M. pneumoniae의 유전체 서열로부터 대사회로 구성 및 분석

화학공학의 이론과 응용 제8권 제1호 2002년

화학공학의 이론과 응용 제8권 제1호 2002년

Theories and Applications of Chem. Eng., 2002, Vol. 8, No. 1

김진식, 이상엽

한국과학기술원 생명화학공학과

In silico construction and analysis of metabolic pathways

from the complete genome sequence of  M. pneumoniae

Jin Sik Kim, Sang Yup Lee

Department of Chemical and Biomolecular Engineering

Korea Advanced Institute of Science and Technology

서론

Completion of genome projects gives us a lot of information to deal with and analyze. From the genomic sequence data, cellular information can be obtained. The complexity of cellular processes can be analyzed not only by the individual components but also by the systematic approaches. However in general, these approaches are limited by the lack of kinetic information on the metabolism. Systematic method can be accomplished by step-by-step approach to resolve and verify the uncertainties of the metabolic model (Edwards and Palsson [2], Schilling et al. [6], Schilling and Palsson [7]).

Figure 1. Schematic Diagram of the method for the construction of metabolic pathways

Mycoplasma pneumoniae is a pathogen causing atypical pneumonia in human beings, and pathogenicity related studies have been extensively carried out (Himmelreich et al. [3]). Basic studies of M. pneumoniae were hampered by the difficulties in cell culture and genetic manipulation. Therefore, in silico metabolic modeling can give clues to the metabolism and physiology of this strain. In this study, we analyzed the genome sequence of M. pneumoniae and developed a static metabolic model.

이론 및 방법

Complete genome sequence was obtained from sequence databases such as GenBank. Protein coding regions were searched using gene identification tools. This microorganism has a genome size of about 816 Kbp and has less than 700 ORFs. The functions of ORFs were predicted by comparing the DNA or protein sequences to non-redundant sequence databases. Similarity searches using BLAST (Altschul et al. [1]) gave several possible functional candidates for each ORFs.

Figure 2. List of 21 reactions catalyzed by the gene products.

The methods for the construction of metabolic network were summarized in Figure 1. In this model, a graph concept was applied to generate the network. Vertices denoted for the substrates and products of the reactions and edges for the relationships of the vertices. Connectors represent the enzymes involved in the reactions.

결과 및 토론

The enzymatic reactions with stoichiometric coefficients were collected from the metabolic databases (Ogata et al. [4]). The reactions were categorized into groups by functions. Reactions in the functional group were synthesized into local metabolic network. Starting from a selected reaction, all reactions were added to the local network. Reactions, which did not have any relations with other reactions, were remained alone.

As a result of annotation procedure, 84 reactions catalyzed by the gene products (proteins) were obtained (Figure 2). Each reaction was obtained from the database search. The abbreviation of metabolites were based on the short names described in the stoichiometric model of E. coli (Parmanik et al. [5]). These reactions were classified into five groups regarding to the functional categories including energy metabolism, glycerolipid metabolism and nucleotide metabolism.

The model shows that M. pneumoniae does not have many components involved in energy

generation and biosynthesis compared with other microorganisms and this is consistent with previous study (Himmelreich et al. [3]).

Some portion of the constructed metabolic pathway was shown in Figure 3. In this pathways, black characters (vertices) and arrows (directional edges) show the result of network construction. Red characters and arrows mean the absence of the components in the model for M. pneumoniae. These absent components mean they exist in other microorganisms. In our case, the number and size of functional group was relatively small and the complexity of connections between groups was not so high.

Figure 3. A portion of constructed metabolic pathways. Red characters and arrows show the missing components.

For the synthesis of metabolic networks using a graph, a large number of possible candidates can be generated as the number of vertices and edges increase. For the selection of correct model, full characterization of the behavior of the microorganism performs important role. We still get close to various approaches for revealing the uncertainties in the cellular metabolism. And these methods can be more powerful to understand the cell.

결론

Complete genome sequence of M. pneumoniae was analyzed and 84 reaction equations were obtained from the result of annotation and organization. The metabolic capabilities of microorganisms are variable according to the residential environments and species-related characteristics. Analysis of the entire metabolic network enables to find the characteristics and usefulness of the microorganism.

감사 (Acknowledgement)

This work was supported by the National Research Laboratory Program (2000-N-NL-01-C-237) of the Korean Ministry of Science and Technology (MOST).

화학공학의 이론과 응용 제8권 제1호 2002년

참고문헌

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[7] Schilling, C. H., Palsson, B. O. : J. theor. Biol., 203, 249-283 (2000).