2005年度　森基金成果報告書

研究課題名

「Genetic Interaction データを用いた生体内ネットワーク予測」

藤本　顕士

慶応義塾大学　政策・メディア研究科　修士１年　

慶應義塾大学先端生命科学研究所　　　　　　　　　　　

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Abstract

Large-scale interpretation of genetic interaction networks has begun to reveal the global organization of Saccharomyces cerevisiae. Recently developed biological experiment methods bring us to amount of interaction data, but biological process networks remains obscure. In this research, I detect two types of cis-network motifs in Saccharomyces cerevisiae gene networks from genetic interaction data and functional-linkages obtained from phylogenetic profiling to focus attention on essential gene and showed two different reason of why essential genes are essential.

Keyword: phylogenetic profiling, network, genetic interaction, Saccharomyces cerevisiae

Introduction

One of the most valuable biological challenges is to interpret post-genomic networks through recent high-throughput approaches and Saccharomyces cerevisiae is appropriate model organism to observe post-genomic networks. The observation that only ~18% of the genes in Saccharomyces cerevisiae are essential for viability especially illustrates the capacity of genetic networks to buffer against genetic perturbation (Giaever, 2002). Direct physical interactions among yeast proteins are being mapped by systematic two-hybrid and mass spectrometric characterization of protein complexes (Ito et al., 2001; Uetz et al., 2000; Gavin et al., 2002;Ho et al., 2002). Recently developed methods for the comprehensive identification of synthetic lethal interactions in Saccharomyces cerevisiae, such as synthetic genetic arrays (SGA) and synthetic lethal analysis by microarrays (SLAM) enables large-scale mapping of genetic interactions (Tong et al., 2001; Ooi et al., 2003; Tong et al., 2004). Synthetic lethality is an extreme case in which two single mutations that cause no evident phenotype individually are lethal in combination. Nature of genetic interaction, it can be a powerful and widespread tool for establishing functional linkages between genes (Zhang et al., 2005; Kelly and Ideker, 2005). And the phylogenetic profiling of protein in multiple genomes is another high-throughput method for establishing functional-linkages (Pellegrini et al., 1999).

In this work, I describe biological process networks discovered from a Saccharomyces cerevisiae network by using functional-linkages between genes predicted from the phylogenetic profiling of protein in multiple genomes and tried to detect two types of root cis-network motif in recognizing the essential genes.

Materials and Methods

Data sources

9226 known physical interaction data and 6389 genetic interaction data were obtained from Munich Information Center for Protein Sequences (MIPS) (Mewes et al., 2002; Mewes et al., 2004).

All of gene information about functions and viability were obtained from the Yeast Protein Database (YPD)(Hodges et al., 1998).

The protein-coding sequences of complete genomes were obtained from the NCBI FTP server.

Phylogenetic profiling

Phylogenetic profiles for the 6326 proteins encoded by the genome of Saccharomyces cerevisiae were computed by aligning each protein sequence using BLAST search with the proteins from 99 other fully sequenced genomes. Phylogenetic profiles were evaluated as if each pair-wised genes coefficient of profiles correlation shows over 0.7, paired genes were considered as it had functional linkage.

Cis-network motif

Cis-network motifs were divided by meaning of role of essential gene into two types. Type I motif had at least two essential gene and two nonessential genes. Nonessential genes had synthetic lethality and had functional linkages between one side of essential genes. Essential genes were also had functional linkages (Figure 1A).

Type II motif had at least one essential gene and four nonessential genes. Essential gene had an even number of functional linkages to nonessential genes and pair of nonessential genes which had functional linkages to essential gene also had synthetic lethality (Figure 1B).

A

B

Figure 1, root motif of cis-network

Results

Functional-linkage networks were predicted including 13998 functional linkages as edges and 1532 genes in Saccharomyces cerevisiae as nodes. This functional linkage networks resembles the nonessential genetic networks in that it has a scale-free topology and most of the interactions were nonoverlapping with protein-protein interaction (Figure 2).

Figure 2, Predicted functional linkage networks

4360 motifs of type I network (eg. MYO2-TPM1, MYO2-NUM1, MYO2-USO1 as functional linkage ; TP1-NUM1as genetic interaction; Figure 3A) and 3 motifs of type II network (eg. HSP60-CCT2, HSP60-CCT4, HSP60-EFT1, HSP60-EFT2 as functional linkage; CCT2-CCT4, EFT1-EFT2 as genetic interaction, Figure 3B, GCD11-RPT4, GCD11-RPT6, GCD11-DBP7, GCD11-DBP6, GCD11-RFC2, GCD11-RFC5 as functional linkage; RPT4-RPT6, DBP6-DBP7, RFC2-RFC5 as genetic interaction, Figure 4) were detected. Each network node was annotated by use of YPD data (Table 1A, Table 1B, Table 2).

A

B

Figure 3, network motif in Saccharomyces cerevisiae

B

A

Table 1, gene function

Figure 4, rare network motif in Saccharomyces cerevisiae

Table 2, gene function for GCD11 network

Discussions

Phylogenetic profiling and genetic interaction is definitely powerful tool to predict biological process networks. In the biological process networks predicted by phylogenetic profiing, essential genes have a important role to maintain networks. Genetic interaction that it represents synthetic lethality is helpful to interpret post-genomic networks. In this work, root of cis-network motifs is detected such as type I and type II motifs. Type I networks like MYO2 network (Figure 3A) is found in large numbers. The feature of type I network is considered that essential gene mediates alternative pathway and functional linkage between essential gene and another is thought to be important in this network motif. For example, TPM1 and NUM1 has genetic interaction and also has same function like Cell_polarity (Table 1A), MYO2 which is essential for cell has functional linkage to TPM1 and MUM1, also has the same function. It shows that MYO2 play a critical role and edge between MYO2 and USO1 may converge to these pathways. Central essential gene of type I have hub role in the network, and large number of existence of type I network in functional linkage networks means that there is a tendency that essential gene have hub function like protein-protein interaction networks.

Type II network like HSP60 networks (Figure 3B) mean bottleneck of biological process networks. CCT2 to CCT4 thorough HSP60 pathway and EFT1 to EFT2 thorough HSP60 pathway is different biological process (Table 1B). This types of network can detect few, this result represent that type II motif is rare because overconcentration of biological process at one gene is too risky for the cell to survive. But undue concentration of biological process network is exists like GCD11 motif (Figure 4). GCD11 networks have several important roles (Table 2), so some sort of biological mechanism for protection of GCD11 may exist.

In this study, we found cis-network motif in Saccharomyces cerevisiae and interpret implication of two types of essential genes.

Acknowledgement

I would like to thank Dr. Rintaro Saito for insightful suggestions and comments. I also thank Noriyuki Kitagawa for significant discussion. I gratitude for Prof. Masaru Tomita gives me the opportunity of this research.
References

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Recent Presentation

• Annual Meeting of Molecular Biology Society Japan

　December 7-10, 2005. Fukuoka, Japan

Prediction of biological process networks in Saccharomyces cerevisiae using phylogenetic profiling and genetic interaction data

Kenji Fujimoto1,2, Rintaro Saito1, Masaru Tomita1 （1Inst. Adv. Biosci., Keio Univ., 2Bioinfo. Prog. Grad.　Sch. Media & Governance, Keio Univ.）