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

Http://rle.cbi.pku.edu.cn

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

produceX 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_BP RL_before_BP Substrate_of_RL Product_of_RL

Human Liver

49 45 78 67

Centre 3 4 6 7

Anabolic 18 19 40 35

Catabolic 14 12 26 24

Energy 1 2 3 2

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)

A variants, i pathway, vi