Modelagem in silico do gene gumD e sua rede de interação em Gluconacetobacter diazotrophicus PAL5

Abstract

Systems biology is a branch of science that aims to understand the interactions and organization of molecular, cellular and organismal parts for the production of complex biological processes. In order to achieve this goal, several experimental methods are employed, including genomics, proteomics and metabolomics, as well as sophisticated computational tools, such as mathematical modeling, simulation and analysis of complex networks. In this context, Gluconacetobacter diazotrophicus PAL5 stands out as an endophytic diazotrophic bacterium, known for its tolerance to air and for playing a fundamental role in biological nitrogen fixation (BNF). Recently, research has shown that the gumD gene of this bacterium is essential for the production of Exopolysaccharides (EPS). The objective of this work is to understand the function of the GumD protein in G. diazotrophicus PAL5, especially related to its interaction with plants. For this, in silico modeling and construction of interaction networks of this protein were used. This approach involved obtaining protein information from databases such as UniProt, NCBI, Prosite and Pfam. 3D modeling was performed using the I-TASSER tool, and the models were refined and evaluated using ModRefiner and MolProbity, respectively. Visualization of the models was donein Chimera 1.16 software. The analysis of the interaction network and clusters, which was carried out using STRING, showed that the protein encoded by the gumD gene is involved in polysaccharide transferase processes. The data obtained suggest that this protein is involved in the transport of polysaccharides, which may facilitate biofilm formation and possibly influence the interaction of the bacterium G. diazotrophicus PAL5 with plants. It is important to highlight that these results are based on computational and predictive analyses, requiring additional experimental studies to validate and confirm the interactions and functions of the GumD protein. Further investigation of these investigations will contribute to a better understanding of the role of this protein in the bacteria-plant relationship and will pave the way for practical applications in agriculture, such as the development of biotechnological tools to improve crop yields.