Repression loop

Fig. 1.19. Tetramerization of the Lac repressor and loop formation of the DNA. The Lac repressor from E. coli binds as a dimer to the two-fold symmetric operator seqnence, whereby each of the monomers contacts a half-site of a recognition sequence. The Lac operon of E. coli possesses three operator sequences Of, 02 and 03, aU three of which are required for complete repression. Of and 03 are separated by 93 bp, and only these two sequences are displayed in the figure above. Between Of and 03 is a binding site for the CAP protein and the contact surface for the RNA polymerase. The Lac repressor acts as a tetramer. It is therefore assumed that two dimers of the repressor associate to form the active tetramer, whereby one of the two dimers is bound to 03, the other dimer binds to Of. The intervening DNA forms a so-caUed repression loop. After Lewis et al., 1996.

Strater N, Jasper B, Scholte M, Krehs B, Duff AP, Langley DB, Han RL, AveriU BA, Freeman HC, Guss JM. 2005. Crystal structures of recomhinant human purple acid phosphatase with and without an inhihitory conformation of the repression loop. J Mol Biol 351 233-246. 

The low torsion constant at a = —0.025 is very similar to that observed in a supercoiled pBR322 that was partially relaxed by saturation binding of Escherichia coli single-strand binding (ssb) protein, and which persisted for over a month.(56) It is also similar to that recently inferred from an in vivo assay based on variation in repression efficiency with size of a putative DNA loop.(234) Indeed, it appears that anomalously low torsion constants may be universally encountered in the course of either partial or complete relaxation of supercoiled DNAs, regardless of whether the superhelix density is reduced by action of topoisomerase I, binding of ssb protein, binding of intercalated... 

Hwang SS, Boyle TJ, Lyerly HK, Cullen BR (1991) Identification of the envelope V3 loop as the primary determinant of cell tropism in HIV-1. Science 253 71—74 Imai K, Okamoto T (2006) Transcriptional repression of Human Immunodeficiency Virus Type 1 by AP-4. J Biol Chem 281 12495-12505... 

Subsequent studies revealed that the transcription of Rev-erba, is regulated by essentially the same mechanisms as those of Per and Cry genes it is activated by BMALl and CLOCK and repressed by PER and CRY. Therefore, REV-ERBa directly connects two antiphasic feedback loops within the positive and negative limbs of the oscillator (Fig. 1). 

In summary, we have shown that VRI is an integral component of the interlocked feedback loop mechanism in Drosophila whose role is to repress Clk... 

Heintzen C, Loros JJ, Dunlap JC 2001 The PAS protein VIVID defines a clock-associated feedback loop that represses light input, modulates gating, and regulates clock resetting. Cell 104 453-464... 

Control by looping. The arabinose utilization operon of E. coli, araBAD, encodes proteins needed for uptake of arabinose and conversion to D-xylulose 5-P. The repressor AraC in the absence of arabinose binds at operator 1 (Oj) to prevent further synthesis of repressor (autorepression) and also at the aral region to repress transcription of operon araBAD. The operator 2 (02) site, which is 211 bp upstream from aral, is also needed for this repression.145-14713 A loop is apparently formed by repressor binding (Fig. 28-7). Binding of arabinose to the repressor converts it into an activator, which stimulates initiation of transcription at the BAD promoter. Further stimulation is provided by the CAP-cAMP complex, which binds next at aral. 

One of the most prominent features of the 50S subunit is the LI protuberance, seen on the left side in Fig. 29-6A. This protuberance is formed almost entirely by protein LI, which is one of the largest ribosomal proteins. It binds to the 2105-2184 loop in domain V of the 23S RNA (see Fig. 29-14).139 LI has an important regulatory role in bacteria in which it represses translation of its own structural gene by binding to a region in its mRNA close to the Shine-Dalgamo sequence. 

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