Two naturally occurring nucleotides, abbreviated as (p)ppGpp, are the long term focus of our lab. These are analogs of GTP and GDP with 3'- pyrophosphate residues that function as important second messengers in bacteria, plants and now arguably in animal cells, including humans. It is well known that nutritional stress signals increase (p)ppGpp to provoke either positive or negative regulation of global gene expression at the transcriptional level in bacteria and plants. Recently another lab discovered genes encoding (p)ppGpp-specific hydrolases, called Mesh 1 in worms, flies and humans (Sun et al., Nature Struct. Mol. Biol. 17:1188-94, 2010). Recent genomic analyses are confirmatory (Atkinson et al., PLoS One 6(8), e23479. 2011). These enzymes are close structural and catalytic mimics of their bacterial counterparts. While it is technically difficult to demonstrate (p)ppGpp itself in animal cells, these observations seem likely to reverse a long held view that (p)ppGpp is limited to bacteria and plant organelles that have evolved from bacteria. This is because genetic studies with Drosophila reveal animal and bacterial genes in (p)ppGpp metabolism function interchangeably, like plant genes. For example, excess (p)ppGpp made in flies by a bacterial synthetase enzyme perturbs embryogenesis with a phenotype similar to what is seen with a deletion of the Mesh1 (p)ppGpp hydrolase gene. Also transcriptional profiles of global regulatory effects of excess (p)ppGpp in flies are reminiscent of similar effects in bacteria. Our research now has a new and exciting goal in addition to continue to define molecular details of (p)ppGpp regulation in bacteria. The new goal is to identify the putative eukaryotic (p)ppGpp synthetase whose existence is implied by the presence of Mesh1 hydrolase or to otherwise account for the hydrolase. The other goal is to continue to define molecular details of (p)ppGpp regulation in bacteria.

Project Start
Project End
Budget Start
Budget End
Support Year
43
Fiscal Year
2011
Total Cost
$535,852
Indirect Cost
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Kamarthapu, Venu; Epshtein, Vitaly; Benjamin, Bradley et al. (2016) ppGpp couples transcription to DNA repair in E. coli. Science 352:993-6
Gaca, Anthony O; Kudrin, Pavel; Colomer-Winter, Cristina et al. (2015) From (p)ppGpp to (pp)pGpp: Characterization of Regulatory Effects of pGpp Synthesized by the Small Alarmone Synthetase of Enterococcus faecalis. J Bacteriol 197:2908-19
Mechold, Undine; Potrykus, Katarzyna; Murphy, Helen et al. (2013) Differential regulation by ppGpp versus pppGpp in Escherichia coli. Nucleic Acids Res 41:6175-89
Vinella, Daniel; Potrykus, Katarzyna; Murphy, Helen et al. (2012) Effects on growth by changes of the balance between GreA, GreB, and DksA suggest mutual competition and functional redundancy in Escherichia coli. J Bacteriol 194:261-73
Edwards, Adrianne N; Patterson-Fortin, Laura M; Vakulskas, Christopher A et al. (2011) Circuitry linking the Csr and stringent response global regulatory systems. Mol Microbiol 80:1561-80
James, Tamara D; Cashel, Michael; Hinton, Deborah M (2010) A mutation within the {beta} subunit of Escherichia coli RNA polymerase impairs transcription from bacteriophage T4 middle promoters. J Bacteriol :
Potrykus, Katarzyna; Murphy, Helen; Chen, Xiongfong et al. (2010) Imprecise transcription termination within Escherichia coli greA leader gives rise to an array of short transcripts, GraL. Nucleic Acids Res 38:1636-51
Blankschien, Matthew D; Potrykus, Katarzyna; Grace, Elicia et al. (2009) TraR, a homolog of a RNAP secondary channel interactor, modulates transcription. PLoS Genet 5:e1000345
Rhee, Hyun-Woo; Lee, Chang-Ro; Cho, Seung-Hyon et al. (2008) Selective fluorescent chemosensor for the bacterial alarmone (p)ppGpp. J Am Chem Soc 130:784-5
Harinarayanan, Rajendran; Murphy, Helen; Cashel, Michael (2008) Synthetic growth phenotypes of Escherichia coli lacking ppGpp and transketolase A (tktA) are due to ppGpp-mediated transcriptional regulation of tktB. Mol Microbiol 69:882-94

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