Strengths in OMICS as a tool for the early detection of an environmental stressor Microbial Response Session 2009 EPA Fellowship Conference Sept. 22, 2009 genomicsproteomics metabolomics

Traditional methods Experimental identification of metabolites Molecular genetic methods (knock –outs, cloning, sequencing…) Biochemical characterization Give information on individual metabolic/genomic/proteomic reactions… …. But cannot adequately elucidate global cellular responses

Seong-Jae Kim, Ohgew Kweon and Carl E Cerniglia, Cur. Opin. Microbiol., 2009, 12,

Case Study-Phenol response From: Pedro M. Santos, Dirk Benndorf and Isabel Sá-Correia, “Insights into Psedomonas putida KT2440 response to phenol-induced stress by quantitative proteomics”, Proteomics 2004, 4, Santos et al.,Proteomics, 2004, 4, 2640

Advantages to this approach Identify specific metabolic processes based on changes in protein expression A proteomic analysis of an organism is a readout of the “environmental state” within the organism. This leads to understanding of physiological response and organism influence on the ecosystem Why specific process are regulation- ideas about what pathways are being evoked by organism under a give stress Physiology!! Goldberg, E. (1986). Environ. Monit. Assess. 7, 91 –103 Gonzalez-Fernandez et. al.(2008),Pure Appl. Chem., 80,

P. putida study of phenol-induced stress 1. Oxidative stress response 2. General Stress response 3. Energetic Metabolism 4. Fatty Acid Biosynthesis 5. Inhibition of Cell Division 6. Cell envelope Biosynthesis 7. Transcriptional Regulation 8. Transport of small molecules Santos et al.,Proteomics, 2004, 4, 2640

Regulation Down regulated proteins- 1.Cell motility 2.Nucleotide biosynthesis Up-regulated proteins- 1. Oxidative stress response – 2.Fatty Acid Biosynthesis- 3.Inhibition of Cell Division – 4.Cell envelope Biosynthesis – 5. Transport of small molecules – Phenol exposure leads to increased reactive oxygen species. Recovery mechanism for oxidatively damaged membrane phospholipids Prevent the multiplication of mutated DNA Adaption to phenol may involve cell envelope modification Phenol efflux from the cell through increased production of transport proteins Decreased motility )contrary to what was believed) may actually enhance phenol resistance. Prevent multiplication of mutated cells Santos et al.,Proteomics, 2004, 4, 2640

Metabolomics Bioaccumulation - readout of organisms metabolic state. Coupled with OMICS- paints picture of pathway Understanding of organisms response to stress Phale P. et al. OMICS, 2007, 11, 252

Conclusions Omics based approaches give physiological conditions. Through integration of genomic/proteomics/metabolomics a good picture of an organisms response to the environment can be obtained Possible markers of an OMIC state can lead to a picture of the environment inside and outside an organism???