User:Jarle Pahr/Stringent response

Notes on the bacterial stringent reponse.

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

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/

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

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

Ann. Rev genetics 1979. http://www.its.caltech.edu/~skopf/ESE_Bi168/files/GALLANT_1979_STRINGENT%20CONTROL%20IN%20ESCHERICHIA-COLI.pdf

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

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

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

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

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

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/

ppGpp Conjures Bacterial Virulence: http://mmbr.asm.org/content/74/2/171.full

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/

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

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

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.full.pdf

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

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