RRNA organization

Fig. 11.2 The Universal tree based on 16S and 18S rRNA, which is not very different from that generated earlier based on the observable characteristics of organisms.

Whereas DNA is mostly located in the nucleus of cells in higher organisms (with some also in mitochondria and in plant chloroplasts), RNA comes in three major and distinct forms, each of which plays a crucial role in protein biosynthesis in the cytoplasm. These are, respectively, ribosomal RNA (rRNA), which represents two-thirds of the mass of the ribosome, messenger RNA (mRNA), which encodes the information for the sequence of proteins, and transfer RNAs (tRNAs) which serve as adaptor molecules, allowing the 4-letter code of nucleic acids to be translated into the 20-letter code of proteins. These latter molecules contain a substantial number of modified bases, which are introduced enzymatically. 

Ribosomes are found in all organisms and consist of two unequal subunits. Prokaryotic ribosomes (e.g., those from Escherichia coli) are the most widely studied and those with which this article will be primarily concerned. The 50 S subunit of the E. coli ribosome consists of one strand each of 5 S and 23 S rRNA, and 32 different proteins. The 30 S subunit contains 16 S rRNA and 21 different proteins. 

Another methodological artifact are chimeric sequences which can be formed during PCR amphfication of mixed template at a frequency of several percent. The assumption that each rRNA sequence is equivalent to a species is as shaky as the still wide spread assumption that from the frequency of an rRNA clone in a library the relative abundance of the respective organism in the environment can be estimated. 

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