1. SRI International Bioinformatics 1 Regulation in Pathway Tools Pathway Tools Workshop August 2009

2. SRI International Bioinformatics 2 What can be regulated? Gene transcription l Transcription initiation l Transcription termination (attenuation) l Sigma factors mRNA translation Substrate-level regulation of enzymes l Allosteric l Competitive A ligand binding to a protein can activate or inactivate it Protein degradation Other…

3. SRI International Bioinformatics 3 The Regulation Class Taxonomy Regulation-of-Enzyme-Activity Regulation-of-Gene-Products l Regulation-of-Degradation l Regulation-of-Production Regulation-of-Reactions Regulation-of-Transcription l Regulation-of-Transcription-Initiation l Transcriptional-Attenuation u Protein-Mediated-Attenuation u Rho-Blocking-Antitermination u Ribosome-Mediated-Attenuation u RNA-Mediated-Attenuation u RNA-Polymerase-Modification u Small-Molecule-Mediated-Attenuation Regulation-of-Translation l RNA-Mediated-Translation-Regulation l Protein-Mediated-Translation-Regulation

4. SRI International Bioinformatics 4 Regulation Statistics for EcoCyc Transcription Initiation: 2551 regulatory interactions, covering 851 transcription units Attenuation : 18 regulatory interactions (16 TUs) l Ribosome-mediated: 11 l Protein-mediated: 4 l Small-molecule-mediated: 1 l Rho-blocking: 1 Translation: 51 regulatory interactions (41 TUs) l RNA-mediated: 32 l Protein-mediated: 16 Enzyme substrate-level regulation: 2431 regulatory interactions (579 enzymes) Regulation of reactions: 20 regulatory interactions

5. SRI International Bioinformatics 5 Display of Transcriptional Regulation

6. SRI International Bioinformatics 6 Editor for Transcription Initiation

7. SRI International Bioinformatics 7 Editor for Transcription Attenuation

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9. 9 More Example Displays…

10. SRI International Bioinformatics 10 Integrating Regulatory Information Now that we have individual regulatory interactions, we can: Show all regulatory interactions that affect a gene Incorporate regulation into pathway displays l substrate-level enzyme regulation and feedback inhibition l regulators of genes involved in pathway l transcription units regulated by signaling pathway When we look at an object, see everything it regulates l transcription factor l RNA polymerase l RNA l small molecule Highlight regulated reactions on cellular overview diagram Regulatory Overview Diagram

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14. SRI International Bioinformatics 14 Regulation section of L-tryptophan display

15. SRI International Bioinformatics 15 Representation of Transcriptional/Translational Regulation Transcription-Unit l Components include genes, a single promoter, zero or more terminators DNA-Binding-Sites, mRNA-Binding-Sites l Linked to regulation frames Regulation frames l Transcriptional Initiation: defines a 3-way pairing between promoter, transcription factor and DNA-binding-site. l Transcriptional Attenuation: defines relationship between terminator and the entity (tRNA, protein, small molecule) that regulates it. Some classes also have mRNA-Binding-Site. l Translational Regulation: defines a 3-way pairing between transcription unit, regulator and mRNA-Binding-Site. May also include link to RNAse or accessory protein.

16. SRI International Bioinformatics 16 Note about Operons and Transcription Units Operon: A set of two or more genes that are transcribed as a unit. May include multiple promoters. Transcription Unit: A set of one or more genes that are transcribed as a unit from a single promoter. Pathway Tools schema does not represent operons explicitly, only transcription-units

17. SRI International Bioinformatics 17 Ontology for Transcriptional Regulation trpLEDCBAp1 trpE trpD trpC trpB trpA trpL reg001 site001 TrpR*trp trpLEDCBA trp apoTrpR rxn001 components left right regulated-by associated-binding-site regulator terminator001 reg002 charged-trp-tRNA regulated-byregulator sigma70 binds-sigma-factor

18. SRI International Bioinformatics 18 Attributes of Regulation Frames Regulator: usually a compound, protein or RNA Regulated-Entity: depends on class of regulation – could be Enzymatic-Reaction, Transcription-Unit, Promoter, Terminator, etc. Mode: +/- for activation/inhibition Comment, citations, evidence Other slots depend on class of regulation l Mechanism: controlled vocabulary depending on class l Associated-binding-site: for transcription initiation, some classes of attenuation, translation regulation l Antiterminator start/end position: for some classes of attenuation l Accessory-Proteins, Associated-RNAse: for translation regulation l Etc…