Genomic data

For the CTX-M family which has been rapidly growing during the last three years genomic data have identified the genome of Kluyvera species as the genetic source of progenitor enzymes (e.g. encoding CTX-Ml, CTX-M2 or CTX-M9). 

Combined analysis of structural and genomic data will certainly get more importance in the near future. Protein folds can be analysed for whole genomes. 

Ellis LB, Hou BK, Kang W, Wackett LP. The University of Minnesota Bioca-talysis/Biodegradation Database post-genomic data mining. Nucleic Acids Res 2003 31 262-5. 

It is interesting to note that the foremost challenges for the detailed modeling of the intact organism (computing time, complexity of interactions, model selection) are very similar to those entailed by the analysis of proteomic or genomic data. In the clinical case, complexity shifts from the richness of the data set to the model formulation, whereas in the proteomic-genomic case the main source of difficulties is the sheer size of the data set however, at least at present, interpretative tools are rather uncomplicated. 

From a drug discovery/development prospective, the significance of genome data is that they provide full sequence information of every protein the organism can produce. This should result in... 

MENDES, P., Modeling large scale biological systems from functional genomic data parameter estimation. In Foundations of Systems Biology (H. Kitano, ed.) MIT Press, Cambridge, MA. 2001, pp. 165-186. 

In this section, we summarize information about five Ci enzymes involved in metabolism of 5-formyl-THF (5-CHO-THF) and formate, whose existence was predicted from genomics data. 5-Formyltetrahydrofolate cycloligase (5-FCL) and S-formylglutathione hydrolase have since been shown to catalyze the anticipated reactions the other three enzymes (10-formyl-THF deformylase, formamidase, and sarcosine oxidase) are still putative. 

More recently, a novel type of halogenating enzyme, named hydroperoxide halolyase, which generates halogenated aldehydes, has been described in the marine diatom Stephanopyxis turris (Wichard and Pohnert 2006). In other microalgae, halogenation of organic compounds was shown to mainly involve methyl halide transferases (Moore et al. 1996 Manley 2002), and no vHPO has yet been identified on genomic data obtained from diatoms (Scala et al. 2002 Armbrust et al. 2004). Clearly, these emissions are not directly associated with an oxidative burst. 

H. Ma and A. P. Zeng, Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 19(2), 270 277 (2003). 

C. H. Schilling, J. S. Edwards, and B. 0. Palsson, Towards metabolic phenomics Analysis of genomic data using flux balances. Biotechnol. Pmg. 15, 288 295 (1999). 

Fig. 1. Errors arising from the incorrect annotation of protein B from genomic data. The correct annotation lies above the dotted line, and incorrect cases lie below the dotted line. Objects colored in red indicate errors. Similar shading of objects implies homology. Other possible errors that are not represented are the incorrect interpretation of single nucleotide polymorphisms (SNPs) of a gene as different genes, and incomplete detection of splice variants.

Develop new technologies to study genes and DNA on a large scale and store genomic data efficiently. 

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