Genetic modularity of protein disulfide isomerase and guanine dissociation inhibitor families: computational and molecular studies and cloning of the regulatory region

Abstract

Understanding mechanisms of redox processes is important in pathophysiology. The redox chaperone protein disulfide isomerase (PDI) functionally modulates the NADPH oxidase complex, a main source of reactive oxygen species in vascular cells. The question addressed in this project has to do with the mechanism of this effect. By means of computational and systems biology methods, PDI interactome algorithms show convergence between Rho family GTPases (involved in cell signaling and activation of NADPH oxidase, including Rac1 and RhoA), and the GTPase regulator RhoGDI. Databases analysis indicate that the chromosomal mapping of PDI (s) and GDI genes shows synteny, i.e., occupation of adjacent chromosomal loci. Syntenic genes may function in coordination, sharing regulatory regions and binding sites for transcription factors. Such synteny was observed at distinct evolutive scale levels in eukaryotes, from fish to humans. In particular, synteny was observed in chromosomes bearing different isoforms of those two families: ie, PDIA1 (PDI P4HB) PDIA2 (PDIP) and PDIA8 (Erp27) are syntenic, respectively, to RhoGDI1, RhoGDI3 and RHOGDI2. The broad objective of our study is to locate and to identify regulatory elements and sites for transcription factor binding in the sequences of such gene paris from PDI and GDI families. This analysis will be done by computer techniques and make functional correlations in cellular model. Our specific objectives are: to evaluate by computational techniques the interaction between PDI (s) and RhoGDI (s) genes with respect to: (1) Genomic structure, (2) Information mapping, (3) gene expression profiles to assess coexpression and (4) Structures of genomic regulatory blocks, looking for conserved regions in different species, (5) In the same genomic blocks, mapping sites of transcription factors (TFBS), and from these sites, definition of the elements in trans (6) Correlation between regulatory structures in these genomic blocks and gene expression (7) From the data obtained above, to clone conserved blocks common to PDI and RhoGDI and develop experimental models for this study. The understanding of a possible co-regulation and analysis of the promoter region of these genes in evolutionary perspective and with the desired functional correlations will clarify the ontogeny and functional regulation of these genes, with potential implications for elucidating redox signaling associated with NADPH oxidase. (AU)