Readings

Course readings.
WEEK #	TOPICS	READINGS
1	Introduction See the Lecture Summary	[No Readings]
2	The general stress response and sporulation See the Lecture Summary	Paper 1 Schultz, J. E., G. I. Latter, and A. Matin. "Differential Regulation by Cyclic AMP of Starvation Protein Synthesis in Escherichia coli." J Bacteriol 170 (1988): 3903-9. Paper 2 Eichenberger, P., M. Fujita, S. T. Jensen, E. M. Conlon, D. Z. Rudner, S. T. Wang, C. Ferguson, K. Haga, T. Sato, J. S. Liu, and R. Losick. "The Program of Gene Transcription for a Single Differentiating Cell Type During Sporulation in Bacillus subtilis." PLoS Biol 2 (2004): 328.
3	Evolution of the general stress response and sporulation See the Lecture Summary	Paper 1 Zambrano, M. M., D. A. Siegele, M. Almirón, A. Tormo, and R. Kolter. "Microbial Competition: Escherichia Coli Mutants that Take Over Stationary Phase Cultures." Science 259 (1993): 1757-60. Paper 2 Veening, J. W., E. J. Stewart, T. W. Berngruber, F. Taddei, O. P. Kuipers, and L. W. Hamoen. "Bet-Hedging and Epigenetic Inheritance in Bacterial Cell Development." Proc Natl Acad Sci USA 105 (2008): 4393-8.
4	Protein-protein interactions: Two-component systems See the Lecture Summary	Paper 1 Bray, D., M. D. Levin, and C. J. Morton-Firth. "Receptor Clustering as a Cellular Mechanism to Control Sensitivity." Nature 393 (1998): 85-8. Paper 2 Skerker, J. M., B. S. Perchuk, A. Siryaporn, E. A. Lubin, O. Ashenberg, M. Goulian, and M. T. Laub. "Rewiring the Specificity of Two-component Signal Transduction Systems." Cell 133 (2008): 1043-54.
5	sRNAs: Regulating translation mRNA of RpoS (the general stress response activator) See the Lecture Summary	Paper1 Sledjeski, D. D., A. Gupta, and S. Gottesman. "The Small RNA, DsrA, is Essential for the Low Temperature Expression of RpoS During Exponential Growth in Escherichia Coli." EMBO J 15 (1996): 3993-4000. Paper 2 Repoila, F., and S. Gottesman. "Signal Transduction Cascade for Regulation of RpoS: Temperature Regulation of DsrA." J Bacteriol 183 (July 2001): 4012-23.
6	Small molecules: The stringent response See the Lecture Summary	Paper 1 Haseltine, W. A., and R. Block. "Synthesis of Guanosine Tetra and Pentaphosphate Requires the Presence of a Codon-Specific Uncharged Transfer Ribonucleic Acid in the Acceptor Site of Ribosomes." Proc Natl Acad Sci USA 70 (1973): 1564–8. Paper 2 Kvint, K., A. Farewell, and T. Nyström. "RpoS-Dependent Promoters Require Guanosine Tetraphosphate for Induction Even in the Presence of High Levels of Sigma(s)." J Biol Chem 275 (2000): 14795-8.
7	Field trip to the Laub laboratory See the Lecture Summary	[No Readings]
8	Pumping out toxins: Antibiotics See the Lecture Summary	Paper 1 Li, X. Z., D. Ma, D. M. Livermore, and H. Nikaido. "Role of Efflux Pump(s) in Intrinsic Resistance of Pseudomonas Aeruginosa: Active Efflux as a Contributing Factor to Beta-Lactam Resistance." Antimicrob Agents Chemother 38 (August 1994): 1742-52. Paper 2 Tikhonova, E. B., and H. I. Zgurskaya. "AcrA, AcrB, and TolC of Escherichia coli Form a Stable Intermembrane Multidrug Efflux Complex." J Biol Chem 279, no. 31 (July 30, 2004): 32116-24.
9	Scavenging toxins: Reactive oxidative species See the Lecture Summary	Paper 1 Carlioz, A., and D. Touati. "Isolation of Superoxide Dismutase Mutants in Escherichia coli: is Superoxide Dismutase Necessary for Aerobic life?" EMBO J 5 (1986): 623-30. Paper 2 Greenberg, J. T., P. Monach, J. H. Chou, P. D. Josephy, and B. Demple. "Positive Control of a Global Antioxidant Defense Regulon Activated by Superoxide-generating Agents in Escherichia Coli." Proc Natl Acad Sci U S A 87 (August 1990): 6181-5.
10	Promoting tolerance: Extreme heat and cold See the Lecture Summary	Paper 1 Mogk, A., T. Tomoyasu, P. Goloubinoff, S. Rüdiger, D. Röder, H. Langen, and B. Bukau. "Identification of Thermolabile Escherichia Coli Proteins: Prevention and Reversion of Aggregation by DnaK and ClpB." EMBO J 18 (December 15, 1999): 6934-49. Paper 2 Guisbert, E., C. Herman, C. Z. Lu, and C. A. Gross. "A Chaperone Network Controls the Heat Shock Response in E. Coli." Genes Dev 18 (2004): 2812-21.
11	Final oral presentations See the Lecture Summary	[No Readings]
12	Repair calls: Single-stranded DNA damage See the Lecture Summary	Paper 1 Sancar, A., and W. D. Rupp. "A Novel Repair Enzyme: UVRABC Excision Nuclease of Escherichia Coli Cuts a DNA Strand on Both Sides of the Damaged Region." Cell 33 (May 1983): 249-60. Paper 2 Mellon, I., and G. N. Champe. "Products of DNA Mismatch Repair Genes mutS and mutL are Required for Transcription-Coupled Nucleotide-Excision Repair of the Lactose Operon in Escherichia Coli." Proc Natl Acad Sci U S A 93 (February 6, 1996): 1292-7.