Human liver rate-limiting enzymes influence metabolic flux via branch points and inhibitors Min Zhao Center for Bioinformatics Peking University

Outline Construction of rate-limiting enzyme database Global analysis of rate-limiting enzyme in human liver

Outline Construction of rate-limiting enzyme database Global analysis of rate-limiting enzyme in human liver

Regulation of metabolic network Living cells are self-regulating chemical engines, tuned to operate on the principle of maximum economy. —A. L. Lehninger A pathway’s activity is often controlled by its end products through feedback inhibition of regulatory enzymes located at the start of the sequence and at branch points.

Rate-limiting enzymes in TCA Krebs(1957) Pacemaker Bücher & Russmannn (1963) Rate-limiting

The properties of rate-limiting enzymes Relatively low velocities High flux-control coefficient To improve the total output of the whole pathway, just need to improve [rate-limiting enzymes] Extensively regulated Defined by function Cyclooxygenases, organisms

Construction of RLEdb

Data contents 387 rate-limiting enzymes from15688 abstracts Number of rate-limiting enzymes in database: 147 (human), 105 (rat), 96 (mouse), 16 (yeast) and 15 (E. coli) Number of transcription factors: 330 Pairs of transcription factors and rate-limiting enzymes: 478

Publication

Discover regulatory relations between rate- limiting enzymes and transcription factors

Outline Construction of rate-limiting enzyme database Global analysis of rate-limiting enzyme in human liver

Branch points >=3 >=1 consume >=1 produce X is branch point (Heijnena,2004)

Datasets and Networks 687 metabolic enzymes of human liver all 1033 products of these 687 enzymes 96 liver rate-limiting enzymes manually collected from 2682 PubMed abstracts 132 branch points curated from KEGG pathway maps 202 enzyme inhibitors collected from the BRENDA database compound conversion network from rpair inhibitory network

The 39 common compounds the 28 compounds which take part in more than 100 reactions 7 energy metabolism related nucleoside monophosphates, Nucleoside diphosphates and Nucleoside triphosphates 4 too general compounds including RNA, DNA, Protein and Peptide

How many branch points are surrounded by rate-limiting enzymes

Topological relations between rate- limiting enzymes and branch points RL_after_BPRL_before_BPSubstrate_of_RLProduct_of_RL Human Liver Centre 3467 Anabolic Catabolic Energy 1232

Rate-limiting enzymes and branch points

Compound conversion network

The role of branch points

Rate-limiting enzymes produced nearly half enzymes inhibitors According our in vivo inhibitor annotation, rate-limiting enzymes in human liver could produce nearly half enzymes inhibitors (99 versus 204)

Inhibitory network

Cross-pathway inhibitory relations

Regulability and Regulatory capacity Regulability: the activity of the regulatory enzyme with which a regulator interacts directly can be altered by the regulator. Regulatory capacity: The ability of the regulatory enzyme to transmit the changes to the rest of the system. - Flux control coeffieicent - Aldose reductase could initiate cell signaling and apoptosis of vascular endothelial cells via TNF-alpha (Ramana et al., 2004)

Summary Construction of RLEdb Rate-limiting enzymes surround 76.5% branch point compounds in total. Branch points show high degree, betweenness centrality and closeness centrality in compound conversion network. Rate-limiting enzymes produced nearly half enzymes inhibitors.

Acknowledge Prof Liping Wei Prof Louis Tao Prof Hong Qu Prof Ge Gao All CBI classmates

Thank you for your attention

Rate-limiting enzyme a relative measure of how much a perturbation affects a system variable (Kacser & Burns 1973, Heinrich & Rapoport 1974, Burns et al. 1985)Kacser & Burns 1973Heinrich & Rapoport 1974 Burns et al A variants, i pathway, vi