1. 6/10/2015 ©T. C. Hazen #1 Center for Environmental Biotechnology Center for Environmental Biotechnology Rapid deduction of bacteria stress response pathways: Genomics, proteomics, metabolomics and bioinformatics Terry C. Hazen & Adam Arkin University of California, Berkeley Lawrence Berkeley National Laboratory Berkeley, California 94720 Terry C. Hazen & Adam Arkin University of California, Berkeley Lawrence Berkeley National Laboratory Berkeley, California 94720

2. 6/10/2015 ©T. C. Hazen #2 Center for Environmental Biotechnology Center for Environmental Biotechnology Workshop Schedule 8:30-9:00Introduction Terry Hazen, Lawrence Berkeley National Laboratory, Berkeley, CA 9:00-10:15Environmental stress responses in metal-reducers David Stahl, University of Washington, Seattle, WA 10:15-10:45BREAK 10:45-12:00Genomic microarrays to determine stress responses Joe Zhou, Oak Ridge National Laboratory, Oak Ridge, TN 12:00-1:00LUNCH 1:00-2:15Proteomics of stress Martin Keller, Diversa Corporation, San Diego, CA 2:15-3:30Metabolomics of stress Jay Keasling, University of California/LBNL, Berkeley, CA 3:30-3:45BREAK 3:45-5:00Bioinformatics to determine stress responses Adam Arkin, University of California/LBNL, Berkeley, CA

3. 6/10/2015 ©T. C. Hazen #3 Center for Environmental Biotechnology Center for Environmental Biotechnology Human Genome Project started in 1986 Human Genome Project started in 1986 Scientific project of the millennia Scientific project of the millennia Great advances in sequencing throughput Great advances in sequencing throughput Since 1995 >150 microorganisms have been sequenced, >100 in the last 2 years Since 1995 >150 microorganisms have been sequenced, >100 in the last 2 years TIGR discovers 1.2 million new bacteria/archea genes in the Sargasso Sea March 2, 2004 TIGR discovers 1.2 million new bacteria/archea genes in the Sargasso Sea March 2, 2004 The current Joint Genome Institute throughput is ~2.0-2.5 billion bases per month The current Joint Genome Institute throughput is ~2.0-2.5 billion bases per month In theory, JGI could sequence >400 microbes per year*, In practice, this would be very difficult to achieve In theory, JGI could sequence >400 microbes per year*, In practice, this would be very difficult to achieve JGI will sequence >100 microbes this year JGI will sequence >100 microbes this year Human Genome Project started in 1986 Human Genome Project started in 1986 Scientific project of the millennia Scientific project of the millennia Great advances in sequencing throughput Great advances in sequencing throughput Since 1995 >150 microorganisms have been sequenced, >100 in the last 2 years Since 1995 >150 microorganisms have been sequenced, >100 in the last 2 years TIGR discovers 1.2 million new bacteria/archea genes in the Sargasso Sea March 2, 2004 TIGR discovers 1.2 million new bacteria/archea genes in the Sargasso Sea March 2, 2004 The current Joint Genome Institute throughput is ~2.0-2.5 billion bases per month The current Joint Genome Institute throughput is ~2.0-2.5 billion bases per month In theory, JGI could sequence >400 microbes per year*, In practice, this would be very difficult to achieve In theory, JGI could sequence >400 microbes per year*, In practice, this would be very difficult to achieve JGI will sequence >100 microbes this year JGI will sequence >100 microbes this year Genomics - How far we have come!

4. 6/10/2015 ©T. C. Hazen #4 Center for Environmental Biotechnology Center for Environmental Biotechnology Tyson et al., Nature (2004) Community structure and metabolism through reconstruction of genomes from the environment Ferroplasma type II

5. 6/10/2015 ©T. C. Hazen #5 Center for Environmental Biotechnology Center for Environmental Biotechnology Plane Parts vs. Flying Completed genomes provide “parts lists” for many microbes, we still have very little understanding of how they give rise to living systems. Completed genomes provide “parts lists” for many microbes, we still have very little understanding of how they give rise to living systems. Knowing the working parts of a 747 jet gives few clues as to how it flies. Knowing the working parts of a 747 jet gives few clues as to how it flies. genes, proteins, metabolites, and multimolecular assemblies (“molecular machines”) interact in an intricate labyrinth of pathways and networks to create, sustain, and reproduce the living cell—complexity well beyond the engineering of a 747. genes, proteins, metabolites, and multimolecular assemblies (“molecular machines”) interact in an intricate labyrinth of pathways and networks to create, sustain, and reproduce the living cell—complexity well beyond the engineering of a 747. A systems approach will transform biology from an empirical and descriptive science to a more quantitative and predictive science having the potential to manipulate and use living systems and their components. A systems approach will transform biology from an empirical and descriptive science to a more quantitative and predictive science having the potential to manipulate and use living systems and their components.

6. 6/10/2015 ©T. C. Hazen #6 Center for Environmental Biotechnology Center for Environmental Biotechnology Integration of new science areas to build a knowledge of how to fly the plane Ecogenomics Ecogenomics Phenomics Phenomics Transcriptomics Transcriptomics Proteomics Proteomics Metabolomics (lipidomics, fluxomics) Metabolomics (lipidomics, fluxomics) Bioinformatics to integrate the pathways and build the models to understand how to fly the plane Bioinformatics to integrate the pathways and build the models to understand how to fly the plane

7. The Virtual Institute of Microbial Stress and Survival U Washington http://vimss.lbl.govhttp://vimss.lbl.gov High Throughput Comparative Molecular Environmental Microbiology for Breakthrough Science and New applications for Bioremediation & Natural Attenuation Strategies

8. Design of Project

9. Phenotypic Microarray Omnilog System - 2000 assays, 50 96-well plates at one time Omnilog System - 2000 assays, 50 96-well plates at one time

10. FTIR Profiling Synchrotron FTIR time course of infrared absorption intensity, indicative of oxidative stress levels in different biologically important molecules in Desulfovibrio vulgaris after exposure to atmospheric oxygen. Also found signatures for Cytochrome B hemes Synchrotron FTIR time course of infrared absorption intensity, indicative of oxidative stress levels in different biologically important molecules in Desulfovibrio vulgaris after exposure to atmospheric oxygen. Also found signatures for Cytochrome B hemes

11. O 2 Stress in Desulfovibrio vulgaris Fischer exact test of GO terms for DE genes as measured by microarrays at 2h revealed numerous up-regulated genes in cell wall and polysaccharide metabolism. Candidates for EPS activity. Also– why all the sugar activity given D.v. doesn’t use hexoses for cell growth? Fischer exact test of GO terms for DE genes as measured by microarrays at 2h revealed numerous up-regulated genes in cell wall and polysaccharide metabolism. Candidates for EPS activity. Also– why all the sugar activity given D.v. doesn’t use hexoses for cell growth?

12. Comparative genomics pipeline 120 annotated microbial genomes already in pipeline High quality function prediction in novel comparative genome browser Operon/regulon analysis yields predictions of co- regulated genes and suggests modules of function Flagellar control chemosensing http://escalante.lbl.gov, username=gtl, password=arkin