Bioinformatics Approaches Interpreting Structure-function Relationship Of Tobacco Cytochrome P450 Mono-oxygenase And Genome-scale Identification Of Cell-wall Related Genes In Arabidopsis

Bioinformatics is an intersection field between computer science and molecular biology, which mainly use the computational method to process and analyze the data from genetics and genomics. The research area of bioinformatics spreads to almost all aspects of current concerned biological studies. Specially, the molecular structure-function study and the analysis of gene-expression data are the current topics in the computational molecular biology. In our research, we use computational methods in these two areas, i.e.1) interpretation the mechanism of nicotine N-demethylation catalyzed by tobacco cytochrome P450 mono-oxygenase. which provides a new insight to understanding of the functional mechanism of P450 proteins: 2) genome-scale identification of cell-wall related genes in Arabidopsis through bi-clustering analyses of gene-expression data, which provides a set of high-quality data source for the plant cell wall studies and sets up a public database.CYP82E4. a cytochrome P450 mono-oxygenase. has the nicotine N-demethylase (NND) activity-that mediates the bioconversion of nicotine to nornicotine in senescing tobacco leaves. Nornicotine is a precursor of the known carcinogen, called tobacco-specific nitrosamine. CYP82E3 is an orthoiog of CYP82E4 with 95% sequence identity, but lacking NND activity. A recent site-directed mutagenesis study discovered that a single amino acid substitution, i.e. cystine to tryptophan at the position 330 in the middle of the protein, rescued entirely the NND activity of CYP82E3. whilst the same amino acid change caused the loss of NND activity to CYP82E4. To address the mechanism of the functional turnover of the two molecules, four 3D structures, i.e. the two molecules and their corresnonding cys-trp mutants were modeled. Simulation studies were performed in different biological scenarios The dynamics trajectories analysis suggested that the single amino acid mutation outside the active site region may have mediated indirectly flexibility of the F-G loop and the B-C loop through helix I. causing a functional turnover of the P450 mono-oxygenase.Plant cell walls (PCW) are mainly composed of polysaccharides and lignins, forming the major component of plant biomass. Identification of novel genes relevant to plant cell-wall synthesis represents a highly important and a challenging problem in plant cell-wall studies. Although substantial efforts have been invested into this area, the vast majority of the PCW related genes remain unknown. Here we present a computational study focused on identification of novel PCW genes in Arabidopsis based on bi-clustering analysis of microarray data collected under 351 conditions. Our analysis identified 217 densely connected co-expression gene clusters, each containing at least one gene annotated as PCW synthesis related according to the Purdue database. We believe that this set of predicted data should facilitate the PCW studies, which are set up a public database.