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In Silico Identification of 6-Phosphogluconolactonase Genes that are Frequently Missing from Completely Sequenced Bacterial Genomes  

Jeong, Hae-Young (Genome Research Center, KRIBB)
F. Kim, Ji-Hyun (Systems Microbiology Research Center, KRIBB)
Park, Hong-Seog (Genome Research Center, KRIBB)
Publication Information
Genomics & Informatics / v.4, no.4, 2006 , pp. 182-187 More about this Journal
Abstract
6-Phosphogluconolactonase (6PGL) is one of the key enzymes in the ubiquitous pathways of central carbon metabolism, but bacterial 6PGL had been long known as a missing enzyme even after complete bacterial genome sequence information became available. Although recent experimental characterization suggests that there are two types of 6PGLs (DevB and YbhE), their phylogenetic distribution is severely biased. Here we present that proteins in COG group previously described as 3-oarboxymuconate cyclase (COG2706) are actually the YbhE-type 6PGLs, which are widely distributed in Proteobacteria and Fimicutes. This case exemplifies how erroneous functional description of a member in the reference database commonly used in transitive genome annotation cause systematic problem in the prediction of genes even with universal cellular functions.
Keywords
6-phosphogluconolactonase; 3-carboxymuconate cyclade; missing enzyme; pentose phosphate pathway; genome annotation;
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1 Galperin, M. Y. and Koonin, E. V. (1998). Sources of systematic error in functional annotation of genomes: Domain rearrangement, non-orthologous gene displacement and operon disruption. In Silico Biol. 1, 55-67
2 Haft, D. H., Selengut, J. D., and White, O. (2003). The TIGRFAMs database of protein families. Nucleic Acids Res. 31, 371-373   DOI   ScienceOn
3 Hager, P. W., Calfee, M. W., and Phibbs, P. V. (2000). The Pseudomonas aeruginosa devB/SOL homolog, pgl, is a member of the hex regulon and encodes 6-phosphoglu-conolactonase. J. Bacteriol. 182, 3934-3941   DOI
4 Tatusov, R. L., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Kiryutin, B., Koonin, E. V., Krylov, D. M., Mazumder, R., Mekhedov, S. L., Nikolskaya, A. N., Rao, B. S., Smirnov, S., Sverdlov, A. V., Vasudevan, S., Wolf, Y. I., Yin, J. J., and Natale, D. A. (2003). The COG database: An updated version includes eukaryotes. BMC Bioinformatics 4, 41   DOI   ScienceOn
5 Wu, C. H., Apweiler, R., Bairoch, A., Natale, D. A., Barker, W. C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M. J., Mazumder, R., O'Donovan, C., Redaschi, N., and Suzek, B. (2006). The Universal Protein Resource (UniProt): An expanding universe of protein information. Nucleic Acids Res. 34, D187-191   DOI   ScienceOn
6 Zimenkov, D., Gulevich, A., Skorokhodova, A., Biriukova, I., Kozlov, Y., and Mashko, S. (2005). Escherichia coli ORF ybhE is pgl gene encoding 6-phosphogluconolactonase (EC 3.1.1.31) that has no homology with known 6PGLs from other organisms. FEMS Microbiol. Lett. 244, 275-280   DOI   ScienceOn
7 Gattiker, A., Michoud, K., Rivoire, C., Auchincloss, A. H., Coudert, E., Lima, T., Kersey, P., Pagni, M., Sigrist, C. J., Lachaize, C., Veuthey, A. L., Gasteiger, E., and Bairoch, A.(2003). Automated annotation of microbial proteomes in Swiss-Prot. Comput. Biol. Chem. 27, 49-58   DOI   ScienceOn
8 Kumar, S., Tamura, K., and Nei, M. (2004). MEGA3: Integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5, 150-163   DOI   ScienceOn
9 Murakami, S., Kohsaka, C., Okuno, T., Takenaka, S., and Aoki, K. (2004). Purification, characterization, and gene cloning of cis,cis-muconate cycloisomerase from benzamide-assimilating Arthrobacter sp. Ba-5-17. FEMS Microbiol. Lett. 231, 119-124   DOI   ScienceOn
10 Devos, D. and Valencia, A. (2001). Intrinsic errors in genome annotation. Trends Genet. 17, 429-431   DOI   ScienceOn
11 Mulder, N. J., Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Binns, D., Bradley, P., Bork, P, Bucher, P., Cerutti, L., Copley, R., Courcelle, E., Das, U., Durbin, R., Fleischmann, W., Gough, J., Haft, D., Harte, N., Hulo, N., Kahn, D., Kanapin, A., Krestyaninova, M., Lonsdale, D., Lopez, R., Letunic, I., Madera, M., Maslen, J., McDowall, J. et al. (2005). InterPro, progress and status in 2005. Nucleic Acids Res. 33, D201-205   DOI   ScienceOn
12 Mazur, P., Henzel, W. J., Mattoo, S., and Kozarich, J. W. (1994). 3-carboxy-cis,cis-muconate lactonizing enzyme from Neurospora crassa: An alternate cycloisomerase motif. J. Bacteriol. 176, 1718-1728   DOI
13 Marchler-Bauer, A., Anderson, J. B., Cherukuri, P. F., DeWeese-Scott, C., Geer, L. Y., Gwadz, M., He, S., Hurwitz, D. I., Jackson, J. D., Ke, Z., Lanczycki, C. J., Liebert, C. A., Liu, C., Lu, F., Marchler, G. H., Mullokandov, M., Shoemaker, B. A., Simonyan, V., Song, J. S. et al. (2005). COD: A conserved domain database for protein classification. Nucleic Acids Res. 33, D192-196   DOI   ScienceOn
14 Brenner, S. E. (1999). Errors in genome annotation. Trends Genet. 15, 132-133   DOI   ScienceOn
15 Cordwell, S. J. (1999). Microbial genomes and "Missing" Enzymes: Redefining biochemical pathways. Arch. Microbiol.172, 269-279   DOI
16 Gaudermann, P, Vogl, I., Zientz, E., Silvar, F. J., Moya, A., Gross, R., and Dandeka, T. (2006). Analysis of and function predictions for previously conserved hypothetical or putative proteins in Blochmannia floridanus. BMC Microbiol. 6, 1   DOI
17 Thomason, L. C., Court, D. L., Datta, A. R., Khanna, R., and Rosner, J. L. (2004). Identification of the Escherichia coli K-12 ybhE gene as pgl, encoding 6-phosphogluconolactonase. J. Bacteriol. 186, 8248-8253   DOI   ScienceOn
18 Collard, F., Collet, J. F., Gerin, I., Veiga-da-Cunha, M., and Van Schaftingen, E. (1999). Identification of the cDNA encoding human 6-phosphogluconolactonase, the enzyme catalyzing the second step of the pentose phosphate pathway(1). FEBS Lett. 459, 223-226   DOI   ScienceOn
19 Kanehisa, M., Goto, S., Hattori, M., Aoki-Kinoshita, K. F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., and Hirakawa, M. (2006). From genomics to chemical genomics: New developments in KEGG. Nucleic Acids Res. 34, D354-357   DOI   ScienceOn
20 Lorite, M. J., Sanjuan, J., Velasco, L., Olivares, J., and Bedmar, E. J. (1998). Characterization of Bradyrhizobium japonicum pcaBDC genes involved in 4-hydroxybenzoate degradation. Biochim. Biophys. Acta 1397, 257-261   DOI   ScienceOn
21 Natale, D. A., Shankavaram, U. T., Galperin, M. Y., Wolf, Y. I., Aravind, L., and Koonin, E. V. (2000). Towards understanding the first genome sequence of a crenarchaeon by genome annotation using clusters of orthologous groups of proteins (COGs). Genome Biol. 1, RESEARCH0009