Boron stress activates the general amino acid control mechanism and inhibits protein synthesis

Bayesian Optimized sample-specific Networks Obtained By Omics data (BONOBO)

Gene regulatory networks (GRNs) are effective tools for inferring complex interactions between molecules that regulate biological processes and hence can provide insights into drivers of biological systems. Inferring co-expression networks is a critical element of GRN inference as the correlation between expression patterns may indicate that genes are coregulated by common factors. However, methods that estimate co-expression networks generally derive an aggregate network representing the mean regulatory properties of the population and so fail to fully capture population heterogeneity. To address these concerns, we introduce BONOBO (Bayesian Optimized Networks Obtained By assimilating Omics data), a scalable Bayesian model for deriving individual sample-specific co-expression networks by recognizing variations in molecular interactions across individuals. For every sample, BONOBO assumes a Gaussian distribution on the log-transformed centered gene expression and a conjugate prior distribution on the sample-specific co-expression matrix constructed from all other samples in the data. Combining the sample-specific gene expression with the prior distribution, BONOBO yields a closed-form solution for the posterior distribution of the sample-specific co-expression matrices, thus making the method extremely scalable. We demonstrate the utility of BONOBO in several contexts, including analyzing gene regulation in yeast transcription factor knockout studies, prognostic significance of miRNA-mRNA interaction in human breast cancer subtypes, and sex differences in gene regulation within human thyroid tissue. We find that BONOBO outperforms other sample-specific co-expression network inference methods and provides insight into individual differences in the drivers of biological processes.

Proteomic Analysis of Rat Duodenum Reveals the Modulatory Effect of Boron Supplementation on Immune Activity

The proper supplementation of boron, an essential trace element, can enhance animal immune function. We utilized the method of TMT peptide labeling in conjunction with LC-MS/MS quantitative proteomics for the purpose of examining the effects of boric acid on a rat model and analyzing proteins from the duodenum. In total, 5594 proteins were obtained from the 0, 10, and 320 mg/L boron treatment groups. Two hundred eighty-four proteins that exhibit differential expression were detected. Among the comparison, groups of 0 vs. 10 mg/L, 0 vs. 320 mg/L, and 10 vs. 320 mg/L of boron, 110, 32, and 179 proteins, respectively, demonstrated differential expression. The results revealed that these differential expression proteins (DEPs) mainly clustered into two profiles. GO annotations suggested that most of the DEPs played a role in the immune system process, in which 2'-5'-oligoadenylate synthetase-like, myxovirus resistance 1, myxovirus resistance 2, dynein cytoplasmic 1 intermediate chain 1, and coiled-coil domain containing 88B showed differential expression. The DEPs had demonstrated an augmentation in the signaling pathways, which primarily include phagosome, antigen processing, and presentation, as well as cell adhesion molecules (CAMs). Our study found that immune responses in the duodenum were enhanced by lower doses of boron and that this effect is likely mediated by changes in protein expression patterns in related signaling pathways. It offers an in-depth understanding of the underlying molecular mechanisms that lead to immune modulation in rats subjected to dietary boron treatment.

Boron stress signal is transmitted through the TOR pathway

Although boron is an essential element for many organisms, an excess amount of it can cause toxicity, and the mechanism behind this toxicity is not yet fully understood. The Gcn4 transcription factor plays a crucial role in the boron stress response by directly activating the expression of the boron efflux pump Atr1. More than a dozen transcription factors and multiple cell signaling pathways have roles in regulating the Gcn4 transcription factor under various circumstances. However, it is unknown which pathways or factors mediate boron signaling to Gcn4. Using the yeast Saccharomyces cerevisiae as a model, we analyzed the factors that converge on the Gcn4 transcription factor to assess their possible roles in boron stress signaling. Our findings show that the GCN system is activated by uncharged tRNA stress in response to boron treatment and that GCN1, which plays a role in transferring uncharged tRNAs to Gcn2, is necessary for the kinase activity of Gcn2. The SNF and PKA pathways were not involved in mediating boron stress, even though they interact with Gcn4. Mutations in TOR pathway genes, such as GLN3 and TOR1, abolished Gcn4 and ATR1 activation in response to boric acid treatment. Therefore, our study suggests that the TOR pathway must be functional to form a proper response against boric acid stress.

Interaction between selenium and essential micronutrient elements in plants: A systematic review

Nutrient imbalance (i.e., deficiency and toxicity) of microelements is an outstanding environmental issue that influences each aspect of ecosystems. Although the crucial roles of microelements in entire lifecycle of plants have been widely acknowledged, the effective control of microelements is still neglected due to the narrow safe margins. Selenium (Se) is an essential element for humans and animals. Although it is not believed to be indispensable for plants, many literatures have reported the significance of Se in terms of the uptake, accumulation, and detoxification of essential microelements in plants. However, most papers only concerned on the antagonistic effect of Se on metal elements in plants and ignored the underlying mechanisms. There is still a lack of systematic review articles to summarize the comprehensive knowledge on the connections between Se and microelements in plants. In this review, we conclude the bidirectional effects of Se on micronutrients in plants, including iron, zinc, copper, manganese, nickel, molybdenum, sodium, chlorine, and boron. The regulatory mechanisms of Se on these micronutrients are also analyzed. Moreover, we further emphasize the role of Se in alleviating element toxicity and adjusting the concentration of micronutrients in plants by altering the soil conditions (e.g., adsorption, pH, and organic matter), promoting microbial activity, participating in vital physiological and metabolic processes, generating element competition, stimulating metal chelation, organelle compartmentalization, and sequestration, improving the antioxidant defense system, and controlling related genes involved in transportation and tolerance. Based on the current understanding of the interaction between Se and these essential elements, future directions for research are suggested.

Transcriptome Profiling of Duodenum Reveals the Importance of Boron Supplementation in Modulating Immune Activities in Rats

As an essential trace element, appropriate boron supplementation can promote immune function of animals. To illustrate the effects of boron in a rat model, RNA-Seq was conducted for the RNA from duodenum after treatment with different concentration of boron in which boron was given in the form of boric acid. More than 47 million reads were obtained in 0, 10, and 320 mg/L boron (0, 57.21, and 1830.66 mg/L boric acid) treatment groups that produced 58 965 402, 48 607 328, and 46 760 660 clean reads, respectively. More than 95% of the clean reads were successfully matched to the rat reference genome and assembled to generate 32 662 transcripts. A total of 624 and 391 differentially expressed candidate genes (DEGs) were found between 0 vs.10 and 0 vs. 320 mg/L boron comparison groups. We also identified transcription start site, transcription terminal site, and skipped exons as the main alternative splicing events. GO annotations revealed most of DEGs were involved in the regulation of immune activity. The DEGs were enriched in influenza A, herpes simplex infection, cytosolic DNA-sensing pathway, and antigen processing and presentation signaling pathways. The expression levels of genes enriched in these signaling pathways indicate that lower doses of boron could achieve better effects on promoting immune response in the duodenum. These effects on the immune system appear to be mediated via altering the expression patterns of genes involved in the related signaling pathways in a dose-dependent pattern. These data provide more insights into the molecular mechanisms of immune regulation in rats in response to dietary boron treatment.

A systematic genome-wide account of binding sites for the model transcription factor Gcn4

Sequence-specific DNA-binding transcription factors are central to gene regulation. They are often associated with consensus binding sites that predict far more genomic sites than are bound in vivo. One explanation is that most sites are blocked by nucleosomes, such that only sites in nucleosome-depleted regulatory regions are bound. We compared the binding of the yeast transcription factor Gcn4 in vivo using published ChIP-seq data (546 sites) and in vitro, using a modified SELEX method (“G-SELEX”), which utilizes short genomic DNA fragments to quantify binding at all sites. We confirm that Gcn4 binds strongly to an AP-1-like sequence (TGACTCA) and weakly to half-sites. However, Gcn4 binds only some of the 1078 exact matches to this sequence, even in vitro. We show that there are only 166 copies of the high-affinity RTGACTCAY site (exact match) in the yeast genome, all occupied in vivo, largely independently of whether they are located in nucleosome-depleted or nucleosomal regions. Generally, RTGACTCAR/YTGACTCAY sites are bound much more weakly and YTGACTCAR sites are unbound, with biological implications for determining induction levels. We conclude that, to a first approximation, Gcn4 binding can be predicted using the high-affinity site, without reference to chromatin structure. We propose that transcription factor binding sites should be defined more precisely using quantitative data, allowing more accurate genome-wide prediction of binding sites and greater insight into gene regulation.

Global analysis of boron-induced ribosome stalling reveals its effects on translation termination and unique regulation by AUG-stops in Arabidopsis shoots

We previously reported that ribosome stalling at AUG-stop sequences in the 5'-untranslated region plays a critical role in regulating the expression of Arabidopsis thaliana NIP5;1, which encodes a boron uptake transporter, in response to boron conditions in media. This ribosome stalling is triggered specifically by boric acid, but the mechanisms are unknown. Although upstream open reading frames (uORFs) are known in many cases to regulate translation through peptides encoded by the uORF, AUG-stop stalling does not involve any peptide synthesis. The unique feature of AUG-stops - that termination follows immediately after initiation - suggests a possible effect of boron on the translational process itself. However, the generality of AUG-stop-mediated translational regulation and the effect of boron on translation at the genome scale are not clear. Here, we conducted a ribosome profiling analysis to reveal the genome-wide regulation of translation in response to boron conditions in A. thaliana shoots. We identified hundreds of translationally regulated genes that function in various biological processes. Under high-boron conditions, transcripts with reduced translation efficiency were rich in uORFs, highlighting the importance of uORF-mediated translational regulation. We found 673 uORFs that had more frequent ribosome association. Moreover, transcripts that were translationally downregulated under high-boron conditions were rich in minimum uORFs (AUG-stops), suggesting that AUG-stops play a global role in the boron response. Metagene analysis revealed that boron increased the ribosome occupancy of stop codons, indicating that this element is involved in global translational termination processes.

Cross species multi-omics reveals cell wall sequestration and elevated global transcript abundance as mechanisms of boron tolerance in plants

Boron toxicity is a world-wide problem for crops, yet we have a limited understanding of the genetic responses and adaptive mechanisms to this stress in plants. We employed a cross-species comparison between boron stress-sensitive Arabidopsis thaliana and its boron stress-tolerant extremophyte relative Schrenkiella parvula, and a multi-omics approach integrating genomics, transcriptomics, metabolomics and ionomics to assess plant responses and adaptations to boron stress. Schrenkiella parvula maintains lower concentrations of total boron and free boric acid than Arabidopsis when grown with excess boron. Schrenkiella parvula excludes excess boron more efficiently than Arabidopsis, which we propose is partly driven by SpBOR5, a boron transporter that we functionally characterize in this study. Both species use cell walls as a partial sink for excess boron. When accumulated in the cytoplasm, excess boron appears to interrupt RNA metabolism. The extremophyte S. parvula facilitates critical cellular processes while maintaining the pool of ribose-containing compounds that can bind with boric acid. The S. parvula transcriptome is pre-adapted to boron toxicity. It exhibits substantial overlaps with the Arabidopsis boron-stress responsive transcriptome. Cell wall sequestration and increases in global transcript levels under excess boron conditions emerge as key mechanisms for sustaining plant growth under boron toxicity.

Ion Release From Prototype Surface Pre-Reacted Glass Ionomer (S-PRG) Sealer and EndoSequence BC Sealer

OBJECTIVE

Bioactive ions, when incorporated in an endodontic sealer, can contribute to the long-term success of endodontic therapy by combating the re-infection of a tooth and promoting the healing of the periapical bone. The objective of this study was to measure the release of boron, strontium, and silicon ions from surface pre-reacted glass ionomer (S-PRG) filler containing prototype endodontic sealer over a sustained period in comparison to EndoSequence BC sealer in a simulated clinical model using extracted human teeth in vitro.

METHODS

Twelve extracted human anterior teeth were instrumented using ProTaper Next (Dentsply Sirona, Johnson City, TN, USA) files up to size X3 (#30/variable taper) with copious 2.5% NaOCl irrigation. Teeth were obturated using a single-cone technique with a matching size tapered gutta-percha point and one of two endodontic sealers: prototype S-PRG (Shofu Inc., Kyoto, Japan) or EndoSequence BC (Brasseler, Savannah, GA, USA). The teeth were soaked in phosphate-buffered saline (PBS) solution for 336 hours. Periodically, 1-mL samples of the PBS were analyzed via an inductively coupled plasma mass spectrometer to determine the concentrations of ions released by the sealers.

RESULTS

The average (S.D.) cumulative release (ng/ml) of boron, silicon, and strontium ions over 2 weeks for the prototype S-PRG sealer was 8614.9 (1264.3), 35758.9 (5986.5), and 3965.2 (145.6), and for EndoSequence BC sealer was 1860.5 (82.7), 164648.7 (16468.1), and 227.7 (4.7). Generalized linear mixed model analysis showed significant differences in ion concentration among boron, silicon, and strontium over time between the two sealer groups (Boron: P<0.0001, Silicon: P=0.010, Strontium: P=0.028). Of the three ions, strontium had the lowest amount of release for both sealers. The prototype S-PRG sealer showed a rapid initial burst followed by a slow, continuous release of strontium ions.

CONCLUSION

The prototype S-PRG sealer released boron and strontium ions in higher cumulative concentrations over 2 weeks compared to the EndoSequence BC sealer. Both the prototype S-PRG and EndoSequence BC sealers released silicon ions, although significantly more were eluted from the EndoSequence BC sealer. Antimicrobial and osteogenic ion release from sealers is expected to positively influence the post-treatment control of microbial infections to improve periapical healing.

Boron-dependent regulation of translation through AUGUAA sequence in yeast

Under high boron (B) conditions, nodulin 26-like intrinsic protein 5;1 (NIP5;1) mRNA, a boric acid channel, is destabilized to avoid excess B entry into roots of Arabidopsis thaliana. In this regulation, the minimum upstream open reading frame (uORF), AUGUAA, in its 5'-untranslated region (5'-UTR) is essential, and high B enhances ribosome stalling at AUGUAA and leads to suppression of translation and mRNA degradation. This B-dependent AUGUAA-mediated regulation occurs also in animal transient expression and reticulocyte lysate translation systems. Thus, uncovering the ubiquitousness of B-dependent unique regulation is important to reveal the evolution of translational regulation. In the present study, we examined the regulation in Saccharomyces cerevisiae. Reporter assay showed that in yeast, carrying ATGTAA in 5'-UTR of NIP5;1 upstream of the reporter gene, the relative reporter activities were reduced significantly under high B conditions compared with control, whereas deletion of ATGTAA abolished such responses. This suggests that AUGUAA mediates B-dependent regulation of translation in Saccharomyces cerevisiae. Moreover, the deletion of ATGTAA resulted in up to 10-fold increase in general reporter activities indicating the suppression effect of AUGUAA on translation of the main ORF. Interestingly, mRNA level of the reporter gene was not affected by B in both yeast cells with and without AUGUAA. This finding reveals that in yeast, unlike the case in plants, mRNA degradation is not associated with AUGUAA regulation. Together, results suggest that B-dependent AUGUAA-mediated translational regulation is common among eukaryotes.

In vitro effects of boric acid on human liver hepatoma cell line (HepG2) at the half-maximal inhibitory concentration

BACKGROUND

Boron is a prominent part of the human diet and one of the essential trace elements for humans. Dietary boron is mostly transformed into boric acid within the body and has been associated with desirable health outcomes. Non-dietary resources of boron, such as boron-based drugs and occupational exposure, might lead to excessive boron levels in the blood and provoke health adversities. The liver might be particularly sensitive to boron intake with ample evidence suggesting a relation between boron and liver function, although the underlying molecular processes remain largely unknown.

METHODS

In order to better understand boron-related metabolism and molecular mechanisms associated with a cytotoxic level of boric acid, the half-maximal inhibitory concentration (IC₅₀) of boric acid for the hepatoma cell line (HepG2) was determined using the XTT assay. Cellular responses followed by boric acid treatment at this concentration were investigated using genotoxicity assays and microarray hybridizations. Enrichment analyses were carried out to find out over-represented biological processes using the list of differentially expressed genes identified within the gene expression analysis.

RESULTS

DNA breaks were detected in HepG2 cells treated with 24 mM boric acid, the estimated IC₅₀-level of boric acid. On the other hand, pleiotropic transcriptomic effects, including cell cycle arrest, DNA repair, and apoptosis as well as altered expression of Phase I and Phase II enzymes, amino acid metabolism, and lipid metabolism were discerned in microarray analyses.

CONCLUSION

HepG2 cells treated with a growth-inhibitory concentration of boric acid for 24 h exhibited a senescence-like transcriptomic profile along with DNA damage. Further studies might help in understanding the concentration-dependent effects and mechanisms of boric acid.

Antioxidant or pro-oxidant? The effects of boron compounds on Saccharomyces cerevisiae BY4741 strain

Boron is one of the most important elements with its indisputable biological importance and widespread use. The most studied derivatives of the boron element are boric acid and its salts. In this article, we searched the effects of boric acid and its lithium salt, lithium metaborate, on enzymatic defense system, cell damage, and cell surface morphology of Saccharomyces cerevisiae BY4741 strain. It was found that while all studied concentrations of boric acid showed toxicity against the yeast, even the highest studied concentration of lithium metaborate could not effectively inhibit cell viability. In addition, we observed reverse effect of lithium metaborate depend on its concentration on yeast cell proliferation and metabolic activity. As a defense mechanism, superoxide dismutase and glutathione S-transferase activities were significantly induced in yeast cells treated with boric acid. But these inductions could not protect cells from boric acid induced lipid peroxidation. It was determined that glutathione S-transferase was the only enzyme induced after lithium metaborate treatment. Finally, we visualized the signs of features of necrotic and early apoptotic mechanisms in yeast cells treated with boric acid and lithium metaborate, respectively, which should be investigated with further studies.

Biolog Phenotype Microarray Is a Tool for the Identification of Multidrug Resistance Efflux Pump Inducers

Multidrug resistance efflux pumps frequently present low levels of basal expression. However, antibiotic-resistant mutants that overexpress these resistance determinants are selected during infection. In addition, increased expression of efflux pumps can be induced by environmental signals/cues, which can lead to situations of transient antibiotic resistance. In this study, we have applied a novel high-throughput methodology in order to identify inducers able to trigger the expression of the Stenotrophomonas maltophilia SmeVWX and SmeYZ efflux pumps. To that end, bioreporters in which the expression of the yellow fluorescent protein (YFP) is linked to the activity of either smeVWX or smeYZ promoters were developed and used for the screening of potential inducers of the expression of these efflux pumps using Biolog phenotype microarrays. YFP production was also measured by flow cytometry, and the levels of expression of smeV and smeY in the presence of a set of selected compounds were also determined by real-time reverse transcription-PCR (RT-PCR). The expression of smeVWX was induced by iodoacetate, clioquinol, and selenite, while boric acid, erythromycin, chloramphenicol, and lincomycin triggered smeYZ expression. The susceptibility to antibiotics that are known substrates of the efflux pumps decreased in the presence of the inducers. However, the analyzed multidrug efflux systems did not contribute to S. maltophilia resistance to the studied inducers. To sum up, the use of fluorescent bioreporters in combination with Biolog plates is a valuable tool for identifying inducers of the expression of bacterial multidrug resistance efflux pumps, and likely of other bacterial systems whose expression is regulated in response to signals/cues.

Influence of boric acid on energy metabolism and stress tolerance of Candida albicans

Boron presents at physiological pH in the form of boric acid (BA), a molecule that has both positive and negative effects on biological processes. In medicine, BA is used as a topical treatment for vaginal yeast infections by Candida species because of its well-documented but poorly understood effect on inhibition of growth in general and of invasive, hyphal growth in particular. The present study examines the influence of BA on carbohydrate energy metabolism of this common human pathogen. Starting from previous findings about an inhibition of key NAD-dependent enzymes by BA in vitro, we confirmed that such an inhibition occurs in permeabilized C. albicans cells. Cultures growing even with moderate concentrations of BA experience mitochondrial failure, increase ethanol production from glucose and decrease the deposition of carbohydrate stores in the form of glycogen. Cells growing on the non-fermentable, FAD-generating carbon source lactate have a higher BA tolerance, which suggests that the toxicity of BA is rooted in an inhibition of NAD-dependent reactions and the increased production of ethanol. Boric acid exposure sensitizes C. albicans selectively to the toxic effects of ethanol. This additive effect suggests that the endogenously produced ethanol increases the load on ethanol resistance mechanisms. Lastly, combination studies showed no interactions of BA with common antifungal drugs, meaning that addition of BA to topical formulations can provide an additive antifungal effect regardless of the chosen active ingredient.

Boron-Dependent Translational Suppression of the Borate Exporter BOR1 Contributes to the Avoidance of Boron Toxicity

Boron (B) is an essential element for plants; however, as high B concentrations are toxic, B transport must be tightly regulated. BOR1 is a borate exporter in Arabidopsis (Arabidopsis thaliana) that facilitates B translocation into shoots under B deficiency conditions. When the B supply is sufficient, BOR1 expression is down-regulated by selective degradation of BOR1 protein, while additional BOR1 regulatory mechanisms are proposed to exist. In this study, we identified a novel B-dependent BOR1 translational suppression mechanism. In vivo and in vitro reporter assays demonstrated that BOR1 translation was reduced in a B-dependent manner and that the 5'-untranslated region was both necessary and sufficient for this process. Mutational analysis revealed that multiple upstream open reading frames in the 5'-untranslated region were required for BOR1 translational suppression, and this process depended on the efficiency of translational reinitiation at the BOR1 open reading frame after translation of the upstream open reading frames. To understand the physiological significance of BOR1 regulation, we characterized transgenic plants defective in either one or both of the BOR1 regulation mechanisms. BOR1 translational suppression was induced at higher B concentrations than those triggering BOR1 degradation. Plants lacking both regulation mechanisms exhibited more severe shoot growth reduction under high-B conditions than did plants lacking BOR1 degradation alone, thus demonstrating the importance of BOR1 translational suppression. This study demonstrates that two mechanisms of posttranscriptional BOR1 regulation, each induced under different B concentrations, contribute to the avoidance of B toxicity in plants.

Arabidopsis nonresponding to oxylipins locus NOXY7 encodes a yeast GCN1 homolog that mediates noncanonical translation regulation and stress adaptation

Stress adaptation and translational regulation was studied using noxy7 (nonresponding to oxylipins7) from a series of Arabidopsis thaliana mutants. We identified the noxy7 mutation in At1g64790, which encodes a homolog of the yeast translational regulator General Control Nonderepressible1 (GCN1) that activates the GCN2 kinase; GCN2 in turn phosphorylates the α subunit of the translation initiation factor eIF2. This regulatory circuit is conserved in yeast and mammals, in which phosphorylated eIF2α (P-eIF2α) facilitates stress adaptation by inhibiting protein synthesis. In phenotypic and de novo protein synthesis studies with Arabidopsis mutants, we found that NOXY7/GCN1 and GCN2 mediate P-eIF2α formation and adaptation to amino acid deprivation; however, P-eIF2α formation is not linked to general protein synthesis arrest. Additional evidence suggested that NOXY7/GCN1 but not GCN2 regulates adaptation to mitochondrial dysfunction, high boron concentration, and activation of plant immunity to infection by Pseudomonas syringae pv tomato (Pst). In these responses, NOXY7/GCN1 acts with GCN20 to regulate translation in a noncanonical pathway independently of GCN2 and P-eIF2α. These results show the lesser functional relevance of GCN2 and P-eIF2α in plants relative to other eukaryotes and highlight the prominent role of NOXY7/GCN1 and GCN20 in regulation of translation and stress adaptation in plants.

The importance of boron in biological systems

Boron is an essential element for plants and probably essential for human and animal health. Boron has a broad range of physiological effects on biological systems at low concentrations, whereas it is toxic to at high concentrations. Eventhough there are many studies on boron's biological effects and toxicity, more information is needed to understand the mechanisms of its action. The aim of the current work is to review boron's function, transport and toxicity in different biological systems.

Boron Tolerance in Aspergillus nidulans Is Sustained by the SltA Pathway Through the SLC-Family Transporters SbtA and SbtB

Microbial cells interact with the environment by adapting to external changes. Signal transduction pathways participate in both sensing and responding in the form of modification of gene expression patterns, enabling cell survival. The filamentous fungal-specific SltA pathway regulates tolerance to alkalinity, elevated cation concentrations and, as shown in this work, also stress conditions induced by borates. Growth of sltA⁻ mutants is inhibited by increasing millimolar concentrations of boric acid or borax (sodium tetraborate). In an attempt to identify genes required for boron-stress response, we determined the boric acid or borax-dependent expression of sbtA and sbtB, orthologs of Saccharomyces cerevisiae bor1, and a reduction in their transcript levels in a ΔsltA mutant. Deletion of sbtA, but mainly that of sbtB, decreased the tolerance to boric acid or borax. In contrast, null mutants of genes coding for additional transporters of the Solute Carrier (SLC) family, sB, sbtD or sbtE, showed an unaltered growth pattern under the same stress conditions. Taken together, our results suggest that the SltA pathway induces, through SbtA and SbtB, the export of toxic concentrations of borates, which have largely recognized antimicrobial properties.

Activation of the EIF2α/ATF4 and ATF6 Pathways in DU-145 Cells by Boric Acid at the Concentration Reported in Men at the US Mean Boron Intake

Fruits, nuts, legumes, and vegetables are rich sources of boron (B), an essential plant nutrient with chemopreventive properties. Blood boric acid (BA) levels reflect recent B intake, and men at the US mean intake have a reported non-fasting level of 10 μM. Treatment of DU-145 prostate cancer cells with physiological concentrations of BA inhibits cell proliferation without causing apoptosis and activates eukaryotic initiation factor 2 (eIF2α). EIF2α induces cell differentiation and protects cells by redirecting gene expression to manage endoplasmic reticulum stress. Our objective was to determine the temporal expression of endoplasmic reticulum (ER) stress-activated genes in DU-145 prostate cells treated with 10 μM BA. Immunoblots showed post-treatment increases in eIF2α protein at 30 min and ATF4 and ATF6 proteins at 1 h and 30 min, respectively. The increase in ATF4 was accompanied by an increase in the expression of its downstream genes growth arrest and DNA damage-induced protein 34 (GADD34) and homocysteine-induced ER protein (Herp), but a decrease in GADD153/CCAAT/enhancer-binding protein homologous protein (CHOP), a pro-apoptotic gene. The increase in ATF6 was accompanied by an increase in expression of its downstream genes GRP78/BiP, calreticulin, Grp94, and EDEM. BA did not activate IRE1 or induce cleavage of XBP1 mRNA, a target of IRE1. Low boron status has been associated with increased cancer risk, low bone mineralization, and retinal degeneration. ATF4 and BiP/GRP78 function in osteogenesis and bone remodeling, calreticulin is required for tumor suppressor p53 function and mineralization of teeth, and BiP/GRP78 and EDEM prevent the aggregation of misfolded opsins which leads to retinal degeneration. The identification of BA-activated genes that regulate its phenotypic effects provides a molecular underpinning for boron nutrition and biology.

Biological effects of tolerable level chronic boron intake on transcription factors

The mechanism of boron effect on human transcription and translation has not been fully understood. In the current study it was aimed to reveal the role of boron on the expression of certain transcription factors that play key roles in many cellular pathways on human subjects chronically exposed to low amounts of boron. The boron concentrations in drinking water samples were 1.57±0.06mg/l for boron group while the corresponding value for the control group was 0.016±0.002mg/l. RNA isolation was performed using PAX gene RNA kit on the blood samples from the subjects. The RNA was then reverse transcribed into cDNA and analyzed using the Human Transcription Factors RT² Profiler™ PCR Arrays. While the boron amount in urine was detected as 3.56±1.47mg/day in the boron group, it was 0.72±0.30mg/day in the control group. Daily boron intake of the boron and control groups were calculated to be 6.98±3.39 and 1.18±0.41mg/day, respectively. The expression levels of the transcription factor genes were compared between the boron and control groups and no statistically significant difference was detected (P>0.05). The data suggest that boron intake at 6.98±3.39mg/day, which is the dose at which beneficial effects might be seen, does not result in toxicity at molecular level since the expression levels of transcription factors are not changed. Although boron intake over this level will seem to increase RNA synthesis, further examination of the topic is needed using new molecular epidemiological data.

Potential toxicity of improperly discarded exhausted photovoltaic cells

Low tech photovoltaic panels (PVPs) installed in the early '80s are now coming to the end of their life cycle and this raises the problem of their proper disposal. As panels contain potentially toxic elements, unconventional, complex and costly procedures are required to avoid environmental health risks and in countries where environmental awareness and economic resources are limited this may be especially problematic. This work was designed to investigate potential risks from improper disposal of these panels. To accomplish this aim an exhausted panel was broken into pieces and these were placed in water for 30 days. The resulting leached solution was analyzed to determine chemical release or used in toto, to determine its potential toxicity in established tests. The end points were seed germination (on Cucumis sativus and Lens culinaris) and effects on early development in three larval models: two crustaceans, Daphnia magna and Artemia salina, and the sea urchin Paracentrotus lividus. Our results show that the panels release small amounts of electrolytes (Na, Ca and Mg) into solution, along with antimony and manganese, with a concentration under the accepted maximum contaminant level, and nickel at a potentially toxic concentration. Developmental defects are seen in the plant and animal test organisms after experimental exposure to the whole solution leached from the broken panel. The toxic effects revealed in in vitro tests are sufficient to attract attention considering that they are exerted on both plants and aquatic animals and that the number of old PVPs in disposal sites will be very high.

Boric acid-dependent decrease in regulatory histone H3 acetylation is not mutagenic in yeast

Candida albicans is a dimorphic yeast commonly found on human mucosal membranes that switches from yeast to hyphal morphology in response to environmental factors. The change to hyphal growth requires histone H3 modifications by the yeast-specific histone acetyltransferase Rtt109. In addition to its role in morphogenesis, Rtt109-dependent acetylation of histone H3 lysine residues 9 and 56 has regulatory functions during DNA replication and repair. Boric acid (BA) is a broad-spectrum agent that specifically inhibits C. albicans hyphal growth, locking the fungus in its harmless commensal yeast state. The present study characterizes the effect of BA on C. albicans histone acetylation in respect to specificity, time-course and significance. We demonstrate that sublethal concentrations of BA reduce H3K9/H3K56 acetylation, both on a basal level and in response to genotoxic stress. Acetylation at other selected histone sites were not affected by BA. qRT-PCR expression analysis of the DNA repair gene Rad51 indicated no elevated level of genotoxic stress during BA exposure. A forward-mutation analysis demonstrated the BA does not increase spontaneous or induced mutations. The findings suggest that DNA repair remains effective even when histone H3 acetylation decreases and dispels the notion that BA treatment impairs genome integrity in yeast.

The major facilitator superfamily transporter Knq1p modulates boron homeostasis in Kluyveromyces lactis

Boron is an essential micronutrient for living cells, yet its excess causes toxicity. To date, the mechanisms of boron toxicity are poorly understood. Recently, the ScATR1 gene has been identified encoding the main boron efflux pump in Saccharomyces cerevisiae. In this study, we analyzed the ScATR1 ortholog in Kluyveromyces lactis--the KNQ1 gene, to understand whether it participates in boron stress tolerance. We found that the KNQ1 gene, encoding a permease belonging to the major facilitator superfamily, is required for K. lactis boron tolerance. Deletion of the KNQ1 gene led to boron sensitivity and its overexpression increased K. lactis boron tolerance. The KNQ1 expression was induced by boron and the intracellular boron concentration was controlled by Knq1p. The KNQ1 promoter contains two putative binding motifs for the AP-1-like transcription factor KlYap1p playing a central role in oxidative stress defense. Our results indicate that the induction of the KNQ1 expression requires the presence of KlYap1p and that Knq1p like its ortholog ScAtr1p in S. cerevisiae functions as a boron efflux pump providing boron resistance in K. lactis.

Boric acid induces cytoplasmic stress granule formation, eIF2α phosphorylation, and ATF4 in prostate DU-145 cells

Dietary boron intake is associated with reduced prostate and lung cancer risk and increased bone mass. Boron is absorbed and circulated as boric acid (BA) and at physiological concentrations is a reversible competitive inhibitor of cyclic ADP ribose, the endogenous agonist of the ryanodine receptor calcium (Ca⁺²) channel, and lowers endoplasmic reticulum (ER) [Ca²⁺]. Low ER [Ca²⁺] has been reported to induce ER stress and activate the eIF2α/ATF4 pathway. Here we report that treatment of DU-145 prostate cells with physiological levels of BA induces ER stress with the formation of stress granules and mild activation of eIF2α, GRP78/BiP, and ATF4. Mild activation of eIF2α and its downstream transcription factor, ATF4, enables cells to reconfigure gene expression to manage stress conditions and mild activation of ATF4 is also required for the differentiation of osteoblast cells. Our results using physiological levels of boric acid identify the eIF2α/ATF pathway as a plausible mode of action that underpins the reported health effects of dietary boron.

cDNA-AFLP analysis reveals the adaptive responses of citrus to long-term boron-toxicity

BACKGROUND

Boron (B)-toxicity is an important disorder in agricultural regions across the world. Seedlings of 'Sour pummelo' (Citrus grandis) and 'Xuegan' (Citrus sinensis) were fertigated every other day until drip with 10 μM (control) or 400 μM (B-toxic) H3BO3 in a complete nutrient solution for 15 weeks. The aims of this study were to elucidate the adaptive mechanisms of citrus plants to B-toxicity and to identify B-tolerant genes.

RESULTS

B-toxicity-induced changes in seedlings growth, leaf CO2 assimilation, pigments, total soluble protein, malondialdehyde (MDA) and phosphorus were less pronounced in C. sinensis than in C. grandis. B concentration was higher in B-toxic C. sinensis leaves than in B-toxic C. grandis ones. Here we successfully used cDNA-AFLP to isolate 67 up-regulated and 65 down-regulated transcript-derived fragments (TDFs) from B-toxic C. grandis leaves, whilst only 31 up-regulated and 37 down-regulated TDFs from B-toxic C. sinensis ones, demonstrating that gene expression is less affected in B-toxic C. sinensis leaves than in B-toxic C. grandis ones. These differentially expressed TDFs were related to signal transduction, carbohydrate and energy metabolism, nucleic acid metabolism, protein and amino acid metabolism, lipid metabolism, cell wall and cytoskeleton modification, stress responses and cell transport. The higher B-tolerance of C. sinensis might be related to the findings that B-toxic C. sinensis leaves had higher expression levels of genes involved in photosynthesis, which might contribute to the higher photosyntheis and light utilization and less excess light energy, and in reactive oxygen species (ROS) scavenging compared to B-toxic C. grandis leaves, thus preventing them from photo-oxidative damage. In addition, B-toxicity-induced alteration in the expression levels of genes encoding inorganic pyrophosphatase 1, AT4G01850 and methionine synthase differed between the two species, which might play a role in the B-tolerance of C. sinensis.

CONCLUSIONS

C. sinensis leaves could tolerate higher level of B than C. grandis ones, thus improving the B-tolerance of C. sinensis plants. Our findings reveal some novel mechanisms on the tolerance of plants to B-toxicity at the gene expression level.

Keeping the eIF2 alpha kinase Gcn2 in check

The protein kinase Gcn2 is present in virtually all eukaryotes and is of increasing interest due to its involvement in a large array of crucial biological processes. Some of these are universally conserved from yeast to humans, such as coping with nutrient starvation and oxidative stress. In mammals, Gcn2 is important for e.g. long-term memory formation, feeding behaviour and immune system regulation. Gcn2 has been also implicated in diseases such as cancer and Alzheimer's disease. Studies on Gcn2 have been conducted most extensively in Saccharomyces cerevisiae, where the mechanism of its activation by amino acid starvation has been revealed in most detail. Uncharged tRNAs stimulate Gcn2 which subsequently phosphorylates its substrate, eIF2α, leading to reduced global protein synthesis and simultaneously to increased translation of specific mRNAs, e.g. those coding for Gcn4 in yeast and ATF4 in mammals. Both proteins are transcription factors that regulate the expression of a myriad of genes, thereby enabling the cell to initiate a survival response to the initial activating cue. Given that Gcn2 participates in many diverse processes, Gcn2 itself must be tightly controlled. Indeed, Gcn2 is regulated by a vast network of proteins and RNAs, the list of which is still growing. Deciphering molecular mechanisms underlying Gcn2 regulation by effectors and inhibitors is fundamental for understanding how the cell keeps Gcn2 in check ensuring normal organismal function, and how Gcn2-associated diseases may develop or may be treated. This review provides a critical evaluation of the current knowledge on mechanisms controlling Gcn2 activation or activity.

Natural sequence variants of yeast environmental sensors confer cell-to-cell expression variability

DNA polymorphisms that change cell-to-cell variability in gene expression are identified in a screen for ‘Probabilistic Trait Loci' in yeast. By modifying transmembrane transporter genes, these natural variants modulate intraclonal phenotypic diversification.

We mapped genetic loci affecting cell–cell variability in gene expression.

One variant enhanced both expression of a transporter and variability in a metabolic pathway.

A sequence change in another transporter also increased pathway variability.

The study invites to apprehend complex traits from a nondeterministic angle.

Living systems may have evolved probabilistic bet hedging strategies that generate cell-to-cell phenotypic diversity in anticipation of environmental catastrophes, as opposed to adaptation via a deterministic response to environmental changes. Evolution of bet hedging assumes that genotypes segregating in natural populations modulate the level of intraclonal diversity, which so far has largely remained hypothetical. Using a fluorescent P_met17-GFP reporter, we mapped four genetic loci conferring to a wild yeast strain an elevated cell-to-cell variability in the expression of MET17, a gene regulated by the methionine pathway. A frameshift mutation in the Erc1p transmembrane transporter, probably resulting from a release of laboratory strains from negative selection, reduced P_met17-GFP expression variability. At a second locus, cis-regulatory polymorphisms increased mean expression of the Mup1p methionine permease, causing increased expression variability in trans. These results demonstrate that an expression quantitative trait locus (eQTL) can simultaneously have a deterministic effect in cis and a probabilistic effect in trans. Our observations indicate that the evolution of transmembrane transporter genes can tune intraclonal variation and may therefore be implicated in both reactive and anticipatory strategies of adaptation.

Role of Hog1, Tps1 and Sod1 in boric acid tolerance of Saccharomyces cerevisiae

In order to identify genetic contributions to boric acid (BA) resistance, a yeast knockout collection was screened for BA-sensitive mutants. Prominent among the BA-sensitive mutants were strains with defects in the cytoplasmic part of the high osmolarity/glycerol (HOG) signalling pathway, the trehalose-synthesis pathway (TPS1/TPS2) and the copper-zinc superoxide dismutase SOD1. An analysis of HOG-pathway mutants and fluorescence microscopy of Hog1-GFP fusions showed that the non-redundant cytoplasmic components of the pathway, Pbs2p and Hog1p, are required to maintain BA resistance, but that import of the activated Hog1p kinase into the nucleus neither occurs during BA stress nor is necessary for wild-type-like BA tolerance. Pbs2p and Hog1p are also required to support normal morphogenesis during BA stress as their absence leads to BA-induced hyperpolarized growth. An analysis of Sod1p and Tps1p expression revealed that BA stress induces superoxide dismutase and increases trehalose synthesis activity, albeit only after a 7 h delay. We conclude that normal BA resistance of Saccharomyces cerevisiae depends on the functioning of HOG signalling, the trehalose synthesis pathway and superoxide dismutase activity.

Parameters Symptomatic for Boron Toxicity in Leaves of Tomato Plants

The incidence of boron (B) toxicity has risen in areas of intensive agriculture close to the Mediterranean sea. The objective of this research was to study the how B toxicity (0.5 and 2 mM B) affects the time course of different indicators of abiotic stress in leaves of two tomato genotypes having different sensitivity to B toxicity (cv. Kosaco and cv. Josefina). Under the treatments of 0.5 and 2 mM B, the tomato plants showed a loss of biomass and foliar area. At the same time, in the leaves of both cultivars, the B concentration increased rapidly from the first day of the experiment. These results were more pronounced in the cv. Josefina, indicating greater sensitivity than in cv. Kosaco with respect to excessive B in the environment. The levels of O2 •− and anthocyanins presented a higher correlation coefficient (r>0.9) than did the levels of B in the leaf, followed by other indicators of stress, such as GPX, chlorophyll b and proline (r>0.8). Our results indicate that these parameters could be used to evaluate the stress level as well as to develop models that could help prevent the damage inflicted by B toxicity in tomato plants.