5.6 Physical Maps and Linkage Maps compared

Some very detailed chromosomal maps for bacteria have been obtained by combining the mapping techniques of interrupted mating, recombination mapping, transformation, and transduction. Today, new genetic markers are typically mapped first into a segment of about 10 to 15 map minutes by using interrupted mating. Then additional, closely linked markers can be mapped in a more fine-scale analysis with the use of P1 cotransduction or recombination.

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By 1963, the E. coli map (Figure 5-34) already detailed the positions of approximately 100 genes. After 27 years of further refinement, the 1990 map depicted the positions of more than 1400 genes. Figure 5-35 shows a 5-minute section of the 1990 map (which is adjusted to a scale of 100 minutes). The complexity of these maps illustrates the power and sophistication of genetic analysis. How well do these maps correspond to physical reality? In 1997, the DNA sequence of the entire E. coli genome of 4,632,221 base pairs was completed, allowing us to compare the exact position of genes on the genetic map with the position of the corresponding coding sequence on the linear DNA sequence (the physical map). The full map is represented in Figure 5-36. Figure 5-37 makes a comparison for a segment of both maps. Clearly, the genetic map is a close match to the physical map.

Figure 5-34: A map of the E. coli genome obtained genetically
Figure 5-34: The 1963 genetic map of E. coli genes with mutant phenotypes. Units are minutes, based on interrupted-mating and recombination experiments. Asterisks refer to map positions that are not as precise as the other positions.
[Data from G. S. Stent, Molecular Biology of Bacterial Viruses.]
Figure 5-35: Part of the physical map of the E. coli genome, obtained by sequencing
Figure 5-35: A linear scale drawing of a sequenced 5-minute section of the 100-minute 1990 E. coli linkage map. The parentheses and asterisks indicate markers for which the exact location was unknown at the time of publication. Arrows above genes and groups of genes indicate the direction of transcription.
[Data from B. J. Bachmann, “Linkage Map of Escherichia coli K-12, Edition 8,” Microbiol. Rev. 54, 1990, 130–197.]
Figure 5-36: Physical map of the E. coli genome
Figure 5-36: This map was obtained from sequencing DNA and plotting gene positions. Key to components from the outside in:

  • The DNA replication origin and terminus are marked.

  • The two scales are in DNA base pairs and in minutes.

  • The orange and yellow histograms show the distribution of genes on the two different DNA strands.

  • The arrows represent genes for rRNA (red) and tRNA (green).

  • The central “starburst” is a histogram of each gene with lines of length that reflect predicted level of transcription.
[F. R. Blattner et al., “The Complete Genome Sequence of Escherichia coli K-12” Science 277, 1997, 1453–1462. DOI: 10.1126/science.277.5331.1453. Reprinted with permission from AAAS. Image courtesy of Dr. Guy Plunkett III.]
Figure 5-37: Proportions of the genetic and physical maps are similar but not identical
Figure 5-37: An alignment of the genetic and physical maps. (a) Markers on the 1990 genetic map in the region near 60 and 61 minutes. (b) The exact positions of every gene, based on the complete sequence of the E. coli genome. (Not every gene is named in this map, for simplicity.) The elongated boxes are genes and putative genes. Each color represents a different type of function. For example, red denotes regulatory functions, and dark blue denotes functions in DNA replication, recombination, and repair. Lines between the maps in parts a and b connect the same gene in each map.
[Data from F. R. Blattner et al., “The Complete Science 277, l997, 1453–1462.]
Figure 5-38: Transposon mutagenesis can be used to map a mutation in the genome sequence
Figure 5-38: The insertion of a transposon inserts a mutation into a gene of unknown position and function. The segment next to the transposon is replicated, sequenced, and matched to a segment in the complete genome sequence.

Chapter 4 considered some ways in which the physical map (usually the full genome sequence) can be useful in mapping new mutations. In bacteria, the technique of insertional mutagenesis is another way to zero in rapidly on a mutation’s position on a known physical map. The technique causes mutations through the random insertion of “foreign” DNA fragments. The inserts inactivate any gene in which they land by interrupting the transcriptional unit. Transposons are particularly useful inserts for this purpose in several model organisms, including bacteria. To map a new mutation, the procedure is as follows. The DNA of a transposon carrying a resistance allele or other selectable marker is introduced by transformation into bacterial recipients that have no active transposons. The transposons insert more or less randomly, and any that land in the middle of a gene cause a mutation. A subset of all mutants obtained will have phenotypes relevant to the bacterial process under study, and these phenotypes become the focus of the analysis.

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The beauty of inserting transposons is that, because their sequence is known, the mutant gene can be located and sequenced. DNA replication primers are created that match the known sequence of the transposon (see Chapter 10). These primers are used to initiate a sequencing analysis that proceeds outward from the transposon into the surrounding gene. The short sequence obtained can then be fed into a computer and compared with the complete genome sequence. From this analysis, the position of the gene and its full sequence are obtained. The function of a homolog of this gene might already have been deduced in other organisms. Hence, you can see that this approach (like that introduced in Chapter 4) is another way of uniting mutant phenotype with map position and potential function. Figure 5-38 summarizes the approach.

As an aside in closing, it is interesting that many of the historical experiments revealing the circularity of bacterial and plasmid genomes coincided with the publication and popularization of J. R. R. Tolkien’s The Lord of the Rings. Consequently, a review of bacterial genetics at that time led off with the following quotation from the trilogy: