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Chapter 30 : Physical Map of the Bacillus subtilis 168 Chromosome

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Physical Map of the Bacillus subtilis 168 Chromosome, Page 1 of 2

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Abstract:

This chapter summarizes information on the physical and genetic maps of the chromosome, the integration of the physical and genetic maps, and the unique features of the genome. Two basic physical maps of bacterial genomes have been developed: (i) a long-range restriction map generated by sequence-specific restriction endonucleases that cleave the bacterial chromosome infrequently and (ii) a detailed restriction map derived from the assembly of overlapping cloned DNA segment. The physical map of the 168 chromosome has been constructed by the first method. The strategy and ideas for its construction are unique and specific to 168, and described briefly. In this chapter, the author uses the map constructed by Itaya and Tanaka because it is complete and sufficiently accurate. Diversity of the genome based on the physical map can be used to evaluate the frequency of DNA rearrangements.

Citation: Itaya M. 1993. Physical Map of the Bacillus subtilis 168 Chromosome, p 463-471. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch30

Key Concept Ranking

Genetic Recombination
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Chromosomal DNA
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DNA Restriction Enzymes
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Figures

Image of Figure 1
Figure 1

Conversion of nucleotide sequences on the chromosome. Circles represent the chromosome. Two hypothetical genes, and are in boxed regions, and and denote the drug resistance gene cassettes. The DNA segments used in transformation steps I through III are prepared in and linearized, x x indicates a double crossover followed by homologous recombination. A net change that the last strain acquires is only the mutations. Details are given in the text.

Citation: Itaya M. 1993. Physical Map of the Bacillus subtilis 168 Chromosome, p 463-471. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch30
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Image of Figure 2
Figure 2

Strategy for determination of restriction enzyme sites on the chromosome. Circles represent the chromosome, and short bars around the circles represent recognition sites of restriction enzymes. The sites can be eradicated, i.e., converted to other sequences, from the chromosome by using the gene-directed mutagenesis method described in the legend to Fig. 1 . The method can be sequentially applied, and the number of recognition sites can be decreased progressively from left to right. Patterns of fragments after enzyme digestion and gel electrophoresis are shown at the bottom. Dotted lines indicate changes of fragments resulting from the loss of the recognition site. Details are described in reference .

Citation: Itaya M. 1993. Physical Map of the Bacillus subtilis 168 Chromosome, p 463-471. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch30
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Image of Figure 3
Figure 3

Separation of chromosome DNA by PFGE after II digestion. (Left) Lane 1, concatemeric lambda DNA size markers. Chromosomal DNA from CU741, a wild-type was digested with I (lane 2), I (lane 3), or DNA from (lane 4). (Right) Lanes 1, 5, and 9 contain concatemeric lambda DNA plus lambda DNA digested with as size standards. Noil-digested chromosomal DNA was from CU741 (lane 2), BEST4041 (lane 3), or BEST4101 (lane 4). I-digested chromosomal DNA was from OA101 (lane 6), BEST3015 (lane 7), or BEST3019 (lane 8). Sizes (in kilobase pairs) are in parentheses. or generates 26 or more than 80 fragments. Designations for each fragment are given in Table 1 . Derivatives constructed by progressive removal of (BEST4041 and BEST4101) or I (BEST3015 and BEST3019) are described in reference 15.

Citation: Itaya M. 1993. Physical Map of the Bacillus subtilis 168 Chromosome, p 463-471. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch30
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Image of Figure 4
Figure 4

and physical map of the 168 chromosome. The map was redrawn on the basis of data in reference 15. Total genome size is 4,165 kb, which is divided into five linearized parts (1,000 kb each). Short horizontal bars across the vertical lines mark sites. Physical distances (in kilobases) are indicated on the left. Locations of genes at arrowheads had been precisely determined and were used as landmarks on the physical map ( Table 2 and text). Genes whose locations on both and fragments have been determined are included beside the segments ( Table 2 ). Open triangles indicate 23-kb deletions found in the standard strain, CU741, used for map construction ( ; see text). Two weakly cleavable sites are indicated by boldface arrows. The region of the SPβ prophage is boxed.

Citation: Itaya M. 1993. Physical Map of the Bacillus subtilis 168 Chromosome, p 463-471. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch30
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Image of Figure 5
Figure 5

Correlation between the genetic and physical maps. Genetic map information given in Table 2 is included. Closed circles indicate gene loci whose precise physical locations have been determined. Vertical bars or open circles represent DNA regions to which cloned genes have been assigned by the results of Southern hybridization. Open arrows indicate regions where the physical location is slightly displaced from that on the genetic map.

Citation: Itaya M. 1993. Physical Map of the Bacillus subtilis 168 Chromosome, p 463-471. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch30
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Image of FIGURE 6
FIGURE 6

Stability and asymmetry of the 168 chromosome. Locations of the site (at 39 kb) and the site (at kb 2012) and regions for naturally occurring DNA deletions on the 168 chromosome (regions I, II, and III) are indicated by arrows. The genome size for 168 (strain CU741) was estimated to be 4,165 kb (see details in the text and Fig. 4 ). The broken circle indicates the lengths for the clockwise segment (1,973 kb) and the counterclockwise segment (2,192 kb).

Citation: Itaya M. 1993. Physical Map of the Bacillus subtilis 168 Chromosome, p 463-471. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch30
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References

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Tables

Generic image for table
Table 1

Assignment of and fragments of CU741 DNA to the physical mapa

Citation: Itaya M. 1993. Physical Map of the Bacillus subtilis 168 Chromosome, p 463-471. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch30
Generic image for table
Table 2

Designation of genes on physical map

Citation: Itaya M. 1993. Physical Map of the Bacillus subtilis 168 Chromosome, p 463-471. In Sonenshein A, Hoch J, Losick R (ed), and Other Gram-Positive Bacteria. ASM Press, Washington, DC. doi: 10.1128/9781555818388.ch30

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