1964-1969

• Freese, E., Park, S.W., and Cashel, M.: The developmental significance of alanine dehydrogenase in Bacillus subtilis. Proc. Natl, Acad. Sci. U.S.A. 51:1164-1172, 1964.
• Cashel, M. and Freese, E.: Excretion of alkaline phosphatase by Bacillus subtilis. Biochem. Biophys. Res. Commun. 16:541-544, 1964.
• Freese, E. and Cashel, M.: Crosslinking of deoxyribonucleic acid by exposure to low pH. Biochim. Biophys. Acta 91:67-77, 1964.
• Cashel, M. and Robbins, F. C.: Glucose-6-phosphate dehydrogenase selection by methylene blue in human cell cultures. Exptl. Cell Res. 38:585-591, 1965.
• Freese, E. and Cashel M.: Initial stages of germination. In Campbell, L. and Halvorson, H.O. (Eds.): Spores III. Ann Arbor, American Society for Microbiology, 1965, pp. 144-151.
• Gallant, J. and Cashel, M.: On the mechanism of amino acid control of RNA biosynthesis. J. Mol. Biol. 25:545-553, 1967.
• Gros, F., Gallant, J., Weisberg, R., and Cashel, M.: Decryptification of RNA polymerase in whole cells of Escherichia coli. J. Mol. Biol. 25:555-557, 1967.
• Wax, R., Freese, E., and Cashel, M.: Separation of two functional roles of L-alanine in the initiation of Bacillus subtilis spore germination. J. Bact. 74:522-529, 1967.
• Cashel, M. and Gallant, J.: Control of RNA synthesis in Escherichia coli. I. Amino acid dependence of the synthesis of the substrates of RNA polymerase. J. Mol. Biol. 34:317-330, 1968.
• Cashel, M. and Gallant, J.: Two compounds implicated in the function of the RC gene of Escherichia coli. Nature 221:838-841, 1969.
• Cashel, M., Lazzarini, R. A., and Kalbacher, B.: An improved method for thin-layer chromatography of nucleotide mixtures containing 32-P-labeled orthophosphate. J. Chromatog. 40:103-109, 1969.
• Cashel, M.: The control of RNA synthesis in Escherichia coli. IV. Relevance of unusual phosphorylated compounds from amino acid starved strains. J. Biol. Chem. 244:3133-3141, 1969.

1970-1979

• Cashel, M. and Kalbacher, B.: The control of RNA synthesis in Escherichia coli V. Characterization of a nucleotide associated with the stringent response. J. Biol. Chem. 245:2309- 2318, 1970.
• Cashel, M.: Inhibition of RNA polymerase by ppGpp, a nucleotide accumulated during the stringent response to amino acid starvation in E. coli. Cold Spring Harbor Symp. Quant. Biol. 35:407-413, 1970.
• Travers, A. A., Kamen, R. I., and Cashel, M.: The in vitro synthesis of ribosomal RNA. Cold Spring Harbor Symp. Quant. Biol. 35:415-417, 1970.
• Lazzarini, R. A., Cashel, M., and Gallant, J.: On the regulation of guanosine-tetraphosphate levels in stringent and relaxed strains of E. coli. J. Biol. Chem. 246:4381-4385, 1971.
• Gallant, J., Irr, J., and Cashel, M.: The mechanism of amino acid control of guanylate and adenylate biosynthesis. J. Biol. Chem. 246:5812-5816, 1971.
• Hochstadt-Ozer, J. and Cashel, M.: 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. 247:7067-7072, 1972.
• Miller, D. L., Cashel, M., and Weissbach, H.: The interaction of guanosine 5'-diphosphate, 2'(3')-diphosphate with the bacterial elongation factor Tu. Archiv. of Biochem. Biophys. 154:675-682, 1973.
• Raue, H. A. and Cashel, M.: Regulation of RNA synthesis in Escherichia coli I. Characterization of cells subjected to simultaneous temperature and osmotic shock. Biochim. Biophys. Acta 12:722-736, 1973.
• Raue, H. A. and Cashel, M.: Preparation of β-[32P] ribonucleoside 5'-triphosphates using permeable cells of Escherichia coli. Analyt. Biochem. 56:129-136, 1973.
• Cashel, M.: Preparation of guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (ppGpp) from Escherichia coli ribosomes. Analyt. Biochem. 57:100-107, 1974.
• Hamel, E. and Cashel, M.: The role of guanine nucleotides in protein synthesis. I. Elongation factor G and guanosine 5'triphosphate, 3'-diphosphate. Proc. Natl. Acad. Sci. U.S.A.  70:3250-3254, 1973.
• Yang, H. L., Zubay, G., Urm, E., Reiness, G., and Cashel, M.: The effects of guanosine tetraphosphate (ppGpp). guanosine pentaphosphate (pppGpp) and beta-gamma methylenylguanosine pentaphosphate (pcppGpp) on Escherichia coli gene expression in vitro. Proc. Natl. Acad. Sci. U.S.A. 71:63-67, 1974.
• Que, L., Willie, G. R., Cashel, M., Bodley, J. W., and Gray, G. R.: Guanosine 5'-diphosphate, 3'-diphosphate: Assignment of structure by 13-C nuclear magnetic resonance spectroscopy. Proc. Natl. Acad. Sci. U.S.A. 70:2563–2566, 1973.
• Hamel, E. and Cashel, M.: Guanine nucleotides in protein synthesis. II. Utilization of pppGpp and dGTP by initiation factor 2 and elongation factor Tu. Arch. Biochem. Biophys. 162:293-300, 1974.
• Cashel, M. and Gallant, J.: Cellular regulation of guanosine tetraphosphate and guanosine pentaphosphate. Ribosomes, Cold Spring Harbor Laboratories 1974, pp. 733-745.
• Raue, H. and Cashel, M.: Regulation of RNA synthesis in Escherichia coli. III. Degradation of guanosine 5'-diphosphate 3' diphosphate in cold-shocked cells. Biochim. Biophys. Acta 383:290-304, 1975.
• Cashel, M.: Bacterial regulation of ppGpp and pppGpp. Pan American Association of Biochemical Societies Revista 4:525-568, 1975.
• Cashel, M.: Regulation of bacterial ppGpp and pppGpp. Ann. Rev. Microbiol. 29:301-318, 1975.
• Cashel, M., Hamel, E., Shapshak, P., and Bouquet, M.: A. Benzon Symposium on Ribosome Regulation 9 "Interactions of ppGpp Structural Analogs with RNA Polymerase" New York, Academic Press, pp. 279-291, 1975.
• Cashel, M.: "Pleiotropic Regulatory Effects of ppGpp in Bacteria" in Regulatory Biology, pp. 46-65, 1975.
• Reiness, G., Yang. H.L., Zubay, G. and Cashel, M.: Effects of guanosine tetraphosphate on cell-free synthesis of Escherichia coli ribosomal RNA and other gene products. Proc. Natl. Acad. Sci. U.S.A. 72:2881-2885, 1975.
• Glaser, G., Enquist, L. and Cashel, M.: ColE1 cloning of a ribosomal RNA promoter region from lambda rifd18 by selection for lambda integration and excision functions. Gene 2:159-172, 1977.
• Engel, J.A., Sylvester, J. and Cashel, M.: Guanosine 3',5'bis(pyrophosphate is a dispensable metabolite. In Koch, G. and Richter, D. (eds.), Regulation of Macromolecular Synthesis  by Low Molecular Weight Mediators. New York, Academic Press, pp. 25-38, 1979.
• Silverman, R., Atherly, A. G., Glaser, G. and Cashel, M.: Radioimmunoassay for ppGpp. In Koch, G. and Richter, D. (eds.) Regulation of Macromolecular Synthesis by Low Molecular Weight Mediators, New York, Academic Press, pp. 107-114, 1979.
• Ota, Y., Kikuchi, A. and Cashel, M.: Gene expression of an E. coli ribosomal promoter fused to a galactose structural gene. Proc. Natl. Acad. Sci. U.S.A. 76:5799-5803, 1979.
• Glaser, G. and Cashel, M.: In vitro transcripts from the rrnB ribosomal RNA cistron originate from two tandem promoters. Cell 16:111-121, 1979.

1980-1989

• Yang, H.-L., Ivashkiv, L., Chen, H.-Z., Zubay, G. and Cashel, M.: Cell-free coupled transcription-translation system for investigation of linear DNA segments. Proc. Natl. Acad. Sci. U.S.A.  77:7029-7033, 1980.
• Sylvester, J. E. and Cashel, M. Stable RNA-DNA-RNA polymerase complexes can  accompany formation of a single phosphodiester bond. Biochem. 19:1069-1074, 1980.
• Sarmientos, P., Sylvester, J. E., Contente, S. and Cashel, M., Differential stringent control of tandem E. coli ribosomal promoters from the rrnA operon expressed in vivo in multicopy plasmids. Cell 32:1337-1346, 1983.
• Glaser, G., Sarmientos, P. and Cashel, M. Functional relationship between two tandem E. coli ribosomal RNA promoters. Nature, 294:74-76, 1983.
• Sarmientos, P., Contente, S., Chinali, G. and Cashel, M. Ribosomal RNA operon promoters Pl and P2 show different regulatory responses. In Gene Expression: UCLA Symposia on  Molecular and Cellular Biology, New Series 8. eds. D. Hamer and R. Rosenberg. Alan R. Liss, Inc. New York, NY, 1983. pp. 65-74.
• Sarmientos, P. and Cashel, M.: Carbon starvation and growth rate dependent regulation of the E. coli ribosomal RNA promoters: differential control of dual promoters. Proc. Nat. Acad. Sci. U.S.A. 80:7010-7013, l983.
• Rudd, K. E., Bochner, B.R., Cashel, M., and Roth, J.R.: Mutations in the spoT gene of Salmonella typhimurium: Effects on his operon expression. J. Bacteriol. 163:534-542, 1985.
• Cashel, M. and Rudd, K.E.: The stringent response. in: Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. F.C. Neidhandt (ed). Americ. Soc. Microbiol. (Washington, DC) vol 2:1410-1438, 1987.
• Sarubbi, E., Rudd, K.E., Cashel, M. Basal ppGpp level adjustments shown by new spot mutants affect steady state growth rates and rrnA ribosomal promoter regulation in Escherichia coli. Mol. Gen. Genet. 213: 214-222, 1988.
• Jin, D.J., Cashel M., Friedman, D.I. Nakamura, Y. Walter, W.A. and Gross, C.A. Effects of rifamipicin resistant rpoB mutations on antitermination and interaction with nusA in Escherichia coli. J. Mol. Biol. 204, 247-261, 1988.
• Metzger, S., Dror, I.B. Aizenman, E., Schrieber, G., Toone, M., Friesen, J.D., Cashel, M., Glaser, G. The nucleotide sequence and characterization of the RelA gene of Escherichia coli. J. Biol. Chem. 263: 15699-15704, 1988.
• Sarubbi, E., Rudd, K.E., Xiao, H., Ikehara, K., Kalman, M., Cashel, M. Characterization of the spot gene of Escherichia coli. J. Biol. Chem. 264: 15074-15082, 1989.
• Metzger, S., Sarubbi, E., Glaser, G., Cashel, M. Protein sequences encoded by the relA and spoT genes of Escherichia coli are interrelated. J. Biol. Chem. 264: 9122-9175, 1989.
• Metzger, S., Schreiber, G., Aizenman, E. Cashel, M. Glaser, G. Characterization of the relA1 mutation and a comparison of relA1 with new relA null alleles in Escherichia coli. J. Biol. Chem. 264:21146-21152, 1989.

1990-1999

• Kalman, M., Kalman, E.T., and Cashel, M. Polymerase chain reaction (PCR) amplification with a single specific primer. Biochem. Biophys. Res. Commun. 167:504-506, 1990.
• Kalman, M., Gentry, D.R., and Cashel, M. Characterization  of the Escherichia coli K-12 gltS glutamate permease gene. Mol. Gen. Genetics 225:379-386, 1991.
• Schreiber, G., Metzger, S., Aizenman, E., Roza, S., Cashel, M., and Glaser, G. Overexpression of the relA gene in Escherichia coli. J. Biol. Chem. 266:3760-3767, 1991.
• Xiao, H., Kalman, M., Ikehara, K., Zemel, S., Glaser, G., and Cashel, M. Residual guanosine 3',5'-bispyrophosphate (ppGpp) synthetic activity of relA null mutants can be eliminated by spoT null mutations. J. Biol. Chem. 266:5980-5990, 1991.
• Gentry, D., Xiao, H., Burgess, R., and Cashel, M. The omega subunit of Escherichia coli is not required for stringent RNA control in vivo. J. Bacteriol. 173:3901-3903, 1991.
• Kalman, M., Murphy, H., and Cashel, M. rhlB, a new E. coli K-12 gene with a RNA helicas-like protein sequence motif, one of at least five such possible genes in a prokaryote. New Biol. 3:886-895, 1991.
• Kalman, M., Murphy, H., and Cashel, M. The nucleotide sequence of recG, the distal spo operon gene in Escherichia coli K-12. Gene 110:95-99, 1992.
• Jones. P.G., Cashel, M., Glaser, G., and Neidhardt, F.C. Function of a relaxed-like state following temperature downshifts in Escherichia coli. J. Bacteriol. 174:3903-3914, 1992.
• Svitil, A.L., Cashel, M., and Zyskind, J.W. Guanosine tetraphosphate inhibits protein synthesis in vivo. A possible protective mechanism for starvation stress in Escherichia coli. J. Biol. Chem. 268:2307-2311, 1993.
• Gentry, D., Bengra, C., Ikehara, K., and Cashel, M. Guanylate kinse of Escherichia coli K-12. J. Biol. Chem. 269:14316-14321, 1993.
• Gentry, D.M., Hernandez, V.J., Nguyen, L.H., Jensen, D.R., and Cashel, M. Synthesis of the stationary-phase sigma factor, sS, is positively regulated by ppGpp. J. Bacteriol.  75:7982-7989. 1993.
• Cashel, M. Detection of (p)ppGpp accumulation patterns in Escherichia coli mutants. In Methods in Molecular Genetics Vol. 3 Molecular Microbiology Techniques Part A (K.W. Adolph, Ed.) Academic Press pp 341-356, 1994.
• Gentry, D.M. and Cashel, M. Cellular localization of SpoT protein. J. Bacteriol. 177:3890-3893, 1995.
• Hernandez, V.J. and Cashel, M. Changes in conserved region 3 of Escherichia coli s70 mediate ppGpp-dependent functions in vivo. J. Mol. Biol. 252:536-549, 1995.
• Cashel, M., Gentry, D.M., Hernandez, V.J., and Vinella, D. The stringent response. In Escherichia coli and Salmonella typhimurium Cellular and Molecular Biology. (F. C. Neidhardt, Ed. in Chief). ASM Press, Washington D.C. vol 1:1458-1496, 1996.
• Hernandez, V.J., Hsu, L.M., and Cashel, M. Conserved region 3 of Escherichia coli s70 is implicated in the process of abortive transcription. J. Biol. Chem. 271:18775-18779, 1996.
• Mechold, U., Cashel, M., Steiner, K., Gentry, D.R., and Malke, H.A. A functional analysis of rel-se, a relA/spoT gene homolog from Streptococcus equisimilis. J. Bacteriol. 178:1401-1411, 1996.
• Gentry, D.M. and Cashel, M. Mutational analysis of the Escherichia coli spoT gene identifies distinct but overlapping regions involved in ppGpp synthesis and degradation. Molec. Microb. 19:1373-1384, 1996.
• Vinella, D., Gagny, B., Joseleau-Petit, D., Dari R., and Cashel, M. Mecillinam Resistance in Escherichia coli is conferred by loss of a second activity of the aroK protein. J. Bacteriol. 178:3818-3826, 1996.
• Kuroda, A., Murphy, H., Cashel, M., and Kornberg, A. Guanosine tetra- and pentaphosphate promoter accumulation of inorganic polyphosphate in Escherichia coli. J. Biol. Chem. 272:21240-21243, 1997.
• Wrobel, B., Murphy, H., Cashel, M., and Wegrzyn, G., Guanosine tetraphosphate (ppGpp)-mediated inhibition of the activity of the bacteriophage lambda PR promoter in Escherichia coli. Mol.Gen. Genet. 257:490-495, 1998.
• Hou. Z., Cashel, M., Fromm, H.J., and Honzatko, R.B., Effectors of the stringent response target the active site of Escherichia coli adenylosuccinate synthetase. J. Biol. Chem. 274: 17505-17510, 1999.

2000-2010

• Cashel, M. The stringent response. In Encyclopedia of Microbiology, 2nd edition. Joshua Lederberg (ed). Academic Press, San Diego CA. pp.467-477, 2000.
• Vinella, D., Cashel, M., and D'Ari, R., Selected Amplification of the cell division genes ftsQ-ftsA-ftsZ in Escherichia coli. Genetics. 156:1483-1492, 2000.
• Mechold, U., Murphy, H., Brown, L., and Cashel, M., Intramolecular regulation of the opposing (p)ppGpp catalytic activities of RelSeq, the Rel/Spo enzyme from Streptococcus equisimilis. J. Bacteriol. 184: 2878-2888, 2002.
• Brown, L., Gentry, D., Elliott, T., and Cashel, M., DksA affects ppGpp induction of RpoS at a translational level. J. Bacteriol. 184(16):4455-4465, 2002.
• Cashel, M., Hsu, L. M., Hernandez, V. J., Changes in conserved region 3 of Escherichia coli sigma-70 reduce abortive transcription and enhance promoter escape. J. Biol. Chem. 278:5539-5547, 2003.
• Murphy, H., Cashel, M. Isolation of RNA polymerase suppressors of a (p)ppGpp deficiency. In Methods in Enzymology, S. Adhya & S. Garges (eds.) Academic Press, San Diego, CA. Vol 371 [44], pp 598-603, 2003.
• Hogg, T., Mechold, U., Malke, H., Cashel, M., and Hilgenfeld, R. Conformational antagonism between opposing active sites in a bifunctional RelA/SpoT homolog modulates (p)ppGpp metabolism during the stringent response [corrected]. Cell. 117:57-68, 2004.
• Vinella, D., Albrecht, C., Cashel, M., and D'Ari, R. Iron limitation induces Spot-dependent accumulation of ppGpp in Escherichia coli.Mol. Microbiol. 56:958-970, 2005.
• Potrykus, K., Vinella, D., Murphy, M., Szalewska-Palasz, A., D'Ari, R., and Cashel, M. Antagonistic regulation of Escherichia coli Ribosomal RNA rrnB P1 promoter activity by GreA and DksA. J. Biol. Chem. 281:15238-15248, 2006.
• Rhee, H-W., Lee, C-R., Cho, S-H., Song, M-R., Cashel, M., Choy, HE., Seok, Y-J., Hong, J-I. Selective fluorescent chemosensor for the bacterial alarmone (p)ppGpp. J. Am. Chem. Soc. 130:784-5, 2008.
• Potrykus, K., Cashel, M., (p)ppGpp: still magical? Ann. Rev. Microbiol. 62: 35-51, 2008.
• Harinarayanan, R., Murphy, H. Cashel, M. Synthetic growth phenotypes of Escherichia coli lacking ppGpp and transketolase A (tktA) are due to ppGpp-mediated transcriptional regulation of tktB. Mol. Microbiol. 69:882-899, 2008.
• Blankschien, M.D., Potrykus K., Grace, E., Choudhary, A., Vinella D., Cashel, M. and Herman, C. TraR, a homolog of a RNAP secondary channel interactor, modulates transcription. 2009 PLOS Genetics 5 (1): e1000345.

2010-2019

• Potrykus, K., Murphy, H. Chen, J. Epstein, J.A. Cashel, M. Imprecise transcription termination within Escherichia coli greA leader gives rise to an array of short transcripts, GraL. 2010 Nucleic Acids Research 38:1636-1651.
• James, T.D. Cashel, M. Hinton, D.M. A mutation within the β subunit of Escherichia coli RNA polymerase impairs transcription from bacteriophage T4 middle promoters. 2010 J. Bacteriology 192:5580-5587.
• Potrykus, K., Murphy, H., Philippe, N., Cashel, M. ppGpp is the major source of growth rate control in Escherichia coli. 2010 Environ. Microbiol. 13:563-576.
• Szalewska-Palasz, A., Potrykus, K., Cashel, M., Wegrzyn, G. 2011. Starvation of bacteria for amino acids as an example of a prokaryotic response to nutritional deprivation. Chapter 4, in Biology of Starvation in Humans and other organisms. ed:  T.C. Merkin, Nova Science Publishers, NewYork.
• Edwards, A.N., Patterson-Fortin, L.M., Vakulskas, C.A., Mercante J.W., Potrykus, K., Vinella, D., Camacho, M.I., Fields, J.A., Thompson, S.A., Georgellis, D., Cashel, M., Babitzke. P., Romeo. T. 2011. Circuitry linking the Csr and stringent response global regulatory systems. Mol. Microbiol. 80:1561-1580.
• Vinella D, Potrykus K, Murphy H, Cashel M. 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.
• Mechold U, Potrykus K, Murphy H, Murakami Ks, Cashel M. 2013. Differential regulation  by ppGpp versus pppGpp in Escherichia coli.Nucleic Acids Research 2013. 41:6175-89.
• Gaca A.O,. Kudrin P, Colomer-Winter C., Beljantseva J., Liu K., Anderson B.., Wang J.D., Rejman D., Potrykus K., Cashel M., Hauryliuk V., Lemos J.A., 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(18):2908-19.
• Kamarthapu V., Epshtein V., Benjamin B., Proshkin S., Mironov A., Cashel M., Nudler E. 2016. ppGpp couples transcription to DNA repair in E. coli.Science. 352:993-6.
• Potrykus K., Cashel M. 2016. Preferential cellular accumulation of ppGpp or pppGpp in Escherichia coli. In: Stress and Environmental Regulation of Gene Expression and Adaptation in Bacteria, Chapter 7.1. Frans J. de Brujin (ed.) John Wiley and Sons Inc.
• Molodtsov V., Sineva E., Zhang L., Huang X., Cashel M., Ades SE, Murakami KS. Allosteric Effector ppGpp Potentiates the Inhibition of Transcript Initiation by DksA. 2018. Molecular Cell 69:828-839.
• Patterson-West J, James TD, Fernandez-Coll L, Iben JR, Moon K, Knipling L, Cashel M, Hinton D. 2018 The E. coli Global Regulator DksA Reduces Transcription during T4 Infection. 2018 Viruses.10(6):308.
• Bruhn-Olszewska B, Molodtsov V, Sobala M, Dylewski M, Murakami KS, Cashel M, Potrykus K. Structure-function comparisons of (p)ppApp vs (p)ppGpp for Escherichia coli RNA polymerase binding sites and for rrnB P1 promoter regulatory responses in vitro. 2018. Biochim Biophys Acta - Gene Regulatory Mechanisms;1861(8):731-742.
• Fernández-Coll L, and Cashel M. Contributions of SpoT hydrolase, SpoT synthetase and RelA synthetase to carbon source diauxic growth transitions in Escherichia coli. 2018. Frontiers Microbiology 9:1802.
• Potrykus K. and Cashel M. Growth at the best and worst of times. Nature Microbiology. 2018 Commentary 8:862-863.
• Fernandez-Coll L., Potrykus K, Cashel M. Puzzling conformational changes affecting proteins binding to RNA polymerase. 2018 Commentary. Proc. Nat'l. Acad. Sci. 115:12550-12552.
• Fernández-Coll L. and Cashel M. Using microtiter dish radiolabeling for multiple in vivo measurements of Escherichia coli (p)ppGpp followed by thin layer chromatography. 2019 JOVE. In press.