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Describing the structural robustness landscape of bacterial small RNAs.

Rodrigo G, Fares MA - BMC Evol. Biol. (2012)

Bottom Line: We found that bacterial sncRNAs are not significantly robust to both mutational and environmental perturbations when compared against artificial, unbiased sequences.We further found that, on average, epistasis in bacterial sncRNAs is significantly antagonistic, and positively correlates with plasticity.As a result, plasticity emerges to link robustness, functionality and evolvability.

View Article: PubMed Central - HTML - PubMed

Affiliation: Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain. guirodta@ibmcp.upv.es

ABSTRACT

Background: The potential role of RNA molecules as gene expression regulators has led to a new perspective on the intracellular control and genome organization. Because secondary structures are crucial for their regulatory role, we sought to investigate their robustness to mutations and environmental changes.

Results: Here, we dissected the structural robustness landscape of the small non-coding RNAs (sncRNAs) encoded in the genome of the bacterium Escherichia coli. We found that bacterial sncRNAs are not significantly robust to both mutational and environmental perturbations when compared against artificial, unbiased sequences. However, we found that, on average, bacterial sncRNAs tend to be significantly plastic, and that mutational and environmental robustness strongly correlate. We further found that, on average, epistasis in bacterial sncRNAs is significantly antagonistic, and positively correlates with plasticity. Moreover, the evolution of robustness is likely dependent upon the environmental stability of the cell, with more fluctuating environments leading to the emergence and fixation of more robust molecules. Mutational robustness also appears to be correlated with structural functionality and complexity.

Conclusion: Our study provides a deep characterization of the structural robustness landscape of bacterial sncRNAs, suggesting that evolvability could be evolved as a consequence of selection for more plastic molecules. It also supports that environmental fluctuations could promote mutational robustness. As a result, plasticity emerges to link robustness, functionality and evolvability.

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Congruent evolution of mutational and environmental robustness. Computation of mutational and environmental robustness (Rm and Re) during a neutral evolution (acceptance of mutations that do not change the structure) of a MicA-like sncRNA (scatter plot in the inset). These two trajectories show a pattern of congruent evolution. One iteration corresponds to 100 mutations (order O(L)).
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Figure 4: Congruent evolution of mutational and environmental robustness. Computation of mutational and environmental robustness (Rm and Re) during a neutral evolution (acceptance of mutations that do not change the structure) of a MicA-like sncRNA (scatter plot in the inset). These two trajectories show a pattern of congruent evolution. One iteration corresponds to 100 mutations (order O(L)).

Mentions: Based on our previous results, we sought to investigate whether mutational robustness correlates with our definition of environmental robustness, provided that the relationship between Rm and 1-P has been already described [27]. We selected micA as a case study, although similar results could be derived with other sncRNAs, and we performed a neutral evolution process (accounting for potential compensatory mutations as described above to enlarge the sequence space). We found a significant correlation between the two types of robustness (Figure 4), although some punctual mutations can entail an opposite effect on these variables (Figure S5). By large, a sequence that evolves to increase its environmental robustness also increases its mutational robustness and vice versa. This reflects a clear dependency of these two magnitudes. Energetic parameters handle the structural robustness in both cases, but while environmental robustness is a global outcome, mutational robustness is local.


Describing the structural robustness landscape of bacterial small RNAs.

Rodrigo G, Fares MA - BMC Evol. Biol. (2012)

Congruent evolution of mutational and environmental robustness. Computation of mutational and environmental robustness (Rm and Re) during a neutral evolution (acceptance of mutations that do not change the structure) of a MicA-like sncRNA (scatter plot in the inset). These two trajectories show a pattern of congruent evolution. One iteration corresponds to 100 mutations (order O(L)).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368786&req=5

Figure 4: Congruent evolution of mutational and environmental robustness. Computation of mutational and environmental robustness (Rm and Re) during a neutral evolution (acceptance of mutations that do not change the structure) of a MicA-like sncRNA (scatter plot in the inset). These two trajectories show a pattern of congruent evolution. One iteration corresponds to 100 mutations (order O(L)).
Mentions: Based on our previous results, we sought to investigate whether mutational robustness correlates with our definition of environmental robustness, provided that the relationship between Rm and 1-P has been already described [27]. We selected micA as a case study, although similar results could be derived with other sncRNAs, and we performed a neutral evolution process (accounting for potential compensatory mutations as described above to enlarge the sequence space). We found a significant correlation between the two types of robustness (Figure 4), although some punctual mutations can entail an opposite effect on these variables (Figure S5). By large, a sequence that evolves to increase its environmental robustness also increases its mutational robustness and vice versa. This reflects a clear dependency of these two magnitudes. Energetic parameters handle the structural robustness in both cases, but while environmental robustness is a global outcome, mutational robustness is local.

Bottom Line: We found that bacterial sncRNAs are not significantly robust to both mutational and environmental perturbations when compared against artificial, unbiased sequences.We further found that, on average, epistasis in bacterial sncRNAs is significantly antagonistic, and positively correlates with plasticity.As a result, plasticity emerges to link robustness, functionality and evolvability.

View Article: PubMed Central - HTML - PubMed

Affiliation: Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Ingeniero Fausto Elio s/n, 46022 Valencia, Spain. guirodta@ibmcp.upv.es

ABSTRACT

Background: The potential role of RNA molecules as gene expression regulators has led to a new perspective on the intracellular control and genome organization. Because secondary structures are crucial for their regulatory role, we sought to investigate their robustness to mutations and environmental changes.

Results: Here, we dissected the structural robustness landscape of the small non-coding RNAs (sncRNAs) encoded in the genome of the bacterium Escherichia coli. We found that bacterial sncRNAs are not significantly robust to both mutational and environmental perturbations when compared against artificial, unbiased sequences. However, we found that, on average, bacterial sncRNAs tend to be significantly plastic, and that mutational and environmental robustness strongly correlate. We further found that, on average, epistasis in bacterial sncRNAs is significantly antagonistic, and positively correlates with plasticity. Moreover, the evolution of robustness is likely dependent upon the environmental stability of the cell, with more fluctuating environments leading to the emergence and fixation of more robust molecules. Mutational robustness also appears to be correlated with structural functionality and complexity.

Conclusion: Our study provides a deep characterization of the structural robustness landscape of bacterial sncRNAs, suggesting that evolvability could be evolved as a consequence of selection for more plastic molecules. It also supports that environmental fluctuations could promote mutational robustness. As a result, plasticity emerges to link robustness, functionality and evolvability.

Show MeSH
Related in: MedlinePlus