Article

Understanding the roadmap of metabolism by pathway analysis.

Department of Bioinformatics, Friedrich-Schiller University of Jena, Germany.
Methods in molecular biology (Clifton, N.J.) 02/2007; 358:199-226. DOI:10.1007/978-1-59745-244-1_12 pp.199-226
Source: PubMed

ABSTRACT The theoretical investigation of the structure of metabolic systems has recently attracted increasing interest. In this chapter, the basic concepts of metabolic pathway analysis are described and various applications are outlined. In particular, the concepts of nullspace and elementary flux modes are explained. The presentation is illustrated by a simple example from tyrosine metabolism and a system describing lysine production in Corynebacterium glutamicum. The latter system gives rise to 37 elementary modes, 36 of which produce lysine with different molar yields. The examples illustrate that metabolic pathway analysis is a useful tool for better understanding the complex architecture of intracellular metabolism, for determining the pathways on which the molar conversion yield of a substrate-product pair under study is maximal, and for assigning functions to orphan genes (functional genomics). Moreover, problems emerging in the modeling of large networks are discussed. An outlook on current trends in the field concludes the chapter.

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Keywords

37 elementary modes
 
assigning functions
 
complex architecture
 
different molar yields
 
elementary flux modes
 
functional genomics
 
intracellular metabolism
 
lysine production
 
metabolic pathway analysis
 
molar conversion yield
 
nullspace
 
orphan genes
 
pathways
 
problems
 
produce lysine
 
simple example
 
substrate-product pair
 
theoretical investigation
 
tyrosine metabolism
 
useful tool