Meaningful Metabolic Logic

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					Meaningful Metabolic Logic

Lynda B.M. Ellis
Laboratory Medicine and Pathology University of Minnesota


Top: Larry Wackett, Michael Turnbull, Kathrin Fenner, Ted LaBelle Bottom: Junfeng (Jeff) Gao, Chunhui Li, Rachael Long, Lynda Ellis

The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD)

Freely available on the World Wide Web

 Focus:  Microbial specialized catabolism  Emphasizing environmental pollutants
 Represents metabolism as pathways

From 1,2-Dichloroethane to 2-Chloroethanol
Graphic of the reaction.
Medline reference Verschueren KH, Seljee F, Rozeboom HJ, Kalk KH, Dijkstra BW Nature (1993) 363(6431): 693-8. Search Medline titles for haloalkane dehalogenase. 64 citations found on August 14, 2005.
1,2-Dichloroethane | | H2O haloalkane | / dehalogenase |/ | Search GenBank, 89 hits on Aug. 14, 2005 Kyoto |\ ExPASy | \ | HCl v 2-Chloroethanol

Reaction Page

Generate a pathway starting from this reaction. UM-BBD Biotransformation rules in accord with this reaction: Alkyl halide -----> Alcohol (bt0022) ______________________________________________________________________

[1,2-Dichloroethane] [BBD Main Menu]
Page Author(s): Renhao Li August 14, 2005 Contact Us
This is the UM-BBD reaction, reacID# r0001. It was generated on August 24, 2005 2:42:28 PM CDT.
© 2005, University of Minnesota.

Metapathway Map meta/meta_map.html

 ~107 compounds in the environment.  The UM-BBD will never contain all such

metabolism.  UM-BBD data might be used to predict reasonable biodegradation schemes for compounds it does not contain.

Prediction Overview

Biotransformation Rule

vic-dihydroxybenzenoid -> extradiol ring cleavage Aerobic Likelihood: Likely

UM-BBD Reaction(s): 2'-Aminobiphenyl-2,3-diol -----> 2-Hydroxy-6-oxo-(2'-aminophenyl)hexa-2E,4Z-dienoate (reacID# r0457) Catechol -----> 2-Hydroxy-cis,cis-muconate semialdehyde (reacID# r0307) 3-Chlorocatechol -----> 3-Chloro-2-hydroxymuconic semialdehyde (reacID# r1022) 4-Chlorocatechol -----> 5-Chloro-2-hydroxymuconic semialdehyde (reacID# r0287) …

Contact Us if you have any comments on rule bt0008.

Biotransformation Rule-base
bt0001: primary alcohol  aldehyde bt0002: secondary alcohol  ketone bt0003: aldehyde  carboxylate bt0005: vic-unsubstituted aromatic  cis-dihydroxydihydroaromatic bt0008: vic-dihydroxybenzenoid  extradiol ring cleavage … bt0255: vic-dihydrodihydroxyaromatic  vic-dihydroxyaromatic bt0259: vic-dihydroxyaromatic  intradiol ring cleavage

Pathway Prediction Example


After five steps

Complexity - 100gm of soil

• 100,000,000,000 bacteria • 100,000 natural chemicals • 10,000 bacterial species • 1 new chemical

PredictBT Workshops
 Since 1998, three workshops held  Fourth, May 4-5, 2007  Second workshop (May, 2005) assigned

aerobic likelihood to btrules

Aerobic Likelihood
 Standard conditions  Aerobic  Soil (moderate moisture) or water  25 C  No other toxic or competing chemicals  Rank Rules: Very Likely, Likely,

Neutral, Unlikely, Very Unlikely, Unknown

Expert Rankings
 7 experts; 6 assigned 50 of the 250 rules,

one ranked all 250.  Each rule ranked by 2-3 experts prior to the workshop (prework), on a 1-5 scale  Unknown rarely used (1-2 per expert)  Most rankings within 1 unit
 

If so, used rank closest to 3 (2,3 = 3; 4,5 = 4). If no, discussed at workshop, consensus reached

 2 experts agreed to rank future rules

Challenges of Likelihood Ranking
 Are two experts enough?  Only 21 of 230 rules based on 10+ reactions  “Them as has, gets” - not likely to improve  How to rank rules for less common reactions?

Challenges, 2


R-COOH + CoA  CoA thioester (unlikely) divided into aliphatic (likely) and aromatic (unlikely) Peroxide  alcohol (very likely)  (neutral) cis-dihydroxyhydrocarboxylate formation

Single ring reactions were Likely

This fused ring reaction was Unlikely

Now all single and fused rings are Likely

Challenges, 3
Over half rules ranked “Neutral”

Summary of BT rule rankings


Number of BT rules


60 48 40 17 10 32


0 very likely likely neutral unlikely very unlikely

Relative Like lihood

Challenges, 4
Based on BBD reactions

Oxidative cleavage of secondary amines (bt0063)
Unlikely, based on BBD exotic examples  Simpler ones are likely  How to separate?

Carbamyl degradation - known, but no BBD or KEGG examples. No btrule.  Should non-BBD-based rules be written?

Challenges, 5
Hydrolytic vs reductive dehalogenation
 Hydrolytic dehalogenation aerobically

likely, unless a highly halogenated compound  “Highly”? X/C ratio >=1 ?
H Cl Cl Cl Cl H Cl H H H Cl H

H Cl Cl H Cl

Cl H H H H Cl Cl

aerobic hydrolytic dehalogenation

anaerobic reductive dehalogenation

Challenges, 6
Decarboxylation (bt0051)
Too general, how to limit?  27 example BBD reactions; more in KEGG  >10 different reaction patterns  Instead, excluded fatty acids  Other exclusions for this rule?  Exclusions for other rules?

Challenges, 7
 Change in software breaks rules
 Change in hardware breaks rules

 Change in personnel breaks rules

Data entry Rule writers


Challenges, 8
Interactive web-based application

Predictions must be fast
Cpd button shows exact match  Smlr button could show similar compounds; but is it quick enough?


All rule patterns are tested against each query; each additional pattern slightly slows predictions

Combinatorial Explosion
Parent compound # possible metabolites # possible pathways

Glyphosate (RoundUp™) Diuron (phenylureas)

14 27

132 2,223

MTBE (methy-t-butyl ether)



Kathrin Fenner, 2007, personal communication

2007 PredictBT Workshop
 May 4-5, 2007, Cargill Building, UM  Goal - to limit PPS predictions in a

meaningful, efficient, effective way  Sponsors:

2007 PredictBT Panel
 John Bumpus  Stefan Kramer

U Northern Iowa  Kathrin Fenner EAWAG, Switzerland  Susumu Goto Kyoto U, Japan

TUM, Germany  Fangping Mu Los Alamos Nat Lab  Mukesh Patel Lhasa Limited, UK  Jeanne VanBriesen Carneige-Mellon U

PredictBT Suggestions
 Ask experts to rerank “neutral” rules  Would need to rerank all  No funding for this  Create list of Readily Degradable

Intermediates (RDIs)  Develop separate, batch, mode
 

Create complete tree Prune

 Even two levels useful;

more chances to find an RDI

PredictBT Suggestions, 2
 Prune tree using thermodynamics  Based on ATP generation, known pathways are in the top 20 percentile of possible pathways.  Prune tree using RDIs  Find the shortest path to an RDI.

PredictBT Suggestions, 3
 Susumo Goto: Use similarity  biological, not chemical, similarity





>.9 Tanimoto




Different RDIs

PredictBT Suggestions, 4
 Use chemical similarity to prescreen queries  If no BBD compounds are chemically similar to the query, PPS predictions are less accurate  Use machine learning to determine which

biotransformations are most likely for a given substructure.
  

Need positive and negative examples Need rules based on 10+ reactions 8/21 are problematic rules

 Started in 2002, funded by Lhasa Limited
 PPS rules  Meteor, forming MEPPS.  Meteor Environmental Pathway Prediction System  Static UM-BBD web pages  MEPPS.

MEPPS links to static UM-BBD btrule web pages via MEPPS Biotransformation screen “Examples” button.

 Aerobic likelihoods added using existing Meteor

metabolic reasoning tools.

MEPPS Prediction



 Implement PredictBT workshop suggestions  Add  pathways  rules  features  Improve guidance for users  Develop MEPPS in parallel with PPS

 Workshop suggestions & MEPPS?  Priority of workshop suggestions?  Other comments?

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