Sequence-specific DNA-binding protein

E7. Ehrlich, K. C., and Ehrlich, M., Highly repeated sites in the apolipoprotein(a) gene recognized by methylated DNA-binding protein, a sequence specific DNA-binding protein. Mol. Celt. Biol. 10, 4957-4960 (1990). 

Song, Z., et al., A novel cysteine-ridi sequence-specific DNA-binding protein interacts with the conserved X-box motif of the human major histocompatibility complex dass II genes via a repeated Cys-His domain and functions as a transcriptional repressor. / Exp Med, 1994, 180(5), 1763-74. 

Gagne et al, 2003). Some non-sequence-specific DNA-binding proteins, such as the linker histone HI, may even have a greater affinity for PAR than DNA (Malanga et al., 1998). Thus, an understanding of PAR is an important aspect of understanding the biology of PARP-1 and other PARPs. 

HMG-box proteins stimulate the binding of certain sequence-specific DNA-binding proteins to their DNA targets... 

The specific transcriptional activators (see 1.4.3.1), represented by the GAL4 protein of yeast, are sequence-specific DNA-binding proteins. They possess both a DNA-binding domain and a trans-activating domain to allow them to interact directly with the transcription apparatus. 

The principle means by which the activity of sequence-specific DNA-binding proteins is controlled have aheady been presented in section 1.2. The importance of these mechanisms for regulation in eucaryotes will be discussed below. Altogether, the demands on eucaryotic organisms with regard to the regulation of transcription activity are much more complex than for procaryotes. This tenet holds for the structure of the transcription apparatus as well as for the mechanism of transcription regulation. 

The steroid hormone receptors are sequence specific DNA binding proteins whose cognate DNA elements are termed hormone responsive elements" (HREs). The HREs known to date possess a common structure. They are composed primarily of two copies of a hexamer sequence. In table 4.1 are listed the hexamer sequences of the HREs of important nuclear receptors. 

Mitchell, P. J., and R. Tjian, Transcriptional regulation in mammalian cells by sequence-specific DNA binding proteins. Science 245 371-378, 1989. 

Fu, Y.-H. Marzluf, G.A. (1990). nit-2, the major positively-acting nitrogen regulatory gene of Neurospora crassa, encodes a sequence-specific DNA-binding protein. Proceedings of the National Academy of Sciences (USA) 87, 5331-4. 

Chang P-K, Ehrlich KC, Yu J, Bhatnagar D, Cleveland TE Increased expression of Aspergillus parasiticus aflR, encoding a sequence-specific DNA-binding protein, relieves nitrate inhibition of aflatoxin biosynthesis. Appl Environ Microbiol 1995 61 2372-2377. 

All the DNA-binding proteins discussed thus far function by inhibiting transcription until some environmental condition, such as the presence of lactose, is met. There are also DNA-binding proteins that stimulate transcription. One particularly well studied example is the catabolite activator protein (CAP), which is also known as the cAMP response protein (CRP). When bound to cAMP, CAP, which also is a sequence-specific DNA-binding protein, stimulates the transcription of lactose- and arabinose-catabolizing genes. Within the lac operon, CAP binds to an inverted repeat that is centered near position -61 relative to the start site for transcription (Figure 31.10). CAP functions as a dimer of identical subunits. 

Figure 31.12. Helix-Tum-Helix Motif. These structures show three sequence-specific DNA-binding proteins that...

These structures show three sequence-specific DNA-binding proteins that interact with DNA through a helix-turn-helix motif (highlighted in yellow). Notice that, in each case, the helix-turn-helix units within a protein dimer are approximately 34 A apart, corresponding to one full turn of DNA. [Drawn from lEFA, IRUN, and ITRO.pdb.]... 

When bound to cAM P, CAP stimulates the transcription of lactose- and arabinose-catabolizing genes. CAP is a sequence-specific DNA-binding protein. Within the lac operon, CAP binds to an inverted repeat that is cen tered near position —61 relative to the start site for transcription (Figure 31.15). CAP functions as a dimer of identical subunits. 

The deacteylase complexes are targeted to specific promotors by interactions with different types of negative regulatory proteins. Among these are sequence-specific DNA-binding proteins, corepressors and the methylated CpG-binding proteins (see Section 1.4.8)... 

Transcription factor A protein that functions to initiate or modulate transcription. Most, but not all, transcription factors are sequence-specific DNA binding proteins. 

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