Use of a global metabolic network to curate organismal metabolic networks.

The difficulty in annotating the vast amounts of biological information poses one of the greatest current challenges in biological research. The number of genomic, proteomic, and metabolomic datasets has increased dramatically over the last two decades, far outstripping the pace of curation efforts. Here, we tackle the challenge of curating metabolic network reconstructions. We predict organismal metabolic networks using sequence homology and a global metabolic network constructed from all available organismal networks. While sequence homology has been a standard to annotate metabolic networks it has been faulted for its lack of predictive power. We show, however, that when homology is used with a global metabolic network one is able to predict organismal metabolic networks that have enhanced network connectivity. Additionally, we compare the annotation behavior of current database curation efforts with our predictions and find that curation efforts are biased towards adding (rather than removing) reactions to organismal networks.

The Arabidopsis thaliana putative sialyltransferase resides in the Golgi apparatus but lacks the ability to transfer sialic acid.

A common feature of the animal sialyltransferases (STs) is the presence of four conserved motifs, namely large (L), small (S), very small (VS) and motif III. Although sialic acid (SA) has not been detected in plants, three orthologues containing sequences similar to the ST motifs have been identified in the Arabidopsis thaliana L. database. In this study, we report that the At3g48820 gene (Gene ID: 824043) codes for a Golgi resident protein lacking the ability to transfer SA to asialofetuin or Galbeta1,3GalNAc and Galbeta1,4GlcNAc oligosaccharide acceptors. Restoration of deteriorated motifs S, VS and motif III by constructing chimeric proteins consisting of the 28-308 amino acid region of the A. thalianaAt3g48820 ST-like protein and the 264-393 amino acid region of the Oryza sativa L. AK107493 ST-like protein, or of the 28-240 amino acid region of the At3g48820 protein and the 204-350 amino acid region of the Homo sapiens L. alpha2,3-ST (NP_008858) was not able to recover sialyltransferase activity. Altering the appropriate amino acid regions of the A. thalianaAt3g48820 ST-like protein to those typical for the mammalian motif III (HHYWE) and VS motif (HDADFE) also did not have any effect. Our data, together with previous results, indicate that A. thaliana in particular, and plants in general, do not have transferases for SA. Substrates for the plant ST-like proteins might be compounds involved in secondary metabolism.