Purple bacteria for lignin degradation: a computational and synthetic biology approach

Lignin, one of the primary components of lignocellulose, represents the most abundant natural source of aromatic scaffold. Despite this, nowadays its exploitation is limited because of the difficulty of its degradation, which lies in its complex three-dimensional structure and in the nature of its units. Although chemical and thermal treatments can be applied to obtain high yields of lignin degradation, drastic conditions, the addiction of toxic materials, expensive molecules and solvents are required. Furthermore, due to lignin structural heterogeneity, the use of these techniques results in a large variety of product species, which requires extensive separation and purification procedures. In contrast, the application of a microbial treatment which exploits microorganisms’ evolutionary adaptation can be effective in obtaining a more sustainable process. This thesis research investigates the potential of purple bacteria, exploiting Rhodopseudomonas palustris as a model species, in lignin degradation via comparative pathway analysis using computational approaches. The potential of this purple non-sulfur bacterium in industrial processes has been well established and depends mainly on its remarkable metabolic adaptation to various stressors and in its ability to synthetize different metabolites starting from what are nowadays considered as waste organic materials. Furthermore, other promising candidate lignin-degrading microorganisms have been evaluated. Lignin depolymerization, dimer and monomer uptake and mineralization steps have been assessed via protein sequence and structural comparison, docking analysis and binding affinity prediction. Lignin depolymerization potential has been investigated searching for DyP peroxidases and laccases in R. palustris, lignin-derived aromatic compounds uptake has been studied analyzing R. palustris ABC transporters and TRAP transporters, while lignin-derived aromatic molecules catabolism has been examined comparing R. palustris proteome to an already characterized lignin-degrading pathway in another organism. Moreover, a microbial consortia process to maximize lignin degradation yield has been proposed. This computational and synthetic biology approach applied to lignin degradation pave the way for experimental validation. However, in the study of a complex problem which is lignin degradation, the application of in silico analysis helped us to more easily select potential organisms, enzymes, transporters and steps to scan in wet lab.