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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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Representation of the S. cerevisiae transcriptional regulatory network. a) Representation of the transcription-factor gene regulatory network of S. cerevisiae. Green circles represent transcription factors, brown circles denote regulated genes, and those with both functions are coloured in red. We also show the network projections onto b) transcription factors and onto c) regulated genes.
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Figure 2: Representation of the S. cerevisiae transcriptional regulatory network. a) Representation of the transcription-factor gene regulatory network of S. cerevisiae. Green circles represent transcription factors, brown circles denote regulated genes, and those with both functions are coloured in red. We also show the network projections onto b) transcription factors and onto c) regulated genes.

Mentions: The E. coli and S. cerevisiae gene regulatory networks are bipartite; i.e. they comprise two kinds of nodes, transcription factors (TF) and regulated genes (RG), with the links being directed from the TF to the RG nodes. Bipartite gene regulatory networks can be projected onto either networks comprising only transcription factors or networks comprising only regulated genes. The projections onto transcription factors are constructed by linking every two nodes regulating a common gene; similarly, the projections onto regulated genes are built by linking every two regulated genes sharing a common regulator. The E. coli and S. cerevisiae original (non-randomized) bipartite and projected networks are respectively pictured in Figures 1 and 2.


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

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

Representation of the S. cerevisiae transcriptional regulatory network. a) Representation of the transcription-factor gene regulatory network of S. cerevisiae. Green circles represent transcription factors, brown circles denote regulated genes, and those with both functions are coloured in red. We also show the network projections onto b) transcription factors and onto c) regulated genes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Representation of the S. cerevisiae transcriptional regulatory network. a) Representation of the transcription-factor gene regulatory network of S. cerevisiae. Green circles represent transcription factors, brown circles denote regulated genes, and those with both functions are coloured in red. We also show the network projections onto b) transcription factors and onto c) regulated genes.
Mentions: The E. coli and S. cerevisiae gene regulatory networks are bipartite; i.e. they comprise two kinds of nodes, transcription factors (TF) and regulated genes (RG), with the links being directed from the TF to the RG nodes. Bipartite gene regulatory networks can be projected onto either networks comprising only transcription factors or networks comprising only regulated genes. The projections onto transcription factors are constructed by linking every two nodes regulating a common gene; similarly, the projections onto regulated genes are built by linking every two regulated genes sharing a common regulator. The E. coli and S. cerevisiae original (non-randomized) bipartite and projected networks are respectively pictured in Figures 1 and 2.

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