Aspects of the Neurospora crassa Sulfur Starvation Response Are Revealed by Transcriptional Profiling and DNA Affinity Purification Sequencing

Identification of nutrients present in the environment is a challenge common to all organisms. Sulfur is an important nutrient source found in proteins, lipids, and electron carriers that are required for the survival of filamentous fungi such as Neurospora crassa .

Aspects of the Neurospora crassa sulfur starvation response are revealed by transcriptional profiling and DNA affinity purification sequencing

Accurate nutrient sensing is important for rapid fungal growth and exploitation of available resources. Sulfur is an important nutrient source found in a number of biological macromolecules, including proteins and lipids. The model filamentous fungus Neurospora crassa is capable of utilizing sulfur found in a variety of sources from amino acids to sulfate. During sulfur starvation, the transcription factor CYS-3 is responsible for upregulation of genes involved in sulfur uptake and assimilation. Using a combination of RNA sequencing and DNA affinity purification sequencing, we performed a global survey of the N. crassa sulfur starvation response and the role of CYS-3 in regulating sulfur responsive genes. Along with genes known to be involved in sulfur metabolism, the CYS-3 transcription factor also directly activated the expression of a number of uncharacterized transporter genes, suggesting that regulating sulfur import is an important aspect of regulation by CYS-3. Additionally, CYS-3 directly regulated the expression of genes involved in mitochondrial electron transfer. During sulfur starvation, genes involved in nitrogen metabolism, such as amino acid and nucleic acid metabolic pathways, along with genes encoding proteases and nucleases that are necessary for scavenging nitrogen, were activated. Sulfur starvation also caused changes in the expression of genes involved in carbohydrate metabolism, such as those encoding glycosyl hydrolases. Thus, our data suggest a connection between sulfur metabolism and other aspects of cellular metabolism.

Transcriptomics Reveals Fast Changes in Salicylate and Jasmonate Signaling Pathways in Shoots of Carbonate-Tolerant Arabidopsis thaliana under Bicarbonate Exposure

High bicarbonate concentrations of calcareous soils with high pH can affect crop performance due to different constraints. Among these, Fe deficiency has mostly been studied. The ability to mobilize sparingly soluble Fe is a key factor for tolerance. Here, a comparative transcriptomic analysis was performed with two naturally selected Arabidopsis thaliana demes, the carbonate-tolerant A1(c+) and the sensitive T6(c−). Analyses of plants exposed to either pH stress alone (pH 5.9 vs. pH 8.3) or to alkalinity caused by 10 mM NaHCO3 (pH 8.3) confirmed better growth and nutrient homeostasis of A1(c+) under alkaline conditions. RNA-sequencing (RNA-seq) revealed that bicarbonate quickly (3 h) induced Fe deficiency-related genes in T6(c−) leaves. Contrastingly, in A1(c+), initial changes concerned receptor-like proteins (RLP), jasmonate (JA) and salicylate (SA) pathways, methionine-derived glucosinolates (GS), sulfur starvation, starch degradation, and cell cycle. Our results suggest that leaves of carbonate-tolerant plants do not sense iron deficiency as fast as sensitive ones. This is in line with a more efficient Fe translocation to aerial parts. In A1(c+) leaves, the activation of other genes related to stress perception, signal transduction, GS, sulfur acquisition, and cell cycle precedes the induction of iron homeostasis mechanisms yielding an efficient response to bicarbonate stress.

The SCFMet30 ubiquitin ligase senses cellular redox state to regulate the transcription of sulfur metabolism genes

In yeast, control of sulfur amino acid metabolism relies upon Met4, a transcription factor which activates the expression of enzymes responsible for the biosynthesis of cysteine and methionine. In times of sulfur abundance, the activity of Met4 is repressed via ubiquitination by the SCFMet30 E3 ubiquitin ligase, but the mechanism by which the F-box protein Met30 senses sulfur status to tune its E3 ligase activity remains unresolved. Here, using a combination of genetics and biochemistry, we show that Met30 utilizes exquisitely redox-sensitive cysteine residues in its WD-40 repeat region to sense the availability of sulfur metabolites in the cell. Oxidation of these cysteine residues in response to sulfur starvation inhibits binding and ubiquitination of Met4, leading to induction of sulfur metabolism genes. Our findings reveal how SCFMet30 dynamically senses redox cues to regulate synthesis of these special amino acids, and further highlight the mechanistic diversity in E3 ligase-substrate relationships.

Effects of Sulfur Starvation on Growth Rates, Biomass and Lipid Contents in the Green Microalga Scenedesmus obliquus

Background:: Scenedesmus obliquus, a green unicellular chlorophycean microalga, is well-established as a lipid and biomass production platform. The nutrient starvation strategy is considered as a robust platform for lipid production from different microalgal strains. Objective: The study aimed to analyse the influences of sulfur starvation on the growth rates, and also biomass and lipid production and composition in a naturally isolated strain of S. obliquus. Methods: The BG-11 culture medium was utilized for preservation and microalgal growth. To monitor the cell growth rates, two different methods, including direct cell counting and also dry cell weight measurement were used. The study was conducted in 28 days composed of two distinct growth modes as 10 days of sulfur-rich and 18 days of sulfur starved media. Results: The studied S. obliquus strain displayed higher lipid and carbohydrate production levels (34.68% and 34.02%) in sulfur starved medium compared with the sulfur-rich medium (25.84% and 29.08%). Nevertheless, a noticeable reduction (51.36%) in biomass contents and also in cell growth rates (63.36%) was observed during sulfur starvation. The investigated strain was composed of some important fatty acids with potential applications as food, feed and biodiesel. Conclusion: The observed results implied the possibility of the sulfur starvation strategy to increase lipid production in S. obliquus strain. Besides, the available data from recently published patents reveals the promising potential of the identified lipids from S. obliquus in this study for bioenergy production and other biotechnological purposes.