Modification of Regulatory Proteins

Post-translational covalent modification of DNA-binding proteins is a mechanism commonly employed among eucaryotes to control the activity of DNA-binding proteins. 

Of particular importance is the phosphorylation of eucaryotic transcription factors. Functional and mechanistic consequences of the phosphorylation of transcription factors will be discussed in more detail in the section on the regulation of eucaryotic transcription (see 1.4.3.2). Specific or non-specific protein phosphatases (see 7.5) can remove the phosphate residues and terminate the phosphorylation signal. 

A singular example of how covalent modification can be used to achieve transcription control is found in the regulation of the adaptive repair of DNA damage in proca- 

repair is induced by alkylation damage. The repair of methylated DNA is performed by, among others, the Ada protein which possesses S-alkyl transferase and transcription activation activity. The Ada protein is methylated during the first repair process. In the methylated form the Ada protein can function as a transcriptional activator. It binds to the corresponding DNA element of an operon which encodes for 

Ada and other proteins. Upon the binding of the methylated Ada protein to its cognate DNA element, the transcription of the genes is stimulated such that more repair proteins are available. 

Covalent modification by methylation or acetylation at Arg or Lys residues can be used to regulate the interaction of transcription factors with other regulatory proteins. As an example, Arg methylation of the transcription factor Statl regulates its dephosphorylation by protein tyrosine phosphatases (Zhu et al., 2002). Acetylation of Lys residues controls the activity of the yeast transcription factor GATA-1 (Boyes et al., 1998). 

The reversible oxidation of cysteine residues has been shown to function as a switch between different states of activity of transcription factors. This has been shown, e.g., for the transcription factor API, which contains cysteine motifs that regulate activity in response to oxidative stress (Karimpour et al., 2002). 

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In contrast to simple charge neutralization effects, the effects on protein recog-nition/recruitment are collectively referred to as the histone code . This hypothesis predicts that specific patterns of histone tail acetylations and other modifications serve as epigenetic marks for distinct sets of regulatory proteins to differentially modulate chromatin structure and function (Strahl and Allis, 2000 Turner, 2000 Jenuwein and Allis, 2001). Indeed, several recent findings have demonstrated that histone acetylation creates a signal for the binding of a bromodomain which has... 

Covalent modification of a protein by the hnkage of an ADP-ribosyl moiety to the protein. The resulting product typically exhibits altered kinetic and/or regulatory properties. ADP-ribosyltransferases catalyze the trans-... 

Phosphorylation of proteins on Ser/Thr residues is one of the most common regulatory modifications of signaling proteins (see Chapters 2 and 7). Only recently has it been recognized that serine/threonine phosphorylation results in the formation of multiprotein signaling complexes through specific interactions between phosphory-lated sequence motifs and the following phosphoserine/threonine-binding domains (review Yaffe and Elia, 2001). 

The step labeled p in Figure 1 represents modification of primary proteins to render them functional examples would be posttranslational covalent modifications (e.g., phosphorylation) and binding with other proteins or other molecules. Represented within the set of steps p are the many regulatory events (other than transcription and translation) affecting gene expression and the overall physiology of the cell. 

It is noteworthy that free mRNP particles are a temporary untranslatable form of mRNA in the cytoplasm and that proteins associated with the active polysomal mRNP or the repressed mRNP are different [6, 7]. There is now some evidence that ribo-nucleoprotein particles are dynamic structures and that protein exchanges occur between the cytoplasmic mRNA-associated proteins and free proteins. Involvement of mRNA-associated proteins in the regulation of protein synthesis has been considered [7-10] and post-translational modification of these proteins as a regulatory mechanism might be considered. 

Posttranslational modification of precursor proteins appears to be an important regulatory step in the synthesis and secretion of complement proteins, as it is with other proteins (Ooi et al. 1980). Hall and CoLTEN (1978) showed in the guinea pig, that deficiency of C3 resulted from a translational defect in the synthesis of C4 protein. Under cell-free conditions, hepatic polysomes from C4-deficient guinea pigs synthesised only nascent C4 polypeptides that remain polysome-bound. Thus, the mRNA appears to be present but not completely translated. 

A model called histone code theory includes more aspects of chromatin regulation which have been identified. The histone code theory predicts that histone acetylation and other posttranslational histone modifications serve as binding sites for regulatory proteins which mediate processes like gene transcription upon recruitment (see Fig. 2b) [3]. In this context histone modifications can be understood as... 

Evolution has provided the cell with a repertoire of 20 amino acids to build proteins. The diversity of amino acid side chain properties is enormous, yet many additional functional groups have been selectively chosen to be covalently attached to side chains and this further increases the unique properties of proteins. Diese additional groups play a regulatory role allowing the cell to respond to changing cellular conditions and events. Known covalent modifications of proteins now include phosphorylation, methylation, acetylation, ubi-quitylation, hydroxylation, uridylylation and glycosyl-ation, among many others. Intense study in this field has shown the addition of a phosphate moiety to a protein... 

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