Eukaryotic transcription

Nuclear factor kappa B (NF-kB) is the generic term for a family of dimeric eukaryotic transcription factors, composed of members of the Rel family of DNA-binding proteins including the mammalian proteins RelA (or p65), cRel, RelB, p50 and p52, and the Drosophila proteins Dorsal, Dif and Relish. These proteins bind with different affinities to a consensus DNA sequence motif (called the kB site) consisting of the sequence 5 -GGGRNNYYCC-3 in which R is a purine, Y is a pyrimidine, and N is any base. 

The Rel homology domain (RHD) is an evolutionarily conserved domain found in some eukaryotic transcription factors, including NF-kB, the nuclear factors of activated T-cells (NFATs) and the drosophila proteins Dif and Relish. Some of these transcription factors form... 

Ghromatin modifications are important in eukaryotic transcription control. 

Tab. 13.1 Transcription factors under the control of RNI. Selected examples for the regulatory impact of RNI on prokaryotic and eukaryotic transcription factors. In a very simplistic way activation versus inhibition by RNI are indicated.

Rodriguez, J. M., Salas, M. L., and Vinuela, E. Genes homologous to ubiquitin-conjugating proteins and eukaryotic transcription factor SII in African swine fever virus. Virology 1992, 386, 40-52. 

Depletion of histone HI after covalent modification from chromatin is a key step in eukaryotic transcription (Lee et al, 1993 Juan et al, 1994 Rice and Allis, 2001). A comparison of the association of the antibiotic Mg + complexes with the normal and HI depleted chromatin suggests that smaller ligands, like anticancer drugs, have better accessibility for HI depleted chromatin compared to native chromatin. HI depleted chromatin is also more prone to aggregation upon association with the complex I of the antibiotic Mg + complexes. It is also less accessible to micrococcal nuclease. We propose that HI depleted chromatin is a better target of these antibiotics compared to native chromatin. This observation is particularly significant in case of neoplastic cells where most of the cell nuclei are transcriptionally active, and, therefore, contain HI depleted chromatin. 

Sandelin, A., Alkema, W., Engstrom, P.,Wasserman, W. W., andLenhard, B. (2004) JASPAR an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 32, D91-D94. 

The correlation between histone acetylation and eukaryotic transcription were recognized many years ago [128,129]. However, it has not been until very recently, with the discovery that both HATs [130-133] and HDACs [134-138] are an integral part of the basal transcriptional machinery, that the molecular link for this correlation was established. This discovery has rekindled interest in this post-translational histone modification with implications ranging from basic chromatin research to applied medical investigations. Indeed, histone acetylation has been linked to cancer [139-144] and certain types of HDAC inhibitors are already being used to treat certain forms of cancer [145]. 

C. Eukaryotic transcription is more complex than in prokaryotes, mainly in terms of the nature of the RNA polymerases, the assembly of the pre-initiation complex, and the need for processing eukaryotic RNAs. 

Poxvirus promoters are not recognized by eukaryotic transcription machinery. Transcription of poxviral genes is initiated only by virally encoded RNA polymerase, normally packaged alongside the DNA in the virion particles. Purified poxvirus DNA is, therefore, non-infectious. 

The eukaryotic transcription factor NFxB also binds DNA via P-sheet structure (Fig. 1.10). Noteworthy is the enshrouding of the DNA by the P-sheets of NFxB. The recognition of the DNA elements is also achieved by interaction with the major groove of the DNA. 

Burley, S.K. DNA-binding motifs from eukaryotic transcription factors (1994) Curr. Op. Struct. Biol. 4, 3-11... 

Kadonaga, J.T. Eukaryotic transcription an interlaced network of transcription factors and chromatin-modifying machines (1998) Cell 92, 307-13. 

Bernas T, Dobrucki JW (2000) The role of plasma membrane in bioreduction of two tetrazolium salts, MTT, and CTC. Arch Biochem Biophys 380 108-116 Best AA, Morrison HG, McArthur AG, Sogin ML, Olsen GJ (2004) Evolution of eukaryotic transcription insights from the genome of Giardia lamblia. Genome Res 14 1537— 1547... 

Subunit Mixing in Eukaryotic Regulatory Proteins Several families of eukaryotic transcription factors have been defined based on close structural similarities. Within each family, dimers can sometimes form between two identical proteins (a homodimer) or between two different members of the family (a heterodimer). A hypothetical family of four different leucine-zipper proteins could thus form up to ten different dimeric species. In many cases, the different combinations appear to have distinct regulatory and functional properties. 

The structure of RNA polymerase, the signals that control transcription, and the varieties of modification that RNA transcripts can undergo dffer among organisms, and particularly from prokaryotes to eukaryotes. Therefore, in this chapter, the discussions of prokaryotic and eukaryotic transcription are presented separately. 

Genes containing introns have been identified in several archaebacteria2"3 2,13 and in certain phage.206 The corresponding transcripts must be spliced, as are most eukaryotic transcripts. 

In bacteria transcription and translation are closely linked. Polyribosomes may assemble on single DNA strands as shown in Fig. 28-5. It has often been assumed that RNA synthesis occurs on loops of DNA that extend out into the cytosol. However, recent studies indicate that most transcription occurs in the dense nucleoid and that assembly of ribosomes takes place in the cytosol.2683 In a similar way eukaryotic transcription occurs in the nucleus and protein synthesis in the cytosol. Nevertheless, some active ribosomes are present in the nucleus.26813... 

Functional Classification of Positive-Acting Eukaryotic Transcription Factors3... 

Discuss two main DNA-recognition motifs found in eukaryotic transcription factors. Describe their structures, indicate how they bind to DNA, and discuss how each specifically recognizes its DNA binding site. 

The most useful inhibitor of eukaryotic transcription has been a-amanitin, a major toxic substance in the poisonous mushroom Amanita phalloides. The toxin preferentially binds to and inhibits RNA polymerase II (see table 28.4). At high concentrations it also can inhibit RNA polymerase III but not RNA polymerase I or bacterial, mitochondrial, or chloroplast RNA polymerases. 

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