Retrieving sequences of enzymes experimentally characterized but erroneously annotated: The case of the putrescine carbamoyltransferase

BMC Genomics

Volumn 5, Issue , 2004, Pages

  Naumoff, Daniil G ^a,c   Xu, Ying ^b   Glansdorff, Nicolas ^b   Labedan, Bernard ^a  

^a UNIVERSITÉ PARIS SACLAY   (France)

^b VRIJE UNIVERSITEIT BRUSSEL   (Belgium)

^c STATE RESEARCH INSTITUTE OF GENETICS AND SELECTION OF INDUSTRIAL MICROORGANISMS   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

CARBAMOYLTRANSFERASE; NUCLEOTIDE; ORNITHINE CARBAMOYLTRANSFERASE; PUTRESCINE CARBAMOYLTRANSFERASE; UNCLASSIFIED DRUG; BACTERIAL PROTEIN; TRANSFERASE;

ACCURACY; AMINO TERMINAL SEQUENCE; ANALYTIC METHOD; ARTICLE; BIOCHEMISTRY; CONTROLLED STUDY; CORRELATION ANALYSIS; DATA ANALYSIS; ENZYME ANALYSIS; ERROR; EXPERIMENTATION; GENE SEQUENCE; GENOME ANALYSIS; INFORMATION RETRIEVAL; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PROTEIN DATABASE; PROTEIN MOTIF; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; AMINO ACID SEQUENCE; BACTERIAL GENE; CHEMISTRY; CLASSIFICATION; COMPARATIVE STUDY; ENTEROCOCCUS FAECALIS; ENZYMOLOGY; GENE ORDER; GENETICS; LACTOBACILLUS; LISTERIA MONOCYTOGENES; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MULTIGENE FAMILY; MYCOPLASMA MYCOIDES; PEDIOCOCCUS; PHYLOGENY; SPECIES DIFFERENCE; STREPTOCOCCUS MUTANS; STRUCTURE ACTIVITY RELATION;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CARBOXYL AND CARBAMOYL TRANSFERASES; DATABASES, PROTEIN; ENTEROCOCCUS FAECALIS; EVOLUTION, MOLECULAR; GENE ORDER; GENES, BACTERIAL; LACTOBACILLUS; LISTERIA MONOCYTOGENES; MOLECULAR SEQUENCE DATA; MULTIGENE FAMILY; MYCOPLASMA MYCOIDES; ORNITHINE CARBAMOYLTRANSFERASE; PEDIOCOCCUS; PHYLOGENY; SEQUENCE HOMOLOGY, AMINO ACID; SPECIES SPECIFICITY; STREPTOCOCCUS MUTANS; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 9144265895     PISSN: 14712164     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2164-5-52     Document Type: Article

References (33)

1. Brenner SE: Errors in genome annotation. Trends Genet 1999, 15:132-133.
2. Gerlt JA, Babbitt PC: Can sequence determine function? Genome Biol 2000, 1:REVIEWS0005.10.
3. Babbitt PC: Definitions of enzyme function for the structural genomics era. Curr Opin Chem Biol 2003, 2: 30-237.
4. Labedan B, Boyen A, Baetens M, Charlier D, Chen P, Cunin R, Durbecq V, Glansdorff N, Hervé G, Legrain C, Liang Z, Purcarea C, Roovers M, Sanchez R, Toong TL, Van de Casteele M, van Vliet F, Xu Y, Zhang YF: The evolutionary history of carbamoyltransferases: a complex set of paralogous genes was already present in the last universal common ancestor. J Mol Evol 1999, 49:461-473.
5. Labedan B, Xu Y, Naumoff DG, Glansdorff N: Using quaternary structures to assess the evolutionary history of proteins : the case of the Aspartate Carbamoyltransferase. Mol Biol Evol 2004, 21:364-73.
6. The SwissProt page for the YgeW protein: [http://www.expasy.org/cgi-bin/niceprot.pl?%20Q46803].
7. Dashuang S, Gallegos R, De Ponte IIIJ, Morizono H, Yu X, Allewell NM, Malamy M, Tuchman M: Crystal structure of a transcarbamylase-like protein from the anaerobic bacterium Bacteroides fragilis at 2.0 A resolution. J Mol Biol 2002, 320: 99-908.
8. Roon RJ, Barker HA: Fermentation of agmatine in Streptococcus faecalis : occurrence of putrescine transcarbamoylase. J Bacteriol 1972, 109:44-50.
9. Wargnies B, Lauwers N, Stalon V: Structure and properties of the putrescine carbamoyltransferase of Streptococcus faecalis. Eur J Biochem 1979, 101:143-52.
10. Simon JP, Stalon V: Enzymes of agmatine degradation and the control of their synthesis in Streptococcus faecalis. J Bacteriol 1982, 152:676-81.
11. Stalon V: Putrescine carbamoyltransferase (Streptococcus faecalis). Methods Enzymol 1983, 94: 39-43.
12. Vander Wauven C, Simon JP, Slos P, Stalon V: Control of enzyme synthesis in the oxalurate catabolic pathway of Streptococcus faecalis ATCC 11700: evidence for the existence of a third carbamate kinase. Arch Microbiol 1986, 145:386-90.
13. Tricot C, De Coen JL, Momin P, Falmagne P, Stalon V: Evolutionary relationships among bacterial carbamoyltransferases. J Gen Microbiol 1989, 135:2453-64.
14. Paulsen I, Banerjei L, Myers GSA, Nelson KE, Seshadri R, Read TD, Fouts DE, Eisen JA, Gill SR, Heidelberg JF, Tettelin H, Dodson RJ, Umayam L, Brinkac L, Beanan M, Daugherty S, DeBoy RT, Durkin S, Kolonay J, Madupu R, Nelson W, Vamathevan J, Tran B, Upton J, Hansen T, Shetty J, Khouri H, Utterback T, Radune D, Ketchum KA, Dougherty BA, Fraser CM: Role of Mobile DNA in the Evolution of Vancomycin-Resistant Enterococcus faecalis. Science 2003, 299:2071-2074.
15. Apweiler R, Bairoch A, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS: UniProt: the Universal Protein Knowledgebase. Nucleic Acids Res 2004, 32:D115-D119 [http://www.expasy.uniprot.org/index.shtml].
16. Nakada Y, Jiang Y, Nishijyo T, Itoh Y, Lu CD: Molecular characterization and regulation of the aguBA operon, responsible for agmatine utilization in Pseudomonas aeruginosa PAO1. J Bacteriol 2001, 183:6517-24.
17. Nakada Y, Itoh Y: Identification of the putrescine biosynthetic genes in Pseudomonas aeruginosa and characterization of agmatine deiminase, N-carbamoylputrescine amidohydrolase of the arginine decarboxylase pathway. Microbiology 2003, 149: 07-14.
18. Janowitz T, Kneifel H, Piotrowski M: Identification and characterization of plant agmatine iminohydrolase, the last missing link in polyamine biosynthesis of plants. FEBS Lett 2003, 544: 58-61.
19. Cunin R, Glansdorff N, Piérard A, Stalon V: Biosynthesis and metabolism of arginine in bacteria. Microbiol Rev 1986, 50:314-352.
20. Sekowska A, Danchin A, Risler JL: Phylogeny of related functions: the case of polyamine biosynthetic enzymes. Microbiology 2000, 146:1815-28.
21. Barcelona-Andres B, Marina A, Rubio V: Gene structure, organization, expression and potential regulatory mechanisms of arginine catabolism in Enterococcus faecalis. J Bacteriol 2002, 184:6289-300.
22. Zuniga M, Perez G, Gonzalez-Candelas F: Evolution of arginine deiminase (ADI) pathway genes. Mol Phylogenet Evol 2002, 25:429-44.
23. Bairoch A: The ENZYME database in 2000. Nucleic Acids Res 2000, 28:304-305 [http://www.expasy.org/enzyme/].
24. Schomburg I, Chang A, Ebeling C, Gremse M, Heldt C, Huhn G, Schomburg D: BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res 2004, 32:D431-D433 [http://www.brenda.uni-koeln.de/].
25. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M: The KEGG resources for deciphering the genome. Nucleic Acids Res 2004, 32:D277-D280 [http://www.genome.ad.jp/kegg].
26. Karp PD, Arnaud M, Collado-Vides J, Ingraham J, Paulsen IT, Saier MH Jr: The E. coli EcoCyc Database: No Longer Just a Metabolic Pathway Database. ASM News 2004, 70:25-30 [http://www.biocyc.org/].
27. The Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res 2004, 32:D258-D261 [http://www.geneontology.org/].
28. Grivell L: Mining the bibliome: searching for a needle in a haystack? EMBO Reports 2002, 3:200-203.
29. Joint Genome Institute (Department of Energy, USA): [http://www.jgi.doe.gov/JGI_microbial/html/index.html].
30. Sanger Institute (Wellcome Trust, United Kingdom): [http://www.sanger.ac.uk/Projects].
31. Hall TA: BioEdit: a user-friendly biological sequence alignment editor and analfysis program for Windows 95/98/NT. Nucl Acids Symp Ser 1999, 41:95-98 [http://www.mbio.ncsu.edu/BioEdit/bioedit.html].
32. Felsenstein J: Inferring phylogenies from protein sequences by parsimony, distance and likelihood methods. Methods Enzymol 1996, 266:418-27 [http://evolution.gs.washington.edu/phylip.html].
33. Gonnet GH, Hallett MT, Korostensky C, Bernardin L: Darwin v. 2.0: an interpreted computer language for the biosciences. Bioinformatics 2000, 16:101-103 [http://cbrg.inf.ethz.ch/welcome.html].