Gene expression profiling of Escherichia coli growth transitions: An expanded stringent response model

Molecular Microbiology

Volumn 45, Issue 2, 2002, Pages 289-306

  Chang, Dong Eun ^a   Smalley, Darren J ^a   Conway, Tyrrell ^a  

^a UNIVERSITY OF OKLAHOMA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTITOXIN; GLUCOSE; GUANOSINE TRIPHOSPHATASE; HYDROGEN PEROXIDE; LACTOSE; TOXIN;

AEROBIC METABOLISM; AMINO ACID SYNTHESIS; ARTICLE; BACTERIAL CELL; BACTERIAL GENOME; BACTERIAL GROWTH; CELL GROWTH; DNA MICROARRAY; DNA REPLICATION; DOWN REGULATION; ESCHERICHIA COLI; GENE EXPRESSION PROFILING; GENETIC CODE; GENETIC TRANSCRIPTION; GROWTH INHIBITION; HALF LIFE TIME; NONHUMAN; NUCLEOTIDE METABOLISM; OPERON; PRIORITY JOURNAL; REGULATORY MECHANISM; REGULON; RNA TRANSLATION;

AMINO ACIDS; CULTURE MEDIA; ENERGY METABOLISM; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; GLUCOSE; GUANINE NUCLEOTIDES; HYDROGEN PEROXIDE; MODELS, GENETIC; NUCLEIC ACIDS; PROTEIN BIOSYNTHESIS; TRANSCRIPTION, GENETIC;

ARCA; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA; PROKARYOTA;

EID: 0036069537     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2958.2002.03001.x     Document Type: Article

References (80)

1. An Escherichia coli chromosomal 'addiction module' regulated by guanosine 3′,5′-bispyrophosphate: A model for programmed bacterial cell death
2. Global gene expression profiling in Escherichia coli K12. The effects of Integration host factor
3. Control of ilvIH transcription during amino acid downshift in stringent and relaxed strains of Escherichia coli
4. Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli
5. Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro
6. The complete genome sequence of Escherichia coli K-12
7. Molecular anatomy of a transcription activation patch: FIS-RNA polymerase interactions at the Escherichia coli rrnB P1 promoter
8. Interplay between global regulators of Escherichia coli: Effect of RpoS, Lrp and H-NS on transcription of the gene osmc
9. Transcript analysis of 1003 novel yeast genes using high-throughput northern hybridizations
10. Two compounds implicated in the function of the RC gene of Escherichia coli
11. The stringent response
12. The control of ribonucleic acid synthesis in Escherichia coli. V. Characterization of a nucleotide associated with the stringent response
13. Coupling of DNA replication to growth rate in Escherichia coli: A possible role for guanosine tetraphosphate
14. RelE, a global inhibitor of translation, is activated during nutritional stress
15. Variation in HU composition during growth of Escherichia coli: The heterodimer is required for long term survival
16. Sigma factor selectivity of Escherichia coli RNA polymerase: Role for CRP, IHF and lrp transcription factors
17. Anaerobic activation of arcA transcription in Escherichia coli: Roles of Fnr and ArcA
18. DNA array analysis in a microsoft windows environment
19. Exploring the metabolic and genetic control of gene expression on a genomic scale
20. Synthesis of the Escherichia coli K-12 nucleoid-associated DNA-binding protein H-NS is subjected to growth-phase control and autoregulation
21. Characterization of transcriptional initiation from promoters P1 and P2 of the pyrBI operon of Escherichia coli K12
22. Cluster analysis and display of genome-wide expression patterns
23. The general stress sigma factor sigmaS of Escherichia coli is induced during diauxic shift from glucose to lactose
24. Purification of the RelB and RelE proteins of Escherichia coli: RelE binds to RelB and to ribosomes
25. Hyperphosphorylation of Msn2p and Msn4p in response to heat shock and the diauxic shift is inhibited by cAMP in Saccharomyces cerevisiae
26. Synthesis of the stationary-phase sigma factor sigmaS is positively regulated by ppGpp
27. Quinones as the redox signal for the arc two-component system of bacteria
28. Toxin-anti-toxin modules may regulate synthesis of macromolecules during nutritional stress
29. Trigger factor depletion or overproduction causes defective cell division but does not block protein export
30. Formation of ppGpp in a relaxed and stringent strain of Escherichia coli during diauxie lag
31. The transcriptional activator Cat8p provides a major contribution to the reprogramming of carbon metabolism during the diauxic shift in Saccharomyces cerevisiae
32. Timing of synthetic activities in the cell cycle
33. Regulation of gene expression during entry into stationary phase
34. Interplay of global regulators and cell physiology in the general stress response of Escherichia coli
35. Regulation of peptidoglycan biosynthesis in relA+ and relA-strains of Escherichia coli during diauxic growth on glucose and lactose
36. Genetic regulatory mechanisms in the synthesis of proteins
37. Role of RpoH, a heat shock regulator protein. Escherichia coli carbon starvation protein synthesis and survival
38. Regulation of ribosome synthesis
39. The stationary phase of the bacterial life cycle
40. Guanosine polyphosphate production of Escherichia coli stringent and relaxed strains in the stationary phase of growth
41. RpoS-dependent promoters require guanosine tetraphosphate for induction even in the presence of high levels of sigma (s)
42. Effects of nutrition and growth rate on Lrp levels in Escherichia coli
43. Cell division
44. Responses to molecular oxygen
45. Catabolite repression
46. Diauxic shift-induced stress resistance against hydroperoxides in Saccharomyces cerevisiae is not an adaptive stress response and does not depend on functional mitochondria
47. The hypothesis is there is no hypothesis. The microarray meeting, Scottsdale, Arizona, USA, 22-25 September 1999
48. Control of spoT-dependent ppGpp synthesis and degradation in Escherichia coli
49. Culture medium for enterobacteria
50. The glucose-starvation stimulon of Escherichia coli: Induced and repressed synthesis of enzymes of central metabolic pathways and role of acetyl phosphate in gene expression and starvation survival
51. To be or not to be: The ultimate decision of the growth-arrested bacterial cell
52. Starvation, cessation of growth and bacterial aging
53. Not quite dead enough: On bacterial life, culturability, senescence, and death
54. The response regulator SprE controls the stability of RpoS
55. Stress response and expression patterns in wine fermentations of yeast genes induced at the diauxic shift
56. Genes and proteins of Escherichia coli K-12
57. The stationary-phase morphogene bolA from Escherichia coli is induced by stress during early stages of growth
58. Dependence on medium and temperature of cell size and chemical composition during balanced growth of Salmonella typhimurium
59. Functional dissection of trigger factor and DnaK: Interactions with nascent polypeptides and thermally denatured proteins
60. Correlation between histidine operon expression and guanosine 5′- diphosphate-3′-diphosphate levels during amino acid downshift in stringent and relaxed strains of Salmonella typhimurium
61. Combined, functional genomic-biochemical approach to intermediary metabolism: Interaction of acivicin, a glutamine amidotransferase inhibitor, with Escherichia coli K-12
62. Guanosine 5′-diphosphate 3′-diphosphate (ppGpp): Positive effector for histidine operon transcription and general signal for amino-acid deficiency
63. Functional genomics: Expression analysis of Escherichia coli growing on minimal and rich media
64. Growth rate related concentration changes of the starvation response regulators sigmaS and ppGpp in glucose-limited fed-batch and continuous cultures of Escherichia coli
65. Crystal structure of Escherichia coli QOR quinone oxidoreductase complexed with NADPH
66. Differential induction of heat shock, SOS, and oxidation stress regulons and accumulation of nucleotides in Escherichia coli
67. Level of messenger RNA transcribed from the histidine operon in repressed, derepressed and histidine-starved Salmonella typhimurium
68. The SOS response of Escherichia coli
69. Functional determinants of the Escherichia coli fis promoter: Roles of -35-10 and transcription initiation regions in the response to stringent control and growth phase-dependent regulation
70. Transcriptional pattern of Escherichia coli ihfB (himD) gene expression
71. High-density microarray-mediated gene expression profiling of Escherichia coli
72. Expression of arg genes of Escherichia coli during arginine limitation dependent upon stringent control of translation
73. Residual guanosine 3′,5′-bispyrophosphate synthetic activity of relA null mutants can be eliminated by spoT null mutations
74. CspD, a novel DNA replication inhibitor induced during the stationary phase in Escherichia coli
75. DNA microarray-mediated transcriptional profiling of the Escherichia coli response to hydrogen peroxide
76. Regulation of proteolysis of the stationary-phase sigma factor RpoS
77. The RssB response regulator directly targets sigma (S) for degradation by ClpXP
78. The rpoB mutants destabilizing initiation complexes at stringently controlled promoters behave like 'stringent' RNA polymerases in Escherichia coli