Crossref journal-article
Public Library of Science (PLoS)
PLoS ONE (340)
Bibliography

Atkinson, G. C., Tenson, T., & Hauryliuk, V. (2011). The RelA/SpoT Homolog (RSH) Superfamily: Distribution and Functional Evolution of ppGpp Synthetases and Hydrolases across the Tree of Life. PLoS ONE, 6(8), e23479.

Authors 3
  1. Gemma C. Atkinson (first)
  2. Tanel Tenson (additional)
  3. Vasili Hauryliuk (additional)
References 101 Referenced 417
  1. 10.1016/j.mib.2009.01.007 / Curr Opin Microbiol / Bacterial nucleotide-based second messengers. by C Pesavento (2009)
  2. {'key': 'ref2', 'first-page': '562', 'article-title': 'cAMP, c-di-GMP, c-di-AMP and now cGMP: bacteria use them all! Mol Microbiol', 'volume': '79', 'author': 'M Gomelsky', 'year': '2011'} / cAMP, c-di-GMP, c-di-AMP and now cGMP: bacteria use them all! Mol Microbiol by M Gomelsky (2011)
  3. {'key': 'ref3', 'first-page': '585', 'article-title': 'Comparative genomics and evolution of genes encoding bacterial (p)ppGpp synthetases/hydrolases (the Rel, RelA and SpoT proteins).', 'volume': '3', 'author': 'G Mittenhuber', 'year': '2001', 'journal-title': 'J Mol Microbiol Biotechnol'} / J Mol Microbiol Biotechnol / Comparative genomics and evolution of genes encoding bacterial (p)ppGpp synthetases/hydrolases (the Rel, RelA and SpoT proteins). by G Mittenhuber (2001)
  4. 10.1016/0092-8674(77)90329-4 / Cell / Anomalous synthesis of ppGpp in growing cells. by J Gallant (1977)
  5. 10.1073/pnas.1102255108 / Single-molecule investigations of the stringent response machinery in living bacterial cells. by BP English (2011)
  6. 10.1016/S0021-9258(18)62023-X / J Biol Chem / On the regulation of guanosine tetraphosphate levels in stringent and relaxed strains of Escherichia coli. by RA Lazzarini (1971)
  7. 10.1128/jb.176.19.5949-5957.1994 / J Bacteriol / Stringent control during carbon starvation of marine Vibrio sp. strain S14: molecular cloning, nucleotide sequence, and deletion of the relA gene. by K Flardh (1994)
  8. 10.1111/j.1365-2958.2005.04601.x / Mol Microbiol / Iron limitation induces SpoT-dependent accumulation of ppGpp in Escherichia coli. by D Vinella (2005)
  9. 10.1111/j.1365-2958.2006.05442.x / Mol Microbiol / Acyl carrier protein/SpoT interaction, the switch linking SpoT-dependent stress response to fatty acid metabolism. by A Battesti (2006)
  10. 10.1128/jb.177.14.4053-4058.1995 / J Bacteriol / Guanosine 3′,5′-bispyrophosphate (ppGpp) synthesis in cells of Escherichia coli starved for Pi. by B Spira (1995)
  11. 10.1073/pnas.70.5.1564 / Proc Natl Acad Sci U S A / Synthesis of guanosine tetra- and pentaphosphate requires the presence of a codon-specific, uncharged transfer ribonucleic acid in the acceptor site of ribosomes. by W Haseltine (1973)
  12. 10.1146/annurev.micro.62.081307.162903 / Annu Rev Microbiol / (p)ppGpp: still magical? by K Potrykus (2008)
  13. 10.1038/221838a0 / Nature / Two compounds implicated in the function of the RC gene of Escherichia coli. by M Cashel (1969)
  14. 10.1038/238381a0 / Nature / MSI and MSII made on ribosome in idling step of protein synthesis. by WA Haseltine (1972)
  15. 10.1016/S0021-9258(18)33039-4 / J Biol Chem / Guanosine 5′-triphosphate, 3′-diphosphate 5′-phosphohydrolase. Purification and substrate specificity. by A Hara (1983)
  16. 10.1073/pnas.70.11.3250 / Proc Natl Acad Sci U S A / Role of guanine nucleotides in protein synthesis. Elongation factor G and guanosine 5′-triphosphate,3′-diphosphate. by E Hamel (1973)
  17. {'key': 'ref17', 'first-page': '293', 'article-title': 'Guanine nucleotides in protein synthesis. Utilization of pppGpp and dGTP by initiation factor 2 and elongation factor Tu.', 'volume': '162', 'author': 'E Hamel', 'year': '1974', 'journal-title': 'Arch Biochem Biophys'} / Arch Biochem Biophys / Guanine nucleotides in protein synthesis. Utilization of pppGpp and dGTP by initiation factor 2 and elongation factor Tu. by E Hamel (1974)
  18. 10.1016/S0021-9258(19)67694-5 / J Biol Chem / Residual guanosine 3′,5′-bispyrophosphate synthetic activity of relA null mutants can be eliminated by spoT null mutations. by H Xiao (1991)
  19. 10.1073/pnas.75.9.4180 / Proc Natl Acad Sci U S A / Mechanism of the in vitro breakdown of guanosine 5′-diphosphate 3′-diphosphate in Escherichia coli. by EA Heinemeyer (1978)
  20. 10.1016/S0968-0004(98)01293-6 / Trends Biochem Sci / The HD domain defines a new superfamily of metal-dependent phosphohydrolases. by L Aravind (1998)
  21. 10.1099/mic.0.26811-0 / Microbiology / Two relA/spoT homologous genes are involved in the morphological and physiological differentiation of Streptomyces clavuligerus. by W Jin (2004)
  22. 10.1074/jbc.271.18.10627 / J Biol Chem / A relA/spoT homologous gene from Streptomyces coelicolor A3(2) controls antibiotic biosynthetic genes. by OH Martinez-Costa (1996)
  23. 10.1128/JB.180.16.4123-4132.1998 / J Bacteriol / The relA/spoT-homologous gene in Streptomyces coelicolor encodes both ribosome-dependent (p)ppGpp-synthesizing and -degrading activities. by OH Martinez-Costa (1998)
  24. 10.1074/jbc.M704828200 / J Biol Chem / A charge reversal differentiates (p)ppGpp synthesis by monofunctional and bifunctional Rel proteins. by M Sajish (2007)
  25. 10.1128/JB.183.11.3488-3498.2001 / J Bacteriol / Functional analysis of relA and rshA, two relA/spoT homologues of Streptomyces coelicolor A3(2). by J Sun (2001)
  26. 10.1111/j.1365-2958.2011.07602.x / Mol Microbiol / The complex logic of stringent response regulation in Caulobacter crescentus: starvation signalling in an oligotrophic environment. by CC Boutte (2011)
  27. 10.1111/j.1365-2958.2007.06018.x / Mol Microbiol / Identification and functional analysis of novel (p)ppGpp synthetase genes in Bacillus subtilis. by H Nanamiya (2008)
  28. 10.1111/j.1365-2958.2007.05897.x / Mol Microbiol / Three gene products govern (p)ppGpp production by Streptococcus mutans. by JA Lemos (2007)
  29. 10.1111/j.1365-2958.2009.06653.x / Mol Microbiol / Stringent response in Vibrio cholerae: genetic analysis of spoT gene function and identification of a novel (p)ppGpp synthetase gene. by B Das (2009)
  30. 10.1038/nsmb.1906 / Nat Struct Mol Biol / A metazoan ortholog of SpoT hydrolyzes ppGpp and functions in starvation responses. by D Sun (2010)
  31. 10.1111/j.1438-8677.2011.00484.x / Signalling by the global regulatory molecule ppGpp in bacteria and chloroplasts of land plants. by Y Tozawa (2011)
  32. 10.1016/j.jmb.2008.01.042 / J Mol Biol / Still looking for the magic spot: the crystallographically defined binding site for ppGpp on RNA polymerase is unlikely to be responsible for rRNA transcription regulation. by CE Vrentas (2008)
  33. 10.1073/pnas.0606384103 / Proc Natl Acad Sci U S A / The nucleotide-binding site of bacterial translation initiation factor 2 (IF2) as a metabolic sensor. by P Milon (2006)
  34. 10.1016/j.jmb.2010.08.016 / J Mol Biol / Thermodynamic characterization of ppGpp binding to EF-G or IF2 and of initiator tRNA binding to free IF2 in the presence of GDP, GTP, or ppGpp. by VA Mitkevich (2010)
  35. 10.1038/emboj.2011.5 / EMBO J / Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase. by U Kanjee (2011)
  36. 10.1016/j.plasmid.2009.11.002 / Plasmid / ppGpp inhibits the activity of Escherichia coli DnaG primase. by M Maciag (2010)
  37. 10.1111/j.1462-2920.2010.02357.x / Environ Microbiol / ppGpp is the major source of growth rate control in E. coli. by K Potrykus (2011)
  38. 10.1016/j.mib.2008.02.001 / Curr Opin Microbiol / Control of bacterial transcription, translation and replication by (p)ppGpp. by A Srivatsan (2008)
  39. 10.1128/MMBR.00046-09 / Microbiol Mol Biol Rev / ppGpp conjures bacterial virulence. by ZD Dalebroux (2010)
  40. 10.1016/S0092-8674(04)00260-0 / Cell / Conformational antagonism between opposing active sites in a bifunctional RelA/SpoT homolog modulates (p)ppGpp metabolism during the stringent response [corrected]. by T Hogg (2004)
  41. 10.1021/bi0505316 / Biochemistry / Functional regulation of the opposing (p)ppGpp synthetase/hydrolase activities of RelMtb from Mycobacterium tuberculosis. by A Avarbock (2005)
  42. 10.1128/JB.183.2.570-579.2001 / J Bacteriol / Regulation of Escherichia coli RelA requires oligomerization of the C-terminal domain. by M Gropp (2001)
  43. 10.1128/JB.184.11.2878-2888.2002 / J Bacteriol / Intramolecular regulation of the opposing (p)ppGpp catalytic activities of Rel(Seq), the Rel/Spo enzyme from Streptococcus equisimilis. by U Mechold (2002)
  44. 10.1074/jbc.M807187200 / J Biol Chem / The significance of EXDD and RXKD motif conservation in Rel proteins. by M Sajish (2009)
  45. 10.1093/nar/gkj149 / Nucleic Acids Res / Pfam: clans, web tools and services. by RD Finn (2006)
  46. 10.1093/nar/gki198 / Nucleic Acids Res / MAFFT version 5: improvement in accuracy of multiple sequence alignment. by K Katoh (2005)
  47. 10.1093/bioinformatics/btl446 / Bioinformatics / RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. by A Stamatakis (2006)
  48. 10.1093/molbev/msq316 / Mol Biol Evol / Evolution of elongation factor G and the origins of mitochondrial and chloroplast forms. by GC Atkinson (2011)
  49. 10.1093/bioinformatics/14.9.755 / Bioinformatics / Profile hidden Markov models. by SR Eddy (1998)
  50. 10.1093/bioinformatics/btg180 / Bioinformatics / MrBayes 3: Bayesian phylogenetic inference under mixed models. by F Ronquist (2003)
  51. 10.1093/oxfordjournals.molbev.a003824 / Mol Biol Evol / Maximum-likelihood approach for gene family evolution under functional divergence. by X Gu (2001)
  52. 10.1093/molbev/msl056 / Mol Biol Evol / A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences. by X Gu (2006)
  53. 10.1093/bioinformatics/18.3.500 / Bioinformatics / DIVERGE: phylogeny-based analysis for functional-structural divergence of a protein family. by X Gu (2002)
  54. 10.1093/bioinformatics/bth195 / Bioinformatics / The DISOPRED server for the prediction of protein disorder. by JJ Ward (2004)
  55. 10.1006/jmbi.2000.3903 / J Mol Biol / Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. by O Emanuelsson (2000)
  56. {'key': 'ref56', 'article-title': 'The PyMOL Molecular Graphics System, Version 1.3r1', 'year': '2010'} / The PyMOL Molecular Graphics System, Version 1.3r1 (2010)
  57. 10.1371/journal.pbio.1000281 / PLoS Biol / The compartmentalized bacteria of the planctomycetes-verrucomicrobia-chlamydiae superphylum have membrane coat-like proteins. by R Santarella-Mellwig (2010)
  58. 10.1016/j.copbio.2006.05.005 / Curr Opin Biotechnol / The Planctomycetes, Verrucomicrobia, Chlamydiae and sister phyla comprise a superphylum with biotechnological and medical relevance. by M Wagner (2006)
  59. 10.1016/j.bpc.2006.12.003 / Biophys Chem / Synthesis and hydrolysis of pppGpp in mycobacteria: a ligand mediated conformational switch in Rel. by V Jain (2007)
  60. 10.1128/JB.01480-09 / J Bacteriol / Phylogeny of gammaproteobacteria. by KP Williams (2010)
  61. 10.1007/PL00006352 / J Mol Evol / Signature sequences in diverse proteins provide evidence of a close evolutionary relationship between the Deinococcus-thermus group and cyanobacteria. by RS Gupta (1998)
  62. 10.1098/rstb.2009.0103 / Philos Trans R Soc Lond B Biol Sci / The endosymbiotic origin, diversification and fate of plastids. by PJ Keeling (2010)
  63. 10.1073/pnas.97.7.3747 / Proc Natl Acad Sci U S A / Arabidopsis RelA/SpoT homologs implicate (p)ppGpp in plant signaling. by EA van der Biezen (2000)
  64. 10.1111/j.1469-185X.2010.00151.x / Biol Rev Camb Philos Soc / Rickettsial evolution in the light of comparative genomics. by V Merhej (2011)
  65. 10.1073/pnas.0611553104 / Proc Natl Acad Sci U S A / The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host-cell interaction genes. by NH Cho (2007)
  66. 10.1371/journal.pbio.0030248 / PLoS Biol / The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite. by H Ogata (2005)
  67. 10.1016/j.resmic.2004.09.002 / Res Microbiol / Transcriptional response of Rickettsia conorii exposed to temperature variation and stress starvation. by C Rovery (2005)
  68. 10.1128/IAI.00048-11 / Infect Immun / Complementation of Rickettsia rickettsii RelA/SpoT Restores a Nonlytic Plaque Phenotype. by TR Clark (2011)
  69. 10.1038/nrg2102 / Nat Rev Genet / Network motifs: theory and experimental approaches. by U Alon (2007)
  70. 10.1016/j.resmic.2009.07.006 / Res Microbiol / Phylogeny of prokaryotes: does it exist and why should we care? by S Gribaldo (2009)
  71. 10.1126/science.1196720 / Science / Evolution. Intermediate steps. by DP Devos (2010)
  72. 10.1038/nature09333 / Nature / Fundamental limits on the suppression of molecular fluctuations. by I Lestas (2010)
  73. 10.1016/j.tcb.2009.08.008 / Trends Cell Biol / A single molecule view of gene expression. by DR Larson (2009)
  74. 10.1038/43199 / Nature / Robustness in simple biochemical networks. by N Barkai (1997)
  75. 10.1126/science.1183372 / Science / Structural sources of robustness in biochemical reaction networks. by G Shinar (2010)
  76. 10.1126/science.1140818 / Science / Noise in gene expression determines cell fate in Bacillus subtilis. by H Maamar (2007)
  77. 10.1371/journal.pone.0001771 / PLoS ONE / Positive feedback and noise activate the stringent response regulator rel in mycobacteria. by K Sureka (2008)
  78. 10.1016/S0966-842X(02)02403-4 / Trends Microbiol / The role of the stringent response in the pathogenesis of bacterial infections. by HP Godfrey (2002)
  79. 10.1073/pnas.1631248100 / Proc Natl Acad Sci U S A / The role of RelMtb-mediated adaptation to stationary phase in long-term persistence of Mycobacterium tuberculosis in mice. by JL Dahl (2003)
  80. 10.1046/j.1365-2958.2003.03779.x / Mol Microbiol / Characterization of the hipA7 allele of Escherichia coli and evidence that high persistence is governed by (p)ppGpp synthesis. by SB Korch (2003)
  81. 10.1126/science.1099390 / Science / Bacterial persistence as a phenotypic switch. by NQ Balaban (2004)
  82. 10.1186/1752-0509-5-18 / BMC Syst Biol / Phenotypic heterogeneity in mycobacterial stringent response. by S Ghosh (2011)
  83. 10.1073/pnas.151588598 / Proc Natl Acad Sci U S A / Intrinsic noise in gene regulatory networks. by M Thattai (2001)
  84. 10.1073/pnas.96.7.3801 / Proc Natl Acad Sci U S A / Horizontal gene transfer among genomes: the complexity hypothesis. by R Jain (1999)
  85. 10.1016/j.molcel.2010.04.015 / Mol Cell / Cost of unneeded proteins in E. coli is reduced after several generations in exponential growth. by I Shachrai (2010)
  86. 10.1074/jbc.M703820200 / J Biol Chem / Calcium-activated (p)ppGpp synthetase in chloroplasts of land plants. by Y Tozawa (2007)
  87. 10.1038/nrg2386 / Nat Rev Genet / Horizontal gene transfer in eukaryotic evolution. by PJ Keeling (2008)
  88. 10.1023/A:1024483829878 / J Muscle Res Cell Motil / cAMP signaling in Dictyostelium. Complexity of cAMP synthesis, degradation and detection. by S Saran (2002)
  89. 10.1128/MMBR.43.1.27-41.1979 / Microbiol Rev / The search for guanosine tetraphosphate (ppGpp) and other unusual nucleotides in eucaryotes. by RH Silverman (1979)
  90. 10.1074/jbc.M900582200 / J Biol Chem / Degradation of ppGpp by nudix pyrophosphatase modulates the transition of growth phase in the bacterium Thermus thermophilus. by T Ooga (2009)
  91. 10.1016/0005-2744(75)90228-4 / Biochim Biophys Acta / Purine nucleotide pyrophosphotransferase from Streptomyces morookaensis, capable of synthesizing pppApp and pppGpp. by T Oki (1975)
  92. 10.1128/JB.186.16.5249-5257.2004 / J Bacteriol / The Escherichia coli GTPase CgtAE cofractionates with the 50S ribosomal subunit and interacts with SpoT, a ppGpp synthetase/hydrolase. by P Wout (2004)
  93. 10.1111/j.1432-1033.1976.tb11103.x / Eur J Biochem / Free 3′-OH group of the terminal adenosine of the tRNA molecule is essential for the synthesis in vitro of guanosine tetraphosphate and pentaphosphate in a ribosomal system from Escherichia coli. by M Sprinzl (1976)
  94. 10.1128/JB.01195-08 / J Bacteriol / Bacteria possessing two RelA/SpoT-like proteins have evolved a specific stringent response involving the acyl carrier protein-SpoT interaction. by A Battesti (2009)
  95. 10.1139/o01-144 / Biochem Cell Biol / Dimerization of the RelA protein of Escherichia coli. by X Yang (2001)
  96. {'key': 'ref96', 'article-title': 'An ancient P-loop GTPase in rice is regulated by a higher plant-specific regulatory protein.', 'author': 'MY Cheung', 'year': '2010', 'journal-title': 'J Biol Chem'} / J Biol Chem / An ancient P-loop GTPase in rice is regulated by a higher plant-specific regulatory protein. by MY Cheung (2010)
  97. 10.1016/j.micpath.2010.12.005 / Microb Pathog / Chlamydia abortus YhbZ, a truncated Obg family GTPase, associates with the Escherichia coli large ribosomal subunit. by A Polkinghorne (2011)
  98. 10.1021/bi101563v / Biochemistry / Multispecific recognition: mechanism, evolution, and design. by A Erijman (2011)
  99. 10.1111/j.1432-1033.1977.tb11573.x / Eur J Biochem / Analysis of the relA gene product of Escherichia coli. by F Pedersen (1977)
  100. {'key': 'ref100', 'article-title': 'Evolution by gene duplication.', 'author': 'S Ohno', 'year': '1970'} / Evolution by gene duplication. by S Ohno (1970)
  101. 10.1038/nrg2689 / Nat Rev Genet / The evolution of gene duplications: classifying and distinguishing between models. by H Innan (2010)
Dates
Type When
Created 14 years ago (Aug. 9, 2011, 4:55 p.m.)
Deposited 3 years, 9 months ago (Nov. 29, 2021, 10:02 p.m.)
Indexed 22 hours, 58 minutes ago (Sept. 2, 2025, 6:43 a.m.)
Issued 14 years ago (Aug. 9, 2011)
Published 14 years ago (Aug. 9, 2011)
Published Online 14 years ago (Aug. 9, 2011)
Funders 0

None

@article{Atkinson_2011, title={The RelA/SpoT Homolog (RSH) Superfamily: Distribution and Functional Evolution of ppGpp Synthetases and Hydrolases across the Tree of Life}, volume={6}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0023479}, DOI={10.1371/journal.pone.0023479}, number={8}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Atkinson, Gemma C. and Tenson, Tanel and Hauryliuk, Vasili}, editor={Stiller, John W.}, year={2011}, month=aug, pages={e23479} }