Abstract
It has recently been proposed that in addition to Nomenclature, Classification and Identification, Comprehending Microbial Diversity may be considered as the fourth tenet of microbial systematics [Staley JT (2010) The Bulletin of BISMiS, 1(1): 1–5]. As this fourth goal implies a fundamental understanding of microbial speciation, this perspective article argues that translation of bacterial genome sequences into metabolic features may contribute to the development of modern polyphasic taxonomic approaches. Genome-scale metabolic network reconstructions (GSMRs), which are the result of computationally predicted and experimentally confirmed stoichiometric matrices incorporating all enzyme and metabolite components encoded by a genome sequence, provide a platform that can illustrate bacterial speciation. As the topology and the composition of GSMRs are expected to be the result of adaptive evolution, the features of these networks may provide the prokaryotic taxonomist with novel tools for reaching the fourth tenet of microbial systematics. Through selected examples from the Actinobacteria, which have been inferred from GSMRs and experimentally confirmed after phenotypic characterisation, it will be shown that this level of information can be incorporated into modern polyphasic taxonomic approaches. In conclusion, three specific examples are illustrated to show how GSMRs will revolutionize prokaryotic systematics, as has previously occurred in many other fields of microbiology.
Similar content being viewed by others
References
Arakawa C, Kuratsu M, Furihata K, Hiratsuka T, Itoh N, Seto H, Dairi T (2011) Diversity of the early step of the futalosine pathway. Antimicrob Agents Chemother 55(2):913–916
Borodina I, Krabben P, Nielsen J (2005) Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism. Genome Res 15(6):820–829
Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100(2):221–230
Collins MD, Goodfellow M, Minnikin DE, Alderson G (1985) Menaquinone composition of mycolic acid-containing actinomycetes and some sporoactinomycetes. J Appl Bacteriol 58(1):77–86
Conrad TM, Lewis NE, Palsson BO (2011) Microbial laboratory evolution in the era of genome-scale science. Mol Syst Biol 7:509
Dairi T, Kuzuyama T, Nishiyama M, Fujii I (2011) Convergent strategies in biosynthesis. Nat Prod Rep 28(6):1054–1086
Feist AM, Herrgard MJ, Thiele I, Reed JL, Palsson BO (2009) Reconstruction of biochemical networks in microorganisms. Nat Rev Microbiol 7(2):129–143
Frisvad JC, Andersen B, Thrane U (2008) The use of secondary metabolite profiling in chemotaxonomy of filamentous fungi. Mycol Res 112(Pt 2):231–240
Hiratsuka T, Furihata K, Ishikawa J, Yamashita H, Itoh N, Seto H, Dairi T (2008) An alternative menaquinone biosynthetic pathway operating in microorganisms. Science 321(5896):1670–1673
Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17(8):754–755
Jamshidi N, Palsson BO (2007) Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets. BMC Syst Biol 1:26
Kindberg C, Suttie JW, Uchida K, Hirauchi K, Nakao H (1987) Menaquinone production and utilization in germ-free rats after inoculation with specific organisms. J Nutr 117(6):1032–1035
Kjeldsen KR, Nielsen J (2009) In silico genome-scale reconstruction and validation of the Corynebacterium glutamicum metabolic network. Biotechnol Bioeng 102(2):583–597
Koch C, Kroppenstedt RM, Stackebrandt E (1996) Intrageneric relationships of the actinomycete genus Micromonospora. Int J Syst Bacteriol 46(2):383–387
Marineo S, Cusimano MG, Limauro D, Coticchio G, Puglia AM (2008) The histidinol phosphate phosphatase involved in histidine biosynthetic pathway is encoded by SCO5208 (hisN) in Streptomyces coelicolor A3(2). Curr Microbiol 56(1):6–13
Nampoothiri KM, Hoischen C, Bathe B, Mockel B, Pfefferle W, Krumbach K, Sahm H, Eggeling L (2002) Expression of genes of lipid synthesis and altered lipid composition modulates l-glutamate efflux of Corynebacterium glutamicum. Appl Microbiol Biotechnol 58(1):89–96
Nett M, Ikeda H, Moore BS (2009) Genomic basis for natural product biosynthetic diversity in the actinomycetes. Nat Prod Rep 26(11):1362–1384
Osterman A, Overbeek R (2003) Missing genes in metabolic pathways: a comparative genomics approach. Curr Opin Chem Biol 7(2):238–251
Sandoval-Calderon M, Geiger O, Guan Z, Barona-Gomez F, Sohlenkamp C (2009) A eukaryote-like cardiolipin synthase is present in Streptomyces coelicolor and in most actinobacteria. J Biol Chem 284(26):17383–17390
Seto H, Jinnai Y, Hiratsuka T, Fukawa M, Furihata K, Itoh N, Dairi T (2008) Studies on a new biosynthetic pathway for menaquinone. J Am Chem Soc 130(17):5614–5615
Seyedsayamdost MR, Traxler MF, Zheng SL, Kolter R, Clardy J (2011) Structure and biosynthesis of amychelin, an unusual mixed-ligand siderophore from Amycolatopsis sp. AA4. J Am Chem Soc 133(30):11434–11437
Staley JT (2010) Comprehending microbial diversity: the fourth goal of microbial taxonomy. The Bulletin of BISMiS 1(1):1–5
Tauch A, Schneider J, Szczepanowski R, Tilker A, Viehoever P, Gartemann KH, Arnold W, Blom J, Brinkrolf K, Brune I, Gotker S, Weisshaar B, Goesmann A, Droge M, Puhler A (2008) Ultrafast pyrosequencing of Corynebacterium kroppenstedtii DSM44385 revealed insights into the physiology of a lipophilic corynebacterium that lacks mycolic acids. J Biotechnol 136(1–2):22–30
Tindall BJ, Rossello-Mora R, Busse HJ, Ludwig W, Kampfer P (2010) Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60(Pt 1):249–266
Trujillo ME, Fernández-Molinero C, Velázquez E, Kroppenstedt RM, Schumann P, Mateos PF, Martínez-Molina E (2005) Micromonospora mirobrigensis sp. nov. Int J Syst Evol Microbiol 55:877–880
Wagner A (2009) Evolutionary constraints permeate large metabolic networks. BMC Evol Biol 9:231
Yim G, Wang HH, Davies J (2007) Antibiotics as signalling molecules. Philos Trans R Soc Lond B Biol Sci 362(1483):1195–1200
Acknowledgments
This work was supported by Conacyt, Mexico (grant No. 82319).
Author information
Authors and Affiliations
Corresponding author
Electronic supplementary material
Below is the link to the electronic supplementary material.
10482_2011_9655_MOESM1_ESM.docx
Supplementary Information. Details on the methods, organisms, genomes and genes analysed herein are provided as supplementary information (DOCX 162 kb)
Rights and permissions
About this article
Cite this article
Barona-Gómez, F., Cruz-Morales, P. & Noda-García, L. What can genome-scale metabolic network reconstructions do for prokaryotic systematics?. Antonie van Leeuwenhoek 101, 35–43 (2012). https://doi.org/10.1007/s10482-011-9655-1
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10482-011-9655-1