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Comparative analysis of the transcription-factor gene regulatory networks of E. coli and S. cerevisiae.

Guzmán-Vargas L, Santillán M - BMC Syst Biol (2008)

Bottom Line: These last results indicate that the observed differences are mostly due to the very different ratios of TF to RG counts of the E. coli and S. cerevisiae bipartite networks, rather than to their having different connectivity patterns.From the results in this paper we conclude that the most important effect such differences have had on the development of the corresponding transcription-factor gene regulatory networks is their very different ratios of TF to RG numbers.An this, to our consideration, indicates that the structure of both networks is optimal from an evolutionary viewpoint.

View Article: PubMed Central - HTML - PubMed

Affiliation: Unidad Profesional Interdisciplinaria en Ingeniería y Tecnologías Avanzadas, Instituto Politécnico Nacional, Av, IPN No, 2580, L, Ticomán, México D,F, 07340, México. lguzmanv@ipn.mx

ABSTRACT

Background: The regulatory interactions between transcription factors (TF) and regulated genes (RG) in a species genome can be lumped together in a single directed graph. The TF's and RG's conform the nodes of this graph, while links are drawn whenever a transcription factor regulates a gene's expression. Projections onto TF nodes can be constructed by linking every two nodes regulating a common gene. Similarly, projections onto RG nodes can be made by linking every two regulated genes sharing at least one common regulator. Recent studies of the connectivity pattern in the transcription-factor regulatory network of many organisms have revealed some interesting properties. However, the differences between TF and RG nodes have not been widely explored.

Results: After analysing the RG and TF projections of the transcription-factor gene regulatory networks of Escherichia coli and Saccharomyces cerevisiae, we found several common characteristic as well as some noticeable differences. To better understand these differences, we compared the properties of the E. coli and S. cerevisiae RG- and TF-projected networks with those of the corresponding projections built from randomized versions of the original bipartite networks. These last results indicate that the observed differences are mostly due to the very different ratios of TF to RG counts of the E. coli and S. cerevisiae bipartite networks, rather than to their having different connectivity patterns.

Conclusion: Since E. coli is a prokaryotic organism while S. cerevisiae is eukaryotic, there are important differences between them concerning processing of mRNA before translation, DNA packing, amount of junk DNA, and gene regulation. From the results in this paper we conclude that the most important effect such differences have had on the development of the corresponding transcription-factor gene regulatory networks is their very different ratios of TF to RG numbers. This ratio is more than three times larger in S. cerevisiae than in E. coli. Our calculations reveal that, both species' gene regulatory networks have very similar connectivity patterns, despite their very different TF to RG ratios. An this, to our consideration, indicates that the structure of both networks is optimal from an evolutionary viewpoint.

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Clustering-coefficient profiles for the TF-projected networks under directed attacks to the best connected transcription factors and regulated genes. In these panels, we show the average clustering coefficient value of TF-projected networks after attacks according to the color scheme shown in the bar. a) E. coli original network. b) S. cerevisiae original network. c) E. coli randomized network. d) S. cerevisiae randomized network. We remark the slightly slower decay of the clustering coefficient in the randomized case of E. coli TF network. For S. cerevisiae network no appreciable differences are observed between the original and randomized cases.
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Figure 6: Clustering-coefficient profiles for the TF-projected networks under directed attacks to the best connected transcription factors and regulated genes. In these panels, we show the average clustering coefficient value of TF-projected networks after attacks according to the color scheme shown in the bar. a) E. coli original network. b) S. cerevisiae original network. c) E. coli randomized network. d) S. cerevisiae randomized network. We remark the slightly slower decay of the clustering coefficient in the randomized case of E. coli TF network. For S. cerevisiae network no appreciable differences are observed between the original and randomized cases.

Mentions: In Figure 6 we illustrate the effect of directed attacks on the clustering coefficient of the TF projected networks. Observe that, for E. coli, both the original and the randomized networks exhibit a similar profile, except for a slightly slower decay of the clustering coefficient in the randomized network. On the other hand, no appreciable difference can be observed between the plots corresponding to the original and randomized networks of S. cerevisiae. Finally, when the E. coli and S. cerevisiae networks are compared, we see that the E. coli networks are more robust to attacks on the regulated genes than they are to attacks on the transcription factors, while the S. cerevisiae networks are a little less robust than those of E. coli RG attacks, but they are much more robust to TF attacks.


Comparative analysis of the transcription-factor gene regulatory networks of E. coli and S. cerevisiae.

Guzmán-Vargas L, Santillán M - BMC Syst Biol (2008)

Clustering-coefficient profiles for the TF-projected networks under directed attacks to the best connected transcription factors and regulated genes. In these panels, we show the average clustering coefficient value of TF-projected networks after attacks according to the color scheme shown in the bar. a) E. coli original network. b) S. cerevisiae original network. c) E. coli randomized network. d) S. cerevisiae randomized network. We remark the slightly slower decay of the clustering coefficient in the randomized case of E. coli TF network. For S. cerevisiae network no appreciable differences are observed between the original and randomized cases.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2268659&req=5

Figure 6: Clustering-coefficient profiles for the TF-projected networks under directed attacks to the best connected transcription factors and regulated genes. In these panels, we show the average clustering coefficient value of TF-projected networks after attacks according to the color scheme shown in the bar. a) E. coli original network. b) S. cerevisiae original network. c) E. coli randomized network. d) S. cerevisiae randomized network. We remark the slightly slower decay of the clustering coefficient in the randomized case of E. coli TF network. For S. cerevisiae network no appreciable differences are observed between the original and randomized cases.
Mentions: In Figure 6 we illustrate the effect of directed attacks on the clustering coefficient of the TF projected networks. Observe that, for E. coli, both the original and the randomized networks exhibit a similar profile, except for a slightly slower decay of the clustering coefficient in the randomized network. On the other hand, no appreciable difference can be observed between the plots corresponding to the original and randomized networks of S. cerevisiae. Finally, when the E. coli and S. cerevisiae networks are compared, we see that the E. coli networks are more robust to attacks on the regulated genes than they are to attacks on the transcription factors, while the S. cerevisiae networks are a little less robust than those of E. coli RG attacks, but they are much more robust to TF attacks.

Bottom Line: These last results indicate that the observed differences are mostly due to the very different ratios of TF to RG counts of the E. coli and S. cerevisiae bipartite networks, rather than to their having different connectivity patterns.From the results in this paper we conclude that the most important effect such differences have had on the development of the corresponding transcription-factor gene regulatory networks is their very different ratios of TF to RG numbers.An this, to our consideration, indicates that the structure of both networks is optimal from an evolutionary viewpoint.

View Article: PubMed Central - HTML - PubMed

Affiliation: Unidad Profesional Interdisciplinaria en Ingeniería y Tecnologías Avanzadas, Instituto Politécnico Nacional, Av, IPN No, 2580, L, Ticomán, México D,F, 07340, México. lguzmanv@ipn.mx

ABSTRACT

Background: The regulatory interactions between transcription factors (TF) and regulated genes (RG) in a species genome can be lumped together in a single directed graph. The TF's and RG's conform the nodes of this graph, while links are drawn whenever a transcription factor regulates a gene's expression. Projections onto TF nodes can be constructed by linking every two nodes regulating a common gene. Similarly, projections onto RG nodes can be made by linking every two regulated genes sharing at least one common regulator. Recent studies of the connectivity pattern in the transcription-factor regulatory network of many organisms have revealed some interesting properties. However, the differences between TF and RG nodes have not been widely explored.

Results: After analysing the RG and TF projections of the transcription-factor gene regulatory networks of Escherichia coli and Saccharomyces cerevisiae, we found several common characteristic as well as some noticeable differences. To better understand these differences, we compared the properties of the E. coli and S. cerevisiae RG- and TF-projected networks with those of the corresponding projections built from randomized versions of the original bipartite networks. These last results indicate that the observed differences are mostly due to the very different ratios of TF to RG counts of the E. coli and S. cerevisiae bipartite networks, rather than to their having different connectivity patterns.

Conclusion: Since E. coli is a prokaryotic organism while S. cerevisiae is eukaryotic, there are important differences between them concerning processing of mRNA before translation, DNA packing, amount of junk DNA, and gene regulation. From the results in this paper we conclude that the most important effect such differences have had on the development of the corresponding transcription-factor gene regulatory networks is their very different ratios of TF to RG numbers. This ratio is more than three times larger in S. cerevisiae than in E. coli. Our calculations reveal that, both species' gene regulatory networks have very similar connectivity patterns, despite their very different TF to RG ratios. An this, to our consideration, indicates that the structure of both networks is optimal from an evolutionary viewpoint.

Show MeSH
Related in: MedlinePlus