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 ressucitate 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 NH(2)-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

Analysis of Large Phenotypic Variability of EEC and SHFM4 Syndromes Caused by K193E Mutation of the TP63 Gene

EEC (ectrodactyly, ectodermal dysplasia, clefting; OMIM 604292) is an autosomal dominant developmental disorder resulting mainly from pathogenic mutations of the DNA-binding domain (DBD) of the TP63 gene. In this study, we showed that K193E mutation in nine affected individuals of a four-generation kindred with a large degree of phenotypic variability causes four different syndromes or TP63-related disorders: EEC, Ectrodactyly-ectodermal dysplasia (EE), isolated ectodermal dysplasia, and isolated Split Hand/Foot Malformation type 4 (SHFM4). Genotype-phenotype and DBD structural modeling analysis showed that the K193-located loop L2-A is associated with R280 through hydrogen bonding interactions, while R280 mutations also often cause large phenotypic variability of EEC and SHFM4. Thus, we speculate that K193 and several other DBD mutation-associated syndromes may share similar pathogenic mechanisms, particularly in the case of the same mutation with different phenotypes. Our study and others also suggest that the phenotypic variability of EEC is attributed, at least partially, to genetic and/or epigenetic modifiers

Crystal and solution structures of di-n-butyltin(IV) complexes of 5-[(E)-2-(4-methoxyphenyl)-1-diazenyl]quinolin-8-ol and benzoic acid derivatives: En route to elegant self-assembly via modulation of the tin coordination geometry

Reactions of nBu2SnCl(L1) (1), where L1 = acid residue of 5-[(E)-2-(4-methoxyphenyl)-1-diazenyl]quinolin-8-ol, with various substituted benzoic acids in refluxing toluene, in the presence of triethylamine, yielded dimeric mixed ligand di-n-butyltin(IV) complexes of composition [nBu2Sn(L1)(L2-6)]2 where L2 = benzene carboxylate (2), L3 = 2-[(E)-2-(2-hydroxy-5-methylphenyl)-1-diazenyl]benzoate (3), L4 = 5-[(E)-2-(4-methylphenyl)-1-diazenyl]-2-hydroxybenzoate (4), L5 = 2-{(E)-4-hydroxy-3-[(E)-4-chlorophenyliminomethyl]-phenyldiazenyl}benzoate (5) and L6 = 2-[(E)-(3-formyl-4-hydroxyphenyl)-diazenyl]benzoate (6). All complexes (1-6) have been characterized by elemental analyses, IR, 1H, 13C and 117Sn NMR and 119Sn Mössbauer spectroscopy and their structures were determined by X-ray crystallography, complemented by 117Sn CP-MAS NMR spectroscopy studies in the solid state. The crystal structure of 1 reveals a distorted trigonal bipyramidal coordination geometry around the Sn-atom where the Cl- and N-atoms of ligand L1 occupy the axial positions. In complexes 2-5, the molecules are centrosymmetric dimers in which the Sn-atoms are connected by asymmetric μ-O bridges through the quinoline O-atom to give an Sn2O2 core. The differences in the Sn–O bond lengths within the bridge range from 0.28-0.48 Å, with the longer of the Sn–O distances being in the range 2.56-2.68 Å and the most symmetrical bridge being in 5. The carboxylate group is almost symmetrically bidentate coordinated to the Sn-atom in 5 (Sn–O distances of 2.327(2) and 2.441(2) Å), unlike the other complexes in which the distance of the carboxylate carbonyl O-atom from the Sn-atom is in the range 2.92-3.03 Å. The structure of 5 displays a more regular pentagonal bipyramidal coordination geometry about each Sn-atom than in 2-4. In contrast, the centrosymmetric dimeric structure of 6 involves asymmetric carboxylate bridges, resulting in a different Sn2C2O4 motif. The Sn–O bond lengths in the bridge differ by about 0.6 Å, with the longer distance involving the carboxylate carbonyl O-atom (2.683(2) and 2.798(2) Å for two molecules in the asymmetric unit). The carboxylate carbonyl O-atom has a second, even longer intramolecular contact to the Sn-atom to which the carboxylate group is primarily coordinated, with these Sn···O distances being as high as 3.085(2) and 2.898(2) Å. If the secondary interactions are considered, all the di-n-butyltin(IV) complexes (2-6) display a distorted pentagonal bipyramidal arrangement about each Sn-atom in which the n-butyl groups occupy the axial positions