1 Institut de Génétique et Microbiologie, CNRS UMR 8621, Université Paris Sud, Bâtiment 409, 91405 Orsay Cedex, France
2 Laboratoire de Microbiologie, Université Libre de Bruxelles and Institut de Recherches Microbiologiques J.M. Wiame, 1, ave E. Gryzon, B-1070 Brussels, Belgium
Correspondence
Bernard Labedan
(bernard.labedan{at}igmors.u-psud.fr)
Incorrect annotation of genes and enzymes is an important source of confusion in phylogenetic studies and analysis of metabolic networks.
We have recently identified as putrescine carbamoyltransferases (PTCases; EC 2.1.3.6, GO: 0050231) a set of enzymes that have been erroneously annotated as ornithine carbamoyltransferases (EC 2.1.3.3, GO: 0009348) on the basis of genomic data (Naumoff et al., 2004). These PTCases are involved in the catabolism of the polyamine agmatine via the agmatine deiminase system (Simon & Stalon, 1982
) present in several Gram-positive bacteria. Accordingly, we have been able to re-annotate the function of the corresponding encoding genes in those bacteria (Enterococcus faecalis, Listeria monocytogenes, Streptococcus mutans and Lactococcus lactis) for which the genomes have been entirely sequenced (Naumoff et al., 2004
). This is summarized in Fig. 1
(see upper part, Cluster A) which also displays more recent data confirming and extending our re-annotation process to other bacteria including one distantly related proteobacterium, Photobacterium profundum [re-annotation of the hypothetical ornithine carbamoyltransferase PBPRB1921 (TrEMBL Q6LG11) as a PTCase].
|
Furthermore, the name aguB has also been used by Voget et al. (2003) to designate a gene encoding a putative
-agarase (see Table 1
) identified from a soil metagenome. This adds to the confusion and should be considered an inappropriate designation also.
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It should be stressed that the uncontrolled misuse of the name aguB has created an intolerable chaos in databases, as shown by the following excerpts from the latest version of TrEMBL (release 27.4, 31 August 2004), which is part of the UniProt knowledgebase (Apweiler et al., 2004). This confusion is clearly apparent in Table 1
, which was obtained by querying UniProt with the text search aguB.
In order to prevent people obtaining such misleading and worthless results where three unrelated enzymic activities are recovered when querying with a unique gene name descriptor, we strongly suggest to use the name aguB to designate exclusively genes encoding N-carbamoylputrescine amidohydrolase as we have specified in the column Annotation is: of Table 1 since both gene aguB and protein AguB have been well studied for a long time and unambiguously characterized as playing a major role in putrescine biosynthesis as well as in agmatine catabolism (Nakada & Itoh, 2003
, and references therein).
With regard to aguA, the use of this name by Griswold et al. (2004a) to designate agmatine deiminase respects the nomenclature proposed by Haas et al. (1984)
and more recently by Nakada et al. (2001)
and Nakada & Itoh (2003)
and is thus correct. By contrast, using aguC for carbamate kinase instead of arcC is again not appropriate since the name arcC is universally recognized as designating carbamate kinases. It must be noted that, in a subsequent article studying in detail the arginine deiminase operon in another Streptococcus species, the same authors went back to using arcC in the case of the corresponding carbamate kinase (Griswold et al., 2004b
).
Interestingly, Fig. 1 further shows that a gene homologous to the transcriptional regulator aguR which has been characterized by Nakada et al. (2001)
and Nakada & Itoh (2003)
as negatively regulating the expression of the aguBA operon in Pseudomonas aeruginosa (cluster B in Fig. 1
) is also found in Photobacterium profundum. However, in Photobacterium profundum, this aguR-like gene is inserted in a set of genes that appear to be homologous to the agmatine deiminase gene cluster (cluster A in Fig. 1
) found in Gram-positive bacteria and encoding PTCase, amino acid permease, agmatine deiminase and carbamate kinase, respectively (Griswold et al., 2004a
; Naumoff et al., 2004
), but with a different gene order. This aguR-like gene does not appear to be evolutionarily related to the putative regulator SMU.261c of the agmatine deiminase pathway in S. mutans (Griswold et al., 2004a
) nor to its homologues EF0731 (E. faecalis) and llrH (Lactococcus lactis). This would appear to be an interesting instance of recruitment of a regulatory gene from one pathway to another and deserves further study.
Acknowledgements
This work was supported by the CNRS (UMR 8621) and by the Flanders Foundation for Joint and Fundamental Research. D. G. N. was supported by a postdoctoral grant from the French Ministère de la Recherche.
REFERENCES
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