(p)ppGpp-dependent activation of gene expression during nutrient limitation
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PROVIDER: PRJNA1293426 | ENA |
REPOSITORIES: ENA
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Project description:As rapidly growing bacteria begin to exhaust nutrients, their growth rate slows, ultimately leading to stasis or quiescence. Adaptation to nutrient limitation requires widespread metabolic remodeling that leads to lower cellular energy consumption. Examples of such changes include attenuated transcription of genes encoding ribosome components, in part mediated by the phosphorylated nucleotides guanosine tetra- and penta-phosphate, collectively (p)ppGpp. In addition, genes such as those encoding specific proteins that facilitate survival exhibit increased expression during nutrient limitation. An example is the hpf gene, encoding a broadly conserved protein responsible for protecting the ribosome from degradation under conditions limiting for ribosome synthesis. Here we show that (p)ppGpp plays a key role in the transcriptional activation of hpf as B. subtilis cells exit rapid growth. Specifically, we demonstrate that hpf transcription during nutrient limitation requires an RNAP holoenzyme containing the alternative sigma factor σH, encoded by sigH, whose expression is normally inhibited by the AbrB repressor. However, when global protein synthesis decreases, in part dependent on (p)ppGpp, AbrB levels fall, leading to increased sigH transcription and consequently hpf activation. This mechanism couples a key physiological consequence of nutrient limitation – reduced protein synthesis – with specific gene activation, thereby linking transcriptional and translational regulation. Finally, we demonstrate that (p)ppGpp is necessary for the gene expression underlying the elaboration of developmental fates including sporulation and genetic competence. Thus, the active attenuation of protein synthesis by (p)ppGpp is not only necessary for the conservation of energetic resources but also for the proper pattern of gene activation during transition to quiescence.
2025-08-04 | GSE303058 | GEO
Project description:This study provides novel insights into archaeal stress response. The effect of nutrient limitation on the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius was monitored over time on transcriptomic, proteomic and metabolic level. To our knowledge, this linkage of transcriptome, proteome, metabolome analysis makes this study a pioneer study to elucidate cellular stress response triggered by nutrient limitation. We further connect previously identified pH and salt stress responsive genes (1) with genes regulated in starvation and suggest that they constitute the core of stress responsive genes active under multiple stress sources.
2018-12-21 | GSE113716 | GEO
Project description:Projected responses of ocean net primary productivity (NPP) to climate change are highly uncertain. The climate sensitivity of phytoplankton nutrient limitation in the low-latitude Pacific plays a crucial role, but field measurements are insufficient to provide suitable constraints. Here we quantify two decades of nutrient limitation in the Equatorial Pacific with satellite observations. Using field nutrient addition experiments, proteomics, and above-water hyperspectral radiometry, we demonstrate that physiological responses of phytoplankton to iron limitation led to ~3-fold increases in chlorophyll-normalized phytoplankton fluorescence. Extension to the >18-year satellite fluorescence record showed that Equatorial Pacific iron limitation was robust to changes in physical forcing through multiple El Niño–Southern Oscillation cycles, despite coherent fluctuations in limitation strength. In contrast, these iron limitation changes were overestimated 2-fold by a state-of-the-art climate model. Such synoptic constraints provide a powerful new approach for benchmarking the realism of model NPP projections to climate changes.
2023-06-26 | PXD030610 | Pride
Project description:Regulated sulfur sequestration promotes multicellularity during nutrient limitation
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Project description:In the intracellular pathogen Brucella spp., the activation of the stringent response, a global regulatory network providing rapid adaptation to a variety of growth-affecting stress conditions such as nutrient deficiency, is essential for replication in the host. A single, bi-functional enzyme Rsh catalyzes synthesis and hydrolysis of the alarmone (p)ppGpp, responsible for differential gene expression under stringent conditions. cDNA microarray analysis allowed characterization of the transcriptional profiles of the B. suis 1330 wild-type and rsh mutant in a synthetic minimal medium, partially mimicking the nutrient-poor environment of the intramacrophagic vacuole. A total of 379 genes (11.6% of the genome) were differentially expressed in a rsh-dependent manner, of which 52% were up-regulated and 48% were down-regulated. The pleiotropic character of the response was confirmed, as the genes encoded factors belonging to various functional groups, comprising an important number of transcriptional regulators, cell envelope proteins, stress factors, transport systems, and energy metabolism proteins. Several virulence genes were under the positive control of (p)ppGpp. Methionine was the only amino acid whose biosynthesis was absolutely dependent on stringent response in B. suis. The study illustrated the complexity of the processes involved in adaptation to nutrient starvation, and contributed to a better understanding of the correlation between stringent response and Brucella virulence. Most interestingly, it clearly indicated (p)ppGpp-dependent cross-talk between at least three stress responses playing a central role in Brucella adaptation to the host: nutrient, oxidative, and low-oxygen stress. Two-condition experiment, wild-type against rsh mutant. Biological replicates: 4 wild-type, 4 rsh mutant, independently grown in minimal medium (under nutrient starvation condition) and harvested. One replicate per array. Please note that Channel 1 (Cy3) on each hybridization was a universal reference (Uref) used as a reference point to merge two (2 channel arrays) into a virtual 2 channel array with wild-type versus rsh mutant.
2013-07-08 | E-GEOD-44688 | biostudies-arrayexpress
Project description:The (p)ppGpp-dependent stress response is required for pathogenic bacteria to survive both outside and inside the host but the mechanisms behind this survival are mostly unknown. In this study, we characterize the (p)ppGpp metabolism in the opportunistic pathogen multi-drug-resistant Acinetobacter baumannii. We show that two stressful conditions potentially encountered during infection – iron starvation and polymyxin exposure – induce (p)ppGpp production. The absence of (p)ppGpp led to multiple consequences on the physiology of A. baumannii, including an increase of surface motility, a decrease in catalase activity, a poor survival upon nutrient starvation, a rapid killing during desiccation and a strong attenuation in a Galleria mellonella model of infection. Using a motility suppressor screen, we isolated multiple independent stringent mutations in rpoB and rpoC that suppress the (p)ppGpp-dependent phenotypes. By combining the suppressor screen with deep sequencing, we isolated dozens of additional mutants, expanding the list of putative stringent RNAP mutations described so far. Furthermore, our transcriptomic data reveal that (p)ppGpp deeply impacts the transcriptional landscape of A. baumannii on solid surface to induce many stress-related genes, including catalase and hydrophilins critical for tolerance to desiccation. This work highlights the functional interplay between (p)ppGpp and RNAP in the successful survival of A. baumannii in the environment but also during infection.
2025-12-10 | GSE302438 | GEO
Project description:Dinitrogenase functions as an electron valve to prevent ROS in Cyanothece 51142 during nutrient limitation
2018-10-24 | PXD002841 | Pride
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2009-03-30 | E-GEOD-14736 | biostudies-arrayexpress
Project description:In the intracellular pathogen Brucella spp., the activation of the stringent response, a global regulatory network providing rapid adaptation to a variety of growth-affecting stress conditions such as nutrient deficiency, is essential for replication in the host. A single, bi-functional enzyme Rsh catalyzes synthesis and hydrolysis of the alarmone (p)ppGpp, responsible for differential gene expression under stringent conditions. cDNA microarray analysis allowed characterization of the transcriptional profiles of the B. suis 1330 wild-type and rsh mutant in a synthetic minimal medium, partially mimicking the nutrient-poor environment of the intramacrophagic vacuole. A total of 379 genes (11.6% of the genome) were differentially expressed in a rsh-dependent manner, of which 52% were up-regulated and 48% were down-regulated. The pleiotropic character of the response was confirmed, as the genes encoded factors belonging to various functional groups, comprising an important number of transcriptional regulators, cell envelope proteins, stress factors, transport systems, and energy metabolism proteins. Several virulence genes were under the positive control of (p)ppGpp. Methionine was the only amino acid whose biosynthesis was absolutely dependent on stringent response in B. suis. The study illustrated the complexity of the processes involved in adaptation to nutrient starvation, and contributed to a better understanding of the correlation between stringent response and Brucella virulence. Most interestingly, it clearly indicated (p)ppGpp-dependent cross-talk between at least three stress responses playing a central role in Brucella adaptation to the host: nutrient, oxidative, and low-oxygen stress.
2013-07-08 | GSE44688 | GEO
Project description:Cellular stress response of Sulfolobus acidocaldarius to nutrient limitation
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