Guanosine-3',5'-bisdiphosphate - (N-6001)

ppGpp, Magic Spot, Guanosine tetraphosphate

This product is now available upon request as a custom synthesis. It is not maintained as a stocked item.


Guanosine-3',5'-Bisdiphosphate (also known as guanosine tetraphosphate, ppGpp or "magic spot*”), is a guanosine analogue containing a diphosphate moiety at both the 5' and 3' hydroxyls. Within the cell, ppGpp regulates transcription of genes affecting important bacterial metabolic processes, such as cell division, motility and adaptation (Potrykus, K., et al., Lemke, J.J., et al.) When prokaryotes and certain plants become nutritionally deficient, amino acid starvation is a direct consequence. During amino acid starvation, guanosine tetraphosphate is an important signal to start the stringent response mechanism. The result of the ppGpp signal is a stop in protein synthesis, leading to adjustments in gene expression levels and causing cells to remain dormant until normal nutritional levels are restored (Artsimovitch, I., et al.) In particular, ppGpp strongly inhibits the synthesis of components of the translation machinery such as tRNA and rRNA (Paul, B.J., et al., Gralla, J.D., et al.) while simultaneously stimulating the transcription of genes involved in amino acid biosynthesis (Artsimovitch, I., et al.). This ppGpp-mediated mechanism prevents the outflow of unnecessary energy resources to help bacteria survive until adequate amino acid levels are reached. Synthesis of ppGpp Guanosine tetraphosphate is synthesized from ATP and GDP during the stringent response mechanism (Figure 1). The RelA and SpoT proteins play a critical role in maintaining the appropriate levels of ppGpp (reviewed in (Potrykus, K., et al.)). Once synthesized, the ppGpp transcription factor binds to the RNA polymerase (Vrentas, C.E., et al.) to regulate the transcription of certain promoters in a process that, in E. coli, is assisted by protein DksA, Figure 2 (Paul, B.J., et al.). In the presence of ppGpp, tRNA and rRNA synthesis is reduced in favor of transcription of amino acid biosynthetic genes. Although the global role of ppGpp is understood, the mechanism by which ppGpp contributes to the regulation of certain promoters has not been fully characterized and varies among different bacteria (Bernardo, L.M., et al.) Molecular mechanisms of ppGpp are still being studied to better understand how different bacteria adapt to extreme circumstances through the stringent response. Stringent Response While ppGpp plays a critical role in cellular survival in vivo, several groups have contributed to our current knowledge of how guanosine tetraphosphate interacts with the RNA polymerase and other transcription factors by in vitro experiments (Lemke, J.J., Vrentas, C.E., Powell, B.S., deLivron, M.A. et al.). Most notably, Richard Gourse’s laboratory at the University of Wisconsin focuses on understanding RNA transcription regulation and the role that ppGpp plays in modulating the response to changing environmental conditions. A well-characterized transcription assay to examine the effects of added ppGpp concentration on promoter activity during in vitro transcription is described in Paul et al. Herein, we provide some general guidelines to follow in any in vitro transcription assay in which the amount of ppGpp is varied to evaluate its effect on the cellular stringent response. * Potrykus and Cashel noted two spots appeared in autoradiograms from extracts of E. coli responding to the stress of aminoacid starvation. According to Irina Artsimovitch of Ohio State University, these spots were tagged as 'magic' because "Microbiologists have wondered for half-century how this small molecule with a relatively simple structure could have such a profound effect on regulating a cell’s survival.” Basic experimental parameters for an in vitro transcription assay using ppGpp: This assay is a basic tool for the study of ppGpp in cell metabolic aspects that are sensitive to changes in the nutrient availability. One of Dr. Gourse’s basic protocols described in Schneider et al. involves the preparation of a reaction mixture that combines the appropriate reaction buffer, a DNA template (supercoiled plasmid or linear), an unbalanced pool of NTPs (where the concentration of UTP is very low), and the RNA polymerase of interest in the presence or absence of ppGpp. The transcription reaction is then incubated for the appropriate time and at the appropriate temperature, quenched using an EDTA and formamide solution, and analyzed by polyacrylamide gel electrophoresis to determine transcription yield. Other notable variations on this protocol have also been described in Krásný and Gourse, Vrentras et al., Paul et al., Carmona et al., and Bernardo et al. NOTE: Control reactions containing buffer instead of ppGpp should be included. NOTE: Salt concentration must be optimized (KCl or NaCl) for each particular promoter. The effects of ppGpp are more pronounced at high salt concentrations (Potrykus, K. et al). "The people I have dealt with have always been professional and have a good working knowledge of products .... a huge plus !!! You offer a product not available through any other source (ppGpp). I have a small lab and even though we could make the compound ourselves, not having to dedicate someone to make the compound speeds up my research endeavors. I think you are great --- really !!!" Victoria Robinson Associate Professor University of Connecticut

Product Details

Catalog No N-6001
Purity ≥85% by AX-HPLC
Extinction Coefficient 13,600 Lmol-1cm-1 at 252 nm
Molecular Formula C10H17N5O17P4 (free acid)
Molecular Weight 603.20 g/mole (free acid)
Salt Form Li+
Concentration 100 mM
Buffer H2O
Recommended Storage -20°C or below
Other Name(s) ppGpp, Magic Spot, Guanosine tetraphosphate
Backbone 3'-5'-Bisdiphosphate
Base Analog(s) Guanosine
Nucleotide Category Bisphosphate

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Vrentas, Catherine E.; Gaal, Tamas; Ross, Wilma; Ebright, Richard H.; Gourse, Richard L. . Response of RNA polymerase to ppGpp: requirement for the omega subunit and relief of this requirement by DksA.

Handke, Luke D.; Shivers, Robert P.; Sonenshein, Abraham L. . Interaction of Bacillus subtilis CodY with GTP

Potrykus, Katarzyna; Cashel, Michael . (p)ppGpp: still magical?

Artsimovitch, Irina; Patlan, Vsevolod; Sekine, Shun-ichi; Vassylyeva, Marina N.; Hosaka, Takeshi; Ochi, Kozo; Yokoyama, Shigeyuki; Vassylyev, Dmitry G. . Structural basis for transcription regulation by alarmone ppGpp.

Blankschien, Matthew D.; Lee, Jeong-Hyun; Grace, Elicia D.; Lennon, Christopher W.; Halliday, Jennifer A.; Ross, Wilma; Gourse, Richard L.; Herman, Christophe . Super DksAs: substitutions in DksA enhancing its effects on transcription initiation.

Burdette, Dara L.; Monroe, Kathryn M.; Sotelo-Troha, Katia; Iwig, Jeff S.; Eckert, Barbara; Hyodo, Mamoru; Hayakawa, Yoshihiro; Vance, Russell E. . STING is a direct innate immune sensor of cyclic di-GMP.

Persky, Nicole S.; Ferullo, Daniel J.; Cooper, Deani L.; Moore, Hayley R.; Lovett, Susan T. . The ObgE/CgtA GTPase influences the stringent response to amino acid starvation in Escherichia coli.

Boehm, Alex; Steiner, Samuel; Zaehringer, Franziska; Casanova, Alain; Hamburger, Fabienne; Ritz, Daniel; Keck, Wolfgang; Ackermann, Martin; Schirmer, Tilman; Jenal, Urs . Second messenger signalling governs Escherichia coli biofilm induction upon ribosomal stress.

Nomura, Yuhta; Takabayashi, Taito; Kuroda, Hiroshi; Yukawa, Yasushi; Sattasuk, Kwanchanok; Akita, Mitsuru; Nozawa, Akira; Tozawa, Yuzuru . ppGpp inhibits peptide elongation cycle of chloroplast translation system in vitro.

Thayil, Seema M.; Morrison, Norman; Schechter, Norman; Rubin, Harvey; Karakousis, Petros C. . The Role of the Novel Exopolyphosphatase MT0516 in Mycobacterium tuberculosis Drug Tolerance and Persistence

Furman, Ran; Sevostyanova, Anastasiya; Artsimovitch, Irina . Transcription initiation factor DksA has diverse effects on RNA chain elongation.

Lee, Jeong-Hyun; Lennon, Christopher W.; Ross, Wilma; Gourse, Richard L. . Role of the coiled-coil tip of Escherichia coli DksA in promoter control.

Konovalova, Anna; Löbach, Stephanie; Søgaard-Andersen, Lotte . A RelA-dependent two-tiered regulated proteolysis cascade controls synthesis of a contact-dependent intercellular signal in Myxococcus xanthus.

Martucci, Nicola M.; Lamberti, Anna; Vitagliano, Luigi; Cantiello, Piergiuseppe; Ruggiero, Immacolata; Arcari, Paolo; Masullo, Mariorosario . The magic spot ppGpp influences in vitro the molecular and functional properties of the elongation factor 1α from the archaeon Sulfolobus solfataricus.

Takeuchi, Kasumi; Yamada, Kosumi; Haas, Dieter . ppGpp controlled by the Gac/Rsm regulatory pathway sustains biocontrol activity in Pseudomonas fluorescens CHA0.

Crépin, Sébastien; Houle, Sébastien; Charbonneau, Marie-Ève; Mourez, Michaël; Harel, Josée; Dozois, Charles M. . Decreased expression of type 1 fimbriae by a pst mutant of uropathogenic Escherichia coli reduces urinary tract infection.

Montero, Manuel; Rahimpour, Mehdi; Viale, Alejandro M.; Almagro, Goizeder; Eydallin, Gustavo; Sevilla, Ángel; Cánovas, Manuel; Bernal, Cristina; Lozano, Ana Belén; Muñoz, Francisco José; Baroja-Fernández, Edurne; Bahaji, Abdellatif; Mori, Hirotada; Codoñer, Francisco M.; Pozueta-Romero, Javier . Systematic production of inactivating and non-inactivating suppressor mutations at the relA locus that compensate the detrimental effects of complete spot loss and affect glycogen content in Escherichia coli.

Mekler, Vladimir; Minakhin, Leonid; Borukhov, Sergei; Mustaev, Arkady; Severinov, Konstantin . Coupling of downstream RNA polymerase-promoter interactions with formation of catalytically competent transcription initiation complex.

Wang, Sufang; Wan, Bin; Zhang, Lianying; Yang, Yu; Guo, Liang-Hong . In vitro inhibition of lysine decarboxylase activity by organophosphate esters.

Zheng, Lin Ling; Huang, Cheng Zhi . Selective and sensitive colorimetric detection of stringent alarmone ppGpp with Fenton-like reagent.

Chatnaparat, Tiyakhon; Li, Zhong; Korban, Schuyler S.; Zhao, Youfu . The bacterial alarmone (p)ppGpp is required for virulence and controls cell size and survival of Pseudomonas syringae on plants.

Roghanian, Mohammad; Zenkin, Nikolay; Yuzenkova, Yulia . Bacterial global regulators DksA/ppGpp increase fidelity of transcription.

Ancona, Veronica; Lee, Jae Hoon; Chatnaparat, Tiyakhon; Oh, Jinrok; Hong, Jong-In; Zhao, Youfu . The bacterial alarmone (p)ppGpp activates the type III secretion system in Erwinia amylovora.

Chatnaparat, Tiyakhon; Li, Zhong; Korban, Schuyler S.; Zhao, Youfu . The Stringent Response Mediated by (p)ppGpp Is Required for Virulence of Pseudomonas syringae pv. tomato and Its Survival on Tomato.

Ihara, Yuta; Ohta, Hiroyuki; Masuda, Shinji . A highly sensitive quantification method for the accumulation of alarmone ppGpp in Arabidopsis thaliana using UPLC-ESI-qMS/MS.

Doniselli, Nicola; Rodriguez-Aliaga, Piere; Amidani, Davide; Bardales, Jorge A.; Bustamante, Carlos; Guerra, Daniel G.; Rivetti, Claudio . New insights into the regulatory mechanisms of ppGpp and DksA on Escherichia coli RNA polymerase-promoter complex.

Fan, Haitian; Hahm, Joseph; Diggs, Stephen; Perry, J. Jefferson P.; Blaha, Gregor . Structural and Functional Analysis of BipA, a Regulator of Virulence in Enteropathogenic Escherichia coli.

González-Olvera, Julio C.; Martínez-Reyes, José; González-Jasso, Eva; Pless, Reynaldo C. . Determination of pKa values for deprotonable nucleobases in short model oligonucleotides.

Sivapragasam, Smitha; Grove, Anne . Streptomyces coelicolor XdhR is a direct target of (p)ppGpp that controls expression of genes encoding xanthine dehydrogenase to promote purine salvage.

Sugliani, Matteo; Abdelkefi, Hela; Ke, Hang; Bouveret, Emmanuelle; Robaglia, Christophe; Caffarri, Stefano; Field, Ben . An Ancient Bacterial Signaling Pathway Regulates Chloroplast Function to Influence Growth and Development in Arabidopsis.

Maouche, Rim; Burgos, Hector L.; My, Laetitia; Viala, Julie P.; Gourse, Richard L.; Bouveret, Emmanuelle . Coexpression of Escherichia coli obgE, Encoding the Evolutionarily Conserved Obg GTPase, with Ribosomal Proteins L21 and L27.

Zhang, Tengfei; Zhu, Jiawen; Wei, Shun; Luo, Qingping; Li, Lu; Li, Shengqing; Tucker, Alexander; Shao, Huabin; Zhou, Rui . The roles of RelA/(p)ppGpp in glucose-starvation induced adaptive response in the zoonotic Streptococcus suis.

Xu, Xiaohui; Yu, Hua; Zhang, Di; Xiong, Junzhi; Qiu, Jing; Xin, Rong; He, Xiaomei; Sheng, Halei; Cai, Wenqiang; Jiang, Lu; Zhang, Kebin; Hu, Xiaomei . Role of ppGpp in Pseudomonas aeruginosa acute pulmonary infection and virulence regulation.

Hood, Rachel D.; Higgins, Sean A.; Flamholz, Avi; Nichols, Robert J.; Savage, David F. . The stringent response regulates adaptation to darkness in the cyanobacterium Synechococcus elongatus.

Monteferrante, C. G.; Jirgensons, A.; Varik, V.; Hauryliuk, V.; Goessens, W. H. F.; Hays, J. P. . Evaluation of the characteristics of leucyl-tRNA synthetase (LeuRS) inhibitor AN3365 in combination with different antibiotic classes.

Berditsch, Marina; Lux, Hannah; Babii, Oleg; Afonin, Sergii; Ulrich, Anne S. . Therapeutic Potential of Gramicidin S in the Treatment of Root Canal Infections.

Gkekas, Sotirios; Singh, Ranjan Kumar; Shkumatov, Alexander V.; Messens, Joris; Fauvart, Maarten; Verstraeten, Natalie; Michiels, Jan; Versées, Wim . Structural and biochemical analysis of Escherichia coli ObgE, a central regulator of bacterial persistence.

Gopalkrishnan, Saumya; Ross, Wilma; Chen, Albert Y.; Gourse, Richard L. . TraR directly regulates transcription initiation by mimicking the combined effects of the global regulators DksA and ppGpp.

Niu, Wenyu; Guo, Jianbo; Lian, Jing; Song, Yuanyuan; Lu, Caicai; Li, Haibo; Han, Yi; Yin, Pengna . Rapid start-up of denitrifying granular sludge by dosing with semi-starvation fluctuation C/N ratio strategy.

Hesketh, Andy; Vergnano, Marta; Wan, Chris; Oliver, Stephen G. . Bacterial Signaling Nucleotides Inhibit Yeast Cell Growth by Impacting Mitochondrial and Other Specifically Eukaryotic Functions.

Katayama, Yuki; Azechi, Takuya; Miyazaki, Motoyasu; Takata, Tohru; Sekine, Miwa; Matsui, Hidehito; Hanaki, Hideaki; Yahara, Koji; Sasano, Hiroshi; Asakura, Kota; Takaku, Tomoiku; Ochiai, Tomonori; Komatsu, Norio; Chambers, Henry F. . Prevalence of Slow-Growth Vancomycin Nonsusceptibility in Methicillin-Resistant Staphylococcus aureus.

Cuthbert, Bonnie J.; Ross, Wilma; Rohlfing, Amy E.; Dove, Simon L.; Gourse, Richard L.; Brennan, Richard G.; Schumacher, Maria A. . Dissection of the molecular circuitry controlling virulence in Francisella tularensis.

Basu, Arnab; Yap, Mee-Ngan F. . Disassembly of the Staphylococcus aureus hibernating 100S ribosome by an evolutionarily conserved GTPase.

Sivapragasam, Smitha; Deochand, Dinesh K.; Meariman, Jacob K.; Grove, Anne . The Stringent Response Induced by Phosphate Limitation Promotes Purine Salvage in Agrobacterium fabrum.

Girard, Mary E.; Gopalkrishnan, Saumya; Grace, Elicia D.; Halliday, Jennifer A.; Gourse, Richard L.; Herman, Christophe . DksA and ppGpp Regulate the σ(S) Stress Response by Activating Promoters for the Small RNA DsrA and the Anti-Adapter Protein IraP.

Ghosh, Anirban; Baltekin, Özden; Wäneskog, Marcus; Elkhalifa, Dina; Hammarlöf, Disa L.; Elf, Johan; Koskiniemi, Sanna . Contact-dependent growth inhibition induces high levels of antibiotic-tolerant persister cells in clonal bacterial populations.

Sherlock, Madeline E.; Sudarsan, Narasimhan; Stav, Shira; Breaker, Ronald R. . Tandem riboswitches form a natural Boolean logic gate to control purine metabolism in bacteria.

Chen, Bin Bin; Liu, Meng Li; Zhan, Lei; Li, Chun Mei; Huang, Cheng Zhi . Terbium(III) Modified Fluorescent Carbon Dots for Highly Selective and Sensitive Ratiometry of Stringent.

Chen, Jia; Huang, Yanni; Yang, Xiaoyan; Zhang, Haijuan; Li, Zhan; Qin, Bo; Chen, Xingguo; Qiu, Hongdeng . Highly sensitive and visual detection of guanosine 3'-diphosphate-5'-di(tri)phosphate (ppGpp) in bacteria based on copper ions-mediated

Knappenberger, Andrew John; Reiss, Caroline Wetherington; Strobel, Scott A. . Structures of two aptamers with differing ligand specificity reveal ruggedness in the functional landscape of RNA.

Tapscott, Timothy; Kim, Ju-Sim; Crawford, Matthew A.; Fitzsimmons, Liam; Liu, Lin; Jones-Carson, Jessica; Vázquez-Torres, Andrés . Guanosine tetraphosphate relieves the negative regulation of Salmonella pathogenicity island-2 gene transcription exerted by the AT-rich ssrA discriminator region.

Schofield, Whitman B.; Zimmermann-Kogadeeva, Maria; Zimmermann, Michael; Barry, Natasha A.; Goodman, Andrew L. . The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut.

Peselis, Alla; Serganov, Alexander . ykkC riboswitches employ an add-on helix to adjust specificity for polyanionic ligands.

Jin, Hui; Lao, Yong Min; Zhou, Jin; Zhang, Huai Jin; Cai, Zhong Hua . A rapid UHPLC-HILIC method for algal guanosine 5'-diphosphate 3'-diphosphate (ppGpp) and the potential separation mechanism.

Lu, Hang; Huang, Yili . Transcriptome Analysis of Novosphingobium pentaromativorans US6-1 Reveals the Rsh Regulon and Potential Molecular Mechanisms of N-acyl-l-homoserine Lactone Accumulation.

Travis, BA;Ramsey, KM;Prezioso, SM;Tallo, T;Wandzilak, JM;Hsu, A;Borgnia, M;Bartesaghi, A;Dove, SL;Brennan, RG;Schumacher, MA; . Structural Basis for Virulence Activation of Francisella tularensis

Schofield, WB;Zimmermann-Kogadeeva, M;Zimmermann, M;Barry, NA;Goodman, AL; . The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut

Wang, B;Svetlov, V;Wolf, YI;Koonin, EV;Nudler, E;Artsimovitch, I; . Allosteric Activation of SARS-CoV-2 RNA-Dependent RNA Polymerase by Remdesivir Triphosphate and Other Phosphorylated Nucleotides

Wang, B;Svetlov, D;Artsimovitch, I; . NMPylation and de-NMPylation of SARS-CoV-2 Nsp9 by the NiRAN domain

B . ppGpp is a bacterial cell size regulator

Bai, K;Yan, H;Chen, X;Lyu, Q;Jiang, N;Li, J;Luo, L; . The Role of RelA and SpoT on ppGpp Production, Stress Response, Growth Regulation, and Pathogenicity in Xanthomonas campestris pv. campestris