NAD captureSeq indicates NAD as a bacterial cap for a subset of regulatory RNAs

Nature

Volumn 519, Issue 7543, 2015, Pages 374-377

  Cahová, Hana ^a   Winz, Marie Luise ^a   Höfer, Katharina ^a   Nübel, Gabriele ^a   Jäschke, Andres ^a  

^a UNIVERSITY OF HEIDELBERG   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL RNA; INORGANIC PYROPHOSPHATASE; MESSENGER RNA; NICOTINAMIDE ADENINE DINUCLEOTIDE; RIBONUCLEASE E; RNA POLYMERASE; TRANSFER RNA; ACID ANHYDRIDE HYDROLASE; CAPPED RNA; ESCHERICHIA COLI PROTEIN; NUCLEOTIDE PYROPHOSPHATASE; RIBONUCLEASE; RPPH PROTEIN, E COLI;

APLYSIA CALIFORNICA; ARTICLE; BACTERIAL STRAIN; CHEMO ENZYMATIC CAPTURE; IN VITRO STUDY; IN VIVO STUDY; NEXT GENERATION SEQUENCING; NONHUMAN; PRIORITY JOURNAL; PROTEIN MODIFICATION; REGULATORY RNA SEQUENCE; RNA CAPPING; RNA CLEAVAGE; RNA DEGRADATION; RNA PROCESSING; RNA SEQUENCE; RNA STABILITY; RNA STRUCTURE; RNA TRANSCRIPTION; SIGNAL TRANSDUCTION; CHEMISTRY; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; SEQUENCE ANALYSIS;

ACID ANHYDRIDE HYDROLASES; ENDORIBONUCLEASES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; NAD; PYROPHOSPHATASES; RNA CAPS; RNA STABILITY; RNA, BACTERIAL; SEQUENCE ANALYSIS;

EID: 84925490079     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature14020     Document Type: Article

References (128)

1. Topisirovic, I., Svitkin, Y. V., Sonenberg, N. & Shatkin, A. J. Cap and cap-binding proteins in the control of gene expression. RNA 2, 277-298 (2011).
2. Chen, Y. G., Kowtoniuk, W. E., Agarwal, I., Shen, Y. & Liu, D. R. LC/MS analysis of cellular RNA reveals NAD-linked RNA. Nature Chem. Biol. 5, 879-881 (2009).
3. Houtkooper, R. H., Cantó , C., Wanders, R. J. & Auwerx, J. The secret life of NAD1: an oldmetabolite controlling newmetabolic signaling pathways. Endocr. Rev. 31, 194-223 (2010).
4. Oppenheimer, N. J. NAD1 and NADP1 as prosthetic groups for enzymes. eLS http://dx.doi/org/10.1002/9780470015902.a0000637.pub2 (2010).
5. Deana, A., Celesnik, H. & Belasco, J. G. The bacterial enzyme RppH triggers messenger RNA degradation by 59 pyrophosphate removal. Nature 451, 355-358 (2008).
6. Mackie, G. A. Ribonuclease E is a 59-end-dependent endonuclease. Nature 395, 720-724 (1998).
7. Frick, D. N.&Bessman, M. J. Cloning, purification, and properties of a novelNADH pyrophosphatase. Evidence for a nucleotide pyrophosphatase catalytic domain in MutT-like enzymes. J. Biol. Chem. 270, 1529-1534 (1995).
8. Walseth, T. F. & Lee, H. C. Synthesis and characterization of antagonists of cyclic-ADP-ribose-inducedCa21release. Biochim.Biophys.Acta1178, 235-242(1993).
9. Preugschat, F., Tomberlin, G. H. & Porter, D. J. The base exchange reaction of NAD1 glycohydrolase: identification of novel heterocyclic alternative substrates. Arch. Biochem. Biophys. 479, 114-120 (2008).
10. Migaud, M. E., Pederick, R. L., Bailey, V. C.&Potter, B. V. Probing Aplysia californica adenosine 59-diphosphate ribosyl cyclase for substrate binding requirements: design of potent inhibitors. Biochemistry 38, 9105-9114 (1999).
11. Rostovtsev, V. V., Green, L. G., Fokin, V. V. & Sharpless, K. B. A stepwise Huisgen cycloaddition process: copper(I)-catalyzed regioselective "ligation" of azides and terminal alkynes. Angew. Chem. Int. Edn Engl. 41, 2596-2599 (2002).
12. Tornøe, C. W., Christensen, C. & Meldal, M. Peptidotriazoles on solid phase: [1, 2, 3]-triazoles by regiospecific copper(I)-catalyzed 1, 3-dipolar cycloadditions of terminal alkynes to azides. J. Org. Chem. 67, 3057-3064 (2002).
13. Huang, F. Efficient incorporation of CoA, NAD and FAD into RNA by in vitro transcription. Nucleic Acids Res. 31, e8 (2003).
14. Opdyke, J. A., Fozo, E. M., Hemm, M. R. & Storz, G. RNase III participates in GadYdependent cleavage of the gadX-gadW mRNA. J. Mol. Biol. 406, 29-43 (2011).
15. Opdyke, J. A., Kang, J. G.& Storz, G. GadY, a small-RNAregulator of acid response genes in Escherichia coli. J. Bacteriol. 186, 6698-6705 (2004).
16. Gerhart, E., Wagner, H. & Nordström, K. Structural analysis of an RNA molecule involved in replication control of plasmid R1. Nucleic Acids Res. 14, 2523-2538 (1986).
17. Lacatena, R. M. & Cesareni, G. Base pairing of RNA I with its complementary sequence in the primer precursor inhibits ColE1 replication. Nature 294, 623-626 (1981).
18. D'Alessio, G. & Josse, J. Glyceraldehyde phosphate dehydrogenase, phosphoglycerate kinase, and phosphoglyceromutase of Escherichia coli. Simultaneous purification and physical properties. J. Biol. Chem. 246, 4319-4325 (1971).
19. Masuda, N. & Church, G. M. Regulatory network of acid resistance genes in Escherichia coli. Mol. Microbiol. 48, 699-712 (2003).
20. Jin, Y., Watt, R. M., Danchin, A. & Huang, J. D. Small noncoding RNA GcvB is a novel regulator of acid resistance in Escherichia coli. BMC Genomics 10, 165 (2009).
21. Hayes, E. T. et al. Oxygen limitation modulates pH regulation of catabolism and hydrogenases, multidrug transporters, and envelope composition in Escherichia coli K-12. BMC Microbiol. 6, 89 (2006).
22. Gustavsson, N., Diez, A. & Nyström, T. The universal stress protein paralogues of Escherichia coli are co-ordinately regulated and co-operate in the defence against DNA damage. Mol. Microbiol. 43, 107-117 (2002).
23. Eguchi, Y. & Tomizawa, J. Complex formed by complementary RNA stem-loops and its stabilization by a protein: function of CoIE1 Rom protein. Cell 60, 199-209 (1990).
24. Dumelin, C. E., Chen, Y., Leconte, A. M., Chen, Y. G. & Liu, D. R. Discovery and biological characterization of geranylated RNA in bacteria. Nature Chem. Biol. 8, 913-919 (2012).
25. Bandyra, K. J. et al. The seed region of a small RNA drives the controlled destruction of the target mRNA by the endoribonuclease RNase E. Mol. Cell 47, 943-953 (2012).
26. McLennan, A. G. Substrate ambiguity among the nudix hydrolases: biologically significant, evolutionary remnant, or both? Cell. Mol. Life Sci. 70, 373-385 (2013).
27. Song, M. G., Bail, S. & Kiledjian, M.Multiple Nudix family proteins possessmRNA decapping activity. RNA 19, 390-399 (2013).
28. Gherardini, P. F., Ausiello, G., Russell, R. B. & Helmer-Citterich, M. Modular architecture of nucleotide-binding pockets. Nucleic Acids Res. 38, 3809-3816 (2010).
29. Bandyra, K. J., Bouvier, M., Carpousis, A. J. & Luisi, B. F. The social fabric of the RNA degradosome. Biochim. Biophys. Acta 1829, 514-522 (2013).
30. Fjeld, C. C., Birdsong, W. T. & Goodman, R. H. Differential binding of NAD1 and NADH allows the transcriptional corepressor carboxyl-terminal binding protein to serve as a metabolic sensor. Proc.Natl Acad. Sci.USA 100, 9202-9207 (2003).
31. Baba, T. et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2, 2006-0008 (2006).
32. Hafner, M. et al. Identification of microRNAs and other small regulatory RNAs using cDNA library sequencing. Methods 44, 3-12 (2008).
33. Lohse, M. et al. RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics. Nucleic Acids Res. 40, W622-W627 (2012).
34. Halbritter, F., Vaidya, H. J. & Tomlinson, S. R. GeneProf: analysis of highthroughput sequencing experiments. Nature Methods 9, 7-8 (2012).
35. Flicek, P. et al. Ensembl 2013. Nucleic Acids Res. 41, D48-D55 (2013).
36. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memoryefficient alignment of shortDNA sequences to the humangenome. GenomeBiol. 10, R25 (2009).
37. Nicol, J. W., Helt, G. A., Blanchard, S. G. Jr, Raja, A. & Loraine, A. E. The Integrated GenomeBrowser: free software for distribution and exploration of genome-scale datasets. Bioinformatics 25, 2730-2731 (2009).
38. Keseler, I. M. et al. EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res. 41, D605-D612 (2013).
39. Bernofsky, C.&Gallagher, W. J.Nonenzymic hydrogen transfer between reduced and oxidized pyridine nucleotides. Biochim. Biophys. Acta 659, 1-6 (1981).
40. Celesnik, H., Deana, A.&Belasco, J. G.PABLOanalysis ofRNA:59-phosphorylation state and 59-end mapping. Methods Enzymol. 447, 83-98 (2008).
41. Celesnik, H., Deana, A.&Belasco, J. G. InitiationofRNAdecay in Escherichia coli by 59 pyrophosphate removal. Mol. Cell 27, 79-90 (2007).
42. Tomcsányi, T. & Apirion, D. Processing enzyme ribonuclease E specifically cleaves RNA I. An inhibitor of primer formation in plasmid DNA synthesis. J. Mol. Biol. 185, 713-720 (1985).
43. Masukata, H. & Tomizawa, J. Control of primer formation for ColE1 plasmid replication: conformational change of the primer transcript. Cell 44, 125-136 (1986).
44. Blomberg, P., Wagner, E. G.& Nordström, K. Control of replication of plasmid R1: the duplex between the antisense RNA, CopA, and its target, CopT, is processed specifically in vivo and in vitro by RNase III. EMBO J. 9, 2331-2340 (1990).
45. Sharma, C. M., Darfeuille, F., Plantinga, T. H. & Vogel, J. A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich elements inside and upstream of ribosome-binding sites. Genes Dev. 21, 2804-2817 (2007).
46. Thomason, M. K., Fontaine, F., De Lay, N. & Storz, G. A small RNA that regulates motility and biofilm formation in response to changes in nutrient availability in Escherichia coli. Mol. Microbiol. 84, 17-35 (2012).
47. Jørgensen, M. G. et al. Small regulatory RNAs control the multi-cellular adhesive lifestyle of Escherichia coli. Mol. Microbiol. 84, 36-50 (2012).
48. Jørgensen, M. G., Thomason, M. K., Havelund, J., Valentin-Hansen, P. & Storz, G. Dual function of the McaS smallRNA in controlling biofilmformation. Genes Dev. 27, 1132-1145 (2013).
49. Rasmussen, A. A. et al. A conserved small RNA promotes silencing of the outer membrane protein YbfM. Mol. Microbiol. 72, 566-577 (2009).
50. Mandin, P.&Gottesman, S.A genetic approach for findingsmallRNAs regulators of genes of interest identifies RybC as regulating the DpiA/DpiB two-component system. Mol. Microbiol. 72, 551-565 (2009).
51. Weilbacher, T. et al. A novel sRNA component of the carbon storage regulatory system of Escherichia coli. Mol. Microbiol. 48, 657-670 (2003).
52. Lease, R. A., Smith, D., McDonough, K. & Belfort, M. The small noncoding DsrA RNA is an acid resistance regulator in Escherichia coli. J. Bacteriol. 186, 6179-6185 (2004).
53. Sledjeski, D. D., Gupta, A.&Gottesman, S. ThesmallRNA, DsrA, is essential for the low temperature expression of RpoS during exponential growth in Escherichia coli. EMBO J. 15, 3993-4000 (1996).
54. Lease, R. A.& Belfort, M. A trans-actingRNA as a control switch in Escherichia coli: DsrA modulates function by forming alternative structures. Proc. Natl Acad. Sci. USA 97, 9919-9924 (2000).
55. Lease, R. A., Cusick, M. E. & Belfort, M. Riboregulation in Escherichia coli: DsrA RNA acts by RNA:RNA interactions at multiple loci. Proc. Natl Acad. Sci. USA 95, 12456-12461 (1998).
56. Göpel, Y., Papenfort, K., Reichenbach, B., Vogel, J. & Görke, B. Targeted decay of a regulatorysmallRNA by an adaptor protein forRNase E and counteraction by an anti-adaptor RNA. Genes Dev. 27, 552-564 (2013).
57. Urban, J. H. & Vogel, J. Two seemingly homologous noncoding RNAs act hierarchically to activate glmS mRNA translation. PLoS Biol. 6, e64 (2008).
58. Reichenbach, B., Maes, A., Kalamorz, F., Hajnsdorf, E. & Görke, B. The small RNA GlmYacts upstreamof the sRNA GlmZin the activation of glmS expression and is subject to regulation by polyadenylation in Escherichia coli. Nucleic AcidsRes. 36, 2570-2580 (2008).
59. Moon, K. & Gottesman, S. A PhoQ/P-regulated small RNA regulates sensitivity of Escherichia coli to antimicrobial peptides. Mol. Microbiol.74, 1314-1330 (2009).
60. Fozo, E. M. et al. Repression of small toxic protein synthesis by the Sib and OhsC small RNAs. Mol. Microbiol. 70, 1076-1093 (2008).
61. Vogel, J. et al. RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria. Nucleic Acids Res. 31, 6435-6443 (2003).
62. Blasi, F. et al. Inhibition of transcription of the histidine operon in vitro by the first enzyme of the histidinepathway.Proc.NatlAcad.Sci.USA70, 2692-2696(1973).
63. Richards, J., Luciano, D. J. & Belasco, J. G. Influence of translation on RppHdependentmRNAdegradation in Escherichia coli.Mol. Microbiol.86, 1063-1072 (2012).
64. Nobelmann, B. & Lengeler, J. W. Molecular analysis of the gat genes from Escherichia coli and of their roles in galactitol transport and metabolism. J. Bacteriol. 178, 6790-6795 (1996).
65. Tucker, D. L., Tucker, N. & Conway, T. Gene expression profiling of the pH response in Escherichia coli. J. Bacteriol. 184, 6551-6558 (2002).
66. Peng, C. A., Oliver, M. J. & Wood, A. J. Is the Rehydrin TrDr3 from Tortula ruralis associated with tolerance to cold, salinity, and reduced pH? Physiological evaluation of the TrDr3-orthologue, HdeD from Escherichia coli in response to abiotic stress. Plant Biol. 7, 315-320 (2005).
67. Lawther, R. P. & Hatfield, G. W. Multivalent translational control of transcription termination at attenuator of ilvGEDA operon of Escherichia coli K-12. Proc. Natl Acad. Sci. USA 77, 1862-1866 (1980).
68. Purta, E. et al. The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase. BMC Mol. Biol. 7, 23 (2006).
69. Elovson, J. & Vagelos, P. R. Acyl carrier protein. X. Acyl carrier protein synthetase. J. Biol. Chem. 243, 3603-3611 (1968).
70. Lu, P., Vogel, C., Wang, R., Yao, X. & Marcotte, E. M. Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation. Nature Biotechnol. 25, 117-124 (2007).
71. Rudolph, F. B. & Fromm, H. J. The purification and properties of aspartase from Escherichia coli. Arch. Biochem. Biophys. 147, 92-98 (1971).
72. Karsten, W. E. & Viola, R. E. Kinetic studies of L-aspartase from Escherichia coli: pH-dependent activity changes. Arch. Biochem. Biophys. 287, 60-67 (1991).
73. Maki, Y., Yoshida, H. & Wada, A. Two proteins, YfiA and YhbH, associated with resting ribosomes in stationary phase Escherichia coli. Genes Cells 5, 965-974 (2000).
74. Agafonov, D. E., Kolb, V. A., Nazimov, I. V. & Spirin, A. S. A protein residing at the subunit interface of the bacterial ribosome. Proc. Natl Acad. Sci. USA 96, 12345-12349 (1999).
75. Vila-Sanjurjo, A., Schuwirth, B. S., Hau, C. W. & Cate, J. H. Structural basis for the control of translation initiation during stress. Nature Struct. Mol. Biol. 11, 1054-1059 (2004).
76. Agafonov, D. E., Kolb, V.A.&Spirin, A. S. Ribosome-associated protein that inhibits translation at the aminoacyl-tRNAbinding stage. EMBO Rep. 2, 399-402 (2001).
77. Kim, K. S. & Lee, Y. Regulation of 6S RNA biogenesis by switching utilization of both sigma factors and endoribonucleases. Nucleic Acids Res. 32, 6057-6068 (2004).
78. Weber, M. M., French, C. L., Barnes, M. B., Siegele, D. A.&McLean, R. J.Apreviously uncharacterized gene, yjfO (bsmA), influences Escherichia coli biofilm formation and stress response. Microbiology 156, 139-147 (2010).
79. Robbins, J. C. & Oxender, D. L. Transport systems for alanine, serine, and glycine in Escherichia coli K-12. J. Bacteriol. 116, 12-18 (1973).
80. Ghrist, A. C. & Stauffer, G. V. The Escherichia coli glycine transport systemand its role in the regulation of the glycine cleavage enzyme system. Microbiology 141, 133-140 (1995).
81. Pulvermacher, S. C., Stauffer, L. T. & Stauffer, G. V. Role of the sRNA GcvB in regulation of cycA in Escherichia coli. Microbiology 155, 106-114 (2009).
82. Hugovieux-Cotte-Pattat, N. & Robert-Baudouy, J. Regulation and transcription direction of exuR, a self-regulated repressor in Escherichia coli K-12. J. Mol. Biol. 156, 221-228 (1982).
83. Rodionov, D. A., Mironov, A. A., Rakhmaninova, A. B. & Gelfand, M. S. Transcriptional regulation of transport and utilization systems for hexuronides, hexuronates and hexonates in gamma purple bacteria. Mol. Microbiol. 38, 673-683 (2000).
84. Cole, S. T. et al. Nucleotide sequence and gene-polypeptide relationships of the glpABC operon encoding the anaerobic sn-glycerol-3-phosphate dehydrogenase of Escherichia coli K-12. J. Bacteriol. 170, 2448-2456 (1988).
85. Schryvers, A., Lohmeier, E. & Weiner, J. H. Chemical and functional properties of the native and reconstituted forms of the membrane-bound, aerobic glycerol-3-phosphate dehydrogenase of Escherichia coli. J. Biol. Chem. 253, 783-788 (1978).
86. Summers, M. C.& Rose, I. A. Proton transfer reactions of methylglyoxal synthase. J. Am. Chem. Soc. 99, 4475-4478 (1977).
87. Plumbridge, J. A. Repression and induction of the nag regulon of Escherichia coli K-12: the roles of nagC and nagA in maintenance of the uninduced state. Mol. Microbiol. 5, 2053-2062 (1991).
88. White, R. J. Control ofamino sugarmetabolismin Escherichia coli and isolation of mutants unable to degrade amino sugars. Biochem. J. 106, 847-858 (1968).
89. Freundlich, M., Ramani, N., Mathew, E., Sirko, A. & Tsui, P. The role of integration host factor in gene expression in Escherichia coli. Mol. Microbiol. 6, 2557-2563 (1992).
90. Nelson, W. C., Howard, M. T., Sherman, J. A.&Matson, S. W. The traY gene product and integration host factor stimulate Escherichia coli DNA helicase I-catalyzed nicking at the F plasmid oriT. J. Biol. Chem. 270, 28374-28380 (1995).
91. Dhavan, G. M., Crothers, D. M., Chance, M. R. & Brenowitz, M. Concerted binding and bending of DNA by Escherichia coli integration host factor. J. Mol. Biol. 315, 1027-1037 (2002).
92. Yanagisawa, T., Sumida, T., Ishii, R., Takemoto, C. & Yokoyama, S. A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P. Nature Struct. Mol. Biol. 17, 1136-1143 (2010).
93. Kaiser, K. & Murray, N. E. Physical characterisation of the "Rac prophage" in E. coli K12. Mol. Gen. Genet. 175, 159-174 (1979).
94. Caldas, T. et al. The FtsJ/RrmJ heat shock protein of Escherichia coli is a 23 S ribosomal RNA methyltransferase. J. Biol. Chem. 275, 16414-16419 (2000).
95. Theobald, A., Springer, M., Grunberg-Manago, M., Ebel, J. P. & Giege, R. Tertiary structure of Escherichia coli tRNAThr 3 in solution and interaction of this tRNAwith the cognate threonyl-tRNA synthetase. Eur. J. Biochem. 175, 511-524 (1988).
96. Serres, M. H. et al. A functional update of the Escherichia coli K-12 genome. Genome Biol. 2, RESEARCH0035 (2001).
97. Tschowri, N., Busse, S. & Hengge, R. The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli. Genes Dev. 23, 522-534 (2009).
98. Daley, D. O. et al. Global topology analysis of the Escherichia coli innermembrane proteome. Science 308, 1321-1323 (2005).
99. Lhoest, J. & Colson, C. Cold-sensitive ribosome assembly in an Escherichia coli mutant lacking a single methyl group in ribosomal protein L3. Eur. J. Biochem. 121, 33-37 (1981).
100. Heurgué-Hamard, V., Champ, S., Engström, A., Ehrenberg, M.&Buckingham, R.H. The hemK gene in Escherichia coli encodes theN5-glutamine methyltransferase that modifies peptide release factors. EMBO J. 21, 769-778 (2002).
101. White, P. J., Millar, G. & Coggins, J. R. The overexpression, purification and completeaminoacid sequence ofchorismate synthase fromEscherichia coliK12 and its comparison with the enzyme from Neurospora crassa. Biochem. J. 251, 313-322 (1988).
102. Imamura, R. et al. Identification of the cpdA gene encoding cyclic39, 59-adenosine monophosphate phosphodiesterase in Escherichia coli. J. Biol. Chem. 271, 25423-25429 (1996).
103. Long, C. W.& Pardee, A. B. Cytidine triphosphate synthetase of Escherichia coli B. I. Purification and kinetics. J. Biol. Chem. 242, 4715-4721 (1967).
104. Py, B., Higgins, C. F., Krisch, H. M. & Carpousis, A. J. A DEAD-box RNA helicase in the Escherichia coli RNA degradosome. Nature 381, 169-172 (1996).
105. Jeanningros, R., Creuzet-Sigal, N., Frixon, C. & Cattaneo, J. Purification and properties of a debranching enzymefromEscherichia coli. Biochim. Biophys. Acta 438, 186-199 (1976).
106. Ballicora, M. A., Iglesias, A. A. & Preiss, J. ADP-glucose pyrophosphorylase, a regulatory enzyme for bacterial glycogen synthesis. Microbiol. Mol. Biol. Rev. 67, 213-225 (2003).
107. Joly, J. C. & Wickner, W. The SecA and SecY subunits of translocase are the nearest neighbors of a translocating preprotein, shielding it fromphospholipids. EMBO J. 12, 255-263 (1993).
108. Wada, A.&Sako, T. Primary structures of and genes for newribosomal proteins A and B in Escherichia coli. J. Biochem. 101, 817-820 (1987).
109. Sparrow, C. P.& Raetz, C. R. Purification and properties of the membrane-bound CDP-diglyceride synthetase from Escherichia coli. J. Biol. Chem. 260, 12084-12091 (1985).
110. Langley, K. E. & Kennedy, E. P. Partial purification and properties of CTP:phosphatidic acid cytidylyltransferase from membranes of Escherichia coli. J. Bacteriol. 136, 85-95 (1978).
111. Kanehara, K., Ito, K. & Akiyama, Y. YaeL (EcfE) activates the sigma(E) pathway of stress response through a site-2 cleavage of anti-sigma(E), RseA. Genes Dev. 16, 2147-2155 (2002).
112. Alba, B. M., Leeds, J. A., Onufryk, C., Lu, C. Z. & Gross, C. A. DegS and YaeL participate sequentially in the cleavage of RseA to activate the sigma(E)-dependent extracytoplasmic stress response. Genes Dev. 16, 2156-2168 (2002).
113. Takeda, K., Akimoto, C. & Kawamukai, M. Effects of the Escherichia coli sfsA gene on mal genes expression and a DNA binding activity of SfsA. Biosci. Biotechnol. Biochem. 65, 213-217 (2001).
114. Kawamukai, M. et al. Nucleotide sequence and characterization of the sfs1 gene: sfs1 is involved in CRP∗-dependent mal gene expression in Escherichia coli. J. Bacteriol. 173, 2644-2648 (1991).
115. Paul, B. J. et al. DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. Cell 118, 311-322 (2004).
116. Clark, R. B. & Ogilvie, J. W. Aspartokinase I-homoserine dehydrogenase I of Escherichia coli K12. Subunit molecular weight and nicotinamide-adenine dinucleotide phosphate binding. Biochemistry 11, 1278-1282 (1972).
117. Starnes, W. L. et al. Threonine-sensitive aspartokinase-homoserine dehydrogenase complex, amino acid composition, molecular weight, and subunit composition of the complex. Biochemistry 11, 677-687 (1972).
118. Burr, B., Walker, J., Truffa-Bachi, P. & Cohen, G. N. Homoserine kinase from Escherichia coli K12. Eur. J. Biochem. 62, 519-526 (1976).
119. Johansen, J., Eriksen, M., Kallipolitis, B.& Valentin-Hansen, P. Down-regulation of outer membrane proteins by noncoding RNAs: unraveling the cAMP-CRP-and sE-dependent CyaR-ompX regulatory case. J. Mol. Biol. 383, 1-9 (2008).
120. De Lay, N. & Gottesman, S. The Crp-activated small noncoding regulatory RNA CyaR (RyeE) links nutritional status to group behavior. J. Bacteriol. 191, 461-476 (2009).
121. Andersen, J., Forst, S. A., Zhao, K., Inouye, M. & Delihas, N. The function of micF RNA. micF RNA is a major factor in the thermal regulation of OmpF protein in Escherichia coli. J. Biol. Chem. 264, 17961-17970 (1989).
122. Deighan, P., Free, A. & Dorman, C. J. A role for the Escherichia coli H-NS-like protein StpA in OmpF porin expression through modulation of micF RNA stability. Mol. Microbiol. 38, 126-139 (2000).
123. Trotochaud, A. E. & Wassarman, K. M. 6S RNA function enhances long-termcell survival. J. Bacteriol. 186, 4978-4985 (2004).
124. Wassarman, K. M. & Storz, G. 6S RNA regulates E. coli RNA polymerase activity. Cell 101, 613-623 (2000).
125. Kim, E. Y., Shin, M. S., Rhee, J. H. & Choy, H. E. Factors influencing preferential utilization of RNA polymerase containing sigma-38 in stationary-phase gene expression in Escherichia coli. J. Microbiol. 42, 103-110 (2004).
126. Muto, A. et al. Structure and function of 10Sa RNA: trans-translation system. Biochimie 78, 985-991 (1996).
127. Roche, E. D.& Sauer, R. T. SsrA-mediated peptide tagging caused by rare codons and tRNA scarcity. EMBO J. 18, 4579-4589 (1999).
128. Kawano, M., Reynolds, A. A., Miranda-Rios, J. & Storz, G. Detection of 59-and 39-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli. Nucleic Acids Res. 33, 1040-1050 (2005).