The Fate of Duplicated Enzymes in Prokaryotes: The Case of Isomerases

The isomerases are a unique enzymatic class of enzymes that carry out a great diversity of chemical reactions at the intramolecular level. This class comprises about 300 members, most of which are involved in carbohydrate and terpenoid/polyketide metabolism. Along with oxidoreductases and translocas...

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Bibliographic Details
Published in:Journal of molecular evolution 2023-02, Vol.91 (1), p.76-92
Main Authors: Álvarez-Lugo, Alejandro, Becerra, Arturo
Format: Article
Language:English
Subjects:
Animal Genetics and Genomics
Archaea
Archaea - genetics
Bacteria - genetics
Biomedical and Life Sciences
Carbohydrate metabolism
Carbohydrates
Cell Biology
Changing environments
Chemical reactions
Environmental changes
Enzymes
Evolution, Molecular
Evolutionary Biology
Gene Duplication
Isomerases - genetics
Life Sciences
Metabolism
Microbiology
Original Article
Plant Genetics and Genomics
Plant Sciences
Prokaryotes
Reproduction (copying)
RNA modification
rRNA
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Summary:The isomerases are a unique enzymatic class of enzymes that carry out a great diversity of chemical reactions at the intramolecular level. This class comprises about 300 members, most of which are involved in carbohydrate and terpenoid/polyketide metabolism. Along with oxidoreductases and translocases, isomerases are one of the classes with the highest ratio of paralogous enzymes. Due to its relatively small number of members, it is plausible to explore it in greater detail to identify specific cases of gene duplication. Here, we present an analysis at the level of individual isomerases and identify different members that seem to be involved in duplication events in prokaryotes. As was suggested in a previous study, there is no homogeneous distribution of paralogs, but rather they accumulate into a few subcategories, some of which differ between Archaea and Bacteria. As expected, the metabolic processes with more paralogous isomerases have to do with carbohydrate metabolism but also with RNA modification (a particular case involving an rRNA-modifying isomerase is thoroughly discussed and analyzed in detail). Overall, our findings suggest that the most common fate for paralogous enzymes is the retention of the original enzymatic function, either associated with a dosage effect or with differential expression in response to changing environments, followed by subfunctionalization and, to a much lesser degree, neofunctionalization, which is consistent with what has been reported elsewhere.
ISSN:0022-2844
1432-1432
DOI:10.1007/s00239-022-10085-x