Benton, H.P., Wong, D.M., Trauger, S.A., Siuzdak, G., 2008. XCMS2:processing tandem mass spectrometry data for metabolite identification and structural characterization. Anal. Chem. 80, 6382-6389.
|
Betts, J.C., Lukey, P.T., Robb, L.C., McAdam, R.A., Duncan, K., 2002. Evaluation of a nutrient starvation model of Mycobacterium tuberculosis persistence by gene and protein expression profiling. Mol. Microbiol. 43, 717-731.
|
Bogdan, C., 2015. Nitric oxide synthase in innate and adaptive immunity:an update. Trends Immunol. 36, 161-178.
|
Boshoff, H.I., Barry 3rd, C.E., 2005. Tuberculosis-metabolism and respiration in the absence of growth. Nat. Rev. Microbiol. 3, 70-80.
|
Boucher, J.L., Moali, C., Tenu, J.P., 1999. Nitric oxide biosynthesis, nitric oxide synthase inhibitors and arginase competition for L-arginine utilization. Cell. Mol. Life Sci. 55, 1015-1028.
|
Bukau, B., Weissman, J., Horwich, A., 2006. Molecular chaperones and protein quality control. Cell 125, 443-451.
|
Bussiere, F.I., Chaturvedi, R., Cheng, Y., Gobert, A.P., Asim, M., Blumberg, D.R., Xu, H., Kim, P.Y., Hacker, A., Casero Jr., R.A., et al., 2005. Spermine causes loss of innate immune response to Helicobacter pylori by inhibition of inducible nitricoxide synthase translation. J. Biol. Chem. 280, 2409-2412.
|
Calogero, S., Gardan, R., Glaser, P., Schweizer, J., Rapoport, G., Debarbouille, M., 1994. RocR, a novel regulatory protein controlling arginine utilization in Bacillus subtilis, belongs to the Ntrc/NifA family of transcriptional activators. J. Bacteriol. 176, 1234-1241.
|
Chan, E.D., Chan, J., Schluger, N.W., 2001. What is the role of nitric oxide in murine and human host defense against tuberculosis? Current knowledge. Am. J. Respir Cell Mol. Biol. 25, 606-612.
|
Chang, C.I., Liao, J.C., Kuo, L., 1998. Arginase modulates nitric oxide production in activated macrophages. Am. J. Physiol. 274, H342-H348.
|
Chattopadhyay, M.K., Tabor, C.W., Tabor, H., 2003. Polyamines protect Escherichia coli cells from the toxic effect of oxygen. Proc. Natl. Acad. Sci. U. S. A. 100, 2261-2265.
|
Cole, S.T., Brosch, R., Parkhill, J., Garnier, T., Churcher, C., Harris, D., Gordon, S.V., Eiglmeier, K., Gas, S., Barry 3rd, C.E., et al., 1998. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393, 537-544.
|
de los Rios, S., Perona, J.J., 2007. Structure of the Escherichia coli leucine-responsive regulatory protein Lrp reveals a novel octameric assembly. J. Mol. Biol. 366, 1589-1602.
|
Deng, W., Wang, H., Xie, J., 2011. Regulatory and pathogenesis roles of Mycobacterium Lrp/AsnC family transcriptional factors. J. Cell. Biochem. 112, 2655-2662.
|
Dougan, D.A., Mogk, A., Bukau, B., 2002. Protein folding and degradation in bacteria:to degrade or not to degrade? That is the question. Cell. Mol. Life Sci. 59, 1607-1616.
|
Ehrt, S., Schnappinger, D., 2009. Mycobacterial survival strategies in the phagosome:defence against host stresses. Cell Microbiol. 11, 1170-1178.
|
El Kasmi, K.C., Qualls, J.E., Pesce, J.T., Smith, A.M., Thompson, R.W., HenaoTamayo, M., Basaraba, R.J., Konig, T., Schleicher, U., Koo, M.S., et al., 2008. Toll-like receptor-induced arginase 1 in macrophages thwarts effective immunity against intracellular pathogens. Nat. Immunol. 9, 1399-1406.
|
Elhai, J., 2015. Highly iterated palindromic sequences (HIPs) and their relationship to DNA methyltransferases. Life 5, 921-948.
|
Fay, A., Glickman, M.S., 2014. An essential nonredundant role for mycobacterial DnaK in native protein folding. PLoS Genet. 10, e1004516.
|
Flesch, I.E., Hess, J.H., Oswald, I.P., Kaufmann, S.H., 1994. Growth inhibition of Mycobacterium bovis by IFN-gamma stimulated macrophages:regulation by endogenous tumor necrosis factor-alpha and by IL-10. Int. Immunol. 6, 693-700.
|
Garbe, T.R., Hibler, N.S., Deretic, V., 1999. Response to reactive nitrogen intermediates in Mycobacterium tuberculosis:induction of the 16-kilodalton a-crystallin homolog by exposure to nitric oxide donors. Infect. Immun. 67, 460-465.
|
Gardan, R., Rapoport, G., Debarbouille, M., 1995. Expression of the rocDEF operon involved in arginine catabolism in Bacillus subtilis. J. Mol. Biol. 249, 843-856.
|
Glaser, P., Kunst, F., Arnaud, M., Coudart, M.P., Gonzales, W., Hullo, M.F., Ionescu, M., Lubochinsky, B., Marcelino, L., Moszer, I., et al., 1993. Bacillus subtilis genome project:cloning and sequencing of the 97 kb region from 325° to 333°. Mol. Microbiol. 10, 371-384.
|
Gobert, A.P., McGee, D.J., Akhtar, M., Mendz, G.L., Newton, J.C., Cheng, Y., Mobley, H.L., Wilson, K.T., 2001. Helicobacter pylori arginase inhibits nitric oxide production by eukaryotic cells:a strategy for bacterial survival. Proc. Natl. Acad. Sci. U. S. A. 98, 13844-13849.
|
Gouzy, A., Poquet, Y., Neyrolles, O., 2014. Nitrogen metabolism in Mycobacterium tuberculosis physiology and virulence. Nat. Rev. Microbiol. 12, 729-737.
|
Hampel, A., Huber, C., Geffers, R., Spona-Friedl, M., Eisenreich, W., Bange, F.C., 2015. Mycobacterium tuberculosis is a natural ornithine aminotransferase (rocD) mutant and depends on Rv2323c for growth on arginine. PLoS One 10, e0136914.
|
Ivanisevic, J., Zhu, Z.J., Plate, L., Tautenhahn, R., Chen, S., O'Brien, P.J., Johnson, C.H., Marletta, M.A., Patti, G.J., Siuzdak, G., 2013. Toward 'omic scale metabolite profiling:a dual separation-mass spectrometry approach for coverage of lipid and central carbon metabolism. Anal. Chem. 85, 6876-6884.
|
Koike, H., Ishijima, S.A., Clowney, L., Suzuki, M., 2004. The archaeal feast/famine regulatory protein:potential roles of its assembly forms for regulating transcription. Proc. Natl. Acad. Sci. U. S. A. 101, 2840-2845.
|
Kwon, D.H., Lu, C.D., 2006. Polyamines induce resistance to cationic peptide, aminoglycoside, and quinolone antibiotics in Pseudomonas aeruginosa PAO1. Antimicrob. Agents Chemother. 50, 1615-1622.
|
Larionov, S., Loskutov, A., Ryadchenko, E., 2008. Chromosome evolution with naked eye:palindromic context of the life origin. Chaos 18, 13105.
|
Lee, J., Sperandio, V., Frantz, D.E., Longgood, J., Camilli, A., Phillips, M.A., Michael, A.J., 2009. An alternative polyamine biosynthetic pathway is widespread in bacteria and essential for biofilm formation in Vibrio cholerae. J. Biol. Chem. 284, 9899-9907.
|
Leonard, P.M., Smits, S.H., Sedelnikova, S.E., Brinkman, A.B., de Vos, W.M., van der Oost, J., Rice, D.W., Rafferty, J.B., 2001. Crystal structure of the Lrp-like transcriptional regulator from the archaeon Pyrococcus furiosus. EMBO J. 20, 990-997.
|
Lupoli, T.J., Fay, A., Adura, C., Glickman, M.S., Nathan, C.F., 2016. Reconstitution of a Mycobacterium tuberculosis proteostasis network highlights essential cofactor interactions with chaperone DnaK. Proc. Natl. Acad. Sci. U. S. A. 113, E7947-E7956.
|
MacMicking, J.D., North, R.J., LaCourse, R., Mudgett, J.S., Shah, S.K., Nathan, C.F., 1997. Identification of nitric oxide synthase as a protective locus against tuberculosis. Proc. Natl. Acad. Sci. U. S. A. 94, 5243-5248.
|
Miller, B.H., Fratti, R.A., Poschet, J.F., Timmins, G.S., Master, S.S., Burgos, M., Marletta, M.A., Deretic, V., 2004. Mycobacteria inhibit nitric oxide synthase recruitment to phagosomes during macrophage infection. Infect. Immun. 72, 2872-2878.
|
Mills, C.D., 2001. Macrophage arginine metabolism to ornithine/urea or nitric oxide/citrulline:a life or death issue. Crit. Rev. Immunol. 21, 399-425.
|
Modolell, M., Corraliza, I.M., Link, F., Soler, G., Eichmann, K., 1995. Reciprocal regulation of the nitric oxide synthase/arginase balance in mouse bone marrow-derived macrophages by TH1 and TH2 cytokines. Eur. J. Immunol. 25, 1101-1104.
|
Nathan, C., Shiloh, M.U., 2000. Reactive oxygen and nitrogen intermediates in the relationship between mammalian hosts and microbial pathogens. Proc. Natl. Acad. Sci. U. S. A. 97, 8841-8848.
|
Nozaki, Y., Hasegawa, Y., Ichiyama, S., Nakashima, I., Shimokata, K., 1997. Mechanism of nitric oxide-dependent killing of Mycobacterium bovis BCG in human alveolar macrophages. Infect. Immun. 65, 3644-3647.
|
Ochoa, J.B., Strange, J., Kearney, P., Gellin, G., Endean, E., Fitzpatrick, E., 2001. Effects of L-arginine on the proliferation of T lymphocyte subpopulations. JPEN J. Parenter. Enter. Nutr. 25, 23-29.
|
Ouhammouch, M., Dewhurst, R.E., Hausner, W., Thomm, M., Geiduschek, E.P., 2003. Activation of archaeal transcription by recruitment of the TATA-binding protein. Proc. Natl. Acad. Sci. U. S. A. 100, 5097-5102.
|
Oves-Costales, D., Kadi, N., Fogg, M.J., Song, L., Wilson, K.S., Challis, G.L., 2007. Enzymatic logic of anthrax stealth siderophore biosynthesis:AsbA catalyzes ATPdependent condensation of citric acid and spermidine. J. Am. Chem. Soc. 129, 8416-8417.
|
Pan, Y.H., Liao, C.C., Kuo, C.C., Duan, K.J., Liang, P.H., Yuan, H.S., Hu, S.T., Chak, K.F., 2006. The critical roles of polyamines in regulating ColE7 production and restricting ColE7 uptake of the colicin-producing Escherichia coli. J. Biol. Chem. 281, 13083-13091.
|
Parti, R.P., Shrivastava, R., Srivastava, S., Subramanian, A.R., Roy, R., Srivastava, B.S., Srivastava, R., 2008. A transposon insertion mutant of Mycobacterium fortuitum attenuated in virulence and persistence in a murine infection model that is complemented by Rv3291c of Mycobacterium tuberculosis. Microb. Pathog. 45, 370-376.
|
Patel, C.N., Wortham, B.W., Lines, J.L., Fetherston, J.D., Perry, R.D., Oliveira, M.A., 2006. Polyamines are essential for the formation of plague biofilm. J. Bacteriol. 188, 2355-2363.
|
Peeters, E., Albers, S.V., Vassart, A., Driessen, A.J., Charlier, D., 2009. Ss-LrpB, a transcriptional regulator from Sulfolobus solfataricus, regulates a gene cluster with a pyruvate ferredoxin oxidoreductase-encoding operon and permease genes. Mol. Microbiol. 71, 972-988.
|
Peteroy-Kelly, M.A., Venketaraman, V., Talaue, M., Seth, A., Connell, N.D., 2003. Modulation of J774.1 macrophage L-arginine metabolism by intracellular Mycobacterium bovis BCG. Infect. Immun. 71, 1011-1015.
|
Pu, Y., Li, Y., Jin, X., Tian, T., Ma, Q., Zhao, Z., Lin, S.Y., Chen, Z., Li, B., Yao, G., et al., 2019. ATP-dependent dynamic protein aggregation regulates bacterial dormancy depth critical for antibiotic tolerance. Mol. Cell. 73, 143-156.
|
Reddy, M.C., Gokulan, K., Jacobs Jr., W.R., Ioerger, T.R., Sacchettini, J.C., 2008. Crystal structure of Mycobacterium tuberculosis LrpA, a leucine-responsive global regulator associated with starvation response. Protein Sci. 17, 159-170.
|
Rodriguez, P.C., Quiceno, D.G., Ochoa, A.C., 2007. L-arginine availability regulates Tlymphocyte cell-cycle progression. Blood 109, 1568-1573.
|
Schut, G.J., Menon, A.L., Adams, M.W., 2001. 2-keto acid oxidoreductases from Pyrococcus furiosus and Thennococcus litoralis. Methods Enzymol. 331, 144-158.
|
Schwaiger, R., Schwarz, C., Furtwangler, K., Tarasov, V., Wende, A., Oesterhelt, D., 2010. Transcriptional control by two leucine-responsive regulatory proteins in Halobacterium salinarum R1. BMC Mol. Biol. 11, 40.
|
Shah, P., Romero, D.G., Swiatlo, E., 2008. Role of polyamine transport in Streptococcus pneumoniae response to physiological stress and murine septicemia. Microb. Pathog. 45, 167-172.
|
Slayden, R.A., Knudson, D.L., Belisle, J.T., 2006. Identification of cell cycle regulators in Mycobacterium tuberculosis by inhibition of septum formation and global transcriptional analysis. Microbiology 152, 1789-1797.
|
Talaue, M.T., Venketaraman, V., Hazbon, M.H., Peteroy-Kelly, M., Seth, A., Colangeli, R., Alland, D., Connell, N.D., 2006. Arginine homeostasis in J774.1 macrophages in the context of Mycobacterium bovis BCG infection. J. Bacteriol. 188, 4830-4840.
|
Tapias, A., Lopez, G., Ayora, S., 2000. Bacillus subtilis lrpc is a sequenceindependent DNA-binding and DNA-bending protein which bridges DNA. Nucleic Acids Res. 28, 552-559.
|
Thaw, P., Sedelnikova, S.E., Muranova, T., Wiese, S., Ayora, S., Alonso, J.C., Brinkman, A.B., Akerboom, J., van der Oost, J., Rafferty, J.B., 2006. Structural insight into gene transcriptional regulation and effector binding by the Lrp/AsnC family. Nucleic Acids Res. 34, 1439-1449.
|
Tiwari, S., van Tonder, A.J., Vilcheze, C., Mendes, V., Thomas, S.E., Malek, A., Chen, B., Chen, M., Kim, J., Blundell, T.L., et al., 2018. Arginine-deprivationinduced oxidative damage sterilizes Mycobacterium tuberculosis. Proc. Natl. Acad. Sci. U. S. A. 115, 9779-9784.
|
Torrey, H.L., Keren, I., Via, L.E., Lee, J.S., Lewis, K., 2016. High persister mutants in Mycobacterium tuberculosis. PLoS One 11, e0155127.
|
Tripathi, P., Parijat, P., Patel, V.K., Batra, J.K., 2018. The amino-terminal domain of Mycobacterium tuberculosis ClpB protein plays a crucial role in its substrate disaggregation activity. FEBS. Open. Bio 8, 1669-1690.
|
Wang, Y., Cen, X.F., Zhao, G.P., Wang, J., 2012. Characterization of a new glnr binding box in the promoter of amtB in Streptomyces coelicolor inferred a Phop/Glnr competitive binding mechanism for transcriptional regulation of amtB. J. Bacteriol. 194, 5237-5244.
|
Yang, M., Gao, C., Cui, T., An, J., He, Z.-G., 2012. A TetR-like regulator broadly affects the expressions of diverse genes in Mycobacterium smegmatis. Nucleic Acids Res 40, 1009-1020.
|
Yokoyama, K., Ishijima, S.A., Koike, H., Kurihara, C., Shimowasa, A., Kabasawa, M., Kawashima, T., Suzuki, M., 2007. Feast/famine regulation by transcription factor FL11 for the survival of the hyperthermophilic archaeon Pyrococcus OT3. Structure 15, 1542-1554.
|
Yurdagul Jr., A., Subramanian, M., Wang, X., Crown, S.B., Ilkayeva, O.R., Darville, L., Kolluru, G.K., Rymond, C.C., Gerlach, B.D., Zheng, Z., et al., 2020. Macrophage metabolism of apoptotic cell-derived arginine promotes continual efferocytosis and resolution of injury. Cell Metabol. 31, 518-533.
|
Zea, A.H., Rodriguez, P.C., Culotta, K.S., Hernandez, C.P., DeSalvo, J., Ochoa, J.B., Park, H.J., Zabaleta, J., Ochoa, A.C., 2004. L-arginine modulates CD3ξ expression and T cell function in activated human T lymphocytes. Cell. Immunol. 232, 21-31.
|