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Genes Within Genes
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interface, one A is shared: TAATG (UAAUG in ribose nucleotides; g. 2). It is the number 3 base of the termination codon and the number 1 base of the initiation codon. The surprises did not end there. At rst, with the sequence of nucleotides spread out in front of them, the researchers could not nd the B and the E genes; they appeared to be missing. Upon careful analysis, however, the scientists found that the B gene was entirely within the A gene and the E gene was entirely within the D gene ( g. 3).Their nding went against theory. We were led to believe, from logical arguments, that genes cannot substantially overlap. There would be too much of a constraint on function: The functional sequence of one gene would also have to be a functional sequence in the other. Similarly, there would be an evolutionary constraint involved. The genes would have to evolve together. But here we have two cases in which genes do overlap. How could overlapping genes come about There are a large number of thymine bases in the X174 genome. In the D gene particularly, many of the codons end with thymine. The imbedded E gene is read on a shifted frame with D so that the terminal bases of D s codons are the middle
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bases of E s. A look at the genetic code (see table 11.4) shows that the codons with U in the middle (E s codons) are mainly for hydrophobic amino acids. Thus, E is a protein with detergent properties. In fact, it is the protein responsible for the dissolution of the outer cell wall of the host bacterium, a process that a detergent can accomplish in vitro. The properties of the E gene, then, are more the properties of its individual amino acids rather than their exact sequence. In the A-B case, there is an indication that the two genes were once autonomous. This indication is based on the patterns of the codons; A s codons tend to end in thymine before the overlap, but thereafter, in the region of overlap, B s codons end in thymine, whereas A s codons do not. Presumably, a mutational event tagged the B material onto the end of the earlier, shorter A gene and improved its enzymatic ability. We can only speculate, however. The amazing arrangement of this viral DNA is one of extreme economy. The protein package is small, yet a minimum of nine genes had to be packed into it. We have seen this kind of economy before in the codon usage of mitochondrial DNA (see chapter 11). As more sequencing has taken place, geneticists have discovered other novel overlap situations. For example, in one case, two genes were transcribed from opposite strands of the same region of DNA from a rat. On one strand, the gonadotropin-releasing hormone gene (GnRH) is located. On the other is a gene (RH) that produces a protein expressed in the heart.
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III. Molecular Genetics
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13. Genomics, Biotechnology, and Recombinant DNA
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Gene overlap is known to occur in bacteria as well. In E. coli, the promoter for the ampC gene (coding for the enzyme -lactamase) begins within the last ten codons for the frdC gene, which codes for a subunit of the enzyme fumarate reductase. There is evidence that in this arrangement the frdC terminator can have some regulatory control of ampC transcription. (See chapter 14 for a discussion of regulatory processes in prokaryotes.)
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With DNA sequence data, including the complete sequences of other chromosomes such as those of SV40 and mitochondria, we have accumulated much information about gene arrangements. Overlap to one degree or another has been found in small viruses ( X174, SV40), large viruses ( ), mitochondrial chromosomes, bacterial DNA, and even eukaryotes, in which several cases are now known in which genes are located
within introns of other genes. In one of the few examples known, three genes are located in an intron of the neuro bromatosis gene, a gene that causes a dis guring neurological disease. Although relatively uncommon, overlap and embedding of genes may have some regulatory role in transcription in addition to minimizing the length of the chromosome.
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