Abstract
In this work, the content of enzymes and DNA-binding transcription factors (TFs) in 794 non-redundant prokaryotic genomes was evaluated. The identification of enzymes was based on annotations deposited in the KEGG database as well as in databases of functional domains (COG and PFAM) and structural domains (Superfamily). For identifications of the TFs, hidden Markov profiles were constructed based on well-known transcriptional regulatory families. From these analyses, we obtained diverse and interesting results, such as the negative rate of incremental changes in the number of detected enzymes with respect to the genome size. On the contrary, for TFs the rate incremented as the complexity of genome increased. This inverse related performance shapes the diversity of metabolic and regulatory networks and impacts the availability of enzymes and TFs. Furthermore, the intersection of the derivatives between enzymes and TFs was identified at 9,659 genes, after this point, the regulatory complexity grows faster than metabolic complexity. In addition, TFs have a low number of duplications, in contrast to the apparent high number of duplications associated with enzymes. Despite the greater number of duplicated enzymes versus TFs, the increment by which duplicates appear is higher in TFs. A lower proportion of enzymes among archaeal genomes (22%) than in the bacterial ones (27%) was also found. This low proportion might be compensated by the interconnection between the metabolic pathways in Archaea. A similar proportion was also found for the archaeal TFs, for which the formation of regulatory complexes has been proposed. Finally, an enrichment of multifunctional enzymes in Bacteria, as a mechanism of ecological adaptation, was detected.
Highlights
An important clue to understanding how prokaryotes have evolved and how they exist in their modern forms can be addressed by comparing their transcriptional and enzymatic repertoires
Enzymes were selected on the basis of their E.C. numbers, PFAM, COG and Superfamily annotations in addition to the annotations deposited in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database
The analysis showed that the increment rate in the number of enzymes is negative, i.e., it diminishes with increasing genome size, and the number of acquired enzymes is always lower in large genomes than in small ones
Summary
An important clue to understanding how prokaryotes have evolved and how they exist in their modern forms can be addressed by comparing their transcriptional and enzymatic repertoires. Assessing the distribution and content of genes associated with enzymatic reactions and gene regulation in sequenced genomes, the evolution of metabolic and regulatory capabilities of prokaryotic cells can be inferred Under this perspective, in this work, an exhaustive analysis of enzymes and DNA-binding transcription factors (TFs) was conducted to evaluate their abundance and distribution across 794 non-redundant genomes from Bacteria and Archaea cellular domains. The rate of change (derivative) associated with the power-law behavior exhibits a negative trend for enzymes, while for TFs is positive These findings suggest that the number of acquired enzymes diminishes as genome size increases; on the contrary, the number of TFs acquired increases as the size of the genome increases. As the genome of an organism becomes larger, it acquires a smaller amount of new tools to perform a new metabolic task because the larger ‘‘toolbox’’
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