Transcription activation domain

What are transcription-activation domains Transcription-Activation Domains 

The three motifs mentioned above are involved in the binding of transcription factors to DNA. Not all transcription factors bind directly to DNA, however. Some hind to other transcription factors and never contact the DNA. An example is GBP, which bridges GREB and the RNA polymerase 11 transcription-initiation complex. The motifs whereby transcription factors recognize other proteins can be broken down into three categories  

Acidic domains are regions rich in acidic amino acids. Gal4 is a transcription factor in yeast that activates the genes for metabolizing galactose. It has a domain of 49 amino acids, 11 of which are acidic. 

A proline-rich domain is seen in the activator CTF-1. It has a domain of 84 amino acids, 19 of which are prolines. GTF-1 is a member of a class of transcription factors that bind to an extended promoter element called a GGAAT box. The N-terminal domain has been shown to regulate transcrip)-tion of certain genes. The G-terminal end is a transcription regulator and is known to bind to histone proteins via the proline repeats. An active area of study is how transcription is linked to the acetylation of histones. The coactivator GBP, which was discussed in the previous section, is also a histone acetyl transferase. See the article by Struhl cited in the bibliography at the end of this chapter. 

Despite the seemingly overwhelming complexity of transcription factors, their elucidation has been made more manageable by the similarities in the motifs described in this section. For example, if a new protein is discovered or a new DNA sequence is elucidated, evidence of its role as a transcription factor can be determined by locating the DNA-binding protein motifs discussed in this section. 

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Rel homology domain (RHD) that encompasses a sequence-specific DNA-binding domain, a dimerization domain and a nuclear translocation signal (NLS) (Fig. la). RelA, cRel, and RelB contain a transcription activation domain (TAD). NF-kB 1 and NF-kB2 are synthesized as large precursors, pi 05 and pi 00, that are posttranslationnally processed to generate the mature forms, p50 and p52, which lack a TAD. 

Figure 5.1. Yeast two-hybrid system. Interaction of proteins X and Y upstream of a reporter gene leads to transcriptional activation. Protein X is part of a fusion protein that binds to a site on DNA upstream of the reporter gene by means of a DNA binding domain. Protein Y is part of a fusion protein that contains a transcriptional activation domain. Interaction of proteins X and Y places the activation domain in the vicinity of the reporter gene and stimulates its transcription.

Figure 8.3 Schematic representation of the general domain structure of a STAT protein. A conserved ( C or con ) domain is located at the N-terminus, followed by the DNA-binding domain (D). Y represents a short se-guence that contains the tyrosine residue phosphorylated by the Janus kinase. The carboxy terminus domain (Tr) represents a transcriptional activation domain...

The participation of the different cofactors that form part of the transcription machinery is not homogeneous. Some, like pl60, can interact with both transcription activator domains of the receptor, TAF1 and TAF2, even though they utilize different pi60 domains. Others, like CBP/p300, do not enter into... 

Figure I. The hetero dimeric Core Binding Factor (CBF) transcription factor is comprised of one of three RUNX family proteins (a snbnnit) and a b-subimit, which is encoded by a single gene. The RUNX proteins contain two conserved and functional domains the runt homology domain (RHD) and the transcription activation domain (TAD). Interactions between the RHD and the hetero dimerization domain (HD) of CBFb are essential for most of the known activities of CBF. Synerigistic activity with a number of different transcription factors is well established.

The observation that steroid hormone receptors act as activators as well as repressors of gene activity suggests that receptors can assume an activating and a repressing conformation. In the latter state, the transcriptional activating domain of the receptors is masked. 

These are but two of the types of domains found to be involved in transcription activation. Undoubtedly, this list will grow in the near future, as will our understanding about how these transcription activation domains work. Thus far they are likely to represent regions that function by contacting other regulatory proteins, transcription factors, and the RNA polymerase itself. 

Apopa PL, He X, Ma Q. 2008. Phosphorylation of Nrf2 in the transcription activation domain by casein kinase 2 (CK2) is critical for the nuclear translocation and transcription activation function of Nrf2 in IMR-32 neuroblastoma cells. J Biochem Mol Toxicol 22 63-76. 

HSF3, identified in chicken, is induced by c-Myb in the absence of cellular stress (Nakai and Morimoto, 1993 Kanei-Ishii et al., 1997). Another isoform of HSF found in human cells, HSF4, possesses transcription represser properties in vivo (Frejtag et al., 2001). Comparisons of HSF protein structure in these organisms indicate the presence of conserved DNA binding domain and three hydrophobic heptad repeats that constitute the trimerization domain. These domains are located within the amino-terminal region of the protein. The stress-responsive transcriptional activation domain is located in the carboxyl-terminal region of the molecule. 

Since the initial paper by Fields and Song, there have been significant technical improvements in the method. DNA-binding domains and transcription activation domains have been optimized to reduce false positives and increase the transcription read-out. A variety of reporter plasmids have been engineered to detect a broad range of protein-protein interactions. Much more is understood about the nature of false positives and how to rout them out. Moreover, in response to the utility of this approach, several laboratories have begun to develop transcription-based assays that can be carried out in bacteria, or protein-protein interaction assays based on alternate readouts such as enzyme complementation or fluorescence resonance energy transfer (FRET). 

N-terminal transcription-activation domain (TAD), also known as activation domain 1 (ADI), which activates transcription factors residues 1-42. 

The NF-kB family can be classified into two subgroups, based on the presence or absence of a transcriptional activation domain. p50 and p52 do not contain distinct transcription activation domain and are, therefore, categorized class I. The homodimers of p50 and p52, and the p50/p52 heterodimer may occupy the NF-KB-binding sites of DNA and, thus, function as repressors of gene transcription (Franzoso et al.,... 

The three other NF-kB family members, p65, c-Rel, and RelB, constitute the class II subgroup. NF-kB dimers containing one or two of these polypeptides act as activators of transcription by virtue of the presence of at least one transcription activation domain. The two most abundant and biologically well-characterized NF-kB dimers are p50 homodimer and p50/p65 heterodimer. 

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