| Date |
Topics |
|---|---|
| Jan 13 |
Introduction |
| 15 |
1 - Benzer, bacteriophage T4,
complementation,
recombination, deletion mapping Benzer, S (1955) Fine structure of a genetic region in bacteriophage. PNAS 41:344-354 Benzer, S (1959) On the topology of the genetic fine structure. PNAS 45:1607-1620 Benzer, S (1961) On the topology of the genetic fine structure. PNAS 47:403-415 |
| 20 |
2 - Complementation analysis II,
quorum
sensing Engebrecht, J and M Silverman (1994) Identification of genes and gene products necessary for bacterial bioluminescence. PNAS 81:4154-4158 Waters, CM and BL Bassler (2005) Quorum sensing: cell-to-cell communication in bacteria. Annu Rev cell Cev Biol 21:319-346 |
| 22 |
3 - DNA and the genetic code Crick, FH, CL Barnett, S Brenner, RJ Watts-Tobin (1961) General nature of the genetic code for proteins. Nature 192:1227-1232 Doring, V and P Marliere (1998) Reassigning cysteine in the genetic code of Escherichia coli. Genetics 150:543-551 |
| 27 |
4 - Supercoiling, DNA topology DiNardo, S, KA Voelkel, and R Sternglanz (1982) Escherichia coli DNA topoisomerase I mutants have compensatory mutations in DNA Gyrase genes. Cell 31:43-51 (To be distributed in class) Deng, S, RA Stein and NP Higgins (2005) Organization of supercoil domains and their reorganization by transcription. Mol Microbiol 57:1511-1521 |
| 29 |
5 - Nucleoid structure Hardy, CD and NR Cozzarelli (2005) A genetic selection for supercoiling mutants of Escherichia coli reveals proteins implicated in chromosome structure. Mol Microbiol 57:1636-1652 Azam, TA, A Iwata, A Nishimura, S Ueda and A Ishihama (1999) Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J. Bacteriol. 181:6361-6370. |
| Feb 3 |
6 - Recombination and
Replication forks Kuzminov, A. and F. W. Stahl (1999) Double-strand end repair via the RecBC pathway in Escherichia coli primes DNA replication. Genes Dev. 13:345-356 |
|
5 |
7 - Recomination: Chi and RecBCD Amundsen, SK and GR Smith (2007) Chi hotspot activity in Exherichia coli without RecBCD exonuclease activity: Implications for the mechanism of recombination. Genetics 175:41-54 |
|
10 |
8 - Chromosomal Replication Christensen, BB, T Atlung, and FG Hansen (1999) DnaA boxes important elements in setting the initiation mass of Escherichia coli. J. Bacteriol. 181:2683-2688 Kaguni, JM (2006) DnaA: controlling the initiation of bacterial DNA replication and more. Annu. Rev. Microbiol. 60:351-71 |
|
12 |
9 - Plasmid Replication I Lin-Chao, S, W-T Chen and T-T Wong (1992) High copy number of pUC plasmid results from a Rom/Rop-suppressible point mutation in RNA II. Mol. Microbiol. 6:3385-3393 Solar, G. and M Espinosa (2000) Plasmid copy number control: an ever-growing story. Mol. Microbiol. 37:492-500 |
| 17 |
10 - Plasmid Replication II McEachern, MJ, MA Bott, PA Tooker and DG Helsinki (1989) Negative control of plasmid R6K replication: possible role of intermolecular coupling of replication origins. PNAS 86:7942-7946 Chattoraj, DK (2000) Control of plasmid DNA replication by iterons: no longer paradoxical. Mol. Microbiol. 37:467-476 |
| 19 |
11 - Mutation Fijalkowska, I J, RL Dunn, RM Schaaper (1993) Mutants of Escherichia coli with increased fidelity of replication. Genetics 134:1023-1-30 |
|
24 |
12 - Mutation II Crotty, S, CE Cameron and R Andino (2001) RNA virus error catastrophe: Direct molecular test by using ribavirin. PNAS 98:6895-6900 Hutchinson, F Alterations in the genome In: Eschrichia coli and Salmonella typhimurium. Ed. Neidhardt, FC. ASM Press, Washington, DC Ch 118 |
| 26 |
13 - DNA Repair Hong, ES, A Yeung, P Funchain, MM Slupska and JH Miller (2005) Mutants with temperature-sensitive defects in the Escherichia coli mismatch repair system: sensitivity to mispairs generated in vivo. J. Bacteriol. 187:840-846. |
| Mar 3 |
14 - DNA Repair Huang, S, J Kang, and MJ Blaser (2006) Antimutator role of the DNA glycosylase mutY gene in Helicobacter pylori. J. Bacteriol. 188:6224-6234 |
|
5 |
15 - Transcription Kuznedelov, K et al. (2002) A role for interaction of the RNA polymerase flap domain with the sigma subunit in promoter recognition. Science 295:855-857 Typas, A, G Becker and R Hengge (2007) The molecular basis of selective promoter activation by the sigmaS subunit of RNA polymerase. Mol. Microbiol. 63:1296-1306. |
| 10 |
Exam 1 |
|
12 |
16 - RNA Stability Gao, J. et al. (2006) Differential modulation of E. coli mRNA abundance by inhibitory proteins that alter the composition of the degradosome. Mol. Microbiol. 61:394-406. Kushner, S. R. (2004) mRNA decay in prokaryotes and eukaryotes: Different approaches to a similar problem. IUBMB 56:585-594. |
|
17 |
17 - Translation Marquez, V, DN Wilson, WP Tate, F. Triana-Alonso, and KH Nierhaus (2004) Maintaining the ribosomal reading frame: the influence of the E site during translational regulation of release factor 2. Cell 118:45-55. |
|
19 |
No Class |
| 31 |
18 - Regulation - Negative Hillerich, B, and J Westpheling (2006) A new GntR family transcriptional regulator in Streptomyces coelicolor is required for morphogenesis and antibiotic production and controls transcription of an ABC transporter in response to carbon source. J. Bacteriol. 188:7477-7487 Browning, DF, and SJW Busby (2004) The regulation of bacterial transcription initiation. Nat. Rev. Microbiol. 2:1-9 |
| Apr 2 |
19 - Regulation - Positive Zheng, M, F Aslund, G Storz (1998) Activation of the OxyR transcription factor by reversible disulfide bond formation. Science 279:1718-1721 Toledano, MB, I Kullik, F Trinh, PT Baird, TD Schneider, G. Storz (1994) Redox-dependent shift in OxyR-DNA contacts along and extended DNA-binding site: a mechanism for differential promoter selection. Cell 78:897-909 |
|
7 |
20 - Regulation - Binary
switches, hysteresis Ozbudak, EM, M Thattai, HN Lim, BI Shraiman and A van Oudenaarden (2004) Multistability in the lactose utilization network of Escherichia coli. Nature 427: 737-740. Supplementary Material |
|
14 |
21 - Regulation - Anti-sigma
factors Ades, SE, LE Connolly, BM Alba, and CA Gross (1999) The Escherichia coli sigma E-dependent extracytoplasmic stress response is controlled by the regulated proteolysis of an anti-sigma factor. Genes Dev. 13:2449-2461. |
| 16 |
22 - Regulation - Small RNAs Morita, T, K Maki and H Aiba (2005) RNase E-based reibonucleoprotein complexes:mechanical basis of mRNA destabilization mediated by bacterial noncoding RNAs. Genes Dev. 19:2176-2186. |
|
21 |
23 - Regulation - Riboswitches Cromie, MJ, Y Shi, T Latifi and EA Groisman (2006) An RNA sensor for intracellular Mg2+. Cell 125:71-84. Grundy, FJ and TM Henkin (2006) From ribosome to riboswitch: control of gene expression in bacteria by RNA structural rearrangements. Crit Rev Biochem Mol Biol 41:329-338. |
| 23 |
25 - Epigenetics Hernday, AD, BA Braaten and DA Low (2003) The mechanism by which DNA adenine methylase and PapI activate the Pap epigenetic switch. Mol. Cell. 12:947-957 Casadesus, J and D. Low (2006) Epigenetic regulation in the bacterial world. Microbiol. Mol. Biol. Rev. 70:830-856. |
|
28 |
26 - Epistasis Beyhan, S, K Bilecen, SR Salama, C Casper-Lindley, and FH Yildiz (2007) Regulation of rugosity and biofilm formation in Vibrio cholerae: Comparison of VpsT and VpsR regulons and epistasis analysis of vpsT, vpsR, and hapR. J. Bacteriol. 189:388-402. |
|
30 |
27 - Pathway analysis Jarvik, J and D Botstein (1973) A genetic method for determining the order of events in a biological pathway. PNAS 70:2046-2050. |
| May 5 |
28 - Bacillus subtilis Dworkin, J and R Losick (2001) Differential gene expression governed by chromosomal spatial asymmetry. Cell 107:339-346. Errington, J (2003) Regulation of endospore formation in Bacillus subtilis. Nat Rev Microbiol 1:117-126. |
| |
Final exam |