In Silico Evolution of Early Metabolism

Ullrich, Alexander; Rohrschneider, Markus; Scheuermann, Gerik; Stadler, Peter F.; Flamm, Christoph

doi:10.1162/artl_a_00021

Cited by 11 publications

(18 citation statements)

References 51 publications

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“…Multifunctional enzymes have been considered a mean for evolution of metabolic pathways. From multifunctional enzymes that catalyze consecutive steps, the pathways might have evolved by duplication and diversification of these precursors to form specific and efficient enzymes that catalyze only one step in the new pathway [19], [20]. Based on this approach, the number of promiscuous enzymes identified was higher, on average, in the bacterial subset (55) than in Archaea (41) (Wilcoxon test p -value = 0.0023) (Table 1).…”

Section: Resultsmentioning

confidence: 99%

Increments and Duplication Events of Enzymes and Transcription Factors Influence Metabolic and Regulatory Diversity in Prokaryotes

et al. 2013

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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.

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Section: Resultsmentioning

confidence: 99%

Increments and Duplication Events of Enzymes and Transcription Factors Influence Metabolic and Regulatory Diversity in Prokaryotes

et al. 2013

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“…Regulation in general makes sense only with specific targets. A future goal is simulation of the coevolution of protocell metabolic network and enzymes, using artificial chemistry [32], which in all likelihood will generate further insight into protocell evolution in general, including membrane-metabolism coevolution [33] that may have led from completely heterotrophic protocells [34] to cells with a rich internal metabolic network.…”

Section: Resultsmentioning

confidence: 99%

Early evolution of efficient enzymes and genome organization

2012

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BackgroundCellular life with complex metabolism probably evolved during the reign of RNA, when it served as both information carrier and enzyme. Jensen proposed that enzymes of primordial cells possessed broad specificities: they were generalist. When and under what conditions could primordial metabolism run by generalist enzymes evolve to contemporary-type metabolism run by specific enzymes?ResultsHere we show by numerical simulation of an enzyme-catalyzed reaction chain that specialist enzymes spread after the invention of the chromosome because protocells harbouring unlinked genes maintain largely non-specific enzymes to reduce their assortment load. When genes are linked on chromosomes, high enzyme specificity evolves because it increases biomass production, also by reducing taxation by side reactions.ConclusionThe constitution of the genetic system has a profound influence on the limits of metabolic efficiency. The major evolutionary transition to chromosomes is thus proven to be a prerequisite for a complex metabolism. Furthermore, the appearance of specific enzymes opens the door for the evolution of their regulation.ReviewersThis article was reviewed by Sándor Pongor, Gáspár Jékely, and Rob Knight.

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“…For this reason only small fragments of fitness landscapes have been determined experimentally [3, 9–13] and progress has been made mostly by studying adaptation in computer-generated landscapes (see e.g. [14–16]) or in simple theoretical models (see e.g. House-of-Cards [17], NK [18], Mount Fuji [19], holey landscapes [20]).…”

Section: Introductionmentioning

confidence: 99%

Beyond the Hypercube: Evolutionary Accessibility of Fitness Landscapes with Realistic Mutational Networks

2016

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Evolutionary pathways describe trajectories of biological evolution in the space of different variants of organisms (genotypes). The probability of existence and the number of evolutionary pathways that lead from a given genotype to a better-adapted genotype are important measures of accessibility of local fitness optima and the reproducibility of evolution. Both quantities have been studied in simple mathematical models where genotypes are represented as binary sequences of two types of basic units, and the network of permitted mutations between the genotypes is a hypercube graph. However, it is unclear how these results translate to the biologically relevant case in which genotypes are represented by sequences of more than two units, for example four nucleotides (DNA) or 20 amino acids (proteins), and the mutational graph is not the hypercube. Here we investigate accessibility of the best-adapted genotype in the general case of K > 2 units. Using computer generated and experimental fitness landscapes we show that accessibility of the global fitness maximum increases with K and can be much higher than for binary sequences. The increase in accessibility comes from the increase in the number of indirect trajectories exploited by evolution for higher K. As one of the consequences, the fraction of genotypes that are accessible increases by three orders of magnitude when the number of units K increases from 2 to 16 for landscapes of size N ∼ 106 genotypes. This suggests that evolution can follow many different trajectories on such landscapes and the reconstruction of evolutionary pathways from experimental data might be an extremely difficult task.

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In Silico Evolution of Early Metabolism

Cited by 11 publications

References 51 publications

Increments and Duplication Events of Enzymes and Transcription Factors Influence Metabolic and Regulatory Diversity in Prokaryotes

Increments and Duplication Events of Enzymes and Transcription Factors Influence Metabolic and Regulatory Diversity in Prokaryotes

Early evolution of efficient enzymes and genome organization

Beyond the Hypercube: Evolutionary Accessibility of Fitness Landscapes with Realistic Mutational Networks

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