References -- Gene Regulation in Prokaryotes

Biochemistry/MCB 568 -- Fall 2007
John W. Little--University of Arizona

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Books and reviews:

Hochschild, A. and Dove, S. L. Cell 92: 597-600 (1998). "Protein-protein contacts that activate and repress prokaryotic transcription".

Ptashne, M. and Gann, A. Curr.Biol. 8: R812-R822 (1998). "Imposing specificity by localization: mechanism and evolvability".

Ptashne, M. and Gann, A. Nature 386: 569-577 (1997). "Transcriptional activation by recruitment".

Ptashne, M. 1992. "A Genetic Switch", 2nd edition, Cell and BSP Press. An excellent introduction to the regulation of the lysis-lysogeny decision, written simply and clearly.

Echols, H. Trends in Genetics 2:26-30 (1986). "Bacteriophage lambda development: temporal switches and the choice of lysis or lysogeny". Another good overview.

Little, J.W. and Mount, D.W. Cell 29:11-22 (1982). "The SOS regulatory system of Escherichia coli". The bacterial regulatory system that leads to prophage induction.

Landick, R. and Yanofsky, C. (1987). "Transcription attenuation". In "Escherichia coli and Salmonella typhimurium", ed. Neidhardt, F.C., ASM Press, pp. 1276- 1301. A PDF is here. The first 8 pages or so deal with trp attenuation as discussed in class.

Little, J.W. in "The Bacteriophages", 2nd edition, edited R.L. Calendar. "Gene regulatory circuitry in phage lambda". PDF is here.

Papers:

Structures:

Benoff, B. et al., Science 297:1562-1566 (2002). "Structural basis of transcription activation: The CAP-aCTD-DNA complex". Shows contact between AR1 in CAP and CTD of RNAP alpha subunit (see Niu reference below).

Jain,D., Nickels,B.E., Hochschild,A., and Darst,S.A. Molecular Cell 13:45-53 (2004). "Structure of a ternary transcription activation complex". Complex between the DNA-binding domain of lambda CI and a portion of the sigma subunit of RNAP. Explains a large body of genetic data about this interaction.

Simple systems:

Niu, W., Kim, Y., Tau, G., Heyduk, T., and Ebright, R. H. Cell 87: 1123-1134 (1996). "Transcription activation at class II CAP-dependent promoters: Two interactions between CAP and RNA polymerase". Can be accessed from here.

Screen shots of a RasMol script showing AR1 and AR2 are here.

Li, M., Moyle, H., and Susskind, M. M. Science 263: 75-77 (1994). "Target of the transcriptional activation function of phage lambda cI protein".

North, A. K. and Kustu, S. J.Mol.Biol. 267: 17-36 (1997). "Mutant forms of the enhancer-binding protein NtrC can activate transcription from solution". NtrC is an activator of 54 holoenzyme; this holoenzyme readily forms closed complexes, but the activator is necessary to allow open complex formation.

Complex systems:

McAdams, H.H. and Shapiro, L. Science 269:650-656 (1995). "Circuit simulation of genetic networks". A complex computer model of the lysis-lysogeny decision. Reviewed by Loomis, W.F. and Sternberg, P.W. Science 269:649 (1995). "Genetic networks".

Little, J. W., Shepley, D. P., and Wert, D. W. EMBO J. 18:4299-4307 (1999). "Robustness of a gene regulatory circuit".

Landick and Yanofsky, J. Mol. Biol. 196, 363-377 (1987). "Isolation and structural analysis of the Escherichia coli trp leader paused transcription complex".

Alternative strategies to the same ends:

Shearwin, K. E., Brumby, A. M., and Egan, J. B. J.Biol.Chem. 273: 5708-5715 (1998). "The Tum protein of coliphage 186 is an antirepressor".

Antson, A. A., Otridge, J., Brzozowski, A. M. et al. Nature 374: 693-700 (1995). "The structure of trp RNA-binding attenuation protein". The B. subtilis protein (TRAP) that regulates attenuation.

Manch, J. N. and Crawford, I. P. J.Mol.Biol. 156: 67-77 (1982). "Genetic evidence for a positive-acting regulatory factor mediating induction in the tryptophan pathway of Pseudomonas aeruginosa".

Olekhnovich, I. and Gussin, G. N. Gene 223: 247-255 (1998). "Recognition of binding sites I and II by the TrpI activator protein of Pseudomonas aeruginosa: efficient binding to both sites requires InGP even when site II is replaced by site I".

Examples of establishment vs. maintenance:

Kramer, S. G., Jinks, T. M., Schedl, P., and Gergen, J. P. Development 126: 191-200 (1999). "Direct activation of Sex-lethal transcription by the Drosophila Runt protein".

Bell, L. R., Horabin, J. I., Schedl, P., and Cline, T. W. Cell 65: 229-239 (1991). "Positive autoregulation of sex-lethal by alternative splicing maintains the female determined state in drosophila".

Pillus, L. & Rine, J. Cell 59:637-647 (1989). "Epigenetic inheritance of transcriptional states in S. cerevisiae".