Regulation eucaryotes

Eucaryotes have many more genes and a broader range of specific transcription factors than procaryotes and gene expression is regulated by using sets of these factors in a combinatorial way. Eucaryotes have found several different solutions to the problem of producing a three-dimensional scaffold that allows a protein to interact specifically with DNA. In the next chapter we shall discuss some of the solutions that have no counterpart in procaryotes. However, the procaryotic helix-turn-helix solution to this problem (see Chapter 8) is also exploited in eucaryotes, in homeodomain proteins and some other families of transcription factors. 

In order to estimate the flux through the SMM cycle and to explore its function, a computer model of methionine metabolism in mature Arabidopsis rosette leaves was developed based on data from radiotracer experiments and on metabolite contents. This model suggested that the cycle serves to stop accumulation of AdoMet, rather than to prevent depletion of free methionine, as proposed by Mudd and Datko.54 Because plants lack the AdoMet feedbacks on MTHFR and AdoMet synthetase that regulate AdoMet pool size in other eucaryotes, the SMM cycle may be the main mechanism whereby plants achieve short-term control of AdoMet level. MMT knockouts of maize and Arabidopsis recently became available, and these can now be used to further investigate the role of the SMM cycle, and to test the predictions of the model. 

Metal ions can serve as effector molecules as well as control the DNA-binding activity of regulatory proteins. An example is the regulation of the metallothionein gene in eucaryotes (Fig. 1.23). The metallothioneins are small, cysteine rich proteins which can specifically bind metal ions like Cu or Zn The complexation of metal ions functions to sequester the ions in a form that is not damaging to the cell. 

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. 

The amoimt of available DNA-binding proteins is, in many situations, a critical factor for the extent of transcription regulation. The concentration of regulatory DNA-binding proteins can be regulated within the framework of the following processes in eucaryotes ... 

The above points will be discussed in more detail in the following section (1.4) in the context of eucaryotic gene regulation. 

A combination of several cis-elements, and thus several transcriptional activators, are often involved in the regulation of eucaryotic transcription. Transcription activation, in these cases, results from the complex concerted action of various specific DNA-binding proteins. 

The formation of an active, regulation-competent initiation complex for transcription in eucaryotes demands the concerted action of a large number of proteins. It is estimated that more than 50 different proteins participate in the initiation of transcription in eucaryotes. The basal transcription complex, consisting of the general initiation factors, as well as RNA polymerase 11, allows only for a slow transcription rate. For a regulated acceleration of this low transcription rate it is necessary to have - apart from the regulatory DNA-binding proteins - mediation by further co-activator proteins. 

The repertoire of mechanisms for control of the activity of eucaryotic transcriptional activators (and also of coactivators) is varied and allows a spatially and temporally coordinated regulation of transcription. 

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 phosphorylation of proteins on Ser, Thr or Tyr residues is a basic tool for the regulation of protein activity (see 7.1). Many eucaryotic transcriptional activators are isolated as phosphorylated proteins. The phosphorylation occurrs mainly on the Ser and Thr residues, but can also be observed on the Tyr residues. The extent of phosphorylation is regulated via specific protein kinases and protein phosphatases, each components of signal transduction pathways (see ch. 7). The phosphorylation of transcriptio-... 

Exemplary is the regulation of the CREB protein of higher eucaryotes, displayed in Fig. 1.37. 

The activity of eucaryotic transcriptional activators can be regulated by the binding of low molecular weight effectors, as well as by the binding of inhibitor proteins (see 1.3.2.3). The most significant example for transcriptional activators regulated by low molecular weight effectors are the nuclear receptors, which will be discussed in more detail in chapter 4. 

An essential instrument for the suppression of transcription activity in heterochromatin, as well as for the differential regulation in euchromatin, is the methylation of DNA on the C5 atom of cytidine in the CpG sequence (Fig. 1.43). CpG sequences occur imevenly distributed in the genome. They may be concentrated in CpG islands. Higher eucaryotes possess a characteristic distribution pattern of 5-methyl cytidine (m C), which remains intact upon cell division. Mechanisms must therefore exist to ensure that the methylation pattern is precisely retained in the daughter cells following cell division. A methyl transferase that carries out hemi-methylation in the CpG sequences (Fig. 1.43) is responsible for the inheritance of the methylation pattern. The methyl group is derived from S-adenosyl methionine. The preferential substrates for the hemi-methylation are DNA sequences in which the complementary strand is already methylated. Such a hemi-methylation occurs, for example, shortly after replication of the sequence. 

In order to allow a better rmderstanding of regulation at the level of translation, some of the specific features of eucaryotic translation will be summarized briefly. 

The de novo synthesis of proteins can be varied in response to external stimuli, such as hormones or heat stress. The regulation of protein biosynthesis ocems primarily via phosphorylation of translation initiation factors. The regulatory points in eucaryotes are, above all, the translation factors eIF-2 and elF-4. 

The phosphorylation of enzymes by specific protein kinases is a widespread mechanism for the regulation of enzyme activity. It represents a flexible and reversible means of regulation and plays a central role in signal transduction chains in eucaryotes. 

The two-component pathway was originaUy discovered in bacteria. It was only recently recognized that this kind of signal transduction is also used in eucaryotes. Bacteria possess signal systems which they use to react to changes in N availability, osmolarity and to chemotactic substances. The signaling pathway responsible for this regulation is... 

The inactivating phosphorylation at Thrl4 and TyrlS can be reversed by specific phosphatases in a regulated marmer. The dephosphorylation is performed by CDC2S phosphatase. This enzyme, first described for S. pombe, is a protein phosphatase with twofold specificity that can cleave phosphate residues from phosphoserine and phosphoty-rosine residues of CDKs. CDC2S phosphatases have also been observed in higher eucaryotes where they have a similar fimction. 

Cellular signaling in higher organisms is a major topic in modem medical and pharmacological research and is of central importance in biomolecular sciences. Accordingly, the book concentrates on signaling and regulation in animal systems and in man. Plant systems could not be considered and results from lower eucaryotes and procaryotes are only cited if they are of exemplary character. 

Cook, H. W., Fatty acid denaturation and chain elongation in eucaryotes. In D. E. Vance, and J. E. Vance (eds.). Biochemistry of Lipids, Lipoproteins and Membranes. Amsterdam Elsevier Science Publishers, 1991. Provides an advanced and current treatment of fatty acid desaturation and its regulation, and cites other key references to this field. 

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