Limits...
Phylophenetic properties of metabolic pathway topologies as revealed by global analysis.

Zhang Y, Li S, Skogerbø G, Zhang Z, Zhu X, Zhang Z, Sun S, Lu H, Shi B, Chen R - BMC Bioinformatics (2006)

Bottom Line: We reconstructed phylophenetic trees for all available metabolic pathways based on topological similarities, and compared them to the corresponding 16S rRNA-based trees.We observed that the topology of different metabolic pathways provided different phylogenetic and phenetic information, depicting the compromise between phylogenetic information and varying evolutionary pressures forming metabolic pathway topologies in different organisms.The phylogenetic information content of the comprehensive tree is substantially higher than that of any tree based on a single pathway, which also gave clues to constraints working on the topology of the global metabolic networks, information that is only partly reflected by the topologies of individual metabolic pathways.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Laboratory and National Laboratory of Bromacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. zhangyong@moon.ibp.ac.cn

ABSTRACT

Background: As phenotypic features derived from heritable characters, the topologies of metabolic pathways contain both phylogenetic and phenetic components. In the post-genomic era, it is possible to measure the "phylophenetic" contents of different pathways topologies from a global perspective.

Results: We reconstructed phylophenetic trees for all available metabolic pathways based on topological similarities, and compared them to the corresponding 16S rRNA-based trees. Similarity values for each pair of trees ranged from 0.044 to 0.297. Using the quartet method, single pathways trees were merged into a comprehensive tree containing information from a large part of the entire metabolic networks. This tree showed considerably higher similarity (0.386) to the corresponding 16S rRNA-based tree than any tree based on a single pathway, but was, on the other hand, sufficiently distinct to preserve unique phylogenetic information not reflected by the 16S rRNA tree.

Conclusion: We observed that the topology of different metabolic pathways provided different phylogenetic and phenetic information, depicting the compromise between phylogenetic information and varying evolutionary pressures forming metabolic pathway topologies in different organisms. The phylogenetic information content of the comprehensive tree is substantially higher than that of any tree based on a single pathway, which also gave clues to constraints working on the topology of the global metabolic networks, information that is only partly reflected by the topologies of individual metabolic pathways.

Show MeSH

Related in: MedlinePlus

The distribution of pathway specific organisms in different phylogenetic categories. The grid color indicates the fraction of organisms in each category containing a certain pathway. The definition of presence or absence of metabolic pathways is given in Methods.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC1483838&req=5

Figure 1: The distribution of pathway specific organisms in different phylogenetic categories. The grid color indicates the fraction of organisms in each category containing a certain pathway. The definition of presence or absence of metabolic pathways is given in Methods.

Mentions: In order to obtain an overview of the distribution of pathways relative to the phylogenetic classification of the 184 organisms studied, we produced a grid showing the fraction of organisms in each KEGG [2] category containing a given pathway, based on the definition given in Methods (Figure 1). Organisms containing any given pathway were far from equally distributed among the phylogenetic categories. Therefore, using equations 1 and 2 separately, pathway specific P-values were assigned to measure whether a pathway specific subset was enriched in or depleted of organisms from a particular category (Figure 2). For pathways found in only a small number of studied organisms, these organisms usually belonged to one or two phylogenetic categories. For example, the C21-steroid hormone pathway (map00140) was present only in three of the organisms studied, all animals (Penriched-value = 9.8 × 10-6). On the other hand, for a pathway conserved in most organisms, there were usually some phylogenetic categories in which none or only a few organisms contained the given pathway. For example, the riboflavin metabolism (map00740) was present in 126 of the 184 organisms, while only 1 of 19 archaea contained it (Pdepleted-value = 1.7 × 10-9), which is consistent with previous findings that several steps in the biosynthesis of riboflavin in archaea were absent [13]. In addition, many metabolic pathways were absent in obligate parasites like Chlamydia and Mollicutes.


Phylophenetic properties of metabolic pathway topologies as revealed by global analysis.

Zhang Y, Li S, Skogerbø G, Zhang Z, Zhu X, Zhang Z, Sun S, Lu H, Shi B, Chen R - BMC Bioinformatics (2006)

The distribution of pathway specific organisms in different phylogenetic categories. The grid color indicates the fraction of organisms in each category containing a certain pathway. The definition of presence or absence of metabolic pathways is given in Methods.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1483838&req=5

Figure 1: The distribution of pathway specific organisms in different phylogenetic categories. The grid color indicates the fraction of organisms in each category containing a certain pathway. The definition of presence or absence of metabolic pathways is given in Methods.
Mentions: In order to obtain an overview of the distribution of pathways relative to the phylogenetic classification of the 184 organisms studied, we produced a grid showing the fraction of organisms in each KEGG [2] category containing a given pathway, based on the definition given in Methods (Figure 1). Organisms containing any given pathway were far from equally distributed among the phylogenetic categories. Therefore, using equations 1 and 2 separately, pathway specific P-values were assigned to measure whether a pathway specific subset was enriched in or depleted of organisms from a particular category (Figure 2). For pathways found in only a small number of studied organisms, these organisms usually belonged to one or two phylogenetic categories. For example, the C21-steroid hormone pathway (map00140) was present only in three of the organisms studied, all animals (Penriched-value = 9.8 × 10-6). On the other hand, for a pathway conserved in most organisms, there were usually some phylogenetic categories in which none or only a few organisms contained the given pathway. For example, the riboflavin metabolism (map00740) was present in 126 of the 184 organisms, while only 1 of 19 archaea contained it (Pdepleted-value = 1.7 × 10-9), which is consistent with previous findings that several steps in the biosynthesis of riboflavin in archaea were absent [13]. In addition, many metabolic pathways were absent in obligate parasites like Chlamydia and Mollicutes.

Bottom Line: We reconstructed phylophenetic trees for all available metabolic pathways based on topological similarities, and compared them to the corresponding 16S rRNA-based trees.We observed that the topology of different metabolic pathways provided different phylogenetic and phenetic information, depicting the compromise between phylogenetic information and varying evolutionary pressures forming metabolic pathway topologies in different organisms.The phylogenetic information content of the comprehensive tree is substantially higher than that of any tree based on a single pathway, which also gave clues to constraints working on the topology of the global metabolic networks, information that is only partly reflected by the topologies of individual metabolic pathways.

View Article: PubMed Central - HTML - PubMed

Affiliation: Bioinformatics Laboratory and National Laboratory of Bromacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China. zhangyong@moon.ibp.ac.cn

ABSTRACT

Background: As phenotypic features derived from heritable characters, the topologies of metabolic pathways contain both phylogenetic and phenetic components. In the post-genomic era, it is possible to measure the "phylophenetic" contents of different pathways topologies from a global perspective.

Results: We reconstructed phylophenetic trees for all available metabolic pathways based on topological similarities, and compared them to the corresponding 16S rRNA-based trees. Similarity values for each pair of trees ranged from 0.044 to 0.297. Using the quartet method, single pathways trees were merged into a comprehensive tree containing information from a large part of the entire metabolic networks. This tree showed considerably higher similarity (0.386) to the corresponding 16S rRNA-based tree than any tree based on a single pathway, but was, on the other hand, sufficiently distinct to preserve unique phylogenetic information not reflected by the 16S rRNA tree.

Conclusion: We observed that the topology of different metabolic pathways provided different phylogenetic and phenetic information, depicting the compromise between phylogenetic information and varying evolutionary pressures forming metabolic pathway topologies in different organisms. The phylogenetic information content of the comprehensive tree is substantially higher than that of any tree based on a single pathway, which also gave clues to constraints working on the topology of the global metabolic networks, information that is only partly reflected by the topologies of individual metabolic pathways.

Show MeSH
Related in: MedlinePlus