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Augmentation of Biotech Products

In silico augumentation of Electricity generation using Geobacter

Microbial Fuel Cells (MFC) are a promising and efficient method for bio-electricity generation. These cells can be operated using electrochemically active microorganisms that generate electricity by degrading organic biomass from waste water. Geobacter sulfurreducens PCA is a bacterial species that produces electricity by oxidizing acetate with an electrode serving as the sole electron acceptor. We followed a robust and integrated bioinformatics approach which uses different 1-Dimensional, 2-Dimensional, and 3-Dimensional bioinformatics tools for functional re-annotation of hypothetical proteins of G.sulfurreducens PCA. Using four different 1-Dimensional tools in addition to BLAST, we predicted new protein functions for 365 hypothetical proteins. Functions of 92 of the 365 proteins were re-annotated with high majority since they were identified by 3-5 tools for 1- Dimensional analysis. Using Swiss-Prot, we could divide the 92 predicted proteins into 14 functional classes. We also analyzed 8 of 92 hypothetical proteins associated with electricity production and biofilm formation, and obtained good BLAST scores or Pfam scores for most of these proteins. Two-Dimensional analysis confirmed that 5 of these 8 proteins encode 3 AAA ATPase, a Cation efflux protein and an ATP-dependent Lon protease. Three-Dimensional analysis for these 5 proteins provided strong structural evidence. A 3-Dimensional model for a newly predicted ATP-dependent Lon protease (NP_953154.1) represents the first report for this hypothetical protein in G. sulfurreducens PCA. Elementary flux mode analysis of the reconstructed central metabolism was carried out and 87 modes were obtained. From the obtained modes, 8 best modes were identified and flux optimization was carried out using Linear Programming in CellNetAnalyzer. Three gene knock-outs namely 2-oxoglutarate synthase, pyruvate synthase, citrate oxaloacetate-lyase were proposed for flux optimization towards succinate. This in silico gene knock-out yielded a increase in flux of succinate from 0.91 to 6.75 mmol/(g dry Weight * h). This study will help in producing a better mutant for electricity production.


  • Ashok S, Venil Sumantran, Nupoor chowdhary and Kumar GR (2014) Prediction and classification of ABC transporters in Geobacter sulfurreducens PCA using computational approaches. Current Bioinformatics, 9(2), 166-172.
  • Ashok S, Subazini TK, Rajadurai CP, Subhashini P & Kumar GR (2013) A Whole Genome pairwise Comparative and Functional analysis of Geobacter sulfurreducens PCA, ISRN Computational Biology, Article ID 850179, 6 pages, doi:10.1155/2013/850179.
  • Ashok S, Nupoor Chowdhary, Rajadurai CP, Naresh R and Kumar GR (2013) Elementary Flux Mode analysis of central carbon metabolism of Geobacter sulfurreducens PCA for Electricity production.Proceeedings of International Conference on recent trends in Information Technology 2013 (ICRTIT 2013), MIT, Chennai(July 25-27).

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