Posttranscriptional RNA Modification

The three principal kinds of RNA—tRNA, rRNA, and niRNA—are all modihed enzymatically after transcription to give rise to the functional form of the RNA in question. The type of processing in prokaryotes can differ greatly from that in eukaryotes, especially in the case of mRNA. The initial size of the RNA transcripts is greater than the hnal size because of leader sequences at the 5 end and trailer sequences at the 3 end. The leader and trailer sequences must be removed, and other forms of trimming are also possible. Terminal sequences can be added after transcription, and base modification is frequently observed, especially in tRNA. 

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In contrast, GRK and arrestin both modulate the internalization of 5-HT2c receptors. Posttranscriptional RNA modification involving adenosine-to-inosine editing in the second intracellular loop generates 14 different isoforms of the... 

Immunoprecipitation analysis can be used to determine if a specific protein, for which an antibody is available, becomes associated with a microinjected RNA. Moreover, antibodies against particular RNA modifications (e.g., 5 cap structures or modified bases) can be employed to determine if an injected RNA undergoes a particular posttranscriptional modification following oocyte injection. 

Most often proteins are the bacterial biopolymers studied using MALDI MS either from fractions or whole cells. They are not the only isolated cellular biopolymers studied by MALDI, nor the first. Very soon after the introduction of MALDI there were a few reports of the analysis of bacterial RNA or DNA from bacterial fractions. One of the first applications of MALDI to bacteria fractions involved analysis of RNA isolated from E. coli,4 Other studies included analysis of PCR-amplified DNA,5 6 DNA related to repair mechanisms7 and posttranscriptional modification of bacterial RNA.8 While most MALDI studies involve the use of UV lasers, IR MALDI has been reported for the analysis of double stranded DNA from restriction enzyme digested DNA plasmids, also isolated from E. coli.9... 

Kirpekar, F. Douthwaite, S. Roepstorff, P. Mapping posttranscriptional modifications in 5S ribosomal RNA by MALDI mass spectrometry. RNA 2000, 6,296-306. 

These processes are summarized in Figure 28-1. We have examined several of these mechanisms in previous chapters. Posttranscriptional modification of mRNA, by processes such as alternative splicing patterns (see Fig. 26-19b) or RNA editing (see Box 27-1), can affect which proteins are produced from an mRNA transcript and in what amounts. A variety of nucleotide sequences in an mRNA can affect the rate of its degradation (p. 1020). Many factors affect the rate at which an mRNA is translated into a protein, as well as the posttranslational modification, targeting, and eventual degradation of that protein (Chapter 27). 

The sequences of all three pieces of RNA in the E. coli ribosomes are known as are those from many other species. These include eukaryotic mitochondrial, plas-tid, and cytosolic rRNA. From the sequences alone, it was clear that these long molecules could fold into a complex series of hairpin loops resembling those in tRNA. For example, the 16S rRNA of E. coli can fold as in Fig. 29-2A and eukaryotic 18S RNA in a similar way (Fig. 29-4).38/39/67 69 The actual secondary structures of 16S and 18S RNAs, within the folded molecules revealed by X-ray crystallography, are very similar to that shown in Fig. 29-2A. Ribosomal RNAs undergo many posttranscriptional alterations. Methylation of 2 -hydroxyls and of the nucleic acid bases as well as conversion to pseudouridines (pp. 1638-1641) predominate over 200 modifications, principally in functionally important locations that have been found in human rRNA.69a... 

All tRNAs contain several ribonucleotides that differ from the usual four (12 in the case of tRNAphe). The structures for some of these are shown in figure 28.4. Only four ribonucleotides are incorporated into RNA in the transcription process. All of the rare bases found in the mature tRNA result from posttranscriptional modification. 

Be able to discuss the posttranscriptional modification and processing of RNAs (rRNA, mRNA, and tRNA). 

Posttranscriptional processing of primary RNA transcripts includes RNA splicing, 50 capping, 30 polyadenylation, and tRNA base modifications. Many of these alterations increase RNA stability and enhance inRNA translation. 

Second, many of the bases in tRNAs are modified posttranscriptionally some of these modifications are uniform among all tRNAs, whereas others are specific for each tRNA. Third, the structural data reveal that there are four intrastrand RNA-RNA helices which are formed by standard (G-C, A-U) and nonstandard (G-U) base pairing. 

The main features of translation are the same in prokaryotes and eukaryotes, but the details differ. The messenger RNAs of eukaryotes are characterized by two major posttranscriptional modifications. The first is the 5 cap, and the second is the 3 poly A tail (Figure 12.19). Both modifications are essential to eukaryotic translation. 

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