were utilized slowly by air microbial communities; and the characteristics of the air community carbon catabolic along the edge of the Taklamakan desert revealed regional feature, which may be affected by environmental factors.

Acetogens and acetoclastic methanosarcinales govern methane formation in abandoned coal mines.

In abandoned coal mines, methanogenic archaea are responsible for the production of substantial amounts of methane. The present study aimed to directly unravel the active methanogens mediating methane release as well as active bacteria potentially involved in the trophic network. Therefore, the stable-isotope-labeled precursors of methane, [(13)C]acetate and H(2)-(13)CO(2), were fed to liquid cultures from hard coal and mine timber from a coal mine in Germany. Guided by methane production rates, samples for DNA stable-isotope probing (SIP) with subsequent quantitative PCR and denaturing gradient gel electrophoretic (DGGE) analyses were taken over 6 months. Surprisingly, the formation of [(13)C]methane was linked to acetoclastic methanogenesis in both the [(13)C]acetate- and the H(2)-(13)CO(2)-amended cultures of coal and timber. H(2)-(13)CO(2) was used mainly by acetogens related to Pelobacter acetylenicus and Clostridium species. Active methanogens, closely affiliated with Methanosarcina barkeri, utilized the readily available acetate rather than the thermodynamically more favorable hydrogen. Thus, the methanogenic microbial community appears to be highly adapted to the low-H(2) conditions found in coal mines.

Clinical approach to renal tubular acidosis in adult patients.

Renal tubular acidosis (RTA) is a group of disorders observed in patients with normal anion gap metabolic acidosis. There are three major forms of RTA: A proximal (type II) RTA and two types of distal RTAs (type I and type IV). Proximal (type II) RTA originates from the inability to reabsorb bicarbonate normally in the proximal tubule. Type I RTA is associated with inability to excrete the daily acid load and may present with hyperkalaemia or hypokalaemia. The most prominent abnormality in type IV RTA is hyperkalaemia caused by hypoaldosteronism. This article extensively reviews the mechanism of hydrogen ion generation from metabolism of normal diet and various forms of RTA leading to disruptions of normal acid-base handling by the kidneys.

Alkalizing reactions streamline cellular metabolism in acidogenic microorganisms.

An understanding of the integrated relationships among the principal cellular functions that govern the bioenergetic reactions of an organism is necessary to determine how cells remain viable and optimise their fitness in the environment. Urease is a complex enzyme that catalyzes the hydrolysis of urea to ammonia and carbonic acid. While the induction of urease activity by several microorganisms has been predominantly considered a stress-response that is initiated to generate a nitrogen source in response to a low environmental pH, here we demonstrate a new role of urease in the optimisation of cellular bioenergetics. We show that urea hydrolysis increases the catabolic efficiency of Streptococcus thermophilus, a lactic acid bacterium that is widely used in the industrial manufacture of dairy products. By modulating the intracellular pH and thereby increasing the activity of ß-galactosidase, glycolytic enzymes and lactate dehydrogenase, urease increases the overall change in enthalpy generated by the bioenergetic reactions. A cooperative altruistic behaviour of urease-positive microorganisms on the urease-negative microorganisms within the same environment was also observed. The physiological role of a single enzymatic activity demonstrates a novel and unexpected view of the non-transcriptional regulatory mechanisms that govern the bioenergetics of a bacterial cell, highlighting a new role for cytosol-alkalizing biochemical pathways in acidogenic microorganisms.

Acid sensing by the Drosophila olfactory system.

The odour of acids has a distinct quality that is perceived as sharp, pungent and often irritating. How acidity is sensed and translated into an appropriate behavioural response is poorly understood. Here we describe a functionally segregated population of olfactory sensory neurons in the fruitfly, Drosophila melanogaster, that are highly selective for acidity. These olfactory sensory neurons express IR64a, a member of the recently identified ionotropic receptor (IR) family of putative olfactory receptors. In vivo calcium imaging showed that IR64a+ neurons projecting to the DC4 glomerulus in the antennal lobe are specifically activated by acids. Flies in which the function of IR64a+ neurons or the IR64a gene is disrupted had defects in acid-evoked physiological and behavioural responses, but their responses to non-acidic odorants remained unaffected. Furthermore, artificial stimulation of IR64a+ neurons elicited avoidance responses. Taken together, these results identify cellular and molecular substrates for acid detection in the Drosophila olfactory system and support a labelled-line mode of acidity coding at the periphery.

Recombinant plant gamma carbonic anhydrase homotrimers bind inorganic carbon.

Gamma carbonic anhydrases (gammaCA) are widespread in Prokaryotes. In Eukaryotes, homologous genes were found only in plant genomes. In Arabidopsis and maize, the corresponding gene products are subunits of mitochondrial Complex I. At present, only gammaCA homotrimers of Methanosarcina thermophila (CAM) show reversible carbon dioxide (CO(2)) hydration activity. In the present work, it is shown that recombinant plant gammaCA2 could form homotrimers and bind H(14)CO(3)(-). However, they are unable to catalyse the reversible hydration of CO(2). These results suggest that plant gammaCAs do not act as carbonic anhydrases but with a related activity possibly contributing to recycle CO(2) in the context of photorespiration.

Evaluation of the metabolic diversity of microbial communities in four different filter layers of a constructed wetland with vertical flow by Biolog analysis.

The community-level substrate utilization test based on direct incubation of environmental samples in Biolog EcoPlates is a suitable and sensitive tool to characterize microbial communities. The aim of this study was to investigate the influence of plant roots and soil structure on the metabolic diversity of microorganisms in a constructed wetland with vertical flow. Sediment samples were taken from different filter depths representing specific filter layers. The color development representing the substrate utilization was measured with the samples over a period of 10 days. The average well color development (AWCD) for all carbon sources was calculated as an indicator of total activity and in order to compensate the influence of the inoculum's density on the color development in the plates. After transformation by dividing by the AWCD, the optical density data were analysed by principal component analysis (PCA). An analysis of the kinetic profile of the AWCD was carried out to increase the analytical power of the method. The corrected data have been successfully fit to the logistic growth equation. Three kinetic model parameters, the asymptote (K), the exponential rate of color change (p) and the time to the midpoint of the exponential portion of the curve (s), were used for statistical analysis of the physiological profile of the microbial community in the different filter layers of the constructed wetland. We found out that in the upper two horizons, which were rooted most densely, mainly easily degradable materials like specific carbohydrates were utilized, while in the lower layers, where only single roots occur, more biochemically inert compounds, e.g. 2-hydroxy benzoic acid, were utilized. Furthermore it could be shown that microorganisms in the surface layer benefited from the plant litter because they can utilize decay products of these. In the lower filter layers specialists took advantage because they had to cope with the biochemically inert materials and the lower nutrient supply.

A brain protein centered view of H+ buffering.

In the traditional approach to buffering of H(+) during metabolic acidosis, the sole focus is on lowering the H(+) concentration, but this overlooks several important points. First, increased binding of H(+) to proteins changes their charge, shape, and possibly function. Second, organs in which buffering of H(+) occurs is not assessed even though it would be advantageous to spare brain proteins in this process. Third, only the arterial and not the capillary PCO(2) of individual organs is considered. This article provides a "brain protein-centered" view, which leads to different conclusions concerning the way H(+) are removed physiologically.

Oxidized tissue proteins after intestinal reperfusion injury in rats

OBJETIVO: Analisar se a mensuração da proteína carbonilada pode ser validada como método capaz de permitir a identificação de um estresse oxidativo intestinal causado por lesões decorrentes da isquemia e reperfusão. MÉTODOS: Vinte e cinco ratos machos da linhagem Wistar, pesando entre 200 e 250g, foram divididos em três grupos. Grupo I – controle (n = 10). Grupo II – simulação (n = 5) e grupo III (n = 10) submetido a 60 minutos de isquemia intestinal e igual intervalo para reperfusão. Para este fim clampeou-se a artéria mesentérica superior no seu terço distal. Alterações histológicas e os níveis de proteínas carboniladas foram determinados em amostras obtidas em todos os grupos. No grupo III foram estudados segmentos ileais reperfundidos e normais. RESULTADOS: Em todos os segmentos reperfundidos houve edema da mucosa e submucosa, além de infiltrado inflamatório da lâmina própria. Os níveis de proteína carbonilada aumentaram no grupo III, inclusive nos segmentos não isquemiados. A sensibilidade e a especificidade da proteína carbonilada no tecido foram, respectivamente, de 94% e 88%. CONCLUSÃO: O procedimento da proteína carbonilada é útil como marcador biológico do estresse oxidativo após isquemia e reperfusão intestinal em ratos. Também foi relevante o efeito do estresse oxidativo, observado à distância do lócus da lesão primária.