application of in silico genomic modeling in bioremediation … · 2018. 9. 27. · bnice bess....

Application ofin silico genomic modeling in

bioremediation processes

Clean up nature from pollutants

Conventional methods- expensive;

- non-specific;

- release of intermediate toxic compounds.

Bioremediation

- ecologically focused process;

- an alternative to physical-chemical processes;

- detoxification and degradation of toxic pollutants either by intracellular accumulation or by enzymatic transformation.

Mycoremdiation

In silico toxicity of compounds

✓More than 70 million compounds have been identified by May 2013;

✓ Quantitative structure-activity relationship model;

✓OSIRIS;

✓SuperToxic database, contains information about multiple toxic compounds (about 60,000).

QSAR model

In silico biodegradation of toxic compounds

➢University of Minnesota Biocatalysis / Biodegradation Database (UMBBD)

➢BESS (Biodegradability Evaluation and Simulation System);

➢Biochemical Network Integrated Computational Explorator (BNICE);

➢The CATABOL software;

➢The MetaRouter System;

➢Biocatalysis Assignment Tool (BAT);

➢KEGG (Kyoto Encyclopedia of Genes and Genomes),

University of Minnesota Biocatalysis/Biodegradation Database (UMBBD)

• 177 metabolic pathways;

• 1220 reactions;

• 1133 compounds,

• 786 enzymes;

• 462 microorganisms of interest.

BNICE BESS

Biodegradative Strain Database (BSD)

Ecological Structure Activity Relationships (ECOSAR)

Evaluates aquatic toxicity:

• Acute toxicity;

• Chronic toxicity.

Uses Structure Activity Relationships (SARs).

Design of bacterial consortium

Heavy metals reduction &radionuclides removal

Deinococcus geothermalis

Biodegradation of pentachlorophenol (PCP)

Sphingobium chlorophenolicum