Identification of functional signatures in the metabolism of the three cellular domains of life

Abstract

In order to identify common and specific enzymatic activities associated with the metabolism of the three cellular domains of life, the conservation and variations between the enzyme contents of Bacteria, Archaea, and Eukarya organisms were evaluated. To this end, the content of enzymes belonging to a particular pathway and their abundance and distribution in 1507 organisms that have been annotated and deposited in the KEGG database were assessed. In addition, we evaluated the consecutive enzymatic reaction pairs obtained from metabolic pathway reactions and transformed into sequences of enzymatic reactions, with catalytic activities encoded in the Enzyme Commission numbers, which are linked by a substrate. Both analyses are complementary: the first considers individual reactions associated with each organism and metabolic map, and the second evaluates the functional associations between pairs of consecutive reactions. From these comparisons, we found a set of five enzymatic reactions that were widely distributed in all the organisms and considered here as universal to Bacteria, Archaea, and Eukarya; whereas 132 pairs out of 3151 reactions were identified as significant, only 5 of them were found to be widely distributed in all the taxonomic divisions. However, these universal reactions are not widely distributed along the metabolic maps, suggesting their dispensability to all metabolic processes. Finally, we found that universal reactions are also associated with ancestral domains, such as those related to phosphorus-containing groups with a phosphate group as acceptor or those related to the ribulose-phosphate binding barrel, triosephosphate isomerase, and D-ribose-5-phosphate isomerase (RpiA) lid domain, among others. Therefore, we consider that this analysis provides clues about the functional constraints associated with the repertoire of enzymatic functions per organism.

Fig 1. Abundance of EC numbers.

a) Archaea, b) Bacteria, and c) Eukarya. The Y-axes indicate the proportion of EC numbers per cellular domain; the X-axes indicate the EC numbers. Each data point corresponds to one EC number. The intersection with the yellow plot indicates the top of the most abundant EC numbers and their percentages. The secondary axes indicate the cumulative proportion of EC numbers. d) The Venn diagram (lower right) shows common and specific EC numbers identified in the three cellular domains.

Fig 2. Clustering of EC numbers displaying the presence of a cluster of enzymatic activities in all organisms.

A total of 195 EC numbers were grouped with an HCA using the Pearson squared correlation as the distance metric. Fifty clusters were obtained using a distance threshold of 0.668. A cluster of five EC numbers (2.7.4, 2.7.7, 2.7.1, 5.3.1, and 5.4.2) are widely distributed in 50 taxonomic divisions, with an RA of ≥ 0.95 (pink branches and highlighted in black).

Fig 3

Ancestrality and abundance of the structural domains of universal enzymatic reactions: a) 2.7.1, b) 2.7.4, c) 2.7.7, d) 5.3.1 and e) 5.4.2. The timeline assigns how ancient each structural domain present in the universal enzymatic reactions is, as suggested by Caetano-Anollés et al [19].