Vacuolar H(+)-ATPase, but not mitochondrial F(1)F(0)-ATPase, is required for NaCl tolerance in Saccharomyces cerevisiae

" Assessing the impact of biochar on microbes in acidic soils: Alleviating the toxicity of aluminum and acidity"

In arable soils, anthropogenic activities such as fertilizer applications have intensified soil acidification in recent years. This has resulted in frequent environmental problems such as aluminum (Al) and H+ stress, which negatively impact crop yields and quality in acidic soils. Biochar, as a promising soil conditioner, has attracted much attention globally. The present study was conducted in a greenhouse by setting up 2% biochar rate to investigate how biochar relieves Al3+ hazards in acidic soil by affecting soil quality, soil environment, and soil microbiomes. The addition of biochar significantly improved soil fertility and enzyme activities, which were attributed to its ability to enhance the utilization of soil carbon sources by influencing the activity of soil microorganisms. Moreover, the Al3+ contents were significantly decreased by 66.61-88.83% compared to the C0 level (without biochar treatment). In particular, the results of the 27Al NMR suggested that forms of AlVI (Al(OH)2+, Al(OH)+ 2, and Al3+) were increased by 88.69-100.44% on the surface of biochar, reducing the Al3+ stress on soil health. The combination of biochar and nitrogen (N) fertilizer contributed to the augmentation of bacterial diversity. The application of biochar and N fertilizer increased the relative abundance of the majority of bacterial species. Additionally, the application of biochar and N fertilizer had a significant impact on soil microbial metabolism, specifically in the biosynthesis of secondary metabolites (lipids and organic acids) and carbon metabolic ability. In conclusion, biochar can enhance soil microbial activity and improve the overall health of acidic soil by driving microbial metabolism. This study offers both theoretical and technical guidance for enhancing biochar in acidified soil and promoting sustainable development in farmland production.

Novel Cesium Resistance Mechanism of Alkaliphilic Bacterium Isolated From Jumping Spider Ground Extract

The radionuclide isotopes (¹³⁴Cs and ¹³⁷Cs) of Cesium (Cs), an alkali metal, are attracting attention as major causes of radioactive contamination. Although Cs⁺ is harmful to the growth of plants and bacteria, alkaliphilic bacterium Microbacterium sp. TS-1, isolated from a jumping spider, showed growth even in the presence of 1.2 M CsCl. The maximum concentration of Cs⁺ that microorganisms can withstand has been reported to be 700 mM till date, suggesting that the strain TS-1 is resistant to a high concentration of Cs ions. Multiple reports of cesium ion-resistant bacteria have been reported, but the detailed mechanism has not yet been elucidated. We obtained Cs ion-sensitive mutants and their revertant mutants from strain TS-1 and identified a Cs ion resistance-related gene, MTS1_00475, by performing SNP analysis of the whole-genome sequence data. When exposed to more than 200 mM Cs⁺ concentration, the intracellular Cs⁺ concentration was constantly lowered by MTS1_00475, which encodes the novel low-affinity Cs⁺/H⁺ antiporter. This study is the first to clarify the mechanism of cesium resistance in unexplained cesium-resistant microorganisms. By clarifying the new cesium resistance mechanism, it can be expected to be used as a bioremediation tool for treating radioactive Cs⁺ contaminated water.

Coordinated gene regulation in the initial phase of salt stress adaptation

Stress triggers complex transcriptional responses, which include both gene activation and repression. We used time-resolved reporter assays in living yeast cells to gain insights into the coordination of positive and negative control of gene expression upon salt stress. We found that the repression of "housekeeping" genes coincides with the transient activation of defense genes and that the timing of this expression pattern depends on the severity of the stress. Moreover, we identified mutants that caused an alteration in the kinetics of this transcriptional control. Loss of function of the vacuolar H(+)-ATPase (vma1) or a defect in the biosynthesis of the osmolyte glycerol (gpd1) caused a prolonged repression of housekeeping genes and a delay in gene activation at inducible loci. Both mutants have a defect in the relocation of RNA polymerase II complexes at stress defense genes. Accordingly salt-activated transcription is delayed and less efficient upon partially respiratory growth conditions in which glycerol production is significantly reduced. Furthermore, the loss of Hog1 MAP kinase function aggravates the loss of RNA polymerase II from housekeeping loci, which apparently do not accumulate at inducible genes. Additionally the Def1 RNA polymerase II degradation factor, but not a high pool of nuclear polymerase II complexes, is needed for efficient stress-induced gene activation. The data presented here indicate that the finely tuned transcriptional control upon salt stress is dependent on physiological functions of the cell, such as the intracellular ion balance, the protective accumulation of osmolyte molecules, and the RNA polymerase II turnover.

Comparative transcriptome analysis of leaves and roots in response to sudden increase in salinity in Brassica napus by RNA-seq

Amphidiploid species in the Brassicaceae family, such as Brassica napus, are more tolerant to environmental stress than their diploid ancestors.A relatively salt tolerant B. napus line, N119, identified in our previous study, was used. N119 maintained lower Na⁺ content, and Na⁺/K⁺ and Na⁺/Ca²⁺ ratios in the leaves than a susceptible line. The transcriptome profiles of both the leaves and the roots 1 h and 12 h after stress were investigated. De novo assembly of individual transcriptome followed by sequence clustering yielded 161,537 nonredundant sequences. A total of 14,719 transcripts were differentially expressed in either organs at either time points. GO and KO enrichment analyses indicated that the same 49 GO terms and seven KO terms were, respectively, overrepresented in upregulated transcripts in both organs at 1 h after stress. Certain overrepresented GO term of genes upregulated at 1 h after stress in the leaves became overrepresented in genes downregulated at 12 h. A total of 582 transcription factors and 438 transporter genes were differentially regulated in both organs in response to salt shock. The transcriptome depicting gene network in the leaves and the roots regulated by salt shock provides valuable information on salt resistance genes for future application to crop improvement.

Intracellular localization and induction of a dynamic RNA-editing event of macro-algal V-ATPase subunit A (VHA-A) in response to copper

A V-ATPase subunit A protein (VHA-A) transcript together with a variant (C793 to U), which introduces a stop codon truncating the subunit immediately downstream of its ATP binding site, was identified within a Fucus vesiculosus cDNA from a heavy metal contaminated site. This is intriguing because the VHA-A subunit is the crucial catalytic subunit responsible for the hydrolysis of ATP that drives ion transport underlying heavy metal detoxification pathways. We employed a chemiluminescent hybridization protection assay to quantify the proportion of both variants directly from mRNA while performing quantification of total transcript using Q-PCR. Polyclonal antisera raised against recombinant VHA-A facilitated simultaneous detection of parent and truncated VHA-A and revealed its cellular and subcellular localization. By exploiting laboratory exposures and samples from an environmental copper gradient, we showed that total VHA-A transcript and protein, together with levels of the truncated variant, were induced by copper. The absence of a genomic sequence representing the truncated variant suggests a RNA editing event causing the production of the truncated VHA-A. Based on these observations, we propose RNA editing as a novel molecular process underpinning VHA trafficking and intracellular sequestration of heavy metals under stress.

Calcium supply effects on wheat cultivars differing in salt resistance with special reference to leaf cytosol ion homeostasis

Salinity causes changes in cytosolic Ca(2+), [Ca(2+)]cyt, Na(+), [Na(+)]cyt and pH, pH cyt , which induce specific reactions and signals. Reactions causing a rebalancing of the physiological homeostasis of the cytosol could result in plant resistance and growth. Two wheat cultivars, Triticum aestivum, Seds1 and Vinjett, were grown in nutrient solution for 7 days under moderate salinity (0 and 50 mM NaCl) with and without extra addition of 5 mM CaSO4 to investigate the seedling-ion homeostasis under salinity. In the leaf protoplasts [Ca(2+) ]cyt, [Na(+)]cyt and pH cyt were detected using acetoxymethyl esters of the ion-specific dyes, Fura 2, SBFI and BCECF, respectively, and fluorescence microscopy. In addition, both cultivars were grown for 3 weeks at 0, 50 and 125 mM NaCl with, or without, extra addition of 5 mM CaSO4 to detect overall Na(+) and Ca(2+) concentrations in leaves and salinity effects on dry weights. In both cultivars, salinity decreased [Ca(2+)]cyt, while at extra Ca(2+) supplied, [Ca(2+)]cyt increased. The [Ca(2+) ]cyt increase was accompanied by increase in the overall Ca(2+) concentrations in leaves and decrease in the overall Na(+) concentration. Moreover, irrespective of Ca(2+) treatment under salinity, the cultivars reacted in different ways; [Na(+) ]cyt significantly increased only in cv. Vinjett, while pH cyt increased only in cv. Seds1. Even at rather high total Na(+) concentrations, the cytosolic concentrations were kept low in both cultivars. It is discussed whether the increase of [Ca(2+)]cyt and pH cyt can contribute to salt tolerance and if the cytosolic changes are due to changes in overall Ca(2+) and Na(+) concentrations.

Statistical optimization of pigment production by Monascus sanguineus under stress condition

Natural pigments are produced by the Monascus sp., which are used for coloring food substances. The intent of this study was to optimize the pigment yield and biomass produced from the unexplored Monascus sanguineus in submerged culture under stress conditions. For inducing thermal stress, the spores were incubated at various temperatures at higher ranges. For inducing osmotic stress, varied concentrations of NaCl, glycerol, and peptone were used. The medium components were optimized by response surface methodology (RSM). The combined effects of the four medium constituents mentioned were studied using a 2⁴ full factorial central composite design (CCD). The relationships between the predicted values and actual values, independent variable, and the response were calculated according to a second-order quadratic model. It was deduced that the variable with the leading effect was the linear effect of glycerol concentration. Furthermore, the quadratic effects of peptone and the interactive effects of temperature and glycerol were more noteworthy than other factors. The optimum values for the test variables in coded factors were found to be spores treated with 70°C for temperature, 0.25 M for glycerol, 0.51% (w/v) for peptone, and 1.25% (w/v) for NaCl, corresponding to a maximum red pigment yield of 55.67 color value units (CVU)/mL. With optimized conditions, the pigment yield was almost three times the yield observed with the control.

New insights on transcriptional responses of genes involved in carbon central metabolism, respiration and fermentation to low ATP levels in Escherichia coli

Adenosine-5-triphosphate (ATP) plays a fundamental role in many cellular processes such as transport, central carbon metabolism, biosynthetic reactions, macromolecular synthesis, signal transduction and cellular division. In addition, the intracellular [ATP]/[ADP] ratio in Escherichia coli plays an important role in controlling the specific rates of growth (µ), glucose consumption (qGlc ) and oxygen uptake (qO2), as well as the transcriptome pattern in the cell, as was recently reported. In the current study, the energetic level (expressed as [ATP]/[ADP] ratio) was substantially reduced in E. coli strains by either over-expressing the F1 -ATPase activity (JMAGD(+)) or inactivating ATP synthase (JMat(-)). The physiological characterization of the wild-type JM101 strain and its derivative JMAGD(+) and JMatp(-) strains was conducted in bioreactors containing minimal medium with glucose. The inactivation of the atp operon and F1 -ATPase overexpression significantly diminished the energetic level and cAMP concentration in derivative strains. Relative transcription levels of 105 genes involved in glucose transport, glycolysis, tricarboxylic acid (TCA) cycle, fermentation, respiration, transcriptional regulators, transcription and genes involved in stress were determined by using qPCR. Interestingly, in the JMAGD(+) and JMatp(-) strains, having a reduced energetic level, many transcripts of glycolysis, TCA cycle and respiratory genes were down-regulated when compared to wild type JM101. The transcriptional responses, detected in the strains with reduced energetic level show down-regulation of genes involved in central carbon metabolism and respiration, these results are apposite to the observed trends of increased metabolic fluxes in glucose consumption, glycolysis, acetate synthesis, TCA cycle and respiration. Regulation mediated by CRP-cAMP complex may explain some observed transcriptional responses of TCA cycle genes, since cAMP concentration and crp transcript level were significant reduced in the JMatp(-) mutant. Therefore, the substantial reduction of [ATP]/[ADP] ratio had a relevant effect on the CRP-cAMP regulatory system (among other global regulators), which may trigger an extensive transcriptional response.

The STF2p hydrophilin from Saccharomyces cerevisiae is required for dehydration stress tolerance

The yeast Saccharomyces cerevisiae is able to overcome cell dehydration; cell metabolic activity is arrested during this period but restarts after rehydration. The yeast genes encoding hydrophilin proteins were characterised to determine their roles in the dehydration-resistant phenotype, and STF2p was found to be a hydrophilin that is essential for survival after the desiccation-rehydration process. Deletion of STF2 promotes the production of reactive oxygen species and apoptotic cell death during stress conditions, whereas the overexpression of STF2, whose gene product localises to the cytoplasm, results in a reduction in ROS production upon oxidative stress as the result of the antioxidant capacity of the STF2p protein.

Chemosensitization of aflatoxigenic fungi to antimycin A and strobilurin using salicylaldehyde, a volatile natural compound targeting cellular antioxidation system

Various species of fungi in the genus Aspergillus are the most common causative agents of invasive aspergillosis and/or producers of hepato-carcinogenic mycotoxins. Salicylaldehyde (SA), a volatile natural compound, exhibited potent antifungal and anti-mycotoxigenic activities to A. flavus and A. parasiticus. By exposure to the volatilized SA, the growth of A. parasiticus was inhibited up to 10-75% at 9.5 mM ≤ SA ≤ 16.0 mM, while complete growth inhibition was achieved at 19.0 mM ≤ SA. Similar trends were also observed with A. flavus. The aflatoxin production, i.e., aflatoxin B(1) and B(2) (AFB(1), AFB(2)) for A. flavus and AFB(1), AFB(2), AFG(1), and AFG(2) for A. parasiticus, in the SA-treated (9.5 mM) fungi was reduced by ~13-45% compared with the untreated control. Using gene deletion mutants of the model yeast Saccharomyces cerevisiae, we identified the fungal antioxidation system as the molecular target of SA, where sod1Δ [cytosolic superoxide dismutase (SOD)], sod2Δ (mitochondrial SOD), and glr1Δ (glutathione reductase) mutants showed increased sensitivity to this compound. Also sensitive was the gene deletion mutant, vph2Δ, for the vacuolar ATPase assembly protein, suggesting vacuolar detoxification plays an important role for fungal tolerance to SA. In chemosensitization experiments, co-application of SA with either antimycin A or strobilurin (inhibitors of mitochondrial respiration) resulted in complete growth inhibition of Aspergillus at much lower dose treatment of either agent, alone. Therefore, SA can enhance antifungal activity of commercial antifungal agents required to achieve effective control. SA is a potent antifungal and anti-aflatoxigenic volatile that may have some practical application as a fumigant.

Cytosolic calcium and pH signaling in plants under salinity stress

Calcium is one of the essential nutrients for growth and development of plants. It is an important component of various structures in cell wall and membranes. Besides some fundamental roles under normal condition, calcium functions as a major secondary-messenger molecule in plants under different developmental cues and various stress conditions including salinity stress. Also changes in cytosolic pH, pH(cyt), either individually, or in coordination with changes in cytosolic Ca(2+) concentration, [Ca(2+)](cyt), evoke a wide range of cellular functions in plants including signal transduction in plant-defense responses against stresses. It is believed that salinity stress, like other stresses, is perceived at cell membrane, either extra cellular or intracellular, which then triggers an intracellular-signaling cascade including the generation of secondary messenger molecules like Ca(2+) and protons. The variety and complexity of Ca(2+) and pH signaling result from the nature of the stresses as well as the tolerance level of the plant species against that specific stress. The nature of changes in [Ca(2+)](cyt) concentration, in terms of amplitude, frequency and duration, is likely very important for decoding the specific downstream responses for salinity stress tolerance in planta. It has been observed that the signatures of [Ca(2+)](cyt) and pH differ in various studies reported so far depending on the techniques used to measure them, and also depending on the plant organs where they are measured, such as root, shoot tissues or cells. This review describes the recent advances about the changes in [Ca(2+)](cyt) and pH(cyt) at both cellular and whole-plant levels under salinity stress condition, and in various salinity-tolerant and -sensitive plant species.

Enhancement of pyruvate productivity by inducible expression of a F(0)F(1)-ATPase inhibitor INH1 in Torulopsis glabrata CCTCC M202019

The aim of this study is to establish a controllable intracellular ATP content regulation system applied to the enhancement of pyruvate production in Torulopsis glabrata. The INH1 gene, which encodes a F(0)F(1)-ATPase inhibitor from Saccharomyces cerevisiae, was expressed under a copper ion inducible promoter in the pyruvate producer Torulopsis glabrata CCTCC M202019. The resultant strain was designated as T. glabrata INH1. The induction efficiency was measured by the inducible expression of an enhanced green fluorescence protein. The copper inducible INH1 gene could control the intracellular ATP content (24 h) in an extensive range between 0.192 mmol/mg protein and 0.642 mmol/mg protein in a flask culture. With T. glabrataINH1, induction with 30 microM of Cu(2+) at 12 h in a 3 L fermentor improved pyruvate yield from glucose on biomass by 29% and its yield by 20%, respectively.

ATP in current biotechnology: regulation, applications and perspectives

Adenosine tri-phosphate (ATP), the most important energy source for metabolic reactions and pathways, plays a vital role in the growth of industrial strain and the production of target metabolites. In this review, current advances in manipulating ATP in industrial strains, including altering NADH availability, and regulating NADH oxidation pathway, oxygen supply, proton gradient, the electron transfer chain activity and the F(0)F(1)-ATPase activity, are summarized and discussed. By applying these strategies, optimal product concentrations, yields and productivity in industrial biotechnology have been achieved. Furthermore, the mechanisms by which ATP extends the substrate utilization spectra and enhances the ability to challenge harsh environmental stress have been elucidated. Finally, three critical issues related to ATP manipulation have been addressed.

The long physiological reach of the yeast vacuolar H+-ATPase

V-ATPases are structurally conserved and functionally versatile proton pumps found in all eukaryotes. The yeast V-ATPase has emerged as a major model system, in part because yeast mutants lacking V-ATPase subunits (vma mutants) are viable and exhibit a distinctive Vma- phenotype. Yeast vma mutants are present in ordered collections of all non-essential yeast deletion mutants, and a number of additional phenotypes of these mutants have emerged in recent years from genomic screens. This review summarizes the many phenotypes that have been associated with vma mutants through genomic screening. The results suggest that V-ATPase activity is important for an unexpectedly wide range of cellular processes. For example, vma mutants are hypersensitive to multiple forms of oxidative stress, suggesting an antioxidant role for the V-ATPase. Consistent with such a role, vma mutants display oxidative protein damage and elevated levels of reactive oxygen species, even in the absence of an exogenous oxidant. This endogenous oxidative stress does not originate at the electron transport chain, and may be extra-mitochondrial, perhaps linked to defective metal ion homeostasis in the absence of a functional V-ATPase. Taken together, genomic data indicate that the physiological reach of the V-ATPase is much longer than anticipated. Further biochemical and genetic dissection is necessary to distinguish those physiological effects arising directly from the enzyme's core functions in proton pumping and organelle acidification from those that reflect broader requirements for cellular pH homeostasis or alternative functions of V-ATPase subunits.

Proteome analysis of leaves from the resurrection plant Boea hygrometrica in response to dehydration and rehydration

Resurrection plants differ from other species in their unique ability to survive desiccation. In order to understand the mechanisms of desiccation tolerance, proteome studies were carried out using leaves of the resurrection plant Boea hygrometrica to reveal proteins that were differentially expressed in response to changes in relative water content. This opportunity was afforded by the rare ability of excised B. hygrometrica leaves to survive and resume metabolism following desiccation in a manner similar to intact plants. From a total of 223 proteins that were reproducibly detected and analyzed, 35% showed increased abundance in dehydrated leaves, 5% were induced in rehydrated leaves and 60% showed decreased or unchanged abundance in dehydrated and rehydrated leaves. Since the induction kinetics fall into clearly defined patterns, we suggest that programmed regulation of protein expression triggered by changes of water status. Fourteen dehydration responsive proteins were analyzed by mass spectrometry. Eight proteins were classified as playing a role in reactive oxygen species scavenging, photosynthesis and energy metabolism. In agreement with these findings, glutathione content and polyphenol oxidase activity were found to increase upon dehydration and rapid recovery of photosynthesis was observed.

Identification and classification of genes required for tolerance to high-sucrose stress revealed by genome-wide screening of Saccharomyces cerevisiae

Yeasts used in bread making are exposed to high concentrations of sucrose during sweet dough fermentation. Despite its importance, tolerance to high-sucrose stress is poorly understood at the gene level. To clarify the genes required for tolerance to high-sucrose stress, genome-wide screening was undertaken using the complete deletion strain collection of diploid Saccharomyces cerevisiae. The screening identified 273 deletions that yielded high sucrose sensitivity, approximately 20 of which were previously uncharacterized. These 273 deleted genes were classified based on their cellular function and localization of their gene products. Cross-sensitivity of the high-sucrose-sensitive mutants to high concentrations of NaCl and sorbitol was studied. Among the 273 sucrose-sensitive deletion mutants, 269 showed cross-sensitivities to sorbitol or NaCl, and four (i.e. ade5,7, ade6, ade8, and pde2) were specifically sensitive to high sucrose. The general stress response pathways via high-osmolarity glycerol and stress response element pathways and the function of the invertase in the ade mutants were similar to those in the wild-type strain. In the presence of high-sucrose stress, intracellular contents of ATP in ade mutants were at least twofold lower than that of the wild-type cells, suggesting that depletion of ATP is a factor in sensitivity to high-sucrose stress. The genes identified in this study might be important for tolerance to high-sucrose stress, and therefore should be target genes in future research into molecular modification for breeding of yeast tolerant to high-sucrose stress.

Controlling food-contaminating fungi by targeting their antioxidative stress-response system with natural phenolic compounds

The antioxidative stress-response system is essential to fungi for tolerating exposure to phenolic compounds. We show how this system can be targeted to improve fungal control by using compounds that inhibit the fungal mitochondrial respiratory chain. Targeting mitochondrial superoxide dismutase with selected phenolic acid derivatives (e.g., vanillyl acetone) resulted in a 100- to 1,000-fold greater sensitivity to strobilurin or carboxin fungicides. This synergism is significantly greater with strobilurin than with carboxin, suggesting that complex III of the mitochondrial respiratory chain is a better target than complex II for fungal control, using phenolics. These results show certain natural compounds are effective synergists to commercial fungicides and can be used for improving control of food-contaminating pathogens. These results suggest that the use of such compounds for fungal control can reduce environmental and health risks associated with commercial fungicides, lower cost for control, and the probability for development of resistance.

Uptake of sodium in protoplasts of salt-sensitive and salt-tolerant cultivars of rice, Oryza sativa L. determined by the fluorescent dye SBFI

In this study, the uptake of Na+ into the cytosol of rice (Oryza sativa L. cvs Pokkali and BRRI Dhan29) protoplasts was measured using the acetoxy methyl ester of the fluorescent sodium-binding benzofuran isopthalate, SBFI-AM, and fluorescence microscopy. By means of inhibitor analyses the mechanisms for uptake and sequestration of Na+ in the salt-sensitive indica rice cv. BRRI Dhan29 and in the salt-tolerant indica rice cv. Pokkali were detected. Less Na+ was taken up into the cytosol of Pokkali than into BRRI Dhan29. The results indicate that K+-selective channels do not contribute to the Na+ uptake in Pokkali, whereas they are the major pathways for Na+ uptake in BRRI Dhan29 along with non-selective cation channels. However, non-selective cation channels seem to be the main pathways for Na+ uptake in Pokkali. Protoplasts from Pokkali leaves took up Na+ only transiently in the presence of extracellular Na+ at 5-100 mM. Therefore, it is likely that the protoplasts have a mechanism for fast extrusion of Na+ out of the cytoplasm. Experiments with protoplasts pretreated with NH4NO3 and NH4VO3 suggest that the salt-tolerant Pokkali extrudes Na+ mainly into the vacuole. After cultivation of both cultivars in the presence of 10 or 50 mM NaCl for 72 h, the isolated protoplasts from Pokkali took up less Na+ than the control protoplasts. The results suggest that the salt-tolerance in Pokkali depends on reduced uptake through K+-selective channels and a fast extrusion of Na+ into the vacuoles.