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Partner 8 (IC-CSIC)

Partner 8 (IC-CSIC). Approaches towards bioremediation of the Mediterranean Sea by exploring its microbial diversity – SICA (Mediterranean Partner Countries) Centre: CSIC – Institute of Catalysis Tel.: +34 91 585 4872 E-mail: mferrer@icp.csic.es Chania, 3 rd July 2011.

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Partner 8 (IC-CSIC)

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  1. Partner 8 (IC-CSIC) Approaches towards bioremediation of the Mediterranean Sea by exploring its microbial diversity – SICA (Mediterranean Partner Countries) Centre: CSIC – Institute of Catalysis Tel.: +34 91 585 4872 E-mail: mferrer@icp.csic.es Chania, 3rd July 2011

  2. IC-CSIC: Scientific achievements • OBJECTIVE • Integrative “omic” investigations for bioremediation strategies associated to MedSea • LIMITATIONS • Omics tools in contaminated-associated MedSea microbial communitiesare limited • A major drawback is the incomplete genomic information that allows elucidating degradation metabolic routes for which the genetic basis has not yet been explored. • This requires cured databases with valid experimental information

  3. Inter. nr. 1 Pollutant nr. 1 Inter. nr. 2 Pollutant nr. 2 Biodegradation networks IC-CSIC: Scientific achievements • PROBLEMS OF OMIC INVESTIGATIONS • There is a serious problem in relation to the quality and degree of completeness of the annotation of (meta-) genomes. • Thus, wrong annotations in enzyme super-families containing multiple families that catalyse different reactions are a large problem that has been recognized • Whereas metabolomic is sequence-independent … • (Meta-) genomic and (meta-) proteomics are sequence-dependent OPTIMIZING ANALYTICAL PROTOCOLS Sediment Sea water

  4. IC-CSIC: Scientific achievements AMINOACID SEQUENCE INHQVETIDDLLKAAYYLQDKRVRIVFGPGRHATSGGYFLYFEGHDGFTFEFSTSDRKVIEDDETYRPRQFALEDASFCLFGAKPDIPEFRR* BLAST NCBI NO POSSIBILITY TO ASSIGN FUNCTIONS NOR PROPER ANNOTATION (wrong annotations) Extradiol dioxygenase of the viccinal chelate superfamily (2,3-dihydroxy-p-cumate dioxygenase)

  5. IC-CSIC: Scientific achievements • SOLUTION AT ULIXES • We have created one in silico screening method to identify enzymes usually catalyzing the aerobic degradation of pollutants via di- and trihydroxylated intermediates: • Intradiol dioxygenases • Extradiol dioxygenases • Gentisate dioxygenases • P450 monooxygenases • Muconate cycloisomerase • Maleylacetate reductase • This cured database contains 1648 proteins (and their sequences) for which a function has been proven and therefore it may provide biochemical valid information that help to elucidate, based on proximity to proteins (in cultivated species with physiology) of known biochemistry, potential catabolic pathways • IC in collaboration with HZI (Dr. D. Pieper; MAGICPAH Project)

  6. IC-CSIC: Scientific achievements Whole degradation networks DNA sample 454 sequence Automatic annotation BLAST database Selection of targets Whole microbial Community metabolism BLAST NCBI Selection of targets *Biodeg reconstruction in MAGICPAH project

  7. IC-CSIC: Scientific achievements Demethylases unknown VI Family: Rieske Subfamily: Phthalate Phenoxybenzoate dioxygenase VII V 3-Nitrobenzoate dioxygenase IV Isophthalate dioxygenases VIII III IX II 1-Oxo-2,3-Dihydroquinoline monooxygenase 3-Chlorobenzoate dioxygenases I X Carbazol dioxygenases Phthalate dioxygenases

  8. IC-CSIC: Scientific achievements Family: EXDO Subfamily: 1.3

  9. IC-CSIC: Scientific achievements • BUT… • Sequence homology per se do not ensure similar biodegradation functions • Thus, it has been well documented that single amino acid difference may have a dramatic influence on enzyme properties. • Therefore, a experimental validation pipiline should be added to the in silico analyses • For such purpose (meta-) proteomics and biochemical analysis are undertaken in ULIXES

  10. IC-CSIC: Scientific achievements DNA sample Screen methods Gene analysis IC-CSIC, IAMC & BU IC-CSIC Cloning Functional IC-CSIC Library screens Characterization IC-CSIC IAMC BU In silico Annotation (Meta-) proteomics IC-CSIC, IAMC & BU -Omics data integration (Meta-) genomics IC-CSIC, IAMC & BU (Meta-) metabolomic IC-CSIC & IAMC

  11. Partner 8 (IC-CSIC) Approaches towards bioremediation of the Mediterranean Sea by exploring its microbial diversity – SICA (Mediterranean Partner Countries) Centre: CSIC – Institute of Catalysis Tel.: +34 91 585 4872 E-mail: mferrer@icp.csic.es Chania, 3rd July 2011

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