Snyder and Champness Molecular Genetics of Bacteria. Tina M. Henkin
The 23S rRNA is the peptidyltransferase enzyme, which joins amino acids into protein on the ribosome. The 23S rRNA therefore acts as a ribozyme, an RNA enzyme (see below). The 16S RNA lacks enzymatic activity but plays crucial roles in initiation and termination of translation, as well as in decoding of the sequence of the mRNA.
The rRNAs and tRNAs make up the bulk of the RNA in cells because of their central role in protein synthesis. In a rapidly growing bacterial cell, much of the total RNA synthesis is devoted to making these RNAs. Also, the rRNAs and tRNAs are far more resistant to degradation than mRNA. With this combination of a high synthesis rate and high stability, the rRNAs and tRNAs together can amount to more than 95% of the total RNA in a rapidly growing bacterial cell.
Not only do the rRNAs physically associate in the ribosome, but they also are synthesized together as long precursor RNAs containing all three forms of rRNA separated by so-called spacer regions. The precursors often contain one or more tRNAs, as well (Figure 2.16), while other tRNAs are encoded in operons that do not include rRNA sequences. The individual rRNAs and tRNAs are released from the precursor RNAs by ribonucleases (RNases). Some of these RNases participate in both rRNA and tRNA processing and RNA degradation, while others are dedicated to a single function; for example, RNase P generates the precise 5′ end of tRNAs. At some point during the processing, individual nucleotides within the rRNA and tRNA precursor molecules are also modified to make the mature rRNAs and tRNAs.
Molecular Phylogeny
The translation apparatus is the most highly conserved of all the cellular components. The structures of ribosomes, translation factors, aaRS enzymes, tRNAs, and the genetic code itself have changed remarkably little in billions of years of evolution. This is why these components have been used extensively in molecular phylogeny. By comparing the sequences of the rRNAs and other components of the translation apparatus and determining how much they have diverged, it has been possible to establish phylogenetic trees that include all organisms on Earth. The high level of conservation probably also explains why so many different antibiotics target the translation apparatus compared to other cellular components. An antibiotic designed to inhibit translation in one type of bacteria will probably inhibit translation in many other types of bacteria.
The conservation of components of the translation apparatus is so high that “rooted” evolutionary trees can be made that include eukaryotes and archaea (see the introduction). Such trees are usually not too different from what has been obtained from physiological and other comparisons, but there are sometimes surprises. Also, the sequence of the translation elongation factors led to the suggestion that the archaea are more closely related to eukaryotes than they are to other bacteria, prompting the change of their name to archaea from the original designation “archaebacteria.”
Many of the initiation and elongation factors in bacteria have counterparts in archaea and eukaryotes. Nevertheless, the major differences in the translation apparatus come in the translation initiation factors. While bacteria have only three initiation factors (some of them have more than one form), archaea and eukaryotes have many more. As is the case with other cellular functions, archaea share more of their initiation factors with eukaryotes than they do with bacteria. Also, some of the initiation factors, while conserved, seem to have somewhat different functions in the three kingdoms of life. These differences may reflect differences in the initiation sites for translation.
References
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Figure 2.16 Precursor of rRNA. The precursor transcript (top) contains the 16S, 23S, and 5S rRNAs, as well as one or more tRNAs. RNases cut the individual rRNAs and tRNAs out of the precursor after it is synthesized.
The faster a cell grows, the more protein it needs to make. Ribosomes are the site of protein synthesis; therefore, cells can increase their growth rate only if they increase the number of ribosomes. In most bacteria, the coding sequences for the rRNAs are repeated in several copies in the genome. Duplication of these genes leads to higher rates of rRNA synthesis in these bacteria. Although the precursor RNAs encoded by these different copies produce identical rRNAs, the rRNA gene clusters often contain different tRNAs and spacer regions.
MODIFICATION OF RNA
Some of the RNAs in cells are modified after they are made. For example, specific nucleotides in the rRNAs are methylated. The tRNAs are probably the most highly processed and modified RNAs in cells (see Björk and Hagervall, Suggested Reading). Figure 2.17 shows a “mature” tRNA that was originally cut out of a much longer molecule that may also have included the rRNAs as well as other tRNAs. Some of the bases within the tRNA are modified by specific enzymes that produce altered bases, such as pseudouracil and dihydrouracil. A CCA sequence is found on the 3′ end of all tRNAs. In some cases this is encoded in the gene, and therefore is part of the precursor RNA, while in others it is added posttranscriptionally by an enzyme called CCA nucleotidyltransferase.
Figure 2.17 Structure of mature tRNAs. (A) Standard clover leaf representation of tRNA, showing the base pairing that holds the molecule together and some of the standard modifications. D is the modified base dihydrouridine. tRNAs also contain thymine (T) and pseudouracil (Ψ) among other modifications. The amino acid is attached to the terminal A of the CCA at the 3′ end. (B) Folding of tRNA into its tertiary structure. The discriminator base (black dot), immediately upstream of the CCA, is important for tRNA recognition by the correct aminoacyl-tRNA synthetase (aaRS).
RNA Degradation
Different classes of RNAs have very