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References

  • Abel, K., Yoder, M.D., Hilgenfeld, R., and Jurnak, F. (1996) An alpha to beta conformational switch in EF-Tu. Structure 4: 11531159.
  • Aberg, A., Shingler, V., and Balsalobre, C. (2006) p)ppGpp regulates type 1 fimbriation of Escherichia coli by modulating the expression of the site-specific recombinase FimB. Mol Microbiol 60: 15201533.
  • Alvarado, J., Ghosh, A., Janovitz, T., Jauregui, A., Hasson, M.S., and Sanders, D.A. (2006) Origin of exopolyphosphatase processivity: fusion of an ASKHA phosphotransferase and a cyclic nucleotide phosphodiesterase homolog. Structure 14: 12631272.
  • Andrews, S.C., and Guest, J.R. (1988) Nucleotide sequence of the gene encoding the GMP reductase of Escherichia coli K12. Biochem J 255: 3543.
  • Aravind, L., and Koonin, E.V. (1998) The HD domain defines a new superfamily of metal-dependent phosphohydrolases. Trends Biochem Sci 23: 469472.
  • Aravind, L., and Koonin, E.V. (1999) Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. J Mol Biol 287: 10231040.
  • Artsimovitch, I., Patlan, V., Sekine, S., Vassylyeva, M.N., Hosaka, T., Ochi, K., et al. (2004) Structural basis for transcription regulation by alarmone ppGpp. Cell 117: 299310.
  • Atkinson, G.C., Tenson, T., and 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: e23479.
  • Barker, M.M., Gaal, T., and Gourse, R.L. (2001a) Mechanism of regulation of transcription initiation by ppGpp. II. Models for positive control based on properties of RNAP mutants and competition for RNAP. J Mol Biol 305: 689702.
  • Barker, M.M., Gaal, T., Josaitis, C.A., and Gourse, R.L. (2001b) Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro. J Mol Biol 305: 673688.
  • Battesti, A., and Bouveret, E. (2006) Acyl carrier protein/SpoT interaction, the switch linking SpoT-dependent stress response to fatty acid metabolism. Mol Microbiol 62: 10481063.
  • Bharat, A., Jiang, M., Sullivan, S.M., Maddock, J.R., and Brown, E.D. (2006) Cooperative and critical roles for both G domains in the GTPase activity and cellular function of ribosome-associated Escherichia coli EngA. J Bacteriol 188: 79927996.
  • Bilder, P., Lightle, S., Bainbridge, G., Ohren, J., Finzel, B., Sun, F., et al. (2006) The structure of the carboxyltransferase component of acetyl-coA carboxylase reveals a zinc-binding motif unique to the bacterial enzyme. Biochemistry 45: 17121722.
  • Bougdour, A., and Gottesman, S. (2007) ppGpp regulation of RpoS degradation via anti-adaptor protein IraP. Proc Natl Acad Sci USA 104: 1289612901.
  • Bourne, H.R., Sanders, D.A., and McCormick, F. (1991) The GTPase superfamily: conserved structure and molecular mechanism. Nature 349: 117127.
  • Bremer, H., and Dennis, P. (2008) Feedback control of ribosome function in Escherichia coli. Biochimie 90: 493499.
  • Brown, E.D. (2005) Conserved P-loop GTPases of unknown function in bacteria: an emerging and vital ensemble in bacterial physiology. Biochem Cell Biol 83: 738746.
  • Buckstein, M.H., He, J., and Rubin, H. (2007) Characterization of Nucleotide Pools as a Function of Physiological State in Escherichia coli. J Bacteriol 190: 718726.
  • Buglino, J., Shen, V., Hakimian, P., and Lima, C.D. (2002) Structural and biochemical analysis of the Obg GTP binding protein. Structure 10: 15811592.
  • Caldon, C.E., and March, P.E. (2003) Function of the universally conserved bacterial GTPases. Curr Opin Microbiol 6: 135139.
  • Cashel, M., Gentry, D.R., Hernandez, V.J., and Vinella, D. (1996) The stringent response. In Escherichia Coli and Salmonella: Cellular and Molecular Biology. Curtiss, R., and Neidhardt, F.C. (eds). Washington, DC: ASM Press, pp. 14581496.
  • Chang, D.E., Smalley, D.J., and Conway, T. (2002) Gene expression profiling of Escherichia coli growth transitions: an expanded stringent response model. Mol Microbiol 45: 289306.
  • Clamp, M., Cuff, J., Searle, S.M., and Barton, G.J. (2004) The Jalview Java alignment editor. Bioinformatics 20: 426427.
  • Daigle, D.M., Rossi, L., Berghuis, A.M., Aravind, L., Koonin, E.V., and Brown, E.D. (2002) YjeQ, an essential, conserved, uncharacterized protein from Escherichia coli, is an unusual GTPase with circularly permuted G-motifs and marked burst kinetics. Biochemistry 41: 1110911117.
  • DeLano, W.L. (2002) The PyMOL Molecular Graphics System. Palo Alto, CA: DeLano Scientific.
  • Dennis, P.P., Ehrenberg, M., and Bremer, H. (2004) Control of rRNA synthesis in Escherichia coli: a systems biology approach. Microbiol Mol Biol Rev 68: 639668.
  • Dietzler, D.N., and Leckie, M.P. (1977) Regulation of ADP-glucose synthetase, the rate-limiting enzyme of bacterial glycogen synthesis, by the pleiotropic nucleotides ppGpp and pppGpp. Biochem Biophys Res Commun 77: 14591467.
  • Dix, D.B., and Thompson, R.C. (1986) Elongation factor Tu.guanosine 3′-diphosphate 5′-diphosphate complex increases the fidelity of proofreading in protein biosynthesis: mechanism for reducing translational errors introduced by amino acid starvation. Proc Natl Acad Sci USA 83: 20272031.
  • Durfee, T., Hansen, A.M., Zhi, H., Blattner, F.R., and Jin, D.J. (2008) Transcription profiling of the stringent response in Escherichia coli. J Bacteriol 190: 10841096.
  • Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 17921797.
  • Eichel, J., Chang, Y.Y., Riesenberg, D., and Cronan, J.E., Jr (1999) Effect of ppGpp on Escherichia coli cyclopropane fatty acid synthesis is mediated through the RpoS sigma factor (sigmaS). J Bacteriol 181: 572576.
  • English, B.P., Hauryliuk, V., Sanamrad, A., Tankov, S., Dekker, N.H., and Elf, J. (2011) Single-molecule investigations of the stringent response machinery in living bacterial cells. Proc Natl Acad Sci USA 108: E365E373.
  • Fast, R., and Skold, O. (1977) Biochemical mechanism of uracil uptake regulation in Escherichia coli B. Allosteric effects on uracil phosphoribosyltransferase under stringent conditions. J Biol Chem 252: 76207624.
  • Ferullo, D.J., and Lovett, S.T. (2008) The stringent response and cell cycle arrest in Escherichia coli. PLoS Genet 4: e1000300.
  • Gallant, J., Irr, J., and Cashel, M. (1971) The mechanism of amino acid control of guanylate and adenylate biosynthesis. J Bio Chem 246: 58125816.
  • Gao, H., Zhou, Z., Rawat, U., Huang, C., Bouakaz, L., Wang, C., et al. (2007) RF3 induces ribosomal conformational changes responsible for dissociation of class I release factors. Cell 129: 929941.
  • Gentry, D.R., and Cashel, M. (1995) Cellular localization of the Escherichia coli SpoT protein. J Bacteriol 177: 38903893.
  • Gentry, D.R., Hernandez, V.J., Nguyen, L.H., Jensen, D.B., and Cashel, M. (1993) Synthesis of the stationary-phase sigma factor sigma s is positively regulated by ppGpp. J Bacteriol 175: 79827989.
  • Gilbert, H.J., Lowe, C.R., and Drabble, W.T. (1979) Inosine 5′-monophosphate dehydrogenase of Escherichia coli. Purification by affinity chromatography, subunit structure and inhibition by guanosine 5′-monophosphate. Biochem J 183: 481494.
  • Greenway, D.L., and England, R.R. (1999) The intrinsic resistance of Escherichia coli to various antimicrobial agents requires ppGpp and sigma s. Lett Appl Microbiol 29: 323326.
  • Guddat, L.W., Vos, S., Martin, J.L., Keough, D.T., and de Jersey, J. (2002) Crystal structures of free, IMP-, and GMP-bound Escherichia coli hypoxanthine phosphoribosyltransferase. Protein Sci 11: 16261638.
  • Gustavsson, N., Diez, A., and Nystrom, T. (2002) The universal stress protein paralogues of Escherichia coli are co-ordinately regulated and co-operate in the defence against DNA damage. Mol Microbiol 43: 107117.
  • Hamel, E., and Cashel, M. (1974) Guanine nucleotides in protein synthesis. Utilization of pppGpp and dGTP by initiation factor 2 and elongation factor Tu. Arch Biochem Biophys 162: 293300.
  • Hara, A., and Sy, J. (1983) Guanosine 5′-triphosphate, 3′-diphosphate 5′-phosphohydrolase. Purification and substrate specificity. J Biol Chem 258: 16781683.
  • Harshman, R.B., and Yamazaki, H. (1971) Formation of ppGpp in a relaxed and stringent strain of Escherichia coli during diauxie lag. Biochemistry 10: 39803982.
  • Harshman, R.B., and Yamazaki, H. (1972) MSI accumulation induced by sodium chloride. Biochemistry 11: 615618.
  • Heath, R.J., Jackowski, S., and Rock, C.O. (1994) Guanosine tetraphosphate inhibition of fatty acid and phospholipid synthesis in Escherichia coli is relieved by overexpression of glycerol-3-phosphate acyltransferase (plsB). J Biol Chem 269: 2658426590.
  • Hernandez, V.J., and Bremer, H. (1993) Characterization of RNA and DNA synthesis in Escherichia coli strains devoid of ppGpp. J Biol Chem 268: 1085110862.
  • Hochstadt, J. (1978) Hypoxanthine phosphoribosyltransferase and guanine phosphoribosyltransferase from enteric bacteria. Methods Enzymol 51: 549558.
  • Hochstadt-Ozer, J., and Cashel, M. (1972) The regulation of purine utilization in bacteria. V. Inhibition of purine phosphoribosyltransferase activities and purine uptake in isolated membrane vesicles by guanosine tetraphosphate. J Biol Chem 247: 70677072.
  • Hochstadt-Ozer, J., and Stadtman, E.R. (1971) The regulation of purine utilization in bacteria. I. Purification of adenine phosphoribosyltransferase from Escherichia coli K12 and control of activity by nucleotides. J Biol Chem 246: 52945303.
  • Hogg, T., Mechold, U., Malke, H., Cashel, M., and Hilgenfeld, R. (2004) Conformational antagonism between opposing active sites in a bifunctional RelA/SpoT homolog modulates (p)ppGpp metabolism during the stringent response [corrected]. Cell 117: 5768.
  • Honzatko, R.B., and Fromm, H.J. (1999) Structure-function studies of adenylosuccinate synthetase from Escherichia coli. Arch Biochem Biophys 370: 18.
  • Hou, Z., Cashel, M., Fromm, H.J., and Honzatko, R.B. (1999) Effectors of the stringent response target the active site of Escherichia coli adenylosuccinate synthetase. J Biol Chem 274: 1750517510.
  • Kanjee, U., Gutsche, I., Ramachandran, S., and Houry, W. (2011a) The enzymatic activities of the Escherichia coli basic aliphatic amino acid decarboxylases exhibit a pH zone of inhibition. Biochemistry 50: 93889398.
  • Kanjee, U., Gutsche, I., Alexopoulos, E., Zhao, B., Thibault, G., Liu, K., et al. (2011b) Linking the bacterial acid stress and stringent responses – the structure of the inducible lysine decarboxylase. EMBO J 30: 931944.
  • al-Karadaghi, S., Aevarsson, A., Garber, M., Zheltonosova, J., and Liljas, A. (1996) The structure of elongation factor G in complex with GDP: conformational flexibility and nucleotide exchange. Structure 4: 555565.
  • Kasai, K., Nishizawa, T., Takahashi, K., Hosaka, T., Aoki, H., and Ochi, K. (2006) Physiological analysis of the stringent response elicited in an extreme thermophilic bacterium, Thermus thermophilus. J Bacteriol 188: 71117122.
  • Keck, J.L., Roche, D.D., Lynch, A.S., and Berger, J.M. (2000) Structure of the RNA polymerase domain of E. coli primase. Science 287: 24822486.
  • Korch, S.B., Henderson, T.A., and Hill, T.M. (2003) Characterization of the hipA7 allele of Escherichia coli and evidence that high persistence is governed by (p)ppGpp synthesis. Mol Microbiol 50: 11991213.
  • Kristensen, O., Ross, B., and Gajhede, M. (2008) Structure of the PPX/GPPA phosphatase from Aquifex aeolicus in complex with the alarmone ppGpp. J Mol Biol 375: 14691476.
  • Kuroda, A., Murphy, H., Cashel, M., and Kornberg, A. (1997) Guanosine tetra- and pentaphosphate promote accumulation of inorganic polyphosphate in Escherichia coli. J Biol Chem 272: 2124021243.
  • Kvint, K., Hosbond, C., Farewell, A., Nybroe, O., and Nystrom, T. (2000) Emergency derepression: stringency allows RNA polymerase to override negative control by an active repressor. Mol Microbiol 35: 435443.
  • Lang, P.T., Brozell, S.R., Mukherjee, S., Pettersen, E.F., Meng, E.C., Thomas, V., et al. (2009) DOCK 6: combining techniques to model RNA-small molecule complexes. RNA 15: 12191230.
  • Lee, S., Kim, M.H., Kang, B.S., Kim, J.S., Kim, G.H., Kim, Y.G., and Kim, K.J. (2008) Crystal structure of Escherichia coli MazG, the regulator of nutritional stress response. J Biol Chem 283: 1523215240.
  • Leesong, M., Henderson, B.S., Gillig, J.R., Schwab, J.M., and Smith, J.L. (1996) Structure of a dehydratase-isomerase from the bacterial pathway for biosynthesis of unsaturated fatty acids: two catalytic activities in one active site. Structure 4: 253264.
  • Legault, L., Jeantet, C., and Gros, F. (1972) Inhibition of in vitro protein synthesis by ppGpp. FEBS Lett 27: 7175.
  • Lehoux, I.E., Mazzulla, M.J., Baker, A., and Petit, C.M. (2003) Purification and characterization of YihA, an essential GTP-binding protein from Escherichia coli. Protein Expr Purif 30: 203209.
  • Lemke, J.J., Sanchez-Vazquez, P., Burgos, H.L., Hedberg, G., Ross, W., and Gourse, R.L. (2011) Direct regulation of Escherichia coli ribosomal protein promoters by the transcription factors ppGpp and DksA. Proc Natl Acad Sci USA 108: 57125717.
  • Liu, S.W., and Milman, G. (1983) Purification and characterization of Escherichia coli guanine-xanthine phosphoribosyltransferase produced by a high efficiency expression plasmid utilizing a lambda PL promoter and CI857 temperature-sensitive repressor. J Biol Chem 258: 74697475.
  • Lohkamp, B., McDermott, G., Campbell, S.A., Coggins, J.R., and Lapthorn, A.J. (2004) The structure of Escherichia coli ATP-phosphoribosyltransferase: identification of substrate binding sites and mode of AMP inhibition. J Mol Biol 336: 131144.
  • Lueking, D.R., and Goldfine, H. (1975) The involvement of guanosine 5-diphosphate-3-diphosphate in the regulation of phospholipid biosynthesis in Escherichia coli. Lack of ppGpp inhibition of acyltransfer from acyl-ACP to sn-glycerol 3-phosphate. J Biol Chem 250: 49114917.
  • Maciag, M., Kochanowska, M., Lyzen, R., Wegrzyn, G., and Szalewska-Palasz, A. (2010) ppGpp inhibits the activity of Escherichia coli DnaG primase. Plasmid 63: 6167.
  • Magnusson, L.U., Farewell, A., and Nystrom, T. (2005) ppGpp: a global regulator in Escherichia coli. Trends Microbiol 13: 236242.
  • Magnusson, L.U., Gummesson, B., Joksimovic, P., Farewell, A., and Nystrom, T. (2007) Identical, independent, and opposing roles of ppGpp and DksA in Escherichia coli. J Bacteriol 189: 51935202.
  • Margus, T., Remm, M., and Tenson, T. (2007) Phylogenetic distribution of translational GTPases in bacteria. BMC Genomics 8: 15.
  • Martinelli, L.K., Ducati, R.G., Rosado, L.A., Breda, A., Selbach, B.P., Santos, D.S., and Basso, L.A. (2011) Recombinant Escherichia coli GMP reductase: kinetic, catalytic and chemical mechanisms, and thermodynamics of enzyme-ligand binary complex formation. Mol Biosyst 7: 12891305.
  • Maurizi, M.R., and Rasulova, F. (2002) Degradation of L-glutamate dehydrogenase from Escherichia coli: allosteric regulation of enzyme stability. Arch Biochem Biophys 397: 206216.
  • Merlie, J.P., and Pizer, L.I. (1973) Regulation of phospholipid synthesis in Escherichia coli by guanosine tetraphosphate. J Bacteriol 116: 355366.
  • Metzger, S., Sarubbi, E., Glaser, G., and Cashel, M. (1989) Protein sequences encoded by the relA and the spoT genes of Escherichia coli are interrelated. J Biol Chem 264: 91229125.
  • Miller, D.L., Cashel, M., and Weissbach, H. (1973) The interaction of guanosine 5′-diphosphate, 2′ (3′)-diphosphate with the bacterial elongation factor Tu. Arch Biochem Biophys 154: 675682.
  • Milon, P., Tischenko, E., Tomsic, J., Caserta, E., Folkers, G., La Teana, A., et al. (2006) The nucleotide-binding site of bacterial translation initiation factor 2 (IF2) as a metabolic sensor. Proc Natl Acad Sci USA 103: 1396213967.
  • Morton, D.P., and Parsons, S.M. (1977) Synergistic inhibition of ATP phosphoribosyltransferase by guanosine tetraphosphate and histidine. Biochem Biophys Res Commun 74: 172177.
  • Nakanishi, N., Abe, H., Ogura, Y., Hayashi, T., Tashiro, K., Kuhara, S., et al. (2006) ppGpp with DksA controls gene expression in the locus of enterocyte effacement (LEE) pathogenicity island of enterohaemorrhagic Escherichia coli through activation of two virulence regulatory genes. Mol Microbiol 61: 194205.
  • Nystrom, T. (2004) Growth versus maintenance: a trade-off dictated by RNA polymerase availability and sigma factor competition? Mol Microbiol 54: 855862.
  • Ochi, K., Kandala, J., and Freese, E. (1982) Evidence that Bacillus subtilis sporulation induced by the stringent response is caused by the decrease in GTP or GDP. J Bacteriol 151: 10621065.
  • Pao, C.C., and Dyess, B.T. (1981) Effect of unusual guanosine nucleotides on the activities of some Escherichia coli cellular enzymes. Biochim Biophys Acta 677: 358362.
  • Paul, B.J., Berkmen, M.B., and Gourse, R.L. (2005) DksA potentiates direct activation of amino acid promoters by ppGpp. Proc Natl Acad Sci USA 102: 78237828.
  • Persky, N.S., Ferullo, D.J., Cooper, D.L., Moore, H.R., and Lovett, S.T. (2009) The ObgE/CgtA GTPase influences the stringent response to amino acid starvation in Escherichia coli. Mol Microbiol 73: 253266.
  • Pingoud, A., Gast, F.U., Block, W., and Peters, F. (1983) The elongation factor Tu from Escherichia coli, aminoacyl-tRNA, and guanosine tetraphosphate form a ternary complex which is bound by programmed ribosomes. J Biol Chem 258: 1420014205.
  • Polakis, S.E., Guchhait, R.B., and Lane, M.D. (1973) Stringent control of fatty acid synthesis in Escherichia coli. Possible regulation of acetyl coenzyme A carboxylase by ppGpp. J Biol Chem 248: 79577966.
  • Potrykus, K., and Cashel, M. (2008) (p)ppGpp: still magical? Annu Rev Microbiol 62: 3551.
  • Potrykus, K., Murphy, H., Philippe, N., and Cashel, M. (2011) ppGpp is the major source of growth rate control in E. coli. Environ Microbiol 13: 563575.
  • Powers, T., and Walter, P. (1995) Reciprocal stimulation of GTP hydrolysis by two directly interacting GTPases. Science 269: 14221424.
  • Rangarajan, E.S., Nadeau, G., Li, Y., Wagner, J., Hung, M.N., Schrag, J.D., et al. (2006) The structure of the exopolyphosphatase (PPX) from Escherichia coli O157:H7 suggests a binding mode for long polyphosphate chains. J Mol Biol 359: 12491260.
  • Rasmussen, U.B., Mygind, B., and Nygaard, P. (1986) Purification and some properties of uracil phosphoribosyltransferase from Escherichia coli K12. Biochim Biophys Acta 881: 268275.
  • Reizer, J., Reizer, A., Saier, M.H., Jr, Bork, P., and Sander, C. (1993) Exopolyphosphate phosphatase and guanosine pentaphosphate phosphatase belong to the sugar kinase/actin/hsp 70 superfamily. Trends Biochem Sci 18: 247248.
  • Rodionov, D.G., and Ishiguro, E.E. (1995) Direct correlation between overproduction of guanosine 3′,5′-bispyrophosphate (ppGpp) and penicillin tolerance in Escherichia coli. J Bacteriol 177: 42244229.
  • Rojas, A.M., Ehrenberg, M., Andersson, S.G., and Kurland, C.G. (1984) ppGpp inhibition of elongation factors Tu, G and Ts during polypeptide synthesis. Mol Gen Genet 197: 3645.
  • Romeo, T., and Preiss, J. (1989) Genetic regulation of glycogen biosynthesis in Escherichia coli: in vitro effects of cyclic AMP and guanosine 5′-diphosphate 3′-diphosphate and analysis of in vivo transcripts. J Bacteriol 171: 27732782.
  • Romeo, T., Gong, M., Liu, M.Y., and Brun-Zinkernagel, A.M. (1993) Identification and molecular characterization of csrA, a pleiotropic gene from Escherichia coli that affects glycogen biosynthesis, gluconeogenesis, cell size, and surface properties. J Bacteriol 175: 47444755.
  • Schreiber, G., Metzger, S., Aizenman, E., Roza, S., Cashel, M., and Glaser, G. (1991) Overexpression of the relA gene in Escherichia coli. J Biol Chem 266: 37603767.
  • Schreiber, G., Ron, E.Z., and Glaser, G. (1995) ppGpp-mediated regulation of DNA replication and cell division in Escherichia coli. Curr Microbiol 30: 2732.
  • Scrima, A., and Wittinghofer, A. (2006) Dimerisation-dependent GTPase reaction of MnmE: how potassium acts as GTPase-activating element. EMBO J 25: 29402951.
  • Shimosaka, M., Fukuda, Y., Murata, K., and Kimura, A. (1985) Purification and properties of orotate phosphoribosyltransferases from Escherichia coli K-12, and its derivative purine-sensitive mutant. J Biochem 98: 16891697.
  • Song, H., Parsons, M.R., Rowsell, S., Leonard, G., and Phillips, S.E. (1999) Crystal structure of intact elongation factor EF-Tu from Escherichia coli in GDP conformation at 2.05 A resolution. J Mol Biol 285: 12451256.
  • Spira, B., and Yagil, E. (1998) The relation between ppGpp and the PHO regulon in Escherichia coli. Mol Gen Genet 257: 469477.
  • Spira, B., Silberstein, N., and Yagil, E. (1995) Guanosine 3′,5′-bispyrophosphate (ppGpp) synthesis in cells of Escherichia coli starved for Pi. J Bacteriol 177: 40534058.
  • Stayton, M.M., and Fromm, H.J. (1979) Guanosine 5′-diphosphate-3′-diphosphate inhibition of adenylosuccinate synthetase. J Biol Chem 254: 25792581.
  • Stein, J.P., Jr, and Bloch, K.E. (1976) Inhibition of E. coli beta-hydroxydecanoyl thioester dehydrase by ppGpp. Biochem Biophys Res Commun 73: 881884.
  • Stent, G.S., and Brenner, S. (1961) A genetic locus for the regulation of ribonucleic acid synthesis. Proc Natl Acad Sci USA 47: 20052014.
  • Svitil, A.L., Cashel, M., and Zyskind, J.W. (1993) Guanosine tetraphosphate inhibits protein synthesis in vivo. A possible protective mechanism for starvation stress in Escherichia coli. J Biol Chem 268: 23072311.
  • Tedin, K., and Norel, F. (2001) Comparison of DeltarelA strains of Escherichia coli and Salmonella enterica serovar Typhimurium suggests a role for ppGpp in attenuation regulation of branched-chain amino acid biosynthesis. J Bacteriol 183: 61846196.
  • Thanbichler, M., Bock, A., and Goody, R.S. (2000) Kinetics of the interaction of translation factor SelB from Escherichia coli with guanosine nucleotides and selenocysteine insertion sequence RNA. J Biol Chem 275: 2045820466.
  • Trautinger, B.W., Jaktaji, R.P., Rusakova, E., and Lloyd, R.G. (2005) RNA polymerase modulators and DNA repair activities resolve conflicts between DNA replication and transcription. Mol Cell 19: 247258.
  • Traxler, M.F., Chang, D.E., and Conway, T. (2006) Guanosine 3′,5′-bispyrophosphate coordinates global gene expression during glucose-lactose diauxie in Escherichia coli. Proc Natl Acad Sci USA 103: 23742379.
  • Traxler, M.F., Summers, S.M., Nguyen, H.T., Zacharia, V.M., Hightower, G.A., Smith, J.T., and Conway, T. (2008) The global, ppGpp-mediated stringent response to amino acid starvation in Escherichia coli. Mol Microbiol 68: 11281148.
  • Traxler, M.F., Zacharia, V.M., Marquardt, S., Summers, S.M., Nguyen, H.T., Stark, S.E., and Conway, T. (2011) Discretely calibrated regulatory loops controlled by ppGpp partition gene induction across the ‘feast to famine’ gradient in Escherichia coli. Mol Microbiol 79: 830845.
  • UniProt Consortium (2011) Ongoing and future developments at the Universal Protein Resource. Nucleic Acids Res 39: D214D219.
  • Vinella, D., Albrecht, C., Cashel, M., and D'Ari, R. (2005) Iron limitation induces SpoT-dependent accumulation of ppGpp in Escherichia coli. Mol Microbiol 56: 958970.
  • Vos, S., Parry, R.J., Burns, M.R., de Jersey, J., and Martin, J.L. (1998) Structures of free and complexed forms of Escherichia coli xanthine-guanine phosphoribosyltransferase. J Mol Biol 282: 875889.
  • Vrentas, C.E., Gaal, T., Berkmen, M.B., Rutherford, S.T., Haugen, S., Vassylyev, D.G., et al. (2008) 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. J Mol Biol 377: 551564.
  • Wang, J.D., Sanders, G.M., and Grossman, A.D. (2007) Nutritional control of elongation of DNA replication by (p)ppGpp. Cell 128: 865875.
  • Wendrich, T.M., Blaha, G., Wilson, D.N., Marahiel, M.A., and Nierhaus, K.H. (2002) Dissection of the mechanism for the stringent factor RelA. Mol Cell 10: 779788.
  • Wolf, Y.I., Aravind, L., Grishin, N.V., and Koonin, E.V. (1999) Evolution of aminoacyl-tRNA synthetases – analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res 9: 689710.
  • Wout, P., Pu, K., Sullivan, S.M., Reese, V., Zhou, S., Lin, B., and Maddock, J.R. (2004) The Escherichia coli GTPase CgtAE cofractionates with the 50S ribosomal subunit and interacts with SpoT, a ppGpp synthetase/hydrolase. J Bacteriol 186: 52495257.
  • Xiao, H., Kalman, M., Ikehara, K., Zemel, S., Glaser, G., and Cashel, M. (1991) Residual guanosine 3′,5′-bispyrophosphate synthetic activity of relA null mutants can be eliminated by spoT null mutations. J Biol Chem 266: 59805990.
  • Yang, X., and Ishiguro, E.E. (2003) Temperature-sensitive growth and decreased thermotolerance associated with relA mutations in Escherichia coli. J Bacteriol 185: 57655771.
  • Zhang, X., Liang, S.T., and Bremer, H. (2006) Feedback control of ribosome synthesis in Escherichia coli is dependent on eight critical amino acids. Biochimie 88: 11451155.