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Dinoflagellates are important primary producers known to form Harmful Algae Blooms (HABs). In water, nutrient availability, pH, salinity and anthropogenic contamination constitute chemical stressors for them. The emergence of OMICs approaches propelled our understanding of dinoflagellates’ responses to stressors. However, in dinoflagellates, these approaches are still biased, as transcriptomic approaches are largely conducted compared to proteomic and metabolomic approaches. Furthermore, integrated OMICs approaches are just emerging. Here, we report recent contributions of the different OMICs approaches to the investigation of dinoflagellates’ responses to chemical stressors and discuss the current challenges we need to face to push studies further despite the lack of genomic resources available for dinoflagellates.

Potassium is one of the principal macronutrients required by all plants, but its mobility is restricted between soil compartments. Numerous studies have shown that Plant Growth Promoting Bacteria (PGPB) can facilitate nutrient uptake. The present work examined the effects of the PGPB (Bacillus megaterium) on rice plants subjected to potassium deprivation. To study only direct effects of B. megaterium, we first checked its lack of capacity to solubilize soil K. Rice plants were provided with 1.5 mM K (100%) or 0.015 mM K (1%) and growth related parameters, nutrient concentrations and gene expression of K transporters were determined. After two weeks, the 1% K treatment reduced growth of non-inoculated plants by about 50% compared with the 100% K treatment. However, there was no effect of reduced K nutrition on growth of inoculated plants. The reduction in growth in non-inoculated plants was accompanied by a similar reduction in K concentration in both roots and leaves and an overall 80% reduction of the plant potassium concentrations. In inoculated plants a 50% reduction occurred only in leaves. The expression of the K transporters HKT1;1, 1;2, 1;5, 2;2, 2;3 and 2;4 was up-regulated by the inoculation of B. megaterium under K deprivation conditions, explaining their higher K tissue concentrations and growth. Thus, the bacterial strain improved plant potassium nutrition without affecting K availability in the soil. The results demonstrate the potential of this bacteria for using as a biofertilizer to reduce the amount of potassium fertilizers to be applied in the field.

We show that E. coli tRNAs are remarkably stable during several days of nutrient starvation, although rRNA is degraded extensively under these conditions. The levels of these two major RNA classes are considered to be strongly coregulated at the level of transcription.tRNAs and ribosomal RNAs are often considered stable RNAs. In contrast to this view, we recently proposed that tRNAs are degraded during amino acid starvation and drug-induced transcription inhibition. However, reevaluation of our experimental approach revealed that common RNA extraction methods suffer from alarming extraction and size biases that can lead to gross underestimation of RNA levels in starved Escherichia coli populations. Quantification of tRNAs suffers additional biases due to differing fractions of tRNAs with base modifications in growing versus starved bacteria. Applying an improved methodology, we measured tRNA levels after starvation for amino acids, glucose, phosphate, or ammonium and transcription inhibition by rifampicin. We report that tRNA levels remain largely unaffected in all tested conditions, including several days of starvation. This confirms that tRNAs are remarkably stable RNAs and serves as a cautionary tale about quantification of RNA from cells cultured outside the steady-state growth regime. rRNA, conversely, is extensively degraded during starvation. Thus, E. coli downregulates the translation machinery in response to starvation by reducing the ribosome pool through rRNA degradation, while a high concentration of tRNAs available to supply amino acids to the remaining ribosomes is maintained.IMPORTANCE We show that E. coli tRNAs are remarkably stable during several days of nutrient starvation, although rRNA is degraded extensively under these conditions. The levels of these two major RNA classes are considered to be strongly coregulated at the level of transcription. We demonstrate that E. coli can control the ratio of tRNAs per ribosome under starvation by

We show that E. coli tRNAs are remarkably stable during several days of nutrient starvation, although rRNA is degraded extensively under these conditions. The levels of these two major RNA classes are considered to be strongly coregulated at the level of transcription.tRNAs and ribosomal RNAs are often considered stable RNAs. In contrast to this view, we recently proposed that tRNAs are degraded during amino acid starvation and drug-induced transcription inhibition. However, reevaluation of our experimental approach revealed that common RNA extraction methods suffer from alarming extraction and size biases that can lead to gross underestimation of RNA levels in starved Escherichia coli populations. Quantification of tRNAs suffers additional biases due to differing fractions of tRNAs with base modifications in growing versus starved bacteria. Applying an improved methodology, we measured tRNA levels after starvation for amino acids, glucose, phosphate, or ammonium and transcription inhibition by rifampicin. We report that tRNA levels remain largely unaffected in all tested conditions, including several days of starvation. This confirms that tRNAs are remarkably stable RNAs and serves as a cautionary tale about quantification of RNA from cells cultured outside the steady-state growth regime. rRNA, conversely, is extensively degraded during starvation. Thus, E. coli downregulates the translation machinery in response to starvation by reducing the ribosome pool through rRNA degradation, while a high concentration of tRNAs available to supply amino acids to the remaining ribosomes is maintained.IMPORTANCE We show that E. coli tRNAs are remarkably stable during several days of nutrient starvation, although rRNA is degraded extensively under these conditions. The levels of these two major RNA classes are considered to be strongly coregulated at the level of transcription. We demonstrate that E. coli can control the ratio of tRNAs per ribosome under starvation by

Although there is some evidence to suggest that LuxR-solo proteins participate in inter-species or even inter-kingdom communication, most of the LuxR-solo protein functions are unknown. We have characterized the LuxR402 regulator of Novosphingobium sp. HR1a, a bacterial strain with the ability to establish high numbers in the plant rhizosphere and able to degrade a wide range of polycyclic aromatic hydrocarbons. LuxR402 controls the aggregation state of the bacterial culture; cultures of a mutant strain lacking this regulator flocculate in less than 3 h without agitation. We have demonstrated that the bacterial surface of the mutant is highly hydrophobic and that the mutant cells assimilate sugars slower than the wild-type. The flocculation mechanism has been demonstrated to be involved in the survival of the strain under unfavorable conditions; the luxR402 gene is repressed and produces flocculation in the presence of salicylate, a substrate that, although being assimilated by Novosphingobium, is toxic to cells at high concentrations. The flocculation of cultures in industrial setups has mainly been achieved through the addition of chemicals; these studies open up the possibility of controlling the flocculation by regulating the level of expression of the luxR402 gene.

The decision to initiate DNA replication is a critical step in the cell cycle of all organisms. In nearly all bacteria, replication initiation requires the activity of the conserved replication initiation protein DnaA. Due to its central role in cell cycle progression, DnaA activity must be precisely regulated. This review summarizes the current state of DnaA regulation in the asymmetrically dividing alpha-proteobacterium Caulobacter crescentus, an important model for bacterial cell cycle studies. Mechanisms will be discussed that regulate DnaA activity and abundance under optimal conditions and in coordination with the asymmetric Caulobacter cell cycle. Furthermore, we highlight recent findings of how regulated DnaA synthesis and degradation collaborate to adjust DnaA abundance under stress conditions. The mechanisms described provide important examples of how DNA replication is regulated in an a-proteobacterium and thus represent an important starting point for the study of DNA replication in many other bacteria. This article is part of a Special Issue entitled: Dynamic gene expression, edited by Prof. Patrick Viollier.

Trichomonas vaginalis is responsible for the most prevalent non-viral sexually transmitted disease worldwide, and yet the mechanisms used by this parasite to establish and maintain infection are poorly understood. We previously identified a T. vaginalis homologue (TvMIF) of a human cytokine, human macrophage migration inhibitory factor (huMIF). TvMIF mimics huMIF's role in increasing cell growth and inhibiting apoptosis in human host cells. To interrogate a role of TvMIF in parasite survival during infection, we asked whether overexpression of TvMIF (TvMIF-OE) confers an advantage to the parasite under nutrient stress conditions by comparing the survival of TvMIF-OE parasites to that of empty vector (EV) parasites. We found that under conditions of serum starvation, overexpression of TvMIF resulted in increased parasite survival. Serum-starved parasites secrete 2.5-fold more intrinsic TvMIF than unstarved parasites, stimulating autocrine and paracrine signaling. Similarly, we observed that addition of recombinant TvMIF increased the survival of the parasites in the absence of serum. Recombinant huMIF likewise increased the parasite survival in the absence of serum, indicating that the parasite may use this host survival factor to resist its own death. Moreover, TvMIF-OE parasites were found to undergo significantly less apoptosis and reactive oxygen species (ROS) generation under conditions of serum starvation, consistent with increased survival being the result of blocking ROS-induced apoptosis. These studies demonstrated that a parasitic MIF enhances survival under adverse conditions and defined TvMIF and huMIF as conserved survival factors that exhibit cross talk in host-pathogen interactions.IMPORTANCE Macrophage migration inhibitory factor (MIF) is a conserved protein found in most eukaryotes which has been well characterized in mammals but poorly studied in other eukaryotes. The limited analyses of MIF proteins found in unicellular eukaryotes have focused excl

Trichomonas vaginalis is responsible for the most prevalent non-viral sexually transmitted disease worldwide, and yet the mechanisms used by this parasite to establish and maintain infection are poorly understood. We previously identified a T. vaginalis homologue (TvMIF) of a human cytokine, human macrophage migration inhibitory factor (huMIF). TvMIF mimics huMIF's role in increasing cell growth and inhibiting apoptosis in human host cells. To interrogate a role of TvMIF in parasite survival during infection, we asked whether overexpression of TvMIF (TvMIF-OE) confers an advantage to the parasite under nutrient stress conditions by comparing the survival of TvMIF-OE parasites to that of empty vector (EV) parasites. We found that under conditions of serum starvation, overexpression of TvMIF resulted in increased parasite survival. Serum-starved parasites secrete 2.5-fold more intrinsic TvMIF than unstarved parasites, stimulating autocrine and paracrine signaling. Similarly, we observed that addition of recombinant TvMIF increased the survival of the parasites in the absence of serum. Recombinant huMIF likewise increased the parasite survival in the absence of serum, indicating that the parasite may use this host survival factor to resist its own death. Moreover, TvMIF-OE parasites were found to undergo significantly less apoptosis and reactive oxygen species (ROS) generation under conditions of serum starvation, consistent with increased survival being the result of blocking ROS-induced apoptosis. These studies demonstrated that a parasitic MIF enhances survival under adverse conditions and defined TvMIF and huMIF as conserved survival factors that exhibit cross talk in host-pathogen interactions.IMPORTANCE Macrophage migration inhibitory factor (MIF) is a conserved protein found in most eukaryotes which has been well characterized in mammals but poorly studied in other eukaryotes. The limited analyses of MIF proteins found in unicellular eukaryotes have focused

[Background]: Rhodococcus jostii RHA1 and other actinobacteria accumulate triglycerides (TAG) under nutrient starvation. This property has an important biotechnological potential in the production of sustainable oils. [Results]: To gain insight into the metabolic pathways involved in TAG accumulation, we analysed the transcriptome of R jostii RHA1 under nutrient-limiting conditions. We correlate these physiological conditions with significant changes in cell physiology. The main consequence was a global switch from catabolic to anabolic pathways. Interestingly, the Entner-Doudoroff (ED) pathway was upregulated in detriment of the glycolysis or pentose phosphate pathways. ED induction was independent of the carbon source (either gluconate or glucose). Some of the diacylglycerol acyltransferase genes involved in the last step of the Kennedy pathway were also upregulated. A common feature of the promoter region of most upregulated genes was the presence of a consensus binding sequence for the cAMP-dependent CRP regulator. [Conclusion]: This is the first experimental observation of an ED shift under nutrient starvation conditions. Knowledge of this switch could help in the design of metabolomic approaches to optimize carbon derivation for single cell oil production.

The aim of this work was to study the stimulation of lipid production on the microalga Ankistrodesmus falcatus by varying cultivation conditions during the stationary phase. The effect of three factors (presence and absence of nitrogen, phosphorus, and light) has been tested once the cultures reached the stationary phase with the aim to increase the value of the biomass for further applications. Lipid content, elemental composition, Nile red fluorescence evolution, and calorific value of microalgal biomass were studied as well as biomass growth. Biomass presented a lipid content of 36.54 % at the end of the first stage, while at the end of the second stage, the experiments with the absence of phosphorus increased their lipid content until 45.94 and 44.55 %, the first with nitrogen and light presence and the second with absence of all factors. The combination of phosphorus absence and nitrogen and light presence achieved the highest lipid productivity (20.27 mg/L/day). The two-stage strategy to culture microalgae is a feasible option to increase the economic or energetic value of biomass.

The aim of this work was to study the stimulation of lipid production on the microalga Ankistrodesmus falcatus by varying cultivation conditions during the stationary phase. The effect of three factors (presence and absence of nitrogen, phosphorus, and light) has been tested once the cultures reached the stationary phase with the aim to increase the value of the biomass for further applications. Lipid content, elemental composition, Nile red fluorescence evolution, and calorific value of microalgal biomass were studied as well as biomass growth. Biomass presented a lipid content of 36.54 % at the end of the first stage, while at the end of the second stage, the experiments with the absence of phosphorus increased their lipid content until 45.94 and 44.55 %, the first with nitrogen and light presence and the second with absence of all factors. The combination of phosphorus absence and nitrogen and light presence achieved the highest lipid productivity (20.27 mg/L/day). The two-stage strategy to culture microalgae is a feasible option to increase the economic or energetic value of biomass.

The gene SPI1, of Saccharomyces cerevisiae, encodes a cell wall protein that is induced in several stress conditions, particularly in the postdiauxic and stationary phases of growth. It has a paralogue, SED1, which shows some common features in expression regulation and in the null mutant phenotype. In this work we have identified homologues in other species of yeasts and filamentous fungi, and we have also elucidated some aspects of the origin of SPI1, by duplication and diversification of SED1. In terms of regulation, we have found that the expression in the post-diauxic phase is regulated by genes related to the PKA pathway and stress response (MSN2/4, YAK1, POP2, SOK2, PHD1, and PHO84) and by genes involved in the PKC pathway (WSC2, PKC1, and MPK1).

Development in the ascomycete A. nidulans is principally determined by environmental signals. Adaptability to oxidative stimuli can derive in changes of growth patterns and/or the activation of sexual or asexual reproductive cycles but this model fungus might also respond to high osmotic or salt concentrations, the redox state, the availability and quantity of carbon or nitrogen sources and the degree or quality of illumination. Since each cell within the colony follows a single morphogenetic program at a time, all these environmental cues might be sensed and integrated into a limited number of intracellular signals which, finally, would activate the required morphogenetic program and repress the others. This signaling mainly occurs through stress response pathways. The present review aims to summarize the available knowledge on how these pathways transduce environmental stimuli to mediate morphological changes in Aspergillus nidulans.

Autophosphorylation of tyrosine residues on the cytoplasmic tail of the epidermal growth factor receptor ( EGFR) upon ligand binding leads to recruitment of the Grb2/Sos complex to the activated receptor and to activation of the Ras pathway. The major aim of this study was to ascertain to which extent the EGFR module ( receptor, Grb2, hSos1) could work in a lower eukaryote, completely devoid of tyrosine kinase receptors but possessing hortologues to mammalian Ras proteins. We show that the EGFR module can be functionally linked to the Ras/cAMP pathway in a Saccharomyces cerevisiae cdc25(ts) strain, as monitored by several independent biological readouts, including drop of budding index, decrease of cAMP level and acquisition of thermotolerance. Autophosphorylation of the receptor is a necessary step for RTK-dependent activation of the yeast Ras pathway, since genetic and pharmacological downregulation of the EGFR catalytic activity abolish coupling with the Ras/cAMP pathway. Thus, our results newly indicate that a RTK-based signal transduction module can be functionally coupled to the yeast Ras/cAMP pathway and that our system can be a valuable tool for the screen of drugs inhibiting the kinase activity of the receptor.

In photosynthetic organisms including unicellular algae, acclimation to and damage by environmental stresses are readily apparent at the level of the photosynthetic apparatus. Phenotypic manifestations of the stress responses include rapid and dramatic reduction of photosynthetic activity and pigment content aimed at mitigating the risk of photooxidative damage. Although the physiological and molecular mechanisms of these events are well known, the ultrastructural picture of the stress responses is often elusive and frequently controversial. We analyzed an extensive set of transmission electron microscopy images of the microalgal cells obtained across species of Chlorophyta and in a wide range of growth conditions. The results of the analysis allowed us to pinpoint distinct ultrastructural changes typical of normal functioning and emergency reduction of the chloroplast membrane system under high light exposure and/or mineral nutrient starvation. We demonstrate the patterns of the stress-related ultrastructural changes including peculiar thylakoid rearrangements and autophagy-like processes and provide an outlook on their significance for implementation of the stress responses. © 2018, Springer-Verlag GmbH Austria, part of Springer Nature.

© 2018 Elsevier B.V. The new species Parietochloris grandis sp. nov. is described from forest soil in the Dnipropetrovsk region, Ukraine. The description is based on morphological features and the phylogenetic analysis of partial SSU rDNA and rbcL genes. Phylogenetic analysis places P. grandis in the Parietochloris clade, within the family Trebouxiophyceae. The novel strain formed a strongly supported monophyletic lineage with the type species of Parietochloris, P. alveolaris. P. grandis differed from other species in the Parietochloris clade by the size and form of vegetative cells and the large number of zoospores in zoosporangia. A number of experiments with different phosphates and nitrates concentrations were conducted to evaluate changes in fatty acid profile and biomass. The dominant fatty acids during cultivation on standard BG-11 medium, as well as with the phosphates concentrations ranged from 0.22 to 2 mM, were linoleic acid (24–25%), palmitic acid (12–14%), linolenic acid (9–12%), and oleic acid (7–11%). The content of arachidonic acid and eicosapentaenoic acid ranged from 3.5 to 4.5% and 0.7% to 0.8%, respectively. The fatty acid profile and total fatty acids varied significantly under different nutrient deficiency. The greatest variation was found for oleic acid (9–46%) and linolenic acid (2–13%). The percentage of arachidonic acid was the highest with a standard nitrates concentration in the medium (5%) and the lowest in the absence of phosphates and nitrates (1.3–1.5%), but the absolute content in dry biomass was similar in all variants of the experiment (6.5–9.3 mg g−1 dry weight). The absence of nitrogen and both nitrogen and phosphorus led to a 3–fold increase in TFA in comparison with the control. Thus, this strain can be considered in biotechnological application as a potential producer of the essential linoleic acid or oleic acid.