In silico analysis of a Rhizobium sp. RC1 putative haloalkanoic permease sequence motif and classification

Aims@#The transport of haloalkanoic acids (haloacids) is important in the metabolism of haloacid pollutants by bacteria. In this study, a computational analysis of Rhizobium sp. RC1 haloacid permease (DehrP) amino acid sequence was conducted to identify its subfamily, sequence motifs and evolutionary position among closely related transporters. @*Conclusion, significance and impact of study@#Blast search in the Pfam and Transmembrane Classification Databases was used to establish the classification and the subfamily of DehrP. Clustal omega sequence alignment approach and MEME Suite motif-based analysis tools were used to locate the transporter motifs of DehrP. Dotplots of DehrP sequence was computed using the EMBOSS Dotmatcher. MEGA7 software was used to analyze the phylogenetic position of DehrP among closely related symporters in the Transmembrane Classification Database. Comparative analysis by Pfam shows that DehrP is a member of the Major Facilitator Superfamily (#2.A.1). PSI-Blast against the Transmembrane Classification Database shows that DehrP is significantly aligned with a subfamily of transporters called the Metabolite: H+ Symporters (#2.A.1.6). DehrP has six similar sequence motifs with the Metabolite: H+ Symporter proteins including the functional motif of GXXXDRXGRR. DehrP is evolutionarily related to Burkholderia caribensis MBA4 Haloacid: H+ Symporters (Dehp2 and Deh4p). @*Methodology and results@#Based on sequence similarity, DehrP is a Major Facilitator Superfamily protein that belongs to the Metabolite: H+ Symporter protein subfamily which might coordinate the transport of a haloacid coupled with a proton (H+). Mutagenesis of DehrP sequence motifs might be useful in the engineering of Rhizobium sp. RC1 for efficient uptake and degradation of haloacids.

The Construction of Regulatory Network for Insulin-Mediated Genes by Integrating Methods Based on Transcription Factor Binding Motifs and Gene Expression Variations

Type 2 diabetes mellitus is a complex metabolic disorder associated with multiple genetic, developmental and environmental factors. The recent advances in gene expression microarray technologies as well as network-based analysis methodologies provide groundbreaking opportunities to study type 2 diabetes mellitus. In the present study, we used previously published gene expression microarray datasets of human skeletal muscle samples collected from 20 insulin sensitive individuals before and after insulin treatment in order to construct insulin-mediated regulatory network. Based on a motif discovery method implemented by iRegulon, a Cytoscape app, we identified 25 candidate regulons, motifs of which were enriched among the promoters of 478 up-regulated genes and 82 down-regulated genes. We then looked for a hierarchical network of the candidate regulators, in such a way that the conditional combination of their expression changes may explain those of their target genes. Using Genomica, a software tool for regulatory network construction, we obtained a hierarchical network of eight regulons that were used to map insulin downstream signaling network. Taken together, the results illustrate the benefits of combining completely different methods such as motif-based regulatory factor discovery and expression level-based construction of regulatory network of their target genes in understanding insulin induced biological processes and signaling pathways.

Functional Role of a Conserved Sequence Motif in the Oxygen-dependent Degradation Domain of Hypoxia-inducible Factor 1 alpha in the Recognition of p53

Hypoxia-inducible factor 1 alpha (HIF1 alpha) is a transcription factor that plays a key role in the adaptation of cells to low oxygen stress and oxygen homeostasis. The oxygen-dependent degradation (ODD) domain of HIF1 alpha is responsible for the negative regulation of HIF1 alpha in normoxia. The interactions of the HIF1 alpha ODD domain with partner proteins such as von Hippel-Lindau tumor suppressor (pVHL) and p53 are mediated by two sequence motifs, the N- and C-terminal ODD (NODD and CODD). Multiple sequence alignment with HIF1 alpha homologs from human, monkey, pig, rat, mouse, chicken, frog, and zebrafish has demonstrated that the NODD and CODD motifs have noticeably high conservation of the primary sequence across different species and isoforms. In this study, we carried out molecular dynamics simulation of the structure of the HIF1 alpha CODD motif in complex with the p53 DNA-binding domain (DBD). The structure reveals specific functional roles of highly conserved residues in the CODD sequence motif of HIF1 alpha for the recognition of p53.