* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Network Reconstruction Slides
Transcriptional regulation wikipedia , lookup
Gene nomenclature wikipedia , lookup
Community fingerprinting wikipedia , lookup
Gene expression wikipedia , lookup
Promoter (genetics) wikipedia , lookup
Genetic engineering wikipedia , lookup
Amino acid synthesis wikipedia , lookup
Biosynthesis wikipedia , lookup
Evolution of metal ions in biological systems wikipedia , lookup
Multi-state modeling of biomolecules wikipedia , lookup
Endogenous retrovirus wikipedia , lookup
Biochemical cascade wikipedia , lookup
Gene expression profiling wikipedia , lookup
Silencer (genetics) wikipedia , lookup
Artificial gene synthesis wikipedia , lookup
Metabolomics wikipedia , lookup
Pharmacometabolomics wikipedia , lookup
Basal metabolic rate wikipedia , lookup
Metabolic network reconstruction “Metabolism is not boring” Systems Biology Paradigm: components -> networks -> computational models -> phenotypes Palsson,BO; Systems Biology, Cambridge University Press 2006 Building a genome-scale metabolic network model Model construction: – Metabolic enzymes – Enzyme specificities Inputs: – Cell objective (e.g. growth, etc.) – Metabolite uptake rates – Genetic or expression changes Predicts: – Growth rate – Pathway usage – Perturbation effects RECONSTRUCTIONS ARE 2D GENOME ANNOTATIONS AND KNOWLEDGE BASES Links and nodes Network Reconstruction are 2D genome annotations Nature Biotechnology, 22:1218(2004) Sequence assembly and bottom-up reconstruction are ‘similar’ processes Bottom-up Network Reconstructions are knowledge bases: Nature Reviews Microbiology, Feb 2009 STEP 1: DEFINING AN INITIAL COMPONENT LIST Automated Generation of Draft Reconstruction Obtain Genome Annotation Identify Candidate Metabolic Functions Obtain candidate metabolic reactions Assemble Draft Reconstruction. Look for EC numbers, GO terms, Comparative genomics Issues associated with automated extraction of content Nat Rev Microbiol. 2009 Feb;7(2):129-43 STEP 2: CURATION AND ADDING CONTENT TO A RECONSTRUCTION The manual curation process Defining Metabolic Reactions hslJ ldhA ydbH Nat Rev Genet. 2006 Feb;7(2):130-41. Nat Rev Genet. 2006 Feb;7(2):130-41. Gene, Protein, Reaction Associations (GPRs) and data mapping The process of forming GPRs Nat Rev Microbiol. 2009 Feb;7(2):129-43 Sources of data for curation Nat Rev Microbiol. 2009 Feb;7(2):129-43 Current Knowledge Status for Organisms SKI = No. Abstracts No. Genes E. coli 55.1 Human 48.5 S. aureus 16-17 Mouse 15.6 H. pylori 13 S. cerevisiae 10.6 20 EMBO Reports. 6(5): 397-9 2005 Lysine Biosynthesis: Gap analysis Example of Integrated Reconstruction Process : Non-Gene • Genome annotation reveals incomplete pathway for lysine biosynthesis Associated • Gap analysis indicates no other routes for lysine production Reactions • Growth physiology data indicates no auxotrophic requirement for lysine • Three additional reactions will be included into the model to complete pathway • These reactions represent hypotheses for future investigation Gene Associated Reactions Knowledge gaps Ubiquinone 10 Biosynthesis Coq2 ? ? Coq3 •physiological data suggest these reactions, not all genes are identified •Some reaction are biochemically not well-defined ? Coq6 ? Score: Coq7 Coq3 Confidence Score: Sources of Evidence Increasing Confidence • Biochemical Enzyme has been tested biochemically. • Genetic Gene overexpression and purification, gene deletions. • Sequence There is significant sequence similarity to another gene with known function. • Physiological There is physiological data to support inclusion in the model. • Modeling Reaction is included to improve simulation results. Kinetic Assay Overexpression 86% Homology Grows on Ascorbate Challenge--Orphan Reactions: Reactions without a known gene. EC classification of enzymes • Several reactions are known to happen, but their associated genes are unknown A large number of metabolic enzymes have no known genetic basis • Many known metabolic reactions with EC numbers are orphan. • Can be probably be found by a combined experimental – computational strategy. • Combination of gene neighborhood, mRNA coexpression data and expts like phenotype profiling and metabolomics measurements. • Distribution of enzymatic activities in orphans reactions BMC Bioinformatics 8:244 (2007) STEP 3: GENOME-SCALE MODELS AND VALIDATION From a reconstruction to a model • Add boundaries • Describe network mathematically The Process of metabolic reconstruction and validation Procedure to generate a biomass function Nat Rev Microbiol. 2009 Feb;7(2):129-43 Computations: Functional states STEP 4: EVALUATION AND ITERATIVE VALIDATION An Example: The process used for reconstructing the human metabolic network Mol Biosyst. 2007 Sep;3(9):598-603. Nat Rev Genet. 2006 Feb;7(2):130-41. USES OF RECONSTRUCTIONS Applications of Genome-Scale metabolic Reconstructions Molec. Sys. Biol, 5:320, 2009 AVAILABLE RECONSTRUCTIONS Growth in Available Reconstructions and their use is exponential Kim et al. Current Opinion in Biotechnology, Volume 23, Issue 4, 2012 Expanding scope in omics data types NEW HORIZONS IN METABOLIC NETWORK RECONSTRUCTION A view of a metabolic network Inclusion of protein structure Science 325:1544 (2009). Brunk et al. BMC Sys Bio (2016). Chang, et al. Science (2013). Environmental applications Nat Rev Micro, 9: 39 (2011) Multiple cells/organs Nature Biotech 28:1279 (2010) Host-Pathogen Mol Sys Biol 6:422 (2010) Microbial interactions Lewis, et al. Nat Rev Microb, 2012 More cellular processes Nat Rev Micro 7:129 (2009) Metabolic Reconstruction • Assume genes are expressed at sufficient quantity • Protein / mRNA synthesis costs are in the biomass objective function Lerman, et al. Nat Communications, 2012 Metabolic + TR/TR • All enzymes must be produced • Biomass objective includes fewer components Lerman, et al. Nat Communications, 2012 Integrating transcription/translation with metabolism • 3-step process • Formulation of transcription & translation reactions for metabolic genes • Formulation of metabolic reactions with enzymes explicitly represented • “Merging” of the networks Thiele et al., plos one, 2012 ME does stuff • Predicts proteome • Finds motifs • Finds gene functions