The stringent response regulates adaptation to darkness in the cyanobacterium
            <i>Synechococcus elongatus</i>

Hood, Rachel D.; Higgins, Sean; Flamholz, Avi I.; Nichols, Robert J.; Savage, David F.

doi:10.1073/pnas.1524915113

Cited by 90 publications

(120 citation statements)

References 65 publications

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“…Transcription of yvyD, the gene encoding BsLHPF, is under the control of the sigma factors r H and r B (Drzewiecki et al, 1998;Tam le et al, 2006;Akanuma et al, 2016), and up-regulated by the presence of the alarmone (p)ppGpp (Eymann et al, 2001;Tagami et al, 2012;Shimada et al, 2013; Fig 7A). Similarly, in the cyanobacterium Synechococcus elongatus, LHPF is also up-regulated by (p)ppGpp to enable dark adaptation (Hood et al, 2016). The up-regulation of LHPF leads to increased 100S formation, indicating that LHPF competes effectively with translation factors, as evidenced by LHPF inhibition of in vitro translation systems (Ueta et al, 2013;Basu & Yap, 2016).…”

Section: Discussionmentioning

confidence: 99%

Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization

et al. 2017

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Under stress conditions, such as nutrient deprivation, bacteria enter into a hibernation stage, which is characterized by the appearance of 100S ribosomal particles. In , dimerization of 70S ribosomes into 100S requires the action of the ribosome modulation factor (RMF) and the hibernation-promoting factor (HPF). Most other bacteria lack RMF and instead contain a long form HPF (LHPF), which is necessary and sufficient for 100S formation. While some structural information exists as to how RMF and HPF mediate formation of 100S (100S), structural insight into 100S formation by LHPF has so far been lacking. Here we present a cryo-EM structure of the hibernating 100S (100S), revealing that the C-terminal domain (CTD) of the LHPF occupies a site on the 30S platform distinct from RMF Moreover, unlike RMF, the HPF-CTD is directly involved in forming the dimer interface, thereby illustrating the divergent mechanisms by which 100S formation is mediated in the majority of bacteria that contain LHPF, compared to some γ-proteobacteria, such as.

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Section: Discussionmentioning

confidence: 99%

Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization

et al. 2017

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“…The 100S disassembly factor and the exact order of HPF release and 100S splitting have yet to be identified. Furthermore, the Firmicutes 100S ribosomes are constitutively produced from the lag-logarithmic phase through the stationary phase (3,14,36), whereas 100S ribosomes are formed only in cyanobacteria and γ-proteobacteria (including E. coli) during darkness and in the stationary phase (1,9). The molecular basis underpinning the variations in temporal abundance of the 100S ribosome in different bacterial systems has remained elusive.…”

Section: Significancementioning

confidence: 99%

“…The 100S ribosome is ubiquitously found in all bacterial phyla and is important for bacterial survival during nutrient limitation (2-6), antibiotic stress (7), host colonization (8), dark adaptation (9), and biofilm formation (10,11). A common feature of these biological processes is that cells generally conserve energy by undergoing metabolic and translational dormancy because protein synthesis accounts for >50% of energy costs (12,13).…”

mentioning

confidence: 99%

Disassembly of theStaphylococcus aureushibernating 100S ribosome by an evolutionarily conserved GTPase

Basu

Yap

2017

Proc. Natl. Acad. Sci. U.S.A.

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The bacterial hibernating 100S ribosome is a poorly understood form of the dimeric 70S particle that has been linked to pathogenesis, translational repression, starvation responses, and ribosome turnover. In the opportunistic pathogen Staphylococcus aureus and most other bacteria, hibernation-promoting factor (HPF) homodimerizes the 70S ribosomes to form a translationally silent 100S complex. Conversely, the 100S ribosomes dissociate into subunits and are presumably recycled for new rounds of translation. The regulation and disassembly of the 100S ribosome are largely unknown because the temporal abundance of the 100S ribosome varies considerably among different bacterial phyla. Here, we identify a universally conserved GTPase (HflX) as a bona fide dissociation factor of the S. aureus 100S ribosome. The expression levels hpf and hflX are coregulated by general stress and stringent responses in a temperature-dependent manner. While all tested guanosine analogs stimulate the splitting activity of HflX on the 70S ribosome, only GTP can completely dissociate the 100S ribosome. Our results reveal the antagonistic relationship of HPF and HflX and uncover the key regulators of 70S and 100S ribosome homeostasis that are intimately associated with bacterial survival.T he biogenesis and function of bacterial 30S and 50S ribosomal subunits and the 70S complex have been studied extensively, but the significance of the 100S ribosome (homodimeric 70S) has only begun to emerge in recent years (1). The 100S ribosome is ubiquitously found in all bacterial phyla and is important for bacterial survival during nutrient limitation (2-6), antibiotic stress (7), host colonization (8), dark adaptation (9), and biofilm formation (10, 11). A common feature of these biological processes is that cells generally conserve energy by undergoing metabolic and translational dormancy because protein synthesis accounts for >50% of energy costs (12, 13). The dimerization of 70S ribosomes has been shown to down-regulate translational efficiency in vivo (3) and in vitro (3,14), and bacteria lacking 100S ribosomes are prone to early cell death concomitant with rapid ribosome degradation (3,10,15,16). These studies lead to a model whereby the formation of the 100S complex sequesters the ribosome pool away from active translation, and 70S self-dimerization prevents ribosome degradation by an unknown pathway (3,17). During the stationary phase, the 100S ribosomes are presumably dissociated and reused for new cycles of translation, thereby maintaining cell viability (1,3,16,18). The process and dissociation factors involved in the reversible transition of silent 100S to a translationally competent 70S ribosome remain poorly understood.By contrast, the 70S dimerizing factor has been characterized in many bacterial species (1,2,4,14). In Firmicutes (such as Staphylococcus aureus and Bacillus subtilis), a single long form of hibernation-promoting factor (HPF) provides the binding platform to conjoin the 30S subunits of the two 70S monomers via a direct inter...

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“…Transient increments in ppGpp levels upon light-to-dark transition have also been reported in the cyanobacterium Synechococcus elongatus (Hood et al 2016;Puszynska and O'Shea 2017), which indicates that the ppGpp-dependent stringent response is universally required to adapt photosynthetic processes to dark conditions in oxygenic phototrophs. Given that cyanobacteria do not contain CRSH homologs (Ito et al 2017), different strategies must be used to upregulate ppGpp synthesis in the dark in a Ca 2+ -independent manner.…”

Section: Discussionmentioning

confidence: 79%

Plastidial (p)ppGpp synthesis by the Ca²⁺-dependent RelA-SpoT homolog regulates the adaptation of chloroplast gene expression to darkness in Arabidopsis

Ono

Suzuki

Ito

et al. 2019

Preprint

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Abbreviations: CRSH, Ca 2+ -activated RSH; flg22, flagellin 22; (p)ppGpp, 5'-di(tri)phosphate 3'-diphosphate; PAMPs; pathogen-associated molecular patterns; RSH, RelA-SpoT homolog; qRT-PCR, quantitative real-time PCR Abstract In bacteria, the hyper-phosphorylated nucleotides, guanosine 5'-diphosphate 3'-diphosphate (ppGpp) and guanosine 5'-triphosphate 3'-diphosphate (pppGpp), function as secondary messengers in the regulation of various metabolic processes of the cell, including transcription, translation, and enzymatic activities, especially under nutrient deficiency. The activity carried out by these nucleotide messengers is known as the stringent response. (p)ppGpp levels are controlled by two distinct enzymes, namely, RelA and SpoT, in Escherichia coli. RelA-SpoT homologs (RSHs) are also conserved in plants and algae where they function in the plastids. The model plant Arabidopsis thaliana contains four RSHs: RSH1, RSH2, RSH3, and Ca 2+ -dependent RSH (CRSH).Genetic characterizations of RSH1, RSH2, and RSH3 were undertaken, which showed that the (p)ppGpp-dependent plastidial stringent response significantly influences plant growth and stress acclimation. However, the physiological significance of CRSH-dependent (p)ppGpp synthesis remains unclear, as no crsh-null mutant has been available. Here to investigate the function of CRSH, a crsh-knockout mutant of Arabidopsis was constructed using a site-specific gene-editing technique, and its phenotype was characterized. A transient increase of ppGpp was observed for 30 min in the wild type (WT) after light-to-dark transition, but this increase was not observed in the crsh mutant. Similar analyzes were performed with the rsh2rsh3 double and rsh1rsh2rsh3 triple mutants of Arabidopsis and showed that the transient increments of ppGpp in the mutants were higher than those in the WT. The increase of (p)ppGpp in the WT and rsh2rsh3 accompanied decrements in the mRNA levels of psbD transcribed by the plastid-encoded plastid RNA polymerase. These results indicated that the transient increase of intracellular ppGpp at night is due to CRSH-dependent ppGpp synthesis and the (p)ppGpp level is maintained by the hydrolytic activities of RSH1, RSH2, and RSH3 to accustom plastidial gene expression to darkness. expression Plants were grown on 0.8% agar-solidified 1/2 MS medium under continuous light (40 µmol photons m −2 s −1 ). Fourteen-day-old plants were transferred to the dark and ~0.1 g shoots were harvested at each of the time points indicated (Fig. 3). Extraction and quantification of ppGpp were as described previously . Western blot analysisProtein content was measured using the Bradford assay Kit (Bio Lab). Total proteins (6 µg each) were applied to an SDS-PAGE gel and electroblotted onto a polyvinylidene difluoride membrane (GE-Healthcare). The membrane was incubated with the CRSH-specific antibody . Immunoreactive proteins were detected using the Alkaline Phosphatase Substrate Kit II (Vector Laboratories).

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The stringent response regulates adaptation to darkness in the cyanobacterium Synechococcus elongatus

Cited by 90 publications

References 65 publications

Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization

Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization

Disassembly of theStaphylococcus aureushibernating 100S ribosome by an evolutionarily conserved GTPase

Plastidial (p)ppGpp synthesis by the Ca²⁺-dependent RelA-SpoT homolog regulates the adaptation of chloroplast gene expression to darkness in Arabidopsis

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The stringent response regulates adaptation to darkness in the cyanobacterium Synechococcus elongatus

Cited by 90 publications

References 65 publications

Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization

Structure of the Bacillus subtilis hibernating 100S ribosome reveals the basis for 70S dimerization

Disassembly of theStaphylococcus aureushibernating 100S ribosome by an evolutionarily conserved GTPase

Plastidial (p)ppGpp synthesis by the Ca2+-dependent RelA-SpoT homolog regulates the adaptation of chloroplast gene expression to darkness in Arabidopsis

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Plastidial (p)ppGpp synthesis by the Ca²⁺-dependent RelA-SpoT homolog regulates the adaptation of chloroplast gene expression to darkness in Arabidopsis