Retrieving sequences of enzymes experimentally characterized but erroneously annotated : the case of the putrescine carbamoyltransferase.
BACKGROUND
Annotating genomes remains an hazardous task. Mistakes or gaps in such a complex process may occur when relevant knowledge is ignored, whether lost, forgotten or overlooked. This paper exemplifies an approach which could help to resuscitate such meaningful data.


RESULTS
We show that a set of closely related sequences which have been annotated as ornithine carbamoyltransferases are actually putrescine carbamoyltransferases. This demonstration is based on the following points : (i) use of enzymatic data which had been overlooked, (ii) rediscovery of a short NH2-terminal sequence allowing to reannotate a wrongly annotated ornithine carbamoyltransferase as a putrescine carbamoyltransferase, (iii) identification of conserved motifs allowing to distinguish unambiguously between the two kinds of carbamoyltransferases, and (iv) comparative study of the gene context of these different sequences.


CONCLUSIONS
We explain why this specific case of misannotation had not yet been described and draw attention to the fact that analogous instances must be rather frequent. We urge to be especially cautious when high sequence similarity is coupled with an apparent lack of biochemical information. Moreover, from the point of view of genome annotation, proteins which have been studied experimentally but are not correlated with sequence data in current databases qualify as "orphans", just as unassigned genomic open reading frames do. The strategy we used in this paper to bridge such gaps in knowledge could work whenever it is possible to collect a body of facts about experimental data, homology, unnoticed sequence data, and accurate informations about gene context.
Naumoff
Daniil G
DG
Institut de Génétique et Microbiologie, CNRS UMR 8621, Université Paris Sud, Bâtiment 409, 91405 Orsay Cedex, France. daniil_naumoff@yahoo.com
Xu
Ying
Y
Glansdorff
Nicolas
N
Labedan
Bernard
B
D020816:Amino Acid Motifs; D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics; D019878:Carboxyl and Carbamoyl Transferases / Q000737:chemistry / Q000145:classification* / Q000235:genetics; D030562:Databases, Protein; D013293:Enterococcus faecalis / Q000201:enzymology / Q000235:genetics; D019143:Evolution, Molecular; D023061:Gene Order; D005798:Genes, Bacterial; D007778:Lactobacillus / Q000201:enzymology / Q000235:genetics; D008089:Listeria monocytogenes / Q000201:enzymology / Q000235:genetics; D008969:Molecular Sequence Data; D005810:Multigene Family; D009176:Mycoplasma mycoides / Q000201:enzymology / Q000235:genetics; D009954:Ornithine Carbamoyltransferase / Q000737:chemistry / Q000145:classification* / Q000235:genetics; D010376:Pediococcus / Q000201:enzymology / Q000235:genetics; D010802:Phylogeny; D017386:Sequence Homology, Amino Acid; D013045:Species Specificity; D013295:Streptococcus mutans / Q000201:enzymology / Q000235:genetics; D013329:Structure-Activity Relationship
D001426:Bacterial Proteins; D019878:Carboxyl and Carbamoyl Transferases; D009954:Ornithine Carbamoyltransferase; C022487:putrescine carbamoyltransferase