User:Jarle Pahr/Stringent response

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Notes on the bacterial stringent reponse.

Measuring (p)ppGpp


Cashel, M. 1994. Detection of (p)ppGpp accumulation patterns in Escherichia coli mutants. Methods Mol. Genet.3: 341–356

A rapid method for the determination of guanosine 5'-diphosphate-3'-diphosphate and guanosine 5'-triphosphate-3'-diphosphate by high-performance liquid chromatography. Analytical Biochemistry Volume 121, Issue 1, 1982, Pages 135-139.


Identification of the bacterial alarmone guanosine 5′-diphosphate 3′-diphosphate (ppGpp) in plants:

EshA Accentuates ppGpp Accumulation and Is Conditionally Required for Antibiotic Production in Streptomyces coelicolor A3(2):

Metabolic Initiation of Differentiation and Secondary Metabolism by Streptomyces griseus: Significance of the Stringent Response (ppGpp) and GTP Content in Relation to A Factor:

Highly selective detection of bacterial alarmone ppGpp with an off–on fluorescent probe of copper-mediated silver nanoclusters:

Selective fluorometric detection of pyrophosphate and stringent alarmone with copper(II)–2,6-bis(2-benzimidazolyl)pyridine complex:

Two Novel Point Mutations in Clinical Staphylococcus aureus Reduce Linezolid Susceptibility and Switch on the Stringent Response to Promote Persistent Infection:

Occurrence of the stringent response in Streptomyces sp. and its significance for the initiation of morphological and physiological differentiation:

Mutant strains

Construction of the Escherichia coli DL11w-3 Strain with spoT relA Double Deletions:

Construction of Escherichia coli K-12 Strain Deficient in relA and SpoT using the lambda Red site-specific recombinase system:

Antibiotic tolerance

Ampicillin Resistance is Increased in Escherichia coli K12 relA and spoT mutants but Sub-inhibitory Pretreatment Does Not Induce Adaptive Resistance:

Antibiotic Tolerance in Escherichia coli under Stringent Response Correlates to Increased Catalase Activity:

Growth rate

Promoter studies

A hyper-mutant of the unusual sigma70-Pr promoter bypasses synergistic ppGpp/DksA co-stimulation.

Fluorescence-based reporters

Sternberg 1999.

  • rrnBp1 coupled to GFP-LVA.

Shah 2006.

  • FACS isolation of persisters, based on fluorescent system from Sternberg 1999.

Rybtke 2012. Fluorescence-Based Reporterfor Gauging Cyclic Di-GMP Levels in Pseudomonas aeruginosa.

Transcriptional profiling

Durfee et al. 2008:

Traxler et al. 2008:

ppGpp synthesis ,degradation and turnover :

"The basal level of ppGpp in NF162 (RC-) is about 0.04 nmole per OD unit (ref 36)." :

"the high level of RpoS in one laboratory strain (MC4100) was partially dependent on an elevated basal level of ppGpp, an alarmone responding to stress and starvation. The elevated ppGpp was caused by two mutations in spoT"

E coli ppGpp biosynthesis pathway at BioCyc:

Indution of stringent response

The stringent response can be inducted by several methods, which increase levels of (p)ppGpp either directly or indirectly.

  • Overexpression of ppGpp synthetase (ex. RelA, RelSeq).
  • Valine treatmet (E. coli K-12)
  • Antibiotics.


Dalebroux and Swanson 2012: "A stress response coordinated by guanosine tetraphosphate and guanosine pentaphosphate, in which cells rapidly inhibit synthesis of stable RNA, ribosomes and proteins, leading to growth arrest."


Mendeley article collection: groups/842261/stringent-response/papers/

Key papers

Original discovery of ppGpp: Mike Cashel and Jonathan Gallant. Nature 221 838-841, 1975. Two Compounds implicated in the Function of the RC Gene of Escherichia coli.

Direct relevance



Gummeson et al. A Proximal Promoter Element Required for Positive Transcriptional Control by ppGpp and DksA during the Stringent Response.:



Chiang et al. 2011: On the Limited Role of relA in Kanamycin and Amino Acid Starvation Induced Stringency and Subsequent Antibiotic Cross- protection in Escherichia coli

Traxler et al. 2011:

2011.Tetracycline Modulates the Valine Induced Stringent Response and Decreases Expressed RpoS in Escherichia coli.

2010: ppGpp conjures bacterial virulence.

When times are good and when times are bad:

See also

2011. The RelA/SpoT Homolog (RSH) Superfamily: Distribution and Functional Evolution of ppGpp Synthetases and Hydrolases across the Tree of Life:


2009. Cell cycle synchronization of E. coli using the stringent response, with fluorescence labeling assays for DNA content and replication:

Ferullo DJ, Lovett ST (2008) The Stringent Response and Cell Cycle Arrest in Escherichia coli. PLoS Genet 4(12): e1000300. doi:10.1371/journal.pgen.1000300

Potrykus & Cashel 2008. (p)ppGpp: still magical?

Traxler et al. 2008. The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli.:

Intramolecular Regulation of the Opposing (p)ppGpp Catalytic Activities of RelSeq, the Rel/Spo Enzyme from Streptococcus equisimilis:


Sternberg et al. 1999. Distribution of Bacterial Growth Activity in Flow-Chamber Biofilms:

Functional interactions between translation, transcription and ppGpp in growing Escherichia coli.


Molecular and General Genetics MGG November 1987, Volume 210, Issue 1, pp 1-4 Hierarchy of the strength of Escherichia coli stringent control signals:

1984. ppGpp inhibition of elongation factors Tu, G and Ts during polypeptide synthesis:


Correlation between the serine sensitivity and the derepressibility of the ilv genes in Escherichia coli relA- mutants.:

Amino Acid Starvation in Escherichia coli K-12: Characteristics of the Translation Process:

1972. On the Turnover of ppGpp in Escherichia coli. JOKATHAN GALLANT, GARY MARGASON, AND BETSY FINCH. THE JOURNAL OF BIOLOGICAL CHEMISTRY. Vol. 247, No. 19, Issue of October 10, pp. 6055-6058, 1972.

From the introduction: "When Escherichia coli cells are deprived of an essential amino acid (1,2) or are unable to activate one (3) there ensues a comprehensive adjustment of cellular activity termed the "stringent" response."

References 1,2 and 3 are [Sands & Robers 1952 J Bacteriol 63, 505], [Pardee and Prestidge LS 1956 J Bacteriol 71, 677] and [Neidhardt FC 1966 Bacteriol Rev 30, 701], respectively.

On the regulation of guanosine tetraphosphate levels in stringent and relaxed strains of Escherichia coli. J. Biol. Chem. 246:4381-4385.


  • The Control of Ribonucleic Acid Synthesis in Escherichia coli

IV. RELEVANCE OF UNUSUAL PHOSPHORYLATED COMPOUNDS FROM AMINO ACID-STARVED STRINGENT STRAINS. Michael Cashel June 25, 1969 The Journal of Biological Chemistry, 244, 3133-3141.

  • Mike Cashel and Jonathan Gallant. Nature 221 838-841, 1969. Two Compounds implicated in the Function of the RC Gene of Escherichia coli.

1968. Bacteriological reviews. Physiology and genetics of the "Ribonucleic acid control" locus of Escherichia coli. Gordon Edlin and Paul Broda.

  • Amino Acid Regulation of the Rates of Synthesis and Chain Elongation of Ribonucleic Acid in Escherichia coli. Robert M. Winslow and Robert A. Lazzarini. June 25, 1969 The Journal of Biological Chemistry, 244, 3387-3392:

Contains the quote. "Various hypotheses have been proposed to explain the stringent response (reviewed in Reference 2)." with reference to Edlin G and Broda P, Bacteriol Rev 32, 206 (1968).

Several articles list this as their reference for the term "Stringent response". The term as quoted does not appear in the article. However, the following quote establishes the "RC" locus nomenclature:

"The amino acid-independent RNA synthesis in this recombinant shows that there must exist a chromosomal locus, which we shall call RC, that in its RCrel allelic state of the 58-161 donor line produces less stringent, i.e., "relaxed," amino acid control of RNA synthesis than its RCSt, or "stringent," allele of the F- recipient line."


Indirect/general relevance and related research

Shared control of gene expression in bacteria by transcription factors and global physiology of the cell:

Indirect and suboptimal control of gene expression is widespread in bacteria:


Dissecting specific and global transcriptional regulation of bacterial gene expression:

Evaluation of the E. coli ribosomal rrnB P1 promoter and phage-derived lysis genes for the use in a biological containment system: A concept study.


(p)ppGpp: still magical? :

Jain 2006. ppGpp: stringent response and survival:

Dalebroux and Swanson. ppGpp - maginc beyond RNA polymerase.

Bacterial lifestyle shapes stringent response activation

Revisiting the stringent response, ppGpp and starvation signaling: Dipankar Chatterji and Anil Kumar Ojha. Current Opinion in Microbiology 2001, 4:160–165.

Magnusson. Trends Microbiol. 2005 May;13(5):236-42. ppGpp: a global regulator in Escherichia coli.:

Bacterial nucleotide-based second messengers:

Cashel 1975. Regulation of Bacterial ppGpp and pppGpp.

Bacterial lifestyle shapes stringent response activation:


Mike Cashel and J Gallant

F C Neidhardt.


The first chronological hit for the search term "Stringent response" in Google Scholar is the article "Effects of amino acid starvation upon constitutive tryptophan messenger RNA synthesis". John D. Stubbs†, Benjamin D. Hall. Journal of Molecular Biology Volume 37, Issue 2, 28 October 1968, Pages 303–312

It contains the quote " Stent & Brenner (1961) found quantitative variations in the stringent response depending upon the amino acid withheld.".