Microsensor studies on Padina from a natural CO2 seep: implications of morphology on acclimation to low pH

Low seawater pH can be harmful to many calcifying marine organisms, but the calcifying macroalgae Padina spp. flourish at natural submarine carbon dioxide seeps where seawater pH is low. We show that the microenvironment created by the rolled thallus margin of Padina australis facilitates supersaturation of CaCO3 and calcifi-cation via photosynthesis-induced elevated pH. Using microsensors to investigate oxygen and pH dynamics in the microenvironment of P. australis at a shallow CO2 seep, we found that, under saturating light, the pH inside the microenvironment (pHME) was higher than the external seawater (pHSW) at all pHSW levels investigated, and the difference (i.e., pHME-pHSW) increased with decreasing pHSW (0.9 units at pHSW 7.0). Gross photosynthesis (Pg) inside the microenvironment increased with decreasing pHSW, but algae from the control site reached a threshold at pH 6.5. Seep algae showed no pH threshold with respect to Pg within the pHSW range investigated. The external carbonic anhydrase (CA) inhibitor, acetazolamide, strongly inhibited Pg of P. australis at pHSW 8.2, but the effect was diminished under low pHSW (6.4-7.5), suggesting a greater dependence on membrane-bound CA for the dehydration of HCO3- ions during dissolved inorganic carbon uptake at the higher pHSW. In comparison, a calcifying green alga, Halimeda cuneata f. digitata, was not inhibited by AZ, suggesting efficient bicarbonate transport. The ability of P. australis to elevate pHME at the site of calcification and its strong dependence on CA may explain why it can thrive at low pHSW.

Combined effects of low pH and low oxygen on the early-life stages of the barnacle Balanus amphitrite

Ocean acidification (OA) is anticipated to interact with the more frequently occurring hypoxic conditions in shallow coastal environments. These could exert extreme stress on the barnacle-dominated fouling communities. However, the interactive effect of these two emerging stressors on early-life stages of fouling organisms remains poorly studied. We investigated both the independent and interactive effect of low pH (7.6 vs. ambient 8.2) and low oxygen (LO; 3 mg/l vs. ambient 5 mg/l) from larval development through settlement (attachment and metamorphosis) and juvenile growth of the widespread fouling barnacle, Balanus amphitrite. In particular, we focused on the critical transition between planktonic and benthic phases to examine potential limiting factors (i.e. larval energy storage and the ability to perceive cues) that may restrain barnacle recruitment under the interactive stressors. LO significantly slowed naupliar development, while the interaction with low pH (LO-LP) seemed to alleviate the negative effect. However, 20-50% of the larvae became cyprid within 4 d post-hatching, regardless of treatment. Under the two stressors interaction (LO-LP), the barnacle larvae increased their feeding rate, which may explain why their energy reserves at competency were not different from any other treatment. In the absence of a settlement-inducing cue, a significantly lower percentage of cyprids (15% lower) settled in LO and LO-LP. The presence of an inducing cue, however, elevated attachment up to 50-70% equally across all treatments. Post-metamorphic growth was not altered, although the condition index was different between LO and LO-LP treatments, potentially indicating that less and/or weaker calcified structures were developed when the two stressors were experienced simultaneously. LO was the major driver for the responses observed and its interaction with low pH should be considered in future studies to avoid underestimating the sensitivity of biofouling species to OA and associated climate change stressors.

In Situ effects of low pH and elevated HCO3 on juvenile massive Porites spp. in Moorea, French Polynesia

Juvenile colonies of massive Porites spp. were exposed to manipulated pH and bicarbonate ([HCO3-]) in situ to test the hypothesis that ocean acidification (OA) does not affect respiration and calcification. Incubations lasted 28 h and exposed corals to ambient temperature and light with ecologically relevant water motion. Three treatments were applied: (1) ambient conditions of pH 8.04 and 1751 µmol HCO3- kg(-1) (Treatment 1), (2) pCO2-induced ocean acidification of pH 7.73 and 2011 µmol HCO3- kg(-1) (Treatment 2), and (3) pCO2 and HCO3--enriched seawater of pH 7.69 and 2730 µmol HCO3- kg(-1) (Treatment 3). The third treatment providing elevated [HCO3-] was used to test for stimulatory effects of dissolved inorganic carbon on calcification under low pH and low saturation of aragonite (Omega arag), but it does not reflect conditions expected to occur under CO2-driven OA. Calcification of juvenile massive Porites spp. was affected by treatments, with an 81% elevation in Treatment 3 versus Treatment 1, but no difference between Treatments 1 and 2; respiration and the metabolic expenditure concurrent with calcification remained unaffected. These findings indicate that juvenile massive Porites spp. are resistant to short exposures to OA in situ, and separately, that they can increase calcification at low pH and low Omega arag if [HCO3-] is elevated. Juvenile Porites spp. may therefore be limited by dissolved inorganic carbon under ambient pCO2 conditions

In vitro selection of self-cleaving RNAs with a low pH optimum

RNAs that undergo a rapid site-specific cleavage at low pH have been selected by in vitro selection (the SELEX process). The cleavage does not require the addition of any divalent metal ions, and is in fact inhibited by divalent metal ions, spermine, or high concentrations of monovalent metal ions. This low pH catalyzed cleavage results in a 2′,3′-cyclic phosphate at the 3′ end and a free hydroxyl at the 5′ end. The reaction proceeds with a calculated rate of 1.1 min−1 at room temperature in cacodylate buffer at pH 5.0. The rate of cleavage is dependent on the pH and shows an optimum around pH 4.0. The rate constant is independent of RNA concentration, indicating to an intramolecular reaction. Autocatalytic cleavage at low pH, in the absence of a metal ion requirement, adds to the reaction possibilities that may have existed on the prebiotic earth.

The vacuolating toxin from Helicobacter pylori forms hexameric pores in lipid bilayers at low pH

Pathogenic strains of Helicobacter pylori secrete a cytotoxin, VacA, that in the presence of weak bases, causes osmotic swelling of acidic intracellular compartments enriched in markers for late endosomes and lysosomes. The molecular mechanisms by which VacA causes this vacuolation remain largely unknown. At neutral pH, VacA is predominantly a water-soluble dodecamer formed by two apposing hexamers. In this report, we show by using atomic force microscopy that below pH ≈5, VacA associates with anionic lipid bilayers to form hexameric membrane-associated complexes. We propose that water-soluble dodecameric VacA proteins disassemble at low pH and reassemble into membrane-spanning hexamers. The surface contour of the membrane-bound hexamer is strikingly similar to the outer surface of the soluble dodecamer, suggesting that the VacA surface in contact with the membrane is buried within the dodecamer before protonation. In addition, electrophysiological measurements indicate that, under the conditions determined by atomic force microscopy for membrane association, VacA forms pores across planar lipid bilayers. This low pH-triggered pore formation is likely a critical step in VacA activity.

A soluble domain of the membrane-anchoring chain of influenza virus hemagglutinin (HA2) folds in Escherichia coli into the low-pH-induced conformation.

The extensive refolding of the membrane-anchoring chain of hemagglutinin (HA) of influenza virus (termed HA2) in cellular endosomes, which initiates viral entry by membrane fusion, suggests that viral HA is meta-stable. HA2 polypeptide residues 38-175 expressed in Escherichia coli are reported here to fold in vivo into a soluble trimer. The structure appears to be the same as the low-pH-induced conformation of viral HA2 by alpha-helical content, thermodynamic stability, protease dissection, electron microscopy, and antibody binding. These results provide evidence that the structure of the low-pH-induced fold of viral HA2 (TBHA2) observed crystallographically is the lowest-energy-state fold of the HA2 polypeptide. They indicate that the HA2 conformation in viral HA before low pH activation of its fusion potential is metastable and suggest that removal of the receptor-binding chain (HA1) is enough to allow HA2 to adopt the stable state. Further, they provide direct evidence that low pH is not required to form the membrane-fusion conformation but acts to make this state kinetically accessible in viral HA.

Determination of chromophore charge states in the low pH color transition of the fluorescent protein Rtms5(H146S) via time-dependent DFT

The red fluorescent protein Rtms5H146S displays a transition from blue (absorbance λmax 590 nm) to yellow (absorbance λmax not, vert, similar453 nm) upon titration to low pH. The pKa of the reaction depends on the concentration of halide, offering promise for new expressible halide sensors. The protonation state involved in the low pH form of the chromophore remains, however, ambiguous. We report calculated excitation energies of different protonation states of an RFP chromophore model. These suggest that the relevant titration site is the phenoxy moiety of the chromophore, and the relevant base and conjugate acid are anionic and neutral chromophore species, respectively.

The role of histidine residues in low-pH-mediated viral membrane fusion

A central event in the invasion of a host cell by an enveloped virus is the fusion of viral and cell membranes. For many viruses, membrane fusion is driven by specific viral surface proteins that undergo large-scale conformational rearrangements, triggered by exposure to low pH in the endosome upon internalization. Here, we present evidence suggesting that in both class I (helical hairpin proteins) and class 11 (beta-structure-rich proteins) pH-dependent fusion proteins the protonation of specific histidine residues triggers fusion via an analogous molecular mechanism. These histidines are located in the vicinity of positively charged residues in the prefusion conformation, and they subsequently form salt bridges with negatively charged residues in the postfusion conformation. The molecular surfaces involved in the corresponding structural rearrangements leading to fusion are highly conserved and thus might provide a suitable common target for the design of antivirals, which could be active against a diverse range of pathogenic viruses.

Nutrient availability affects the response of the calcifying chlorophyte Halimeda opuntia (L.) J.V. Lamouroux to low pH

Atmospheric carbon dioxide emissions cause a decrease in the pH and aragonite saturation state of surface ocean water. As a result, calcifying organisms are expected to suffer under future ocean conditions, but their physiological responses may depend on their nutrient status. Because many coral reefs experience high inorganic nutrient loads or seasonal changes in nutrient availability, reef organisms in localized areas will have to cope with elevated carbon dioxide and changes in inorganic nutrients. Halimeda opuntia is a dominant calcifying primary producer on coral reefs that contributes to coral reef accretion. Therefore, we investigated the carbon and nutrient balance of H. opuntia exposed to elevated carbon dioxide and inorganic nutrients. We measured tissue nitrogen, phosphorus and carbon content as well as the activity of enzymes involved in inorganic carbon uptake and nitrogen assimilation (external carbonic anhydrase and nitrate reductase, respectively). Inorganic carbon content was lower in algae exposed to high CO2, but calcification rates were not significantly affected by CO2 or inorganic nutrients. Organic carbon was positively correlated to external carbonic anhydrase activity, while inorganic carbon showed the opposite correlation. Carbon dioxide had a significant effect on tissue nitrogen and organic carbon content, while inorganic nutrients affected tissue phosphorus and N:P ratios. Nitrate reductase activity was highest in algae grown under elevated CO2 and inorganic nutrient conditions and lowest when phosphate was limiting. In general, we found that enzymatic responses were strongly influenced by nutrient availability, indicating its important role in dictating the local responses of the calcifying primary producer H. opuntia to ocean acidification.

Proteomic analysis of Rhizobium freirei PRF 81 responses to low pH.

Rhizobium freirei PRF 81 is employed in common bean commercial inoculants in Brazil, due to its outstanding efficiency in fixing nitrogen, competitiveness and tolerance to abiotic stresses. Among the environmental conditions faced by rhizobia in soils, acidity is perhaps the encountered most, especially in Brazil. So, we used proteomics based approaches to study the responses of PRF 81 to a low pH condition. R. freirei PRF 81 was grown in TY medium until exponential phase in two treatments: pH 6,8 and pH 4,8. Whole-cell proteins were extracted and separated by two-dimensional gel electrophoresis, using IPG-strips with pH range 4-7 and 12% polyacrilamide gels. The experiment was performed in triplicate. Protein spots were detected in the high-resolution digitized gel images and analyzed by Image Master 2D Platinum v 5.0 software. Relative volumes (%vol) of compared between the two conditions tested and were statistically evaluated (p ≤ 0.05). Even knowing that R. freirei PRF 81 can still grow in more acid conditions, pH 4.8 was chosen because didn´t affect significantly the bacterial growth kinetics, a factor that could compromise the analysis. Using a narrow pH range, the gel profiles displayed a better resolution and reprodutibility than using broader pH range. Spots were mostly concentrated between pH 5-7 and molecular masses between 17-95 kDa. From the six hundred well-defined spots analyzed, one hundred and sixty-three spots presented a significant change in % vol, indicating that the pH led to expressive changes in the proteome of R. freirei PRF 81. Of these, sixty-one were up-regulated and one hundred two was downregulated in pH 4.8 condition. Also, fourteen spots were only identified in the acid condition, while seven spots was exclusively detected in pH 6.8. Ninety-five differentially expressed spots and two exclusively detected in pH 4,8 were selected for Maldi-Tof identification. Together with the genome sequencing and the proteome analysis of heat stress, we will search for molecular determinants of PRF 81 related to capacity to adapt to stressful tropical conditions.

Review of stress corrosion cracking of pipeline steels in "low" and "high" pH solutions

This paper reviews the current understanding of the mechanisms of stress corrosion cracking of pipeline steels. The similarities, the differences and the influencing factors are considered for the high pH stress corrosion cracking caused by a concentrated bicarbonate-carbonate solution, and for the low pH stress corrosion cracking due to a diluter solution. For high pH stress corrosion cracking, it is well accepted that the mechanism involves anodic dissolution for crack initiation and propagation. In contrast, it has been suggested that the low pH stress corrosion cracking is associated with the dissolution of the crack tip and sides, accompanied by the ingress of hydrogen into the pipeline steel. But the precise influence of hydrogen on the mechanism needs to be further studied. (C) 2003 Kluwer Academic Publishers.

Effect of low extracellular pH on NF-κB activation in macrophages

Objective: Many diseases, including atherosclerosis, involve chronic inflammation. The master transcription factor for inflammation is NF-κB. Inflammatory sites have a low extracellular pH. Our objective was to demonstrate the effect of pH on NF-κB activation and cytokine secretion. Methods: Mouse J774 macrophages or human THP-1 or monocyte-derived macrophages were incubated at pH 7.0–7.4 and inflammatory cytokine secretion and NF-κB activity were measured. Results: A pH of 7.0 greatly decreased pro-inflammatory cytokine secretion (TNF or IL-6) by J774 macrophages, but not THP-1 or human monocyte-derived macrophages. Upon stimulation of mouse macrophages, the levels of IκBα, which inhibits NF-κB, fell but low pH prevented its later increase, which normally restores the baseline activity of NF-κB, even though the levels of mRNA for IκBα were increased. pH 7.0 greatly increased and prolonged NF-κB binding to its consensus promoter sequence, especially the anti-inflammatory p50:p50 homodimers. Human p50 was overexpressed using adenovirus in THP-1 macrophages and monocyte-derived macrophages to see if it would confer pH sensitivity to NF-κB activity in human cells. Overexpression of p50 increased p50:p50 DNA-binding and in THP-1 macrophages inhibited considerably TNF and IL-6 secretion, but there was still no effect of pH on p50:p50 DNA binding or cytokine secretion. Conclusion: A modest decrease in pH can sometimes have marked effects on NF-κB activation and cytokine secretion and might be one reason to explain why mice normally develop less atherosclerosis than do humans.

Photosynthate translocation increases in response to low seawater pH in a coral-dinoflagellate symbiosis

This study has examined the effect of low seawater pH values (induced by an increased CO2 partial pressure) on the rates of photosynthesis, as well as on the carbon budget and carbon translocation in the scleractinian coral species Stylophora pistillata, using a new model based on 13C labelling of the photosynthetic products. Symbiont photosynthesis contributes to a large part of the carbon acquisition in tropical coral species, and it is thus important to know how environmental changes affect this carbon acquisition and allocation. For this purpose, nubbins of S. pistillata were maintained for six months at two pHTs (8.1 and 7.2, by bubbling seawater with CO2). The lowest pH value was used to tackle how seawater pH impacts the carbon budget of a scleractinian coral. Rates of photosynthesis and respiration of the symbiotic association and of isolated symbionts were assessed at each pH. The fate of 13C photosynthates was then followed in the symbionts and the coral host for 48 h. Nubbins maintained at pHT 7.2 presented a lower areal symbiont concentration, and lower areal rates of gross photosynthesis and carbon incorporation compared to nubbins maintained at pHT 8.1. The total carbon acquisition was thus lower under low pH. However, the total percentage of carbon translocated to the host as well as the amount of carbon translocated per symbiont cell were significantly higher under pHT 7.2 than under pHT 8.1 (70% at pHT 7.2 vs. 60% at pHT 8.1), such that the total amount of photosynthetic carbon received by the coral host was equivalent under both pHs (5.5 to 6.1 µg C/cm**2/h). Although the carbon budget of the host was unchanged, symbionts acquired less carbon for their own needs (0.6 compared to 1.8 µg C/cm**2/h), explaining the overall decrease in symbiont concentration at low pH. In the long term, such decrease in symbiont concentration might severely affect the carbon budget of the symbiotic association.

Effect of galactose metabolising and non-metabolising strains of Streptococcus thermophilus as a starter culture adjunct on the properties of Cheddar cheese made with low or high pH at whey drainage

Cheddar cheese was made using control culture (Lactococcus lactis subsp. lactis), or with control culture plus a galactose-metabolising (Gal+) or galactose-non-metabolising (Gal-) Streptococcus thermophilus adjunct; for each culture type, the pH at whey drainage was either low (pH 6.15) or high (pH 6.45). Sc. thermophilus affected the levels of residual lactose and galactose, and the volatile compound profile and sensory properties of the mature cheese (270 d) to an extent dependent on the drain pH and phenotype (Gal+ or Gal-). For all culture systems, reducing drain pH resulted in lower levels of moisture and lactic acid, a higher concentration of free amino acids, and higher firmness. The results indicate that Sc. thermophilus may be used to diversify the sensory properties of Cheddar cheese, for example from a fruity buttery odour and creamy flavour to a more acid taste, rancid odour, and a sweaty cheese flavour at high drain pH.