Ambient pH Controls Glycogen Levels by Regulating Glycogen Synthase Gene Expression in Neurospora crassa. New Insights into the pH Signaling Pathway

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Control of ambient pH on growth and stable isotopes in phytoplanktonic calcifying algae

The present work examines the relationship between pH-induced changes in growth and stable isotopic composition of coccolith calcite in two coccolithophore species with a geological perspective. These cells (Gephyrocapsa oceanica and Coccolithus pelagicus) with differing physiologies and vital effects possess a growth optimum corresponding to average pH of surface seawater in the geological period during their first known occurrence. Diminished growth rates outside of their optimum pH range are explained by the challenge of proton translocation into the extracellular environment at low pH, and enhanced aqueous CO2 limitation at high pH. These diminished growth rates correspond to a lower degree of oxygen isotopic disequilibrium in G. oceanica. In contrast, the slower growing and ancient species C. pelagicus, which typically precipitates near-equilibrium calcite, does not show any modulation of oxygen isotope signals with changing pH. In CO2-utilizing unicellular algae, carbon and oxygen isotope compositions are best explained by the degree of utilization of the internal dissolved inorganic carbon (DIC) pool and the dynamics of isotopic re-equilibration inside the cell. Thus, the "carbonate ion effect" may not apply to coccolithophores. This difference with foraminifera can be traced to different modes of DIC incorporation into these two distinct biomineralizing organisms. From a geological perspective, these findings have implications for refining the use of oxygen isotopes to infer more reliable sea surface temperatures (SSTs) from fossil carbonates, and contribute to a better understanding of how climate-relevant parameters are recorded in the sedimentary archive.

Transcription of the Hsp30, Hsp70, and Hsp90 heat shock protein genes is modulated by the PalA protein in response to acid pH-sensing in the fungus Aspergillus nidulans

Heat shock proteins are molecular chaperones linked to a myriad of physiological functions in both prokaryotes and eukaryotes. In this study, we show that the Aspergillus nidulans hsp30 (ANID_03555.1), hsp70 (ANID_05129.1), and hsp90 (ANID_08269.1) genes are preferentially expressed in an acidic milieu, whose expression is dependent on the palA (+) background under optimal temperature for fungal growth. Heat shock induction of these three hsp genes showed different patterns in response to extracellular pH changes in the palA(+) background. However, their accumulation upon heating for 2 h was almost unaffected by ambient pH changes in the palA (-) background. The PalA protein is a member of a conserved signaling cascade that is involved in the pH-mediated regulation of gene expression. Moreover, we identified several genes whose expression at pH 5.0 is also dependent on the palA (+) background. These results reveal novel aspects of the heat- and pH-sensing networks of A. nidulans.

Transcriptional profiling reveals genes in the human pathogen Trichophyton rubrum that are expressed in response to pH signaling

Trichophyton rubrum is a dermatophyte that infects human skin and nails. Its growth on keratin as its carbon source shifts the ambient pH from acidic to alkaline, which may be an efficient strategy for its successful infection and maintenance in the host. In this study, we used suppression subtractive hybridization to identify genes preferentially expressed in T rubrum incubated at either pH 5.0 or pH 8.0. The functional grouping of the 341 overexpressed unigenes indicated proteins putatively involved in diverse cellular processes, such as membrane remodeling, cellular transport, metabolism, cellular protection, fungal pathogenesis, gene regulation, interaction with the environment, and iron uptake. Although the basic metabolic machinery identified under both growth conditions seems to be functionally similar, distinct genes are upregulated at acidic or alkaline pHs. We also isolated a large number of genes of unknown function, probably unique to T rubrum or dermatophytes. Interestingly, the transcriptional profiling of several genes in a pacC mutant suggests that, in T rubrum, the transcription factor PacC has a diversity of metabolic functions, in response to either acidic or alkaline ambient pH. (C) 2009 Elsevier Ltd. All rights reserved.

Climate driven changes in temperature, pH and food quality : effects on copepod reproduction

Increased emissions of greenhouse gases into the atmosphere are causing an anthropogenic climate change. The resulting global warming challenges the ability of organisms to adapt to the new temperature conditions. However, warming is not the only major threat. In marine environments, dissolution of carbon dioxide from the atmosphere causes a decrease in surface water pH, the so called ocean acidification. The temperature and acidification effects can interact, and create even larger problems for the marine flora and fauna than either of the effects would cause alone. I have used Baltic calanoid copepods (crustacean zooplankton) as my research object and studied their growth and stress responses using climate predictions projected for the next century. I have studied both direct temperature and pH effects on copepods, and indirect effects via their food: the changing phytoplankton spring bloom composition and toxic cyanobacterium. The main aims of my thesis were: 1) to find out how warming and acidification combined with a toxic cyanobacterium affect copepod reproductive success (egg production, egg viability, egg hatching success, offspring development) and oxidative balance (antioxidant capacity, oxidative damage), and 2) to reveal the possible food quality effects of spring phytoplankton bloom composition dominated by diatoms or dinoflagellates on reproducing copepods (egg production, egg hatching, RNA:DNA ratio). The two copepod genera used, Acartia sp. and Eurytemora affinis are the dominating mesozooplankton taxa (0.2 – 2 mm) in my study area the Gulf of Finland. The 20°C temperature seems to be within the tolerance limits of Acartia spp., because copepods can adapt to the temperature phenotypically by adjusting their body size. Copepods are also able to tolerate a pH decrease of 0.4 from present values, but the combination of warm water and decreased pH causes problems for them. In my studies, the copepod oxidative balance was negatively influenced by the interaction of these two environmental factors, and egg and nauplii production were lower at 20°C and lower pH, than at 20°C and ambient pH. However, presence of toxic cyanobacterium Nodularia spumigena improved the copepod oxidative balance and helped to resist the environmental stress, in question. In addition, adaptive maternal effects seem to be an important adaptation mechanism in a changing environment, but it depends on the condition of the female copepod and her diet how much she can invest in her offspring. I did not find systematic food quality difference between diatoms and dinoflagellates. There are both good and bad diatom and dinoflagellate species. Instead, the dominating species in the phytoplankton bloom composition has a central role in determining the food quality, although copepods aim at obtaining as a balanced diet as possible by foraging on several species. If the dominating species is of poor quality it can cause stress when ingested, or lead to non-optimal foraging if rejected. My thesis demonstrates that climate change induced water temperature and pH changes can cause problems to Baltic Sea copepod communities. However, their resilience depends substantially on their diet, and therefore the response of phytoplankton to the environmental changes. As copepods are an important link in pelagic food webs, their future success can have far reaching consequences, for example on fish stocks.

Transcription of the Hsp30, Hsp70, and Hsp90 heat shock protein genes is modulated by the PalA protein in response to acid pH-sensing in the fungus Aspergillus nidulans

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Seawater carbonate chemistry, gross photosynthesis and metabolically induced rate of pH change during experiments with macroalgae, 2012

Ocean acidification (OA) is a reduction in oceanic pH due to increased absorption of anthropogenically produced CO2. This change alters the seawater concentrations of inorganic carbon species that are utilized by macroalgae for photosynthesis and calcification: CO2 and HCO3 increase; CO32 decreases. Two common methods of experimentally reducing seawater pH differentially alter other aspects of carbonate chemistry: the addition of CO2 gas mimics changes predicted due to OA, while the addition of HCl results in a comparatively lower [HCO3]. We measured the short-term photosynthetic responses of five macroalgal species with various carbon-use strategies in one of three seawater pH treatments: pH 7.5 lowered by bubbling CO2 gas, pH 7.5 lowered by HCl, and ambient pH 7.9. There was no difference in photosynthetic rates between the CO2, HCl, or pH 7.9 treatments for any of the species examined. However, the ability of macroalgae to raise the pH of the surrounding seawater through carbon uptake was greatest in the pH 7.5 treatments. Modeling of pH change due to carbon assimilation indicated that macroalgal species that could utilize HCO3 increased their use of CO2 in the pH 7.5 treatments compared to pH 7.9 treatments. Species only capable of using CO2 did so exclusively in all treatments. Although CO2 is not likely to be limiting for photosynthesis for the macroalgal species examined, the diffusive uptake of CO2 is less energetically expensive than active HCO3 uptake, and so HCO3-using macroalgae may benefit in future seawater with elevated CO2.

CO2-driven decrease in pH disrupts olfactory behaviour and increases individual variation in deep-sea hermit crabs

Deep-sea species are generally thought to be less tolerant of environmental variation than shallow-living species due to the relatively stable conditions in deep waters for most parameters (e.g. temperature, salinity, oxygen, and pH). To explore the potential for deep-sea hermit crabs (Pagurus tanneri) to acclimate to future ocean acidification, we compared their olfactory and metabolic performance under ambient (pH 7.6) and expected future (pH 7.1) conditions. After exposure to reduced pH waters, metabolic rates of hermit crabs increased transiently and olfactory behaviour was impaired, including antennular flicking and prey detection. Crabs exposed to low pH treatments exhibited higher individual variation for both the speed of antennular flicking and speed of prey detection, than observed in the control pH treatment, suggesting that phenotypic diversity could promote adaptation to future ocean acidification.

Antarctic crustacean grazer assemblages exhibit resistance following exposure to decreased pH

Anthropogenic atmospheric CO2 concentrations are increasing rapidly, resulting in declining seawater pH (ocean acidification). The majority of ocean acidification research to date has focused on the effects of decreased pH in single-species experiments. To assess how decreased pH may influence natural macroalgal-grazer assemblages, we conducted a mesocosm experiment with the common, chemically defended Antarctic brown macroalga Desmarestia menziesii and natural densities of its associated grazer assemblage, predominantly amphipods. Grazer assemblages were collected from the immediate vicinity of Palmer Station (64°46'S, 64°03'W) in March 2013. Assemblages were exposed for 30 days to three levels of pH representing present-day mean summer ambient conditions (pH 8.0), predicted near-future conditions (2100, pH 7.7), and distant-future conditions (pH 7.3). A significant difference was observed in the composition of mesograzer assemblages in the lowest pH treatment (pH 7.3). The differences between assemblages exposed to pH 7.3 and those maintained in the other two treatments were driven primarily by decreases in the abundance of the amphipod Metaleptamphopus pectinatus with decreasing pH, reduced copepod abundance at pH 7.7, and elevated ostracod abundance at pH 7.7. Generally, the assemblages maintained at pH 7.7 were not significantly different from those at ambient pH, demonstrating resistance to short-term decreased pH. The relatively high prevalence of generalist amphipods may have contributed to a net stabilizing effect on the assemblages exposed to decreased pH. Overall, our results suggest that crustacean grazer assemblages associated with D. menziesii, the dominant brown macroalgal species of the western Antarctic Peninsula, may be resistant to short-term near-future decreases in seawater pH.

Transcriptional profiling reveals the expression of novel genes in response to various stimuli in the human dermatophyte Trichophyton rubrum

Background: Cutaneous mycoses are common human infections among healthy and immunocompromised hosts, and the anthropophilic fungus Trichophyton rubrum is the most prevalent microorganism isolated from such clinical cases worldwide. The aim of this study was to determine the transcriptional profile of T. rubrum exposed to various stimuli in order to obtain insights into the responses of this pathogen to different environmental challenges. Therefore, we generated an expressed sequence tag (EST) collection by constructing one cDNA library and nine suppression subtractive hybridization libraries. Results: The 1388 unigenes identified in this study were functionally classified based on the Munich Information Center for Protein Sequences (MIPS) categories. The identified proteins were involved in transcriptional regulation, cellular defense and stress, protein degradation, signaling, transport, and secretion, among other functions. Analysis of these unigenes revealed 575 T. rubrum sequences that had not been previously deposited in public databases. Conclusion: In this study, we identified novel T. rubrum genes that will be useful for ORF prediction in genome sequencing and facilitating functional genome analysis. Annotation of these expressed genes revealed metabolic adaptations of T. rubrum to carbon sources, ambient pH shifts, and various antifungal drugs used in medical practice. Furthermore, challenging T. rubrum with cytotoxic drugs and ambient pH shifts extended our understanding of the molecular events possibly involved in the infectious process and resistance to antifungal drugs.

The conserved and divergent roles of carbonic anhydrases in the filamentous fungi Aspergillus fumigatus and Aspergillus nidulans

P>Carbon dioxide (CO(2)) and its hydration product bicarbonate (HCO(3)-) are essential molecules in various physiological processes of all living organisms. The reversible interconversion between CO(2) and HCO(3)- is in equilibrium. This reaction is slow without catalyst, but can be rapidly facilitated by Zn2+-metalloenzymes named carbonic anhydrases (CAs). To gain an insight into the function of multiple clades of fungal CA, we chose to investigate the filamentous fungi Aspergillus fumigatus and A. nidulans. We identified four and two CAs in A. fumigatus and A. nidulans, respectively, named cafA-D and canA-B. The cafA and cafB genes are constitutively, strongly expressed whereas cafC and cafD genes are weakly expressed but CO(2)-inducible. Heterologous expression of the A. fumigatus cafB, and A. nidulans canA and canB genes completely rescued the high CO(2)-requiring phenotype of a Saccharomyces cerevisiae Delta nce103 mutant. Only the Delta cafA Delta cafB and Delta canB deletion mutants were unable to grow at 0.033% CO(2), of which growth defects can be restored by high CO(2). Defects in the CAs can affect Aspergilli conidiation. Furthermore, A. fumigatus Delta cafA, Delta cafB, Delta cafC, Delta cafD and Delta cafA Delta cafB mutant strains are fully virulent in a low-dose murine infection.

Identification of genes differentially expressed in a strain of the mold Aspergillus nidulans carrying a loss-of-function mutation in the palA gene

To identify genes differentially expressed in a strain of the mold Aspergillus nidulans carrying a loss-of-function mutation in palA, a gene in the pH-responsive signal transduction pathway, suppression subtractive hybridization was performed between RNA isolated from the biA1 and biA1 palA1 strains grown under limiting inorganic phosphate at pH 5.0. We have identified several genes upregulated in the biA1 palA1 mutant strain that play important roles in mitotic fidelity, stress responses, enzyme secretion, signal transduction mechanisms, development, genome stability, phosphate sensing, and transcriptional regulation among others. The upregulation of eight of these transcripts was also validated by Northern blot. Moreover, we show that a loss of function mutation in the palA gene drastically reduced the neutral sugar content of the acid phosphatase PacA secreted by the fungus A. nidulans grown at pH 5.0 compared with a control strain.

The dermatophyte Trichophyton rubrum secretes an EDTA-sensitive alkaline phosphatase on high-phosphate medium

In this communication, we show that the growth of isolate H6 of the dermatophyte Trichophyton rubrum on non-buffered medium and under saturating phosphate conditions is dependent on the initial growth pH, with an apparent optimum at pH 4.0. In addition, irrespective of the initial growth pH, the pH of the medium altered during cultivation reaching values that ranged from 8.3 to 8.9. Furthermore, this isolate synthesized and secreted almost the same levels of an alkaline phosphatase with an apparent optimum pH ranging from 9.0 to 10.0 when grown on both low- and high-phosphate medium. Also, this alkaline phosphatase is activated by Mg2+ and is EDTA-sensitive. On the other hand, the very low levels of the enzyme retained by the mycelium grown on buffered medium at pH 5.0-5.2 suggest that this enzyme is encoded by an alkaline gene, i.e., a gene responsive to ambient pH signaling.

Apple latent infection caused by Neofabraea alba: host-pathogen interaction and disease management

Apple latent infection caused by Neofabraea alba: host-pathogen interaction and disease management Bull’s eye rot (BER) caused by Neofabraea alba is one of the most frequent and damaging latent infection occurring in stored pome fruits worldwide. Fruit infection occurs in the orchard, but disease symptoms appear only 3 months after harvest, during refrigerated storage. In Italy BER is particularly serious for late harvest apple cultivar as ‘Pink Lady™’. The purposes of this thesis were: i) Evaluate the influence of ‘Pink Lady™’ apple primary metabolites in N. alba quiescence ii) Evaluate the influence of pH in five different apple cultivars on BER susceptibility iii) To find out not chemical method to control N. alba infection iv) Identify some fungal volatile compounds in order to use them as N. alba infections markers. Results regarding the role of primary metabolites showed that chlorogenic, quinic and malic acid inhibit N. alba development. The study based on the evaluation of cultivar susceptibility, showed that Granny Smith was the most resistant apple cultivar among the varieties analyzed. Moreover, Granny Smith showed the lowest pH value from harvest until the end of storage, supporting the thesis that ambient pH could be involved in the interaction between N. alba and apple. In order to find out new technologies able to improve lenticel rot management, the application of a non-destructive device for the determination of chlorophyll content was applied. Results showed that fruit with higher chlorophyll content are less susceptible to BER, and molecular analyses comforted this result. Fruits with higher chlorophyll content showed up-regulation of PGIP and HCT, genes involved in plant defence. Through the application of PTR-MS and SPME GC-MS, 25 volatile organic compounds emitted by N. alba were identified. Among them, 16 molecules were identified as potential biomarkers.

Seawater carbonate chemistry and concentration boundary layers around complex assemblages of macroalgae in a laboratory experiment

Metabolic processes have the potential to modulate the effects of ocean acidification (OA) in nearshore macroalgal beds. We investigated whether natural mixed assemblages of the articulate coralline macroalgae Arthrocardia corymbosa and understory crustose coralline algae (CCA) altered pH and O2 concentrations within and immediately above their canopies. In a unidirectional flume, we tested the effect of water velocity (0-0.1 m/s), bulk seawater pH (ambient pH 8.05, and pH 7.65), and irradiance (photosynthetically saturating light and darkness) on pH and O2 concentration gradients, and the derived concentration boundary layer (CBL) thickness. At bulk seawater pH 7.65 and slow velocities (0 and 0.015 m/s), pH at the CCA surface increased to 7.90-8.00 in the light. Although these manipulations were short term, this indicates a potential daytime buffering capacity that could alleviate the effects of OA. Photosynthetic activity also increased O2 concentrations at the surface of the CCA. However, this moderating capacity was flow dependent; the CBL thickness decreased from an average of 26.8 mm from the CCA surface at 0.015 m/s to 4.1 mm at 0.04 m/s. The reverse trends occurred in the dark, with respiration causing pH and O2 concentrations to decrease at the CCA surface. At all flow velocities the CBL thicknesses (up to 68 mm) were much greater than those previously published, indicating that the presence of canopies can alter the CBL substantially. In situ, the height of macroalgal canopies can be an order of magnitude larger than those used here, indicating that the degree of buffering to OA will be context dependent.