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1.
Mol Microbiol ; 117(1): 143-159, 2022 01.
Artículo en Inglés | MEDLINE | ID: mdl-34523176

RESUMEN

Previously, we reported that RelA protein facilitates Hfq-mediated mRNA-sRNA regulation by binding sRNAs carrying a Shine-Dalgarno-like GGAG sequence. In turn, sRNA-Hfq monomers are stabilized, enabling the attachment of more Hfq subunits to form a functional hexamer. Here, using CLIP-seq, we present a global analysis of RelA-bound RNAs showing that RelA interacts with sRNAs as well as with mRNAs carrying a GGAG motif. RelA binding of mRNAs carrying GGAG at position -7 relative to the initiation codon (AUG) inhibits translation by interfering with the binding of 30S ribosomes. The extent of inhibition depends on the distance of GGAG relative to the AUG, as shortening the spacing between GGAG and AUG abrogates RelA-mediated inhibition. Interestingly, RelA binding of target mRNAs carrying GGAG in the coding sequence or close to AUG facilitates target gene regulation by sRNA partners that lack GGAG. However, translation inhibition caused by RelA binding of mRNAs carrying GGAG at position -7 relative to the AUG renders sRNA-mRNA basepairing regulation ineffective. Our study indicates that by binding RNAs carrying GGAG the ribosome-associated RelA protein inhibits translation of specific newly synthesized incoming mRNAs or enables basepairing regulation by their respective sRNA partners, thereby introducing a new regulatory concept for the bacterial response.


Asunto(s)
Proteínas de Escherichia coli/metabolismo , Escherichia coli/genética , GTP Pirofosfoquinasa/metabolismo , ARN Mensajero/metabolismo , ARN Pequeño no Traducido/metabolismo , Emparejamiento Base , Proteínas de Escherichia coli/genética , GTP Pirofosfoquinasa/genética , Motivos de Nucleótidos , Biosíntesis de Proteínas , ARN Bacteriano/genética , ARN Bacteriano/metabolismo , ARN Mensajero/genética , ARN Pequeño no Traducido/genética , Proteínas de Unión al ARN/genética , Proteínas de Unión al ARN/metabolismo , Ribosomas/metabolismo
2.
Microbiol Spectr ; 9(3): e0205721, 2021 12 22.
Artículo en Inglés | MEDLINE | ID: mdl-34935430

RESUMEN

The alarmone ppGpp plays an important role in the survival of bacteria by triggering the stringent response when exposed to environmental stress. Although Xanthomonas campestris pv. campestris (Xcc), which causes black rot disease in crucifers, is a representative species of Gram-negative phytopathogenic bacteria, relatively little is known regarding the factors influencing the stringent response in this species. However, previous studies in other Gram-negative bacteria have indicated that RelA and SpoT play a critical role in ppGpp synthesis. The current study found that these proteins also had an important role in Xcc, with a ΔrelAΔspoT double mutant being unable to produce ppGpp, resulting in changes to phenotype including reduced production of exopolysaccharides (EPS), exoenzymes, and biofilm, as well the loss of swarming motility and pathogenicity. The ppGpp-deficient mutant also exhibited greater sensitivity to environment stress, being almost incapable of growth on modified minimal medium (mMM) and having a much greater propensity to enter the viable but nonculturable (VBNC) state in response to oligotrophic conditions (0.85% NaCl). These findings much advance our understanding of the role of ppGpp in the biology of Xcc and could have important implications for more effective management of this important pathogen. IMPORTANCE Xanthomonas campestris pv. campestris (Xcc) is a typical seedborne phytopathogenic bacterium that causes large economic losses worldwide, and this is the first original research article to investigate the role of ppGpp in this important species. Here, we revealed the function of RelA and SpoT in ppGpp production, physiology, pathogenicity, and stress resistance in Xcc. Most intriguingly, we found that ppGpp levels and downstream ppGpp-dependent phenotypes were mediated predominantly by SpoT, with RelA having only a supplementary role. Taken together, the results of the current study provide new insight into the role of ppGpp in the biology of Xcc, which could also have important implications for the role of ppGpp in the survival and pathogenicity of other pathogenic bacteria.


Asunto(s)
Proteínas Bacterianas/metabolismo , GTP Pirofosfoquinasa/metabolismo , Guanosina Tetrafosfato/biosíntesis , Enfermedades de las Plantas/microbiología , Pirofosfatasas/metabolismo , Xanthomonas campestris/crecimiento & desarrollo , Xanthomonas campestris/patogenicidad , Proteínas Bacterianas/genética , GTP Pirofosfoquinasa/genética , Pirofosfatasas/genética , Raphanus/microbiología , Virulencia , Xanthomonas campestris/enzimología , Xanthomonas campestris/genética
3.
Mol Cell ; 81(16): 3310-3322.e6, 2021 08 19.
Artículo en Inglés | MEDLINE | ID: mdl-34416138

RESUMEN

Amino acid starvation is sensed by Escherichia coli RelA and Bacillus subtilis Rel through monitoring the aminoacylation status of ribosomal A-site tRNA. These enzymes are positively regulated by their product-the alarmone nucleotide (p)ppGpp-through an unknown mechanism. The (p)ppGpp-synthetic activity of Rel/RelA is controlled via auto-inhibition by the hydrolase/pseudo-hydrolase (HD/pseudo-HD) domain within the enzymatic N-terminal domain region (NTD). We localize the allosteric pppGpp site to the interface between the SYNTH and pseudo-HD/HD domains, with the alarmone stimulating Rel/RelA by exploiting intra-NTD autoinhibition dynamics. We show that without stimulation by pppGpp, starved ribosomes cannot efficiently activate Rel/RelA. Compromised activation by pppGpp ablates Rel/RelA function in vivo, suggesting that regulation by the second messenger (p)ppGpp is necessary for mounting an acute starvation response via coordinated enzymatic activity of individual Rel/RelA molecules. Control by (p)ppGpp is lacking in the E. coli (p)ppGpp synthetase SpoT, thus explaining its weak synthetase activity.


Asunto(s)
Regulación Alostérica/genética , Proteínas de Escherichia coli/genética , GTP Pirofosfoquinasa/genética , Guanosina Pentafosfato/genética , Pirofosfatasas/genética , Aminoácidos/metabolismo , Bacillus subtilis/genética , Bacillus subtilis/metabolismo , Dominio Catalítico/genética , Escherichia coli/genética , Escherichia coli/metabolismo , Hidrolasas/genética , Ribosomas/genética , Ribosomas/metabolismo , Inanición/genética , Inanición/metabolismo
4.
Elife ; 102021 07 29.
Artículo en Inglés | MEDLINE | ID: mdl-34323689

RESUMEN

Bacteria regulate their metabolism to adapt and survive adverse conditions, in particular to stressful downshifts in nutrient availability. These shifts trigger the so-called stringent response, coordinated by the signaling molecules guanosine tetra and pentaphosphate collectively referred to as (p)ppGpp. In Escherichia coli, accumulation of theses alarmones depends on the (p)ppGpp synthetase RelA and the bifunctional (p)ppGpp synthetase/hydrolase SpoT. A tight regulation of these intracellular activities is therefore crucial to rapidly adjust the (p)ppGpp levels in response to environmental stresses but also to avoid toxic consequences of (p)ppGpp over-accumulation. In this study, we show that the small protein NirD restrains RelA-dependent accumulation of (p)ppGpp and can inhibit the stringent response in E. coli. Mechanistically, our in vivo and in vitro studies reveal that NirD directly binds the catalytic domains of RelA to balance (p)ppGpp accumulation. Finally, we show that NirD can control RelA activity by directly inhibiting the rate of (p)ppGpp synthesis.


Asunto(s)
Proteínas de Escherichia coli/genética , Escherichia coli/genética , GTP Pirofosfoquinasa/genética , Nitrito Reductasas/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/metabolismo , GTP Pirofosfoquinasa/metabolismo , Guanosina Pentafosfato/metabolismo , Nitrito Reductasas/metabolismo , Estrés Fisiológico
5.
Nat Commun ; 12(1): 2249, 2021 04 21.
Artículo en Inglés | MEDLINE | ID: mdl-33883550

RESUMEN

The RNA chaperone Hfq, acting as a hexamer, is a known mediator of post-transcriptional regulation, expediting basepairing between small RNAs (sRNAs) and their target mRNAs. However, the intricate details associated with Hfq-RNA biogenesis are still unclear. Previously, we reported that the stringent response regulator, RelA, is a functional partner of Hfq that facilitates Hfq-mediated sRNA-mRNA regulation in vivo and induces Hfq hexamerization in vitro. Here we show that RelA-mediated Hfq hexamerization requires an initial binding of RNA, preferably sRNA to Hfq monomers. By interacting with a Shine-Dalgarno-like sequence (GGAG) in the sRNA, RelA stabilizes the initially unstable complex of RNA bound-Hfq monomer, enabling the attachment of more Hfq subunits to form a functional hexamer. Overall, our study showing that RNA binding to Hfq monomers is at the heart of RelA-mediated Hfq hexamerization, challenges the previous concept that only Hfq hexamers can bind RNA.


Asunto(s)
Proteínas de Escherichia coli/metabolismo , GTP Pirofosfoquinasa/metabolismo , Proteína de Factor 1 del Huésped/metabolismo , ARN Bacteriano/metabolismo , Sustitución de Aminoácidos , Secuencia de Bases , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/genética , GTP Pirofosfoquinasa/química , GTP Pirofosfoquinasa/genética , Proteína de Factor 1 del Huésped/química , Modelos Biológicos , Unión Proteica , Multimerización de Proteína , Estabilidad Proteica , Estructura Cuaternaria de Proteína , Subunidades de Proteína , ARN Bacteriano/química , ARN Bacteriano/genética , ARN Pequeño no Traducido/química , ARN Pequeño no Traducido/genética , ARN Pequeño no Traducido/metabolismo , Eliminación de Secuencia
6.
Sci Rep ; 10(1): 6091, 2020 04 08.
Artículo en Inglés | MEDLINE | ID: mdl-32269250

RESUMEN

Genetic circuit-based biosensors have emerged as an effective analytical tool in synthetic biology; these biosensors can be applied to high-throughput screening of new biocatalysts and metabolic pathways. Sigma 54 (σ54)-dependent transcription factor (TF) can be a valuable component of these biosensors owing to its intrinsic silent property compared to most of the housekeeping sigma 70 (σ70) TFs. Here, we show that these unique characteristics of σ54-dependent TFs can be used to control the host cell state to be more appropriate for high-throughput screening. The acclimation of cell state was achieved by using guanosine (penta)tetraphosphate ((p)ppGpp)-related genes (relA, spoT) and nutrient conditions, to link the σ54 TF-based reporter expression with the target enzyme activity. By controlling stringent programmed responses and optimizing assay conditions, catalytically improved tyrosine phenol lyase (TPL) enzymes were successfully obtained using a σ54-dependent DmpR as the TF component, demonstrating the practical feasibility of this biosensor. This combinatorial strategy of biosensors using σ factor-dependent TFs will allow for more effective high-throughput enzyme engineering with broad applicability.


Asunto(s)
Proteínas Bacterianas/genética , Ensayos Analíticos de Alto Rendimiento/métodos , Ingeniería de Proteínas/métodos , Transactivadores/genética , Activación Transcripcional , Tirosina Fenol-Liasa/genética , Aclimatación , Técnicas Biosensibles/métodos , Escherichia coli , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , GTP Pirofosfoquinasa/genética , GTP Pirofosfoquinasa/metabolismo , Regiones Promotoras Genéticas , Pseudomonas putida , Pirofosfatasas/genética , Pirofosfatasas/metabolismo , Factor sigma/genética , Factor sigma/metabolismo , Tirosina Fenol-Liasa/metabolismo
7.
Appl Microbiol Biotechnol ; 104(7): 3061-3079, 2020 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-32009198

RESUMEN

Pseudomonas protegens H78 produces multiple secondary metabolites, including antibiotics and iron carriers. The guanosine pentaphosphate or tetraphosphate ((p)ppGpp)-mediated stringent response is utilized by bacteria to survive during nutritional starvation and other stresses. RelA/SpoT homologues are responsible for the biosynthesis and degradation of the alarmone (p)ppGpp. Here, we investigated the global effect of relA/spoT dual deletion on the transcriptomic profiles, physiology, and metabolism of P. protegens H78 grown to mid- to late log phase. Transcriptomic profiling revealed that relA/spoT deletion globally upregulated the expression of genes involved in DNA replication, transcription, and translation; amino acid metabolism; carbohydrate and energy metabolism; ion transport and metabolism; and secretion systems. Bacterial growth was partially increased, while the cell survival rate was significantly reduced by relA/spoT deletion in H78. The utilization of some nutritional elements (C, P, S, and N) was downregulated due to relA/spoT deletion. In contrast, relA/spoT mutation globally inhibited the expression of secondary metabolic gene clusters (plt, phl, prn, ofa, fit, pch, pvd, and has). Correspondingly, antibiotic and iron carrier biosynthesis, iron utilization, and antibiotic resistance were significantly downregulated by the relA/spoT mutation. This work highlights that the (p)ppGpp-mediated stringent response regulatory system plays an important role in inhibiting primary metabolism and activating secondary metabolism in P. protegens.


Asunto(s)
Guanosina Pentafosfato/metabolismo , Guanosina Tetrafosfato/metabolismo , Pseudomonas/metabolismo , Metabolismo Secundario/genética , Antibacterianos/biosíntesis , Antibacterianos/farmacología , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Farmacorresistencia Bacteriana/genética , Metabolismo Energético/genética , GTP Pirofosfoquinasa/genética , GTP Pirofosfoquinasa/metabolismo , Eliminación de Gen , Perfilación de la Expresión Génica , Regulación Bacteriana de la Expresión Génica , Viabilidad Microbiana/genética , Pseudomonas/efectos de los fármacos , Pseudomonas/genética , Pseudomonas/crecimiento & desarrollo , Pirofosfatasas/genética , Pirofosfatasas/metabolismo
8.
Amino Acids ; 51(10-12): 1577-1592, 2019 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-31617110

RESUMEN

Increased intracellular cysteine poses a potential danger to cells due to the high ability of cysteine to reduce free iron and promote the Fenton reaction. Here, we studied ways to maintain cysteine homeostasis in E. coli cells while inhibiting protein synthesis with valine or chloramphenicol. When growing wild-type bacteria on minimal medium with sulfate, an excess of cysteine resulting from the inhibition of protein synthesis is mainly incorporated into glutathione (up to 90%), which, therefore, can be considered as cysteine buffer. The share of hydrogen sulfide, which is the product of cysteine degradation by cysteine synthase B (CysM), does not exceed 1-3%, the rest falls on free cysteine, exported from cells. As a result, intracellular free cysteine is maintained at a low level (about 0.1 mM). The lack of glutathione in the gshA mutant increases H2S production and excretion of cysteine and leads to a threefold increase in the level of intracellular cysteine in response to valine and chloramphenicol. The relA mutants, exposed to valine, produce more H2S, dramatically accelerate the export of glutathione and accumulate more cysteine in the cytoplasm than their parent, which indicates that the regulatory nucleotide (p)ppGpp is involved in maintaining cysteine homeostasis. Disruption of cysteine homeostasis in gshA and relA mutants increases their sensitivity to peroxide stress.


Asunto(s)
Cisteína/metabolismo , Escherichia coli/fisiología , Homeostasis , Biosíntesis de Proteínas , Cloranfenicol/farmacología , Escherichia coli/genética , Escherichia coli/metabolismo , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , GTP Pirofosfoquinasa/genética , GTP Pirofosfoquinasa/metabolismo , Glutatión/metabolismo , Glutatión Sintasa/genética , Glutatión Sintasa/metabolismo , Homeostasis/genética , Peróxido de Hidrógeno/metabolismo , Peróxido de Hidrógeno/farmacología , Sulfuro de Hidrógeno/metabolismo , Viabilidad Microbiana , Mutación , Estrés Oxidativo , Biosíntesis de Proteínas/efectos de los fármacos , Valina/metabolismo
9.
J Bacteriol ; 201(19)2019 10 01.
Artículo en Inglés | MEDLINE | ID: mdl-31331975

RESUMEN

Type II fatty acid biosynthesis in bacteria can be broadly classified into the initiation and elongation phases. The biochemical functions defining each step in the two phases have been studied in vitro Among the ß-ketoacyl-acyl carrier protein (ACP) synthases, FabH catalyzes the initiation reaction, while FabB and FabF, which primarily catalyze the elongation reaction, can also drive initiation as side reactions. A role for FabB and FabF in the initiation of fatty acid biosynthesis would be supported by the viability of the ΔfabH mutant. In this study, we show that the ΔfabH and ΔyiiD mutations were synthetically lethal and that ΔfabH ΔrelA ΔspoT and ΔfabH ΔdksA synthetic lethality was rescued by the heterologous expression of yiiD In the ΔfabH mutant, the expression of yiiD was positively regulated by (p)ppGpp. The growth defect, reduced cell size, and altered fatty acid profile of the ΔfabH mutant and the growth defect of the ΔfabH ΔfabF fabB15(Ts) mutant in oleate- and palmitate-supplemented medium at 42°C were rescued by the expression of yiiD from a multicopy plasmid. Together, these results indicate that the yiiD-encoded function supported initiation of fatty acid biosynthesis in the absence of FabH. We have renamed yiiD as fabYIMPORTANCE Fatty acid biosynthesis is an essential process conserved across life forms. ß-Ketoacyl-ACP synthases are essential for fatty acid biosynthesis. FabH is a ß-ketoacyl-ACP synthase that contributes to the initiation of fatty acid biosynthesis in Escherichia coli In this study, we present genetic and biochemical evidence that the yiiD (renamed fabY)-encoded function contributes to the biosynthesis of fatty acid in the absence of FabH activity and that under these conditions, the expression of FabY was regulated by the stringent response factors (p)ppGpp and DksA. Combined inactivation of FabH and FabY resulted in growth arrest, possibly due to the loss of fatty acid biosynthesis. A molecule(s) that inhibits the two activities can be an effective microbicide.


Asunto(s)
Acetiltransferasas/genética , Proteínas de Escherichia coli/genética , Escherichia coli/crecimiento & desarrollo , Ácidos Grasos/biosíntesis , 3-Oxoacil-(Proteína Transportadora de Acil) Sintasa/genética , Escherichia coli/genética , Escherichia coli/metabolismo , Acido Graso Sintasa Tipo II/genética , GTP Pirofosfoquinasa/genética , Regulación Bacteriana de la Expresión Génica , Guanosina Pentafosfato/metabolismo , Mutación , Mutaciones Letales Sintéticas
10.
Cell Microbiol ; 21(8): e13034, 2019 08.
Artículo en Inglés | MEDLINE | ID: mdl-31013389

RESUMEN

How Salmonella enterica serovar Typhi (S. Typhi), an important human pathogen, survives the stressful microenvironments inside the gastrointestinal tract and within macrophages remains poorly understood. We report here that S. Typhi has a bonafide stringent response (SR) system, which is mediated by (p)ppGpp and regulates multiple virulence-associated traits and the pathogenicity of the S. Typhi Ty2 strain. In an iron overload mouse model of S. Typhi infection, the (p)ppGpp0 (Ty2ΔRelAΔSpoT) strain showed minimal systemic spread and no mortality, as opposed to 100% death of the mice challenged with the isogenic wild-type strain. Ty2ΔRelAΔSpoT had markedly elongated morphology with incomplete septa formation and demonstrated severely attenuated motility and chemotaxis due to the loss of flagella. Absence of the Vi-polysaccharide capsule rendered the mutant strain highly susceptible to complement-mediated lysis. The phenotypes of Ty2ΔRelAΔSpoT was contributed by transcriptional repression of several genes, including fliC, tviA, and ftsZ, as found by reverse transcriptase quantitative polymerase chain reaction and gene complementation studies. Finally, Ty2ΔRelAΔSpoT had markedly reduced invasion into intestinal epithelial cells and significantly attenuated survival within macrophages. To the best of our knowledge, this was the first study that addressed SR in S. Typhi and showed that (p)ppGpp was essential for optimal pathogenic fitness of the organism.


Asunto(s)
Proteínas Bacterianas/genética , Guanosina Pentafosfato/metabolismo , Interacciones Huésped-Patógeno/genética , Salmonella typhi/genética , Salmonella typhi/patogenicidad , Fiebre Tifoidea/microbiología , Animales , Proteínas Bacterianas/metabolismo , Células CACO-2 , Modelos Animales de Enfermedad , GTP Pirofosfoquinasa/deficiencia , GTP Pirofosfoquinasa/genética , Regulación Bacteriana de la Expresión Génica , Células HT29 , Humanos , Sobrecarga de Hierro/metabolismo , Sobrecarga de Hierro/microbiología , Sobrecarga de Hierro/mortalidad , Sobrecarga de Hierro/patología , Hígado/metabolismo , Hígado/microbiología , Hígado/patología , Ratones , Ratones Endogámicos BALB C , Ratones Noqueados , Polisacáridos Bacterianos/deficiencia , Pirofosfatasas/deficiencia , Pirofosfatasas/genética , Células RAW 264.7 , Salmonella typhi/crecimiento & desarrollo , Salmonella typhi/metabolismo , Transducción de Señal , Bazo/metabolismo , Bazo/microbiología , Bazo/patología , Análisis de Supervivencia , Células THP-1 , Fiebre Tifoidea/metabolismo , Fiebre Tifoidea/mortalidad , Fiebre Tifoidea/patología , Virulencia
11.
Artículo en Inglés | MEDLINE | ID: mdl-30509938

RESUMEN

We developed a simple, efficient, and cost-effective method, named the replica plating tolerance isolation system (REPTIS), to detect the antibiotic tolerance potential of a bacterial strain. This method can also be used to quantify the antibiotic-tolerant subpopulation in a susceptible population. Using REPTIS, we isolated ciprofloxacin (CPFX)-tolerant mutants (mutants R2, R3, R5, and R6) carrying a total of 12 mutations in 12 different genes from methicillin-sensitive Staphylococcus aureus (MSSA) strain FDA209P. Each mutant carried multiple mutations, while few strains shared the same mutation. The R2 strain carried a nonsense mutation in the stress-mediating gene, relA Additionally, two strains carried the same point mutation in the leuS gene, encoding leucyl-tRNA synthetase. Furthermore, RNA sequencing of the R strains showed a common upregulation of relA Overall, transcriptome analysis showed downregulation of genes related to translation; carbohydrate, fat, and energy metabolism; nucleotide synthesis; and upregulation of amino acid biosynthesis and transportation genes in R2, R3, and R6, similar to the findings observed for the FDA209P strain treated with mupirocin (MUP0.03). However, R5 showed a unique transcription pattern that differed from that of MUP0.03. REPTIS is a unique and convenient method for quantifying the level of tolerance of a clinical isolate. Genomic and transcriptomic analyses of R strains demonstrated that CPFX tolerance in these S. aureus mutants occurs via at least two distinct mechanisms, one of which is similar to that which occurs with mupirocin treatment.


Asunto(s)
Antibacterianos/farmacología , Ciprofloxacina/farmacología , Farmacorresistencia Bacteriana/genética , Pruebas de Sensibilidad Microbiana/métodos , Staphylococcus aureus/efectos de los fármacos , Staphylococcus aureus/genética , GTP Pirofosfoquinasa/genética , Perfilación de la Expresión Génica/métodos , Humanos , Leucina-ARNt Ligasa/genética , Mupirocina/farmacología , Staphylococcus aureus/aislamiento & purificación
12.
J Microbiol Biotechnol ; 26(12): 2106-2115, 2016 Dec 28.
Artículo en Inglés | MEDLINE | ID: mdl-27558436

RESUMEN

To identify the global effects of (p)ppGpp in the gram-positive bacterium Deinococcus radiodurans, which exhibits remarkable resistance to radiation and other stresses, RelA/SpoT homolog (RSHs) mutants were constructed by direct deletion mutagenesis. The results showed that RelA has both synthesis and hydrolysis domains of (p)ppGpp, whereas RelQ only synthesizes (p)ppGpp in D. radiodurans. The growth assay for mutants and complementation analysis revealed that deletion of relA and relQ sensitized the cells to H2O2, heat shock, and amino acid limitation. Comparative proteomic analysis revealed that the bifunctional RelA is involved in DNA repair, molecular chaperone functions, transcription, the tricarboxylic acid cycle, and metabolism, suggesting that relA maintains the cellular (p)ppGpp levels and plays a crucial role in oxidative resistance in D. radiodurans. The D. radiodurans relA and relQ genes are responsible for (p)ppGpp synthesis/hydrolysis and (p)ppGpp hydrolysis, respectively. (p)ppGpp integrates a general stress response with a targeted re-programming of gene regulation to allow bacteria to respond appropriately towards heat shock, oxidative stress, and starvation. This is the first identification of RelA and RelQ involvement in response to oxidative, heat shock, and starvation stresses in D. radiodurans, which further elucidates the remarkable resistance of this bacterium to stresses.


Asunto(s)
Proteínas Bacterianas/metabolismo , Deinococcus/enzimología , GTP Pirofosfoquinasa/metabolismo , Proteínas Bacterianas/genética , Reparación del ADN , Deinococcus/genética , Deinococcus/crecimiento & desarrollo , Deinococcus/metabolismo , GTP Pirofosfoquinasa/genética , Regulación Bacteriana de la Expresión Génica , Guanosina Tetrafosfato/metabolismo , Estrés Oxidativo
13.
Nature ; 534(7606): 277-280, 2016 06 09.
Artículo en Inglés | MEDLINE | ID: mdl-27279228

RESUMEN

In order to survive, bacteria continually sense, and respond to, environmental fluctuations. Stringent control represents a key bacterial stress response to nutrient starvation that leads to rapid and comprehensive reprogramming of metabolic and transcriptional patterns. In general, transcription of genes for growth and proliferation is downregulated, while those important for survival and virulence are upregulated. Amino acid starvation is sensed by depletion of the aminoacylated tRNA pools, and this results in accumulation of ribosomes stalled with non-aminoacylated (uncharged) tRNA in the ribosomal A site. RelA is recruited to stalled ribosomes and activated to synthesize a hyperphosphorylated guanosine analogue, (p)ppGpp, which acts as a pleiotropic secondary messenger. However, structural information about how RelA recognizes stalled ribosomes and discriminates against aminoacylated tRNAs is missing. Here we present the cryo-electron microscopy structure of RelA bound to the bacterial ribosome stalled with uncharged tRNA. The structure reveals that RelA utilizes a distinct binding site compared to the translational factors, with a multi-domain architecture that wraps around a highly distorted A-site tRNA. The TGS (ThrRS, GTPase and SpoT) domain of RelA binds the CCA tail to orient the free 3' hydroxyl group of the terminal adenosine towards a ß-strand, such that an aminoacylated tRNA at this position would be sterically precluded. The structure supports a model in which association of RelA with the ribosome suppresses auto-inhibition to activate synthesis of (p)ppGpp and initiate the stringent response. Since stringent control is responsible for the survival of pathogenic bacteria under stress conditions, and contributes to chronic infections and antibiotic tolerance, RelA represents a good target for the development of novel antibacterial therapeutics.


Asunto(s)
Aminoácidos/deficiencia , Proteínas de Escherichia coli/metabolismo , Escherichia coli/genética , GTP Pirofosfoquinasa/metabolismo , ARN de Transferencia/metabolismo , Ribosomas/metabolismo , Estrés Fisiológico , Adenosina/metabolismo , Sitios de Unión , Microscopía por Crioelectrón , Escherichia coli/metabolismo , Escherichia coli/patogenicidad , Escherichia coli/ultraestructura , Proteínas de Escherichia coli/antagonistas & inhibidores , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/ultraestructura , GTP Pirofosfoquinasa/antagonistas & inhibidores , GTP Pirofosfoquinasa/genética , GTP Pirofosfoquinasa/ultraestructura , Regulación Bacteriana de la Expresión Génica , Guanosina Tetrafosfato/química , Guanosina Tetrafosfato/metabolismo , Redes y Vías Metabólicas , Modelos Moleculares , Fosforilación , Biosíntesis de Proteínas , Conformación Proteica , Estructura Terciaria de Proteína , ARN de Transferencia/química , ARN de Transferencia/genética , ARN de Transferencia/ultraestructura , Aminoacil-ARN de Transferencia/química , Aminoacil-ARN de Transferencia/genética , Aminoacil-ARN de Transferencia/metabolismo , Ribosomas/química , Ribosomas/ultraestructura , Sistemas de Mensajero Secundario
14.
Nucleic Acids Res ; 44(13): 6471-81, 2016 07 27.
Artículo en Inglés | MEDLINE | ID: mdl-27226493

RESUMEN

Under stress conditions, such as nutrient starvation, deacylated tRNAs bound within the ribosomal A-site are recognized by the stringent factor RelA, which converts ATP and GTP/GDP to (p)ppGpp. The signaling molecules (p)ppGpp globally rewire the cellular transcriptional program and general metabolism, leading to stress adaptation. Despite the additional importance of the stringent response for regulation of bacterial virulence, antibiotic resistance and persistence, structural insight into how the ribosome and deacylated-tRNA stimulate RelA-mediated (p)ppGpp has been lacking. Here, we present a cryo-EM structure of RelA in complex with the Escherichia coli 70S ribosome with an average resolution of 3.7 Å and local resolution of 4 to >10 Å for RelA. The structure reveals that RelA adopts a unique 'open' conformation, where the C-terminal domain (CTD) is intertwined around an A/T-like tRNA within the intersubunit cavity of the ribosome and the N-terminal domain (NTD) extends into the solvent. We propose that the open conformation of RelA on the ribosome relieves the autoinhibitory effect of the CTD on the NTD, thus leading to stimulation of (p)ppGpp synthesis by RelA.


Asunto(s)
Nucleótidos de Guanina/química , Ligasas/química , ARN de Transferencia/química , Ribosomas/química , Escherichia coli/química , Escherichia coli/genética , GTP Pirofosfoquinasa/química , GTP Pirofosfoquinasa/genética , Regulación Bacteriana de la Expresión Génica , Nucleótidos de Guanina/biosíntesis , Ligasas/genética , Conformación Molecular , ARN de Transferencia/genética , Ribosomas/genética
15.
Curr Microbiol ; 69(4): 436-44, 2014 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-24838666

RESUMEN

RelA and SpoT synthesize ppGpp, a key effector molecule that facilitates the adaptation of bacteria to nutrient starvation and other stresses, known as the stringent response. To investigate the role of Rsh Bant , a putative RelA/SpoT homolog (encoded by BAS4302) in Bacillus anthracis, we examined the alteration of the secretome profiles after the overexpression of a functional His-Rsh Bant protein in the B. anthracis strain Sterne at the stationary growth phase. In the ppGpp-deficient E. coli mutant strain CF1693, overexpression of Rsh Bant restored a ppGpp-dependent growth defect on minimal glucose media. The secretome profiles obtained using a two-dimensional electrophoresis (2-DE) analysis were altered by overexpression of Rsh Bant in B. anthracis. Among the 66 protein spots differentially expressed >1.5-fold, the 29 proteins were abundant for further identification using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Functional categorization of those proteins implicated their involvement in various biological activities. Taken together, our results imply that overexpression of a functional His-Rsh Bant can lead to the increased levels of intracellular ppGpp in B. anthracis, resulting in the significant changes in its secretome profiling. The stringent response-controlled proteins identified are likely useful as potential targets for serodiagnostic applications.


Asunto(s)
Bacillus anthracis/enzimología , Proteínas Bacterianas/metabolismo , GTP Pirofosfoquinasa/metabolismo , Bacillus anthracis/genética , Bacillus anthracis/metabolismo , Proteínas Bacterianas/química , Proteínas Bacterianas/genética , Sistemas de Secreción Bacterianos , Electroforesis en Gel Bidimensional , GTP Pirofosfoquinasa/química , GTP Pirofosfoquinasa/genética , Regulación Bacteriana de la Expresión Génica , Proteómica
16.
Cell ; 117(1): 57-68, 2004 Apr 02.
Artículo en Inglés | MEDLINE | ID: mdl-15066282

RESUMEN

Enzymes of the Rel/Spo family enable bacteria to survive prolonged periods of nutrient limitation by producing an intracellular signaling alarmone, (p)ppGpp, which triggers the so-called stringent response. Both the synthesis of (p)ppGpp from ATP and GDP(GTP), and its hydrolysis to GDP(GTP) and pyrophosphate, are catalyzed by Rel/Spo proteins. The 2.1 A crystal structure of the bifunctional catalytic fragment of the Rel/Spo homolog from Streptococcus dysgalactiae subsp. equisimilis, Rel(Seq), reveals two conformations of the enzyme corresponding to known reciprocal activity states: (p)ppGpp-hydrolase-OFF/(p)ppGpp-synthetase-ON and hydrolase-ON/synthetase-OFF. The hydrolase and synthetase domains bear remarkable similarities to the catalytic domains of the cyclic phosphodiesterase and nucleotidyltransferase superfamilies, respectively. The active sites, separated by more than 30 A, contain bound nucleotides including an unusual (p)ppGpp derivative, GDP-2':3'-cyclic monophosphate. Reciprocal regulation of the antagonistic catalytic activities, suggested by the structure, is supported by mutagenesis experiments and appears to involve ligand-induced signal transmission between the two active sites.


Asunto(s)
Bacterias/enzimología , GTP Pirofosfoquinasa/metabolismo , Guanosina Pentafosfato/metabolismo , Ligasas/metabolismo , Secuencia de Aminoácidos , Bacterias/genética , Sitios de Unión/fisiología , Dominio Catalítico/fisiología , Cristalografía por Rayos X , Metabolismo Energético/fisiología , GTP Pirofosfoquinasa/genética , Ligasas/química , Ligasas/genética , Modelos Moleculares , Datos de Secuencia Molecular , Nucleótidos/metabolismo , Conformación Proteica , Estructura Terciaria de Proteína , Homología de Secuencia de Aminoácido , Transducción de Señal/fisiología , Inanición/metabolismo , Relación Estructura-Actividad
17.
J Bacteriol ; 175(4): 1203-5, 1993 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-8432714

RESUMEN

The Escherichia coli lytB gene, which is involved in penicillin tolerance and control of the stringent response, was identified as a previously described open reading frame designated orf316 located in the ileS-lsp operon (0.4 min on the linkage map).


Asunto(s)
Resistencia a la Ampicilina , Escherichia coli/genética , Genes Bacterianos , Clonación Molecular , GTP Pirofosfoquinasa/genética , Regulación Bacteriana de la Expresión Génica , Prueba de Complementación Genética , Operón , Mapeo Restrictivo , Eliminación de Secuencia
18.
Biochem Biophys Res Commun ; 182(1): 355-60, 1992 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-1731792

RESUMEN

The Drosophila glutathione S-transferase D genes encode a family of isozymes. We have determined the amino acid sequence of a new member of this family by nucleotide sequence analysis of a genomic DNA clone. The open reading frame of this intronless gene should encode an isozyme subunit of 211 amino acids. This sequence has significant homology to the E. coli stringent starvation protein, SSP, which is also a protein of two identical 211 amino acid subunits. The two proteins have very similar overall amino acid composition as well. It is possible that SSP may be a glutathione S-transferase(s) in E. coli or is evolutionarily related to glutathione S-transferases. Because SSP is known to be tightly associated with the RNA polymerase holoenzyme during purification, it is conceivable that Drosophila glutathione S-transferase(s) may potentially interact with the transcription machinery in a fashion similar to SSP's interaction with E. coli RNA polymerase holoenzyme.


Asunto(s)
Proteínas Bacterianas/genética , Drosophila melanogaster/genética , Proteínas de Escherichia coli , Escherichia coli/genética , GTP Pirofosfoquinasa/genética , Glutatión Transferasa/genética , Secuencia de Aminoácidos , Aminoácidos/análisis , Animales , Drosophila melanogaster/enzimología , Escherichia coli/enzimología , Datos de Secuencia Molecular , Homología de Secuencia de Ácido Nucleico
19.
J Biol Chem ; 264(35): 21146-52, 1989 Dec 15.
Artículo en Inglés | MEDLINE | ID: mdl-2556396

RESUMEN

The most widely studied "relaxed" mutant of the relA locus, the relA1 allele, is shown here to consist of an IS2 insertion between the 85th and 86th codons of the otherwise wild-type relA structural gene, which normally encodes a 743-amino acid (84 kDa) protein. The RelA protein is a ribosome-dependent ATP:GTP (GDP) pyrophosphoryltransferase that is activated during the stringent response to amino acid starvation and thereby occasions the accumulation of guanosine 3',5'-bispyrophosphate (ppGpp). We propose that the IS2 insertion functionally splits the RelA protein into two (alpha and beta) peptide fragments which can complement each other in trans to yield residual ppGpp synthetic activity; neither fragment shows this activity when expressed alone. Cell strains with a single copy relA null allele show physiological behavior that is much the same as relA1 mutant strains. Both relA1 and relA null strains accumulate ppGpp during glucose starvation and do not accumulate ppGpp during the stringent response. The presence of ppGpp in verifiable relA null strains is interpreted as unequivocal evidence for an alternate route of ppGpp synthesis that exists in addition to the relA-dependent reaction.


Asunto(s)
Alelos , Escherichia coli/genética , GTP Pirofosfoquinasa/genética , Genes Bacterianos , Mutación , Fosfotransferasas/genética , Secuencia de Aminoácidos , Secuencia de Bases , Southern Blotting , Western Blotting , Clonación Molecular , ADN Bacteriano/genética , Genotipo , Datos de Secuencia Molecular , Peso Molecular , Hibridación de Ácido Nucleico , Plásmidos , Mapeo Restrictivo , Transcripción Genética
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