Eukaryotic specificity

Table I shows that many domain families are widespread among fungi, plants, and metazoa and yet are absent from prokaryotes. It is assumed that these domains arose in early eukaryotes before the emergence of these three major eukaryotic lineages. Consideration of the known functions of these domains, and the proteins in which they occur, strongly suggests that emergence of several cellular functions that are unique to eukaryotes occurred in early eukaryotic history. These functions are likely to have coevolved with the abilities of the protoeukaryotic cell to reproduce sexually and to partake in cell—cell communication. Here we review several eukaryotic-specific domain families as illustrations of the coevolution of domain families with cellular functions.

These GTPases cycle between inactive GDP-bound forms and active GTP-bound forms. Eukaryotic-specific domain families have evolved that either promote GTPase activities (GTPase activator proteins, GAPs ) or promote exchange of GDP for GTP (guanine nucleotide exchange... 

We have demonstrated that this insect cell-free protein synthesis system is one of the most effective protein synthesis systems among those based on animal extracts (2). Furthermore, it has the potential to perform eukaryote-specific protein modifications such as protein W-myristoylation and prenylation (3, 4). Thus, we expect that the insect cell-free protein synthesis system will be a useful method for target protein production in the reverse chemical genetics era, as well as for postgenomic studies. In this chapter, we describe standard protocols to synthesize proteins of interest using the insect cell-free protein synthesis system. 

We confirmed that the Insect Cell Extract has the ability to perform eukaryote-specific protein modifications, such as AT-myristoylation (3) and prenylation (4). To obtain such modified proteins effectively, specific substrates for each protein modification should be added to the translation reaction mixture. 

The 1980 view assumed that the prokaryote-to-eukaryote transition occurred via gradualist mechanisms such as point mutation and hence did not involve symbiosis at all (van Valen and Maiorana 1980 Doolittle 1980) and culminated with a cell that possessed a nucleus, but lacked mitochondria. This is what Doolittle (1998) has called the standard model . In this view, mitochondria are interpreted as a small tack-on to, and mechanistically unrelated to, the process that made eukaryotic cells nucleated and complex (Cavalier-Smith 2002). In the standard model, mitochondria (and chloro-plasts) are descended from endosymbionts, but the nuts-and-bolts of the prokaryote-to-eukaryote transition (the origin of eukaryote-specific traits) was seen as having occurred independently from, and prior to, the origin of mitochondria. The paper by van Valen and Maiorana (1980) expresses this view in clear physiological terms the host was assumed to be an amoeboid, anaerobic, fermenting cell related to archaebacteria, the advantage of the mitochondrial endosymbiont was to supply ATP. 

In chapter 30 we discussed DNA-binding proteins that regulate transcription in prokaryotes. In prokaryotes and eukaryotes specific recognition is dominated by H bond interactions that take place in the major groove of the DNA. In both cases the a helix is the most common element used for DNA recognition. 

An important caution to be heeded in using fresh material directly is to ensure that all contaminating organisms are removed (washed, picked, etc.) from the desired specimen. This may not always be possible, and use of taxon-specific primers in the PCR may overcome the problem. For example, the presence of bacterial contaminants on an eukaryote would be of little consequence if eukaryote-specific primers were being used in the case of lichens, fungus- or alga-specific primers might be used.24... 

Another important difference between DNA replication in prokaryotes and in eukaryotes is that prokaryotic DNA is not complexed to histones, as is eukaryotic DNA. Histone biosynthesis occurs at the same time and at the same rate as DNA biosynthesis. In eukaryotic replication, histones are associated with DNA as it is formed. An important aspect of DNA replication in eukaryotes, specifically affecting humans, is described in the Biochemical Connections box on pages 282 and 283. 

Because of low levels of protein synthesis and undesirable preparation requirements, plant and fungal laceases are often recombinantly expressed using recombinant yeast systems. An exhaustive list and description of heterologously produced laceases can be found in Ref. [13]. Saccharomyces cerevisiae and Pichia pastoris are two common hosts for laccase expression. The yeasts have advantage over native sources because they will grow to high density in liquid cultures and stiU complete eukaryote-specific posttranslational modifications [13]. 

Many polysaccharides of eukaryotic origin show non-specific anti-viral activity and this property may be shared by some of the exopolysaccharides. The structural requirements for activity are not immediately evident as the polysaccharides exhibiting this activity are very diverse. 

Ferri, S. R., and Meighen, E. A. (1991). A Lux-specific myristoyl transferase in luminescent bacteria related to eukaryotic serine esterases. J. Biol. Chem. 266 12852-12857. 

The Ca2+-binding subunit TN-C is homologous to calmodulin with four EF-hands. In contrast to calmodulin, which is ubiquitously expressed in multicellular eukaryotic organisms and interacts with many targets, troponin specifically regulates muscle contraction. There are some structural differences between Troponin C in skeletal and cardiac muscles reflecting their physiological differences. 

The inhibitors of RNA polymerase, which generates RNA from DNA, inhibit a crucial step in gene expression. Inhibition of the eukaryotic form of RNA polymerase is used in cancer chemotherapy and is also an important experimental tool. For example, actinomy-cin D binds to the guanine residues in DNA and blocks the movement of the eukaryotic RNA polymerase. Specific inhibitors of bacterial RNA polymerase can be used as antibacterial agents. Most of these inhibitors like rifamycin bind to the prokaryotic enzyme. 

Microtubules are universally present in eukaryotes from protozoa to the cells of higher animals and plants (Porter, 1966 Hardham and Gunning, 1978 Lloyd, 1987), but they are absent in mammalian erythrocytes and in prokaryotes. Microtubules participate in a number of cellular functions including the maintenance of cell shape and polarity, mitosis, cytokinesis, the positioning of organelles, intracellular transport to specific domains, axoplasmic transport, and cell locomotion. The diversity of microtubule fimctions suggests that not all microtubules are identical and that different classes of microtubules are present in different cell types or are localized in distinct domains in the same cell type (Ginzburg et al., 1989). 

Silver, P.A. Way, J.C. (1993). Eukaryotic DnaJ homologs and the specificity of hsp70 activity. Cell 74, 5-6. 

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