Open Access Research article

Global genome analysis of the shikimic acid pathway reveals greater gene loss in host-associated than in free-living bacteria

Jurica Zucko12, Walter C Dunlap3, J Malcolm Shick4, John Cullum1, François Cercelet56, Bijal Amin5, Lena Hammen57, Timothy Lau5, Jamal Williams5, Daslav Hranueli2 and Paul F Long5*

Author Affiliations

1 Department of Genetics, University of Kaiserslautern, Postfach 3049, 67653 Kaiserslautern, Germany

2 Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia

3 Centre for Marine Microbiology and Genetics, Australian Institute of Marine Science, PMB 3 Townsville MC, Townsville, Queensland, 4810 Australia

4 School of Marine Sciences, University of Maine, 5751 Murray Hall, Orono, ME 04469-5751 USA

5 The School of Pharmacy, University of London, 29/39 Brunswick Square, London WC1N 1AX, UK

6 Department of Bioengineering, Polytech'Nice-Sophia, 930 Route des Colles, 145-06903, Sophia Antipolis, Cedex, France

7 Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany

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BMC Genomics 2010, 11:628  doi:10.1186/1471-2164-11-628

Published: 11 November 2010

Additional files

Additional file 1:

Distribution of genes encoding enzymes of the shikimic acid pathway in non-host associated (free-living) Bacteria.

Format: XLS Size: 157KB Download file

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Additional file 2:

Distribution of genes encoding enzymes of the shikimic acid pathway in host-associated Bacteria.

Format: XLS Size: 571KB Download file

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Additional file 3:

Distribution of genes encoding enzymes of the shikimic acid pathway in Archaea.

Format: XLS Size: 65KB Download file

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Additional file 4:

Distribution of the gene encoding KDPGal aldolase in non-host-associated (free-living) Bacteria.

Format: XLS Size: 47KB Download file

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Additional file 5:

Distribution of the gene encoding KDPGal aldolase in host- associated Bacteria.

Format: XLS Size: 79KB Download file

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Additional file 6:

Distribution of the gene encoding KDPGal aldolase in Archaea.

Format: XLS Size: 28KB Download file

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Additional file 7:

Comparison of the distribution of the shikimic acid pathway in 85 non-host associated bacteria using HMM and BioCyc database searching.

Format: XLS Size: 62KB Download file

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Additional file 8:

Comparison of the distribution of the shikimic acid pathway in 204 host-associated bacteria using HMM and BioCyc database searching.

Format: XLS Size: 117KB Download file

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Additional file 9:

Comparison of the distribution of the shikimic acid pathway in 33 Archaea using HMM and BioCyc database searching.

Format: XLS Size: 38KB Download file

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Additional file 10:

Genetic architecture of the shikimic acid pathway across a range of taxonomically different prokaryote genomes shows that the genes encoding the pathway are not clustered.

Format: XLS Size: 643KB Download file

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