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The hidden universal distribution of amino acid biosynthetic networks: a genomic perspective on their origins and evolution.

Hernández-Montes G, Díaz-Mejía JJ, Pérez-Rueda E, Segovia L - Genome Biol. (2008)

Bottom Line: We suggest that the origin of alternative branches is closely related to different environmental metabolite sources and life-styles among species.The multi-organismal seed strategy employed in this work improves the precision of dating and determining evolutionary relationships among amino acid biosynthetic branches.Additionally, we introduce the concept of 'alternolog', which not only plays an important role in the relationships between structure and function in biological networks, but also, as shown here, has strong implications for their evolution, almost equal to paralogy and analogy.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av, Universidad, Col, Chamilpa, Cuernavaca, Morelos, México.

ABSTRACT

Background: Twenty amino acids comprise the universal building blocks of proteins. However, their biosynthetic routes do not appear to be universal from an Escherichia coli-centric perspective. Nevertheless, it is necessary to understand their origin and evolution in a global context, that is, to include more 'model' species and alternative routes in order to do so. We use a comparative genomics approach to assess the origins and evolution of alternative amino acid biosynthetic network branches.

Results: By tracking the taxonomic distribution of amino acid biosynthetic enzymes, we predicted a core of widely distributed network branches biosynthesizing at least 16 out of the 20 standard amino acids, suggesting that this core occurred in ancient cells, before the separation of the three cellular domains of life. Additionally, we detail the distribution of two types of alternative branches to this core: analogs, enzymes that catalyze the same reaction (using the same metabolites) and belong to different superfamilies; and 'alternologs', herein defined as branches that, proceeding via different metabolites, converge to the same end product. We suggest that the origin of alternative branches is closely related to different environmental metabolite sources and life-styles among species.

Conclusion: The multi-organismal seed strategy employed in this work improves the precision of dating and determining evolutionary relationships among amino acid biosynthetic branches. This strategy could be extended to diverse metabolic routes and even other biological processes. Additionally, we introduce the concept of 'alternolog', which not only plays an important role in the relationships between structure and function in biological networks, but also, as shown here, has strong implications for their evolution, almost equal to paralogy and analogy.

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Average taxonomic distribution of amino acid biosynthetic enzymes partially distributed across the three domains of life. TDs for enzymes with an average normalized distribution <50% (see Materials and methods). Labels and colors are as in Figure 2.
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Figure 4: Average taxonomic distribution of amino acid biosynthetic enzymes partially distributed across the three domains of life. TDs for enzymes with an average normalized distribution <50% (see Materials and methods). Labels and colors are as in Figure 2.

Mentions: The biosynthesis of L-methionine can be carried out by at least three different superpathways (Figure 1). One involves the degradation of cystathionine via homocysteine using either cystathionine β-synthase (EC:4.2.1.22) or cystathionine β-lyase (EC:4.4.1.8), followed by methionine synthase (EC:2.1.1.13). These three enzymes are widely distributed across the three domains (Figure 4) and, hence, this branch could occur in the LCA. Alternatively, the second superpathway, also called the L-methionine salvage cycle, which begins with EC:4.4.1.14 via S-adenosyl-L-methionine and finishes in L-methionine using EC:2.6.1.5 via 2-oxo-4-methylthiobutanoate (Figure 1), is widely distributed in Eukarya but almost absent in Archaea and Bacteria. An exception to this distribution is the step from L-methionine to S-adenosyl-L-methionine, which can be catalyzed by one of two analog methionine adenosyltransferases (EC:2.5.1.6). These analogs show an almost perfect anti-correlation in their TDs (Figure 4); one is restricted to Archaea, while the other occurs in Bacteria and Eukarya. Complementarily, a third superpathway, characterized in plants as the so-called S-adenosyl-L-methionine cycle, converts S-adenosyl-L-methionine to L-methionine via S-adenosyl-L-homocysteine (Figure 1). We found that one of this cycle's enzymes, S-adenosylhomocysteine hydrolase (EC:3.3.1.1), is widely distributed across the three domains. In summary, we suggest that the LCA was able to produce L-methionine, degrading cysthationine via homocysteine.


The hidden universal distribution of amino acid biosynthetic networks: a genomic perspective on their origins and evolution.

Hernández-Montes G, Díaz-Mejía JJ, Pérez-Rueda E, Segovia L - Genome Biol. (2008)

Average taxonomic distribution of amino acid biosynthetic enzymes partially distributed across the three domains of life. TDs for enzymes with an average normalized distribution <50% (see Materials and methods). Labels and colors are as in Figure 2.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2481427&req=5

Figure 4: Average taxonomic distribution of amino acid biosynthetic enzymes partially distributed across the three domains of life. TDs for enzymes with an average normalized distribution <50% (see Materials and methods). Labels and colors are as in Figure 2.
Mentions: The biosynthesis of L-methionine can be carried out by at least three different superpathways (Figure 1). One involves the degradation of cystathionine via homocysteine using either cystathionine β-synthase (EC:4.2.1.22) or cystathionine β-lyase (EC:4.4.1.8), followed by methionine synthase (EC:2.1.1.13). These three enzymes are widely distributed across the three domains (Figure 4) and, hence, this branch could occur in the LCA. Alternatively, the second superpathway, also called the L-methionine salvage cycle, which begins with EC:4.4.1.14 via S-adenosyl-L-methionine and finishes in L-methionine using EC:2.6.1.5 via 2-oxo-4-methylthiobutanoate (Figure 1), is widely distributed in Eukarya but almost absent in Archaea and Bacteria. An exception to this distribution is the step from L-methionine to S-adenosyl-L-methionine, which can be catalyzed by one of two analog methionine adenosyltransferases (EC:2.5.1.6). These analogs show an almost perfect anti-correlation in their TDs (Figure 4); one is restricted to Archaea, while the other occurs in Bacteria and Eukarya. Complementarily, a third superpathway, characterized in plants as the so-called S-adenosyl-L-methionine cycle, converts S-adenosyl-L-methionine to L-methionine via S-adenosyl-L-homocysteine (Figure 1). We found that one of this cycle's enzymes, S-adenosylhomocysteine hydrolase (EC:3.3.1.1), is widely distributed across the three domains. In summary, we suggest that the LCA was able to produce L-methionine, degrading cysthationine via homocysteine.

Bottom Line: We suggest that the origin of alternative branches is closely related to different environmental metabolite sources and life-styles among species.The multi-organismal seed strategy employed in this work improves the precision of dating and determining evolutionary relationships among amino acid biosynthetic branches.Additionally, we introduce the concept of 'alternolog', which not only plays an important role in the relationships between structure and function in biological networks, but also, as shown here, has strong implications for their evolution, almost equal to paralogy and analogy.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av, Universidad, Col, Chamilpa, Cuernavaca, Morelos, México.

ABSTRACT

Background: Twenty amino acids comprise the universal building blocks of proteins. However, their biosynthetic routes do not appear to be universal from an Escherichia coli-centric perspective. Nevertheless, it is necessary to understand their origin and evolution in a global context, that is, to include more 'model' species and alternative routes in order to do so. We use a comparative genomics approach to assess the origins and evolution of alternative amino acid biosynthetic network branches.

Results: By tracking the taxonomic distribution of amino acid biosynthetic enzymes, we predicted a core of widely distributed network branches biosynthesizing at least 16 out of the 20 standard amino acids, suggesting that this core occurred in ancient cells, before the separation of the three cellular domains of life. Additionally, we detail the distribution of two types of alternative branches to this core: analogs, enzymes that catalyze the same reaction (using the same metabolites) and belong to different superfamilies; and 'alternologs', herein defined as branches that, proceeding via different metabolites, converge to the same end product. We suggest that the origin of alternative branches is closely related to different environmental metabolite sources and life-styles among species.

Conclusion: The multi-organismal seed strategy employed in this work improves the precision of dating and determining evolutionary relationships among amino acid biosynthetic branches. This strategy could be extended to diverse metabolic routes and even other biological processes. Additionally, we introduce the concept of 'alternolog', which not only plays an important role in the relationships between structure and function in biological networks, but also, as shown here, has strong implications for their evolution, almost equal to paralogy and analogy.

Show MeSH
Related in: MedlinePlus