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

BMC Genomics

Research Article

Walter C Dunlap¹  John Cullum²  Jurica Zucko³  J Malcolm Shick⁴  Daslav Hranueli⁵  Bijal Amin⁶  Jamal Williams⁶  Paul F Long⁶  Timothy Lau⁶  François Cercelet⁷  Lena Hammen⁸ 

[1] Centre for Marine Microbiology and Genetics, Australian Institute of Marine Science, PMB 3 Townsville MC, 4810, Townsville, Queensland, Australia;Department of Genetics, University of Kaiserslautern, Postfach 3049, 67653, Kaiserslautern, Germany;Department of Genetics, University of Kaiserslautern, Postfach 3049, 67653, Kaiserslautern, Germany;Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000, Zagreb, Croatia;School of Marine Sciences, University of Maine, Murray Hall, 575104469-5751, Orono, ME, USA;Section for Bioinformatics, Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000, Zagreb, Croatia;The School of Pharmacy, University of London, 29/39 Brunswick Square, WC1N 1AX, London, UK;The School of Pharmacy, University of London, 29/39 Brunswick Square, WC1N 1AX, London, UK;Department of Bioengineering, Polytech'Nice-Sophia, 930 Route des Colles, 145-06903, Sophia Antipolis, Cedex, France;The School of Pharmacy, University of London, 29/39 Brunswick Square, WC1N 1AX, London, UK;Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, D-69120, Heidelberg, Germany;

关键词: Shikimic Acid;    Shikimate Pathway;    Shikimic Acid Pathway;    Shikimate Kinase;    Chorismic Acid;   

DOI  :  10.1186/1471-2164-11-628

 received in 2010-02-09, accepted in 2010-11-11,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundA central tenet in biochemistry for over 50 years has held that microorganisms, plants and, more recently, certain apicomplexan parasites synthesize essential aromatic compounds via elaboration of a complete shikimic acid pathway, whereas metazoans lacking this pathway require a dietary source of these compounds. The large number of sequenced bacterial and archaean genomes now available for comparative genomic analyses allows the fundamentals of this contention to be tested in prokaryotes. Using Hidden Markov Model profiles (HMM profiles) to identify all known enzymes of the pathway, we report the presence of genes encoding shikimate pathway enzymes in the hypothetical proteomes constructed from the genomes of 488 sequenced prokaryotes.ResultsAmongst free-living prokaryotes most Bacteria possess, as expected, genes encoding a complete shikimic acid pathway, whereas of the culturable Archaea, only one was found to have a complete complement of recognisable enzymes in its predicted proteome. It may be that in the Archaea, the primary amino-acid sequences of enzymes of the pathway are highly divergent and so are not detected by HMM profiles. Alternatively, structurally unrelated (non-orthologous) proteins might be performing the same biochemical functions as those encoding recognized genes of the shikimate pathway. Most surprisingly, 30% of host-associated (mutualistic, commensal and pathogenic) bacteria likewise do not possess a complete shikimic acid pathway. Many of these microbes show some degree of genome reduction, suggesting that these host-associated bacteria might sequester essential aromatic compounds from a parasitised host, as a 'shared metabolic adaptation' in mutualistic symbiosis, or obtain them from other consorts having the complete biosynthetic pathway. The HMM results gave 84% agreement when compared against data in the highly curated BioCyc reference database of genomes and metabolic pathways.ConclusionsThese results challenge the conventional belief that the shikimic acid pathway is universal and essential in prokaryotes. The possibilities that non-orthologous enzymes catalyse reactions in this pathway (especially in the Archaea), or that there exist specific uptake mechanisms for the acquisition of shikimate intermediates or essential pathway products, warrant further examination to better understand the precise metabolic attributes of host-beneficial and pathogenic bacteria.

【 授权许可】

Unknown   
© Zucko et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.