28 May 2019

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

DOI : 10.1371/journal.pone.0217083

Ernesto Pérez-Rueda, PhD.

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.

Participating Center Researchers

External Researchers Participants

Ernesto Pérez-Rueda



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