User:Jarle Pahr/Stringent response

Notes on the bacterial stringent reponse.

Measuring (p)ppGpp

Methods:

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

http://pubs.acs.org/stoken/beta/select/pdf/10.1021/ja0759139

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.

Applications:

Identification of the bacterial alarmone guanosine 5′-diphosphate 3′-diphosphate (ppGpp) in plants: http://www.pnas.org/content/101/12/4320.full

EshA Accentuates ppGpp Accumulation and Is Conditionally Required for Antibiotic Production in Streptomyces coelicolor A3(2): http://jb.asm.org/content/188/13/4952.full

Metabolic Initiation of Differentiation and Secondary Metabolism by Streptomyces griseus: Significance of the Stringent Response (ppGpp) and GTP Content in Relation to A Factor: http://jb.asm.org/content/169/8/3608.full.pdf+html

http://jb.asm.org/content/169/8/3608.abstract?ijkey=3f49d1f5e244870e580f7b04bd69cdbff46e7494&keytype2=tf_ipsecsha

http://jb.asm.org/content/179/8/2658.abstract?ijkey=ee16ad05d68c3fe53e4eef5feb7aab39ea4a0ac6&keytype2=tf_ipsecsha

http://jb.asm.org/content/177/17/5161.full.pdf

Highly selective detection of bacterial alarmone ppGpp with an off–on fluorescent probe of copper-mediated silver nanoclusters: http://www.sciencedirect.com/science/article/pii/S0956566313003904

Selective fluorometric detection of pyrophosphate and stringent alarmone with copper(II)–2,6-bis(2-benzimidazolyl)pyridine complex: http://www.sciencedirect.com/science/article/pii/S095656631100649X

Two Novel Point Mutations in Clinical Staphylococcus aureus Reduce Linezolid Susceptibility and Switch on the Stringent Response to Promote Persistent Infection: http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1000944

Occurrence of the stringent response in Streptomyces sp. and its significance for the initiation of morphological and physiological differentiation: http://www.ncbi.nlm.nih.gov/pubmed/3794657

Mutant strains

Construction of the Escherichia coli DL11w-3 Strain with spoT relA Double Deletions: http://www.microbiology.ubc.ca/sites/default/files/roles/drupal_ungrad/JEMI/16/JEMI16_96-100.pdf

Construction of Escherichia coli K-12 Strain Deficient in relA and SpoT using the lambda Red site-specific recombinase system: http://www.microbiology.ubc.ca/sites/default/files/roles/drupal_ungrad/JEMI/16/JEMI16_90-95.pdf

Antibiotic tolerance

Ampicillin Resistance is Increased in Escherichia coli K12 relA and spoT mutants but Sub-inhibitory Pretreatment Does Not Induce Adaptive Resistance: http://www.microbiology.ubc.ca/sites/default/files/roles/drupal_ungrad/JEMI/17/07.3A.pdf

Antibiotic Tolerance in Escherichia coli under Stringent Response Correlates to Increased Catalase Activity: http://www.microbiology.ubc.ca/sites/default/files/roles/drupal_ungrad/JEMI/17/08.1C.pdf

Growth rate

http://www.ncbi.nlm.nih.gov/pubmed/7815948

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC135074/

http://jb.asm.org/content/173/3/1168

Promoter studies

A hyper-mutant of the unusual sigma70-Pr promoter bypasses synergistic ppGpp/DksA co-stimulation. http://www.ncbi.nlm.nih.gov/pubmed/21447563

Fluorescence-based reporters

http://stringentresponse.blogspot.no/2012/07/igem2011-gfp-based-readout-for-ppgpp.html

Sternberg 1999. http://aem.asm.org/content/65/9/4108.full

• rrnBp1 coupled to GFP-LVA.

Shah 2006. http://www.biomedcentral.com/1471-2180/6/53

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

Rybtke 2012. Fluorescence-Based Reporterfor Gauging Cyclic Di-GMP Levels in Pseudomonas aeruginosa. http://www.ncbi.nlm.nih.gov/pubmed/22582064

Transcriptional profiling

Durfee et al. 2008: http://jb.asm.org/content/190/3/1084.full

Traxler et al. 2008: http://onlinelibrary.wiley.com/doi/10.1111/j.1365-2958.2008.06229.x/abstract

ppGpp synthesis ,degradation and turnover

http://www.jbc.org/content/247/19/6055.full.pdf+html :

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

http://mic.sgmjournals.org/content/154/9/2887.long :

"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: http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=PPGPPMET-PWY

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.

Definitions

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."

Bibliography

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

2010s

2013:

Gummeson et al. A Proximal Promoter Element Required for Positive Transcriptional Control by ppGpp and DksA during the Stringent Response.: http://www.jbc.org/content/early/2013/06/07/jbc.M113.479998.long

2012:'

Relacin: http://www.ncbi.nlm.nih.gov/pubmed/23028324

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 http://www.microbiology.ubc.ca/sites/default/files/roles/drupal_ungrad/JEMI/15/JEMI15_59-63.pdf

Traxler et al. 2011: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3073637/

2011.Tetracycline Modulates the Valine Induced Stringent Response and Decreases Expressed RpoS in Escherichia coli. http://www.microbiology.ubc.ca/sites/default/files/roles/drupal_ungrad/JEMI/15/JEMI15_117-124.pdf

2010: ppGpp conjures bacterial virulence. http://mmbr.asm.org/content/74/2/171.full

When times are good and when times are bad: http://www.gs.washington.edu/academics/courses/manoil/former/41108/lecture/lectureMarch7.pdf

See also http://stringentresponse.blogspot.no/2011/02/kinetics-of-stringent-response-revealed.html

2011. The RelA/SpoT Homolog (RSH) Superfamily: Distribution and Functional Evolution of ppGpp Synthetases and Hydrolases across the Tree of Life: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3153485/

2000s

2009. Cell cycle synchronization of E. coli using the stringent response, with fluorescence labeling assays for DNA content and replication: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2746677/

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 http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000300

Potrykus & Cashel 2008. (p)ppGpp: still magical? http://www.ncbi.nlm.nih.gov/pubmed/18454629

Traxler et al. 2008. The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli.: http://www.ncbi.nlm.nih.gov/pubmed/18430135

Intramolecular Regulation of the Opposing (p)ppGpp Catalytic Activities of RelSeq, the Rel/Spo Enzyme from Streptococcus equisimilis: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC135074/

1990s

Sternberg et al. 1999. Distribution of Bacterial Growth Activity in Flow-Chamber Biofilms: http://aem.asm.org/content/65/9/4108.full

Functional interactions between translation, transcription and ppGpp in growing Escherichia coli. http://www.ncbi.nlm.nih.gov/pubmed/7918639

1980s

Molecular and General Genetics MGG November 1987, Volume 210, Issue 1, pp 1-4 Hierarchy of the strength of Escherichia coli stringent control signals: http://link.springer.com/content/pdf/10.1007%2FBF00337750.pdf

1984. ppGpp inhibition of elongation factors Tu, G and Ts during polypeptide synthesis: http://link.springer.com/article/10.1007/BF00327920

1970s

Correlation between the serine sensitivity and the derepressibility of the ilv genes in Escherichia coli relA- mutants.: http://www.ncbi.nlm.nih.gov/pubmed/362163

http://www.its.caltech.edu/~skopf/ESE_Bi168/files/GALLANT_1979_STRINGENT%20CONTROL%20IN%20ESCHERICHIA-COLI.pdf

Amino Acid Starvation in Escherichia coli K-12: Characteristics of the Translation Process: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC233124/pdf/jbacter00319-0030.pdf

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. http://www.jbc.org/content/247/19/6055.full.pdf+html

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. http://www.jbc.org/content/246/14/4381.full.pdf

1960s

• 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. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC408295/

• 1968. Isolation of "Relaxed" Mutants of Escherichia coli N. FIIL AND J.D. FRIESEN': http://jb.asm.org/content/95/2/729.full.pdf

• 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: http://www.jbc.org/content/244/12/3387.full.pdf+html

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).

• Proc Natl Acad Sci U S A. 1961 December; 47(12): 2005–2014. Gunther S. Stent* and Sydney Brenner. A GENETIC LOCUS FOR THE REGULATION OF RIBONUCLEIC ACID SYNTHESIS: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC223254/

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:

http://www.nature.com/msb/journal/v9/n1/full/msb201270.html?WT.mc_id=%20TOC_MSB_13

Indirect and suboptimal control of gene expression is widespread in bacteria: http://www.nature.com

/msb/journal/v9/n1/full/msb201316.html?WT.mc_id=%20TOC_MSB_13

Dissecting specific and global transcriptional regulation of bacterial gene expression: http://www.nature.com/msb/journal/v9/n1/full/msb201314.html?WT.mc_id=%20TOC_MSB_13

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. http://www.sciencedirect.com/science/article/pii/0168165695000039

Reviews

(p)ppGpp: still magical? :http://www.ncbi.nlm.nih.gov/pubmed/18454629

Jain 2006. ppGpp: stringent response and survival: http://www.ncbi.nlm.nih.gov/pubmed/16554711

Dalebroux and Swanson. ppGpp - maginc beyond RNA polymerase. http://www.nature.com/nrmicro/journal/v10/n3/full/nrmicro2720.html

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.: http://www.ncbi.nlm.nih.gov/pubmed/15866041

Bacterial nucleotide-based second messengers: http://www.ncbi.nlm.nih.gov/pubmed/19318291

http://www.horizonpress.com/jmmb/v3/v3n4/12.pdf

Cashel 1975. Regulation of Bacterial ppGpp and pppGpp. http://www.annualreviews.org/doi/pdf/10.1146/annurev.mi.29.100175.001505

Bacterial lifestyle shapes stringent response activation: http://www.ncbi.nlm.nih.gov/pubmed/23419217

Persons

Mike Cashel and J Gallant

F C Neidhardt.

Timeline

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.".