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Chapter 12 :

Authors: Jean F. Challacombe1, Richard T. Okinaka2, A. Christine Munk4, Thomas S. Brettin5, Paul Keim6
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Affiliations: 1: Bioscience Division and DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545; 2: Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545; 3: The Microbial Genetics and Genomics Center, Northern Arizona University, Flagstaff, AZ 86011; 4: Bioscience Division and DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545; 5: Bioscience Division and DOE Joint Genome Institute, Los Alamos National Laboratory, Los Alamos, NM 87545; 6: Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, and The Microbial Genetics and Genomics Center; 7: The Translational Genomics Research Institute, Northern Arizona University, Flagstaff, AZ 86011
Content Type: Monograph
Publication Year: 2011

Category: Applied and Industrial Microbiology; Food Microbiology

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Abstract:

is the putative ancestor of all strains, which obtained two virulence plasmids (pXO1 and pXO2) and at least one chromosomal mutation that inactivated the plcR gene. Identification of the molecular signals that trigger germination and the spore surface receptors involved is critical to understanding the pathogenesis of . Sporulation and pathogenesis are opposite processes, while germination and virulence gene expression are synergistic, since transition from dormant spores to vegetative cells is essential for the virulence of . One of the enzymes within the basal layer of spores is an alanine racemase capable of converting the spore germinant L-alanine to the germination inhibitor D-alanine. Comparative genomic studies have contributed significantly to our understanding of the virulence properties, host specificity, ecology, and adaptations of and other species comprising the group. While all Banthracis strains examined so far contain four prophages of the lambda family inserted at defined loci, most of the other sequenced group genomes do not contain homologous prophages inserted at these sites. With the advent of next-generation sequencing technologies, which promise to deliver even more sequence data over shorter periods of time, and with metagenomics and community genomics approaches on the rise, the future of pathogen genomics is bright and growing fast.

Citation: Challacombe J, Okinaka R, Munk A, Brettin T, Keim P. 2011. , p 165-183. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch12
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Bacillus anthracis
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Citation: Challacombe J, Okinaka R, Munk A, Brettin T, Keim P. 2011. , p 165-183. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch12
/content/10.1128/9781555816902.ch12.ch12fig01
Figure 1
Phylogenetic tree representing the evolution of is the putative ancestor of all strains, which obtained two virulence plasmids (pXO1 and pXO2) and at least one chromosomal mutation that inactivated the gene.
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10.1128/9781555816902/f0167-01.gif
Image of Figure 1
Figure 1

Phylogenetic tree representing the evolution of is the putative ancestor of all strains, which obtained two virulence plasmids (pXO1 and pXO2) and at least one chromosomal mutation that inactivated the gene.

Citation: Challacombe J, Okinaka R, Munk A, Brettin T, Keim P. 2011. , p 165-183. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch12
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Figure 2
Dot plot homology analysis of the Ames strain gene. A sliding window (nine nucleotides) is used with two different match criteria (A, 100%; B, 70%) to compare the gene sequence with itself to identify repeated regions. This figure was kindly provided by Mr. James Schupp (Northern Arizona University).
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10.1128/9781555816902/f0168-01.gif
Image of Figure 2
Figure 2

Dot plot homology analysis of the Ames strain gene. A sliding window (nine nucleotides) is used with two different match criteria (A, 100%; B, 70%) to compare the gene sequence with itself to identify repeated regions. This figure was kindly provided by Mr. James Schupp (Northern Arizona University).

Citation: Challacombe J, Okinaka R, Munk A, Brettin T, Keim P. 2011. , p 165-183. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch12
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Figure 3
Mauve alignments of Ames ancestor and Ames chromosomes with near neighbors E33L, and Al Hakam.
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10.1128/9781555816902/f0171-01.gif
Image of Figure 3
Figure 3

Mauve alignments of Ames ancestor and Ames chromosomes with near neighbors E33L, and Al Hakam.

Citation: Challacombe J, Okinaka R, Munk A, Brettin T, Keim P. 2011. , p 165-183. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch12
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Figure 4
Genome map of the Al Hakam circular phage pALH1. Top blastp hits are indicated below each ORE. This phage has a mosaic structure, but the coding sequences share the highest similarity with other phage, prophage, and plasmid sequences. Arrows are shaded based on the origin of the top hit: polka dots indicate that the top hit of the Al Hakam phage coding sequence was to G9241; diagonal lines, 03BB108; cross-hatching, W; burlap, top hit was to both 03BB108 and W; plaid, 059799; capsules, phage IEBH; vertical lines, single hits to additional genomes; solid white, solid black, little or no similarity; black with white spots, top hit to phage sequence from non- species.
10.1128/9781555816902/f0172-01_thmb.gif
10.1128/9781555816902/f0172-01.gif
Image of Figure 4
Figure 4

Genome map of the Al Hakam circular phage pALH1. Top blastp hits are indicated below each ORE. This phage has a mosaic structure, but the coding sequences share the highest similarity with other phage, prophage, and plasmid sequences. Arrows are shaded based on the origin of the top hit: polka dots indicate that the top hit of the Al Hakam phage coding sequence was to G9241; diagonal lines, 03BB108; cross-hatching, W; burlap, top hit was to both 03BB108 and W; plaid, 059799; capsules, phage IEBH; vertical lines, single hits to additional genomes; solid white, solid black, little or no similarity; black with white spots, top hit to phage sequence from non- species.

Citation: Challacombe J, Okinaka R, Munk A, Brettin T, Keim P. 2011. , p 165-183. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch12
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Figure 5
Mauve (left column) and MUMmer (right column) alignments of the Al Hakam phage sequence with other group phage and plasmid sequences. From top to bottom, panels A to C show alignments of the Al Hakam phage sequence with the G9241 pBClin29 prophage region (A), the W plasmid PW_87 (B), and the 03BB108_42 plasmid (C).
10.1128/9781555816902/f0173-01_thmb.gif
10.1128/9781555816902/f0173-01.gif
Image of Figure 5
Figure 5

Mauve (left column) and MUMmer (right column) alignments of the Al Hakam phage sequence with other group phage and plasmid sequences. From top to bottom, panels A to C show alignments of the Al Hakam phage sequence with the G9241 pBClin29 prophage region (A), the W plasmid PW_87 (B), and the 03BB108_42 plasmid (C).

Citation: Challacombe J, Okinaka R, Munk A, Brettin T, Keim P. 2011. , p 165-183. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch12
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Figure 6
Exosporium gene neighborhoods in Ames and Ames ancestor compared to other group genomes. Genes with analogous functional categories are colored the same in each genome. This comparative view of the gene neighborhoods was generated using the Integrated Microbial Genomes system (http://img.jgi.doe.gov/).
10.1128/9781555816902/f0178-01_thmb.gif
10.1128/9781555816902/f0178-01.gif
Image of Figure 6
Figure 6

Exosporium gene neighborhoods in Ames and Ames ancestor compared to other group genomes. Genes with analogous functional categories are colored the same in each genome. This comparative view of the gene neighborhoods was generated using the Integrated Microbial Genomes system (http://img.jgi.doe.gov/).

Citation: Challacombe J, Okinaka R, Munk A, Brettin T, Keim P. 2011. , p 165-183. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch12
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Tables

Bacillus anthracis
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Citation: Challacombe J, Okinaka R, Munk A, Brettin T, Keim P. 2011. , p 165-183. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch12
/content/10.1128/9781555816902.ch12.ch12tab01
Table 1
General features of and near neighbor genomes
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Table 1

General features of and near neighbor genomes

Citation: Challacombe J, Okinaka R, Munk A, Brettin T, Keim P. 2011. , p 165-183. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch12
/content/10.1128/9781555816902.ch12.ch12tab02
Table 2
Sporulation and germination genes
Generic image for table
Table 2

Sporulation and germination genes

Citation: Challacombe J, Okinaka R, Munk A, Brettin T, Keim P. 2011. , p 165-183. In Fratamico P, Liu Y, Kathariou S (ed), Genomes of Foodborne and Waterborne Pathogens. ASM Press, Washington, DC. doi: 10.1128/9781555816902.ch12

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