Other Functions of Ribosomes

In other respects, the archaea lie much closer to the eukaryotes. Although they do not have as many genes as eukaryotes, archaea have on average more than twice as many genes as bacteria. The DNA of archaea is not naked, but is wrapped in proteins similar to those used by eukaryotes. The detailed mechanism of DNA replication and protein synthesis is much closer to that of the eukaryotes. For example, they switch their genes on and off using mechanisms very similar to those in eukaryotes. The protein constituents of the ribosomes also resemble those of the eukaryotes in their structure. Other details of ribosomal function, includ-... 

On the other hand, studies on the structure and function of ribosomes have extensively been performed [22-25]. Quite recently. Ban et al. [26] and Nissen et al. [27] have published reports on the first observation that peptidyltransferase activity in 50S ribosomal subunit is carried out by a 23S ribosomal RNA, the so-called ribozyme, present in the same subunit. The 508 ribosomal subunit was obtained from a gram-negative halophilic Archaean bacterium, H. marismortui or from E. coli [28]. Moreover, Wimberly et al. [29] and Carter et al. [30] reported that the 308 ribosomal subunit originates from a gram-negative heat-loving bacterium, Thermus thermophilus. 

In the cell, nucleic acids are involved in the storage of genomic information and the production of proteins. However, other functions of nucleic acids, especially RNA, have been discovered. For example, ribosomal RNAs not only fold the structure of the ribosome but play an important role in protein synthesis (Moore and Steitz, 2002), and the RNA-induced silencing complex (RICS) is composed of a guide strand of siRNA or microRNA and proteins to control gene expression through RNA interference (Filipowicz, 2005). Those RNAs and proteins work cooperatively to achieve complicated tasks. This means that if we could engineer a nucleic acid-protein complex, we could construct more functional biosensor systems. 

There are at least two assembly domains, namely the L20 domain and the L15 domain, in the 50 S assembly map (Fig. 15). Proteins within the L20 domain are essential for the assembly but not for the function of the 50 S subunit whereas those in the L15 domain are functionally important proteins whose assembly occurs at a late state. As with the 30 S subunit, the assembly map of the 50 S subunit (Rohl and Nierhaus, 1982) not only reflects the assembly dependence but also the topographical relationship of the proteins within the ribosomal particle. This conclusion is supported by a good correspondence between the assembly map on the one hand, and results from cross-linking studies and from the sequential removal of proteins from the particle by LiCl on the other hand. There is also a correlation between the interdependence of proteins during the assembly process and the arrangement of their genes on the E. coli chromosome (Rbhl et al., 1982). 

This definition expands our earlier thoughts in two ways. First, we have included specification of RNA molecules as well as proteins. As noted above, many RNA molecules serve a role as message carrier from DNA to the protein-synthesizing machinery (mRNA) and are translated into protein structures. Other RNA molecules serve other functions as components of the ribosome, rRNA, or as an interface between mRNA and amino acids in protein synthesis, tRNA. Finally, we have the very small RNA molecules known as siRNA. These species of RNA are not translated into proteins and this requires that the definition of a gene include the specification of their structure. 

Although FdUrd produces only DNA-medicated cyotoxicity, 5-FU can also be metabolized to fluorouracil monophosphate (FUMP) and ultimately to fluorouracil triphosphate (FUTP), which can be incorporated into RNA in place of uridine triphosphate (UTP). In other words, incorporation of 5-FU into RNA mimics uracil de novo synthesis and affects the production of ribosomal RNAs (rRNAs) (16,17). 5 -FU also affects several aspects of messenger RNA (mRNA) function, including transcription (18), translation (19), and slicing (20). 

Ribosomal proteins Ribosomal proteins are present in considerably greater numbers in eukaryotic ribosomes than in prokaryotic ribosomes. These proteins play a number of roles in the structure and function of the ribosome and its interactions with other components of the translation system. 

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