Eukarya/eukaryotes

Some biologists prefer a three-domain classification scheme— Bacteria (eubacteria), Archaea (archaebacteria), and Eukarya (eukaryotes)—to the five-kingdom classification (Figure 1.19). The basis for this preference is the emphasis on biochemistry as the basis for classification. 

However, the packing of DNA into nucleosome-like structures is not unique to eukarya similar structures appear in archaea (reviewed in Reeve et al., 1997). Additionally, histones and minichromosome maintenance proteins (MCM) are widespread among eukarya and archaea and absent in prokarya, and the eukaryotic chromo domain has a structure that is highly reminiscent of archaeal histones that are involved in formation of archaeal chromatin (Ball et al., 1997). Consequently, it is possible that chromatin remodeling in eukaryotes is an elaboration of a similar cellular mechanism in archaea. 

Eukaryotes are differentiated from the Archaea and Eubacteria by the possession of a nucleus in the cell enclosed by a membrane as well as by membrane-enclosed subcellular organelles. The nucleus houses the basic genetic information of these organisms, their genomes, as I will describe in chapter 14. The eukaryotes are a diverse set of species, including but not limited to all plants and animals. Remarkably, the Archaea are more closely related to Eukarya than they are to the Eubacteria. This reflects a striking origin of the eukaryotic cell. 

With regard to selenocysteine biosynthesis in archaea and eukarya, a tRNA has been known for some time, which accepts L-serine and possesses an anticodon complementary to UGA. It shares a number of structural featmes with tRNA from E. coli, such as extended aminoacyl acceptor and D-arms. In eukarya, the serine residue attached to this tRNA can be phosphorylated by a specific kinase and it was first assumed that this tRNA inserts phosphoserine into proteins. However, closer examination revealed that this tRNA carries selenocysteine in vivo and certainly is the pendant to tRNA from E. coli. It is still elusive whether (9-phosphoseryl-tRNA is the biosynthetic intermediate for selenocysteyl-tRNA formation in eukaryotes also, there is no evidence yet of an eukaryal and archaeal enzyme, equivalent in its function to selenocysteine synthase from bacteria. 

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