A systems biology approach to studying Enterobacteria Joshua Adkins Center for Systems Biology of EnteroPathogens SBWG Web-Conference January 26,

Family of the Enterobacteriaceae Gram-negative, rod-shaped, facultative anaerobes Important members of the gut microbiome A number of important human pathogens including Salmonella Yersinia Shigella Escherichia Diseases caused include, systemic bacteremia, gastroenteritis, urinary infections, respiratory infections, nosocomial infections, broadly opportunistic, etc. >1 billion cases of human disease per year by some estimates for Salmonella alone* 2 *Pang et al. Trends Micro (1995)

Center of Systems Biology for EnteroPathogens Scott Peterson Genomics Dick Smith LC-MS Omics Fred Heffron Salmonella Bernhard Palsson Modeling and E. coli Vladimir Motin Yersinia 3

Team Interactions-Dependant on Regular Teleconferences 4

Biology Focus 1.Adaptation to the host environment 2.Regulation and order of interactions within the host Omics Approaches 1.Sample matched measurements 2.High-throughput global analysis for transcripts, proteins, soluble/insoluble metabolites 3.Targeted measurements as necessary Modeling Approaches 1.Genome-Scale Reconstruction of metabolic and regulatory networks 2.Inference-based analysis when reconstruction is unavailable Conceptually Simply Projects In Practice Challenging 5

Adaptation-factors versus virulence-effectors Adaptation factors: proteins required by the bacterium to survive on the nutrients available to it (metabolic, transport, structural, etc) Virulence-effectors: proteins (or other biomolecules) that are part of the “active” response to the host Causes changes in the host’s function Subverts or destroys the host’s response(s) to infection Make the host more conducive to pathogen growth 6

Yersinia and Salmonella Compared Diseases caused by members of each genus can be systemic, gastrointestinal, and sometimes auto-immune Successful infections require both adaptation to and modification of the host environment In vitro models Growth on defined media, media that induce “infectious”- like responses Ex vivo models Intracellular growth in host-derived cell lines that are relevant to in vivo infections In vivo models Animal models relevant to human disease 7

Yersinia and Salmonella Contrasted Signals for infectious like conditions Low [Ca 2+ ] and 37 °C Gastroenteritis food borne and systemic is vector borne Extracellular lifecycle Intracellular at early stage of infection in phagosome 8 Yersinia Salmonella Signals for infectious like conditions Low pH, iron, [Mg 2+ ] Gastroenteritis and systemic are both food and water borne Intracellular lifecycle is propagated in early phagosome-like structures

Recent Successes Data acquisition nearly complete for first major cross-site efforts for both Salmonella and Yersinia projects. (transcriptomics, proteomics, and metabolic reconstructions) Multiple rounds of metabolomics and lipidomics methods refinement, finalizing the global protocols Completed community consensus Genome-Scale Reconstruction of the Salmonella metabolic network, Thiele et al. submitted to J. Bac. Integrating community available “omics” results for initial model testing. Publication of early project efforts. Shi et al. 2009, Infection and Immunity (macrophage infection) Shi et al. 2009, J. Proteomics and Bioinformatics (growth condition refinement) Auberry et al. 2010, J. Proteomics and Bioinformatics (proteomics, metabolomics, and lipidomics dissemination site) 9

Changes since the first annual meeting Limited technical changes, but emphasis areas have adapted (increase planning for pathogen-host interactions) Stronger interconnections and better sense of team Sub-projects refined and made more efficient, in some cases moving to application rather than refinements Increased emphasis on multi-site collaborations PI strategy session discussing opportunities for truly impactful work On-line data analysis jamborees (balance individual and team needs) Improving what is meant by “data integration” Adding a sense of urgency (“18 months”) 10

The SysBEP Team OHSU-Heffron Fred Heffron Afshan Kidwai Jie Li George Niemann Hyunjin Yoon UCSD-Palsson Bernhard Palsson Pep Charusanti Daniel Hyduke JCVI-Peterson Scott Peterson Marcus Jones UTMB-Motin Vladimir Motin Sadhana Chauhan WSU-McAteer Kate McAteer PNNL – Adkins Joshua AdkinsMeagan BurnetJason McDermott Richard Smith, Co-PISaiful ChowdhuryMatthew Monroe Gordon AndersonMichelle CostaKarin Rodland Charles Ansong, PMYoung-Mo KimAlexandra Schrimpe-Rutledge Heather BrewerTom MetzLiang Shi Roslyn BrownJessica MartinMudita Singhal NIH/DHHS NIAID IAA Y1-AI SysBEP.org 11

Genome Scale-Metabolic Reconstruction of Salmonella: Community Driven Consensus 12 Thiele et al., submitted to J Bac Thiele, Hyduke, & Palsson

Discovery of Novel Type III Secreted Effectors 13 Niemann, Brown, Li, Brewer, & Heffron

Secretion of SrfN via Outer Membrane Vesicles 14 NMR structure of STM0082 aka SrfN, pdb: 2JNA NESGC Yoon et al., in revision Yoon, Ansong, McDermott, Gritsenko, & Heffron