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Tamarin: Principles of Genetics, Seventh Edition
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III. Molecular Genetics
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10. Gene Expression: Transcription
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Gene Expression: Transcription
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EXON II 3
UACUAAC
U6 U4
U2 U6 Ub U5 U4 U1
U6 Ub U5
U6 U2 U5
EXON I EXON II
Sequence of steps, explained in the text, in which U1, U2, U4, U5, and U6 snRNPs take part in intron removal in a nuclear RNA.
Evidence exists to support both views. Gilbert s exonshuf ing view is supported by the analysis of some genes that do indeed t the pattern of exons coding for functional domains of a protein. (Analysis consists of DNA sequencing, RNA sequencing, and protein structural analysis.) For example, the second of three exons of the globin gene binds heme. Similarly, the human low-density lipoprotein receptor is a mosaic of exon-encoded modules shared with several other proteins. Autocatalytic properties of introns lend credence to the view that RNA was the original genetic material and that introns can move within a genome. Additional evidence for the introns-early hypothesis includes the discovery of several introns in phage genes and introns in transfer RNA and ribosomal RNA genes in ancient bacteria (archaebacteria). Until recently, however, no introns were known in the true bacteria (eubacteria). That changed with recent work from the labs
of D. Shub and J. Palmer, who independently discovered an intron in a transfer RNA gene in seven species of cyanobacteria (blue-green algae of the eubacteria). This intron was suspected to exist because it occurred in the equivalent chloroplast gene; the chloroplast evolved from an invading cyanobacterium. However, this discovery has been viewed as supporting both the intronsearly and introns-late view. The introns-early supporters say this evidence con rms that introns arose before the eukaryotes-prokaryotes split. Introns-late supporters say they expect to see some introns in prokaryotes because of the mobility these bits of genetic material have. Both the introns-early and the introns-late views may be correct. It is possible that introns arose early, were lost by the prokaryotes, which prioritized small genomes and rapid, ef cient DNA replication, and later evolved to produce exon shuf ing in eukaryotes.
Tamarin: Principles of Genetics, Seventh Edition
III. Molecular Genetics
10. Gene Expression: Transcription
The McGraw Hill Companies, 2001
Updated Information About the Flow of Genetic Information
RNA Editing
In the last few years, several examples have arisen in which DNA sequence does not predict protein sequence. In several cases, changes in the protein occur that could have only come about by inserting or deleting nucleotides in the messenger RNA before it is translated. This insertion or deletion is almost exclusively of uridines. The process is termed RNA editing. RNA editing was particularly evident in the mitochondrial proteins of a group of parasites, the trypanosomes (some of which cause African sleeping sickness); in one case, more than 50% of the nucleotides in the messenger RNA were added uridines. Uridines were also deleted from the original sequence. These parasites had another mysterious trait the existence of minicircles and maxicircles of DNA in specialized mitochondria called kinetoplasts. In the average kinetoplast, there are about fty maxicircles and about ve thousand minicircles, concatenated like chain links ( g. 10.38a). The maxicircles contain genes for mitochondrial function (see chapter 17); as L. Simpson and his colleagues showed in 1990, both maxicircles and minicircles are templates for guide RNA (gRNA), RNA that guides the process of messenger editing. The guide RNA forms a complement with the messenger RNA to be edited; however, the guide RNA has the sequence complementary to that of the nal messenger RNA, the one with bases added. Since the bases have not yet been added, a bulge occurs in the guide RNA where the complement to be added is ( g. 10.38b). The messenger RNA is then cleaved opposite the bulge by an editing endonuclease. A uridylate (U) is brought into the messenger RNA as a complement to the adenine (A) with the enzyme terminal-U-transferase. An RNA ligase then closes the nick in the messenger RNA, which now has a uridylate added. An exciting outcome of this research, aside from learning about a novel mechanism of messenger RNA processing, is the possibility of clinical rewards. Anytime there is a specialized pathway in a parasite not found in its host, it is possible to use that pathway to attack the parasite. Thus, this research might lead to new ways of combating these trypanosome parasites. RNA editing also occurs in other species and by different mechanisms. For example, in the apolipoprotein-B (apoB) gene in mammals, one gene produces two forms of the protein. In one case, nucleotide 6666, a cytosine, is modi ed by deamination to a uracil in the messenger RNA, resulting in the termination of translation and a protein about half the normal size. RNA editing also occurs in plant mitochondria and chloroplasts in which the usual change is also a cytosine to a uracil. RNA editing is thus routinely seen in speci c examples of posttranscriptional RNA modi cation in both animals and plants.
(a) 5 A A G G G A A A 3 3 U U C C A Cleavage by an editing endonuclease A A G G U U C C G A A A A C U U U Addition of U from UTP by terminal-U-transferase A A G G U G A A A U U C C A C U U U RNA ligase A A G G U G A A A U U C C (b) Figure 10.38 RNA editing. (a) Eight hundred seventy base pair minicircles of DNA from Leishmania tarentolae. (b) Mechanism by which a guide RNA is involved in the editing of a messenger RNA. After the cycle shown, a uridine-containing nucleotide has been added to the messenger RNA. The guide RNA has the sequence complementary to the messenger RNA with the base already added. ([a] Courtesy of Larry Simpson.) A C U U U C U U U 5 mRNA Guide RNA
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