Limits...
Empirical demonstration of environmental sensing in catalytic RNA: evolution of interpretive behavior at the origins of life.

Lehman N, Bernhard T, Larson BC, Robinson AJ, Southgate CC - BMC Evol. Biol. (2014)

Bottom Line: Yet a variant of this sequence containing five mutations that alter its ability to utilize the Ca(2+) ion engenders a strong interpretive characteristic in this RNA.We have shown that RNA molecules in a test tube can meet the minimum criteria for the evolution of interpretive behaviour in regards to their responses to divalent metal ion concentrations in their environment.Interpretation in RNA molecules provides a property entirely dependent on natural physico-chemical interactions, but capable of shaping the evolutionary trajectory of macromolecules, especially in the earliest stages of life's history.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Portland State University, Portland, OR, USA. niles@pdx.edu.

ABSTRACT

Background: The origins of life on the Earth required chemical entities to interact with their environments in ways that could respond to natural selection. The concept of interpretation, where biotic entities use signs in their environment as proxy for the existence of other items of selective value in their environment, has been proposed on theoretical grounds to be relevant to the origins and early evolution of life. However this concept has not been demonstrated empirically.

Results: Here, we present data that certain catalytic RNA sequences have properties that would enable interpretation of divalent cation levels in their environment. By assaying the responsiveness of two variants of the Tetrahymena ribozyme to the Ca(2+) ion as a sign for the more catalytically useful Mg(2+) ion, we show an empirical proof-of-principle that interpretation can be an evolvable trait in RNA, often suggested as a model system for early life. In particular we demonstrate that in vitro, the wild-type version of the Tetrahymena ribozyme is not interpretive, in that it cannot use Ca(2+) as a sign for Mg(2+). Yet a variant of this sequence containing five mutations that alter its ability to utilize the Ca(2+) ion engenders a strong interpretive characteristic in this RNA.

Conclusions: We have shown that RNA molecules in a test tube can meet the minimum criteria for the evolution of interpretive behaviour in regards to their responses to divalent metal ion concentrations in their environment. Interpretation in RNA molecules provides a property entirely dependent on natural physico-chemical interactions, but capable of shaping the evolutionary trajectory of macromolecules, especially in the earliest stages of life's history.

Show MeSH

Related in: MedlinePlus

Assays of the ribozymes in various divalent ion concentrations. (A) Preliminary pick-up-the-tail assays were performed with 2.5-fold substrate excess as described in the text for activity after 60 minutes at 37°C. (Note: the original selection of the PV ribozyme [12] was performed at 3.25 h, at which time the PV activity surpasses that of the CG activity). The fraction of the initial amount of ribozyme RNA that reacted under conditions of 2.5-fold excess substrate was measured for each variant in the absence (green lines) or presence (red lines) of 10 mM CaCl2 under concentrations of MgCl2 ranging from 0.5–25 mM. Above 5 mM no increase in activity was observed. In the absence of a CaCl2 a slight inhibition of activity with increasing MgCl2 was observed above 0.1 mM, as noted before [8]. From these data, the conditions for formal analysis of interpretive behaviour were chosen near the endpoints of these curves: at, and well above, the point of maximum separation (0.5 mM MgCl2, indicated with the dashed black line). These conditions were 25 mM MgCl2 + 10 mM CaCl2 (O1), 0.5 mM MgCl2 + 10 mM CaCl2 (O2), 25 mM MgCl2 (O3), and 0.5 mM MgCl2 (O4). (B) Example gels of ribozyme reacted for 0–60 min with 2.5-fold excess S-1t substrate at 37°C (lower band: unreacted ribozyme; upper band: ribozyme reacted with S-1t substrate). Summarized data from all assays is shown in Table 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
getmorefigures.php?uid=PMC4260251&req=5

Fig3: Assays of the ribozymes in various divalent ion concentrations. (A) Preliminary pick-up-the-tail assays were performed with 2.5-fold substrate excess as described in the text for activity after 60 minutes at 37°C. (Note: the original selection of the PV ribozyme [12] was performed at 3.25 h, at which time the PV activity surpasses that of the CG activity). The fraction of the initial amount of ribozyme RNA that reacted under conditions of 2.5-fold excess substrate was measured for each variant in the absence (green lines) or presence (red lines) of 10 mM CaCl2 under concentrations of MgCl2 ranging from 0.5–25 mM. Above 5 mM no increase in activity was observed. In the absence of a CaCl2 a slight inhibition of activity with increasing MgCl2 was observed above 0.1 mM, as noted before [8]. From these data, the conditions for formal analysis of interpretive behaviour were chosen near the endpoints of these curves: at, and well above, the point of maximum separation (0.5 mM MgCl2, indicated with the dashed black line). These conditions were 25 mM MgCl2 + 10 mM CaCl2 (O1), 0.5 mM MgCl2 + 10 mM CaCl2 (O2), 25 mM MgCl2 (O3), and 0.5 mM MgCl2 (O4). (B) Example gels of ribozyme reacted for 0–60 min with 2.5-fold excess S-1t substrate at 37°C (lower band: unreacted ribozyme; upper band: ribozyme reacted with S-1t substrate). Summarized data from all assays is shown in Table 1.

Mentions: Example payoff matrix for interpretive behaviour. Payoff values O1–O4 are evaluated for each pair-wise combination of environmental conditions and genotype traits as discussed in the text. The ion concentrations refer to those used in the assays of the Tetrahymena ribozyme, as described in Figures 2, 3 and 4.


Empirical demonstration of environmental sensing in catalytic RNA: evolution of interpretive behavior at the origins of life.

Lehman N, Bernhard T, Larson BC, Robinson AJ, Southgate CC - BMC Evol. Biol. (2014)

Assays of the ribozymes in various divalent ion concentrations. (A) Preliminary pick-up-the-tail assays were performed with 2.5-fold substrate excess as described in the text for activity after 60 minutes at 37°C. (Note: the original selection of the PV ribozyme [12] was performed at 3.25 h, at which time the PV activity surpasses that of the CG activity). The fraction of the initial amount of ribozyme RNA that reacted under conditions of 2.5-fold excess substrate was measured for each variant in the absence (green lines) or presence (red lines) of 10 mM CaCl2 under concentrations of MgCl2 ranging from 0.5–25 mM. Above 5 mM no increase in activity was observed. In the absence of a CaCl2 a slight inhibition of activity with increasing MgCl2 was observed above 0.1 mM, as noted before [8]. From these data, the conditions for formal analysis of interpretive behaviour were chosen near the endpoints of these curves: at, and well above, the point of maximum separation (0.5 mM MgCl2, indicated with the dashed black line). These conditions were 25 mM MgCl2 + 10 mM CaCl2 (O1), 0.5 mM MgCl2 + 10 mM CaCl2 (O2), 25 mM MgCl2 (O3), and 0.5 mM MgCl2 (O4). (B) Example gels of ribozyme reacted for 0–60 min with 2.5-fold excess S-1t substrate at 37°C (lower band: unreacted ribozyme; upper band: ribozyme reacted with S-1t substrate). Summarized data from all assays is shown in Table 1.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4260251&req=5

Fig3: Assays of the ribozymes in various divalent ion concentrations. (A) Preliminary pick-up-the-tail assays were performed with 2.5-fold substrate excess as described in the text for activity after 60 minutes at 37°C. (Note: the original selection of the PV ribozyme [12] was performed at 3.25 h, at which time the PV activity surpasses that of the CG activity). The fraction of the initial amount of ribozyme RNA that reacted under conditions of 2.5-fold excess substrate was measured for each variant in the absence (green lines) or presence (red lines) of 10 mM CaCl2 under concentrations of MgCl2 ranging from 0.5–25 mM. Above 5 mM no increase in activity was observed. In the absence of a CaCl2 a slight inhibition of activity with increasing MgCl2 was observed above 0.1 mM, as noted before [8]. From these data, the conditions for formal analysis of interpretive behaviour were chosen near the endpoints of these curves: at, and well above, the point of maximum separation (0.5 mM MgCl2, indicated with the dashed black line). These conditions were 25 mM MgCl2 + 10 mM CaCl2 (O1), 0.5 mM MgCl2 + 10 mM CaCl2 (O2), 25 mM MgCl2 (O3), and 0.5 mM MgCl2 (O4). (B) Example gels of ribozyme reacted for 0–60 min with 2.5-fold excess S-1t substrate at 37°C (lower band: unreacted ribozyme; upper band: ribozyme reacted with S-1t substrate). Summarized data from all assays is shown in Table 1.
Mentions: Example payoff matrix for interpretive behaviour. Payoff values O1–O4 are evaluated for each pair-wise combination of environmental conditions and genotype traits as discussed in the text. The ion concentrations refer to those used in the assays of the Tetrahymena ribozyme, as described in Figures 2, 3 and 4.

Bottom Line: Yet a variant of this sequence containing five mutations that alter its ability to utilize the Ca(2+) ion engenders a strong interpretive characteristic in this RNA.We have shown that RNA molecules in a test tube can meet the minimum criteria for the evolution of interpretive behaviour in regards to their responses to divalent metal ion concentrations in their environment.Interpretation in RNA molecules provides a property entirely dependent on natural physico-chemical interactions, but capable of shaping the evolutionary trajectory of macromolecules, especially in the earliest stages of life's history.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Portland State University, Portland, OR, USA. niles@pdx.edu.

ABSTRACT

Background: The origins of life on the Earth required chemical entities to interact with their environments in ways that could respond to natural selection. The concept of interpretation, where biotic entities use signs in their environment as proxy for the existence of other items of selective value in their environment, has been proposed on theoretical grounds to be relevant to the origins and early evolution of life. However this concept has not been demonstrated empirically.

Results: Here, we present data that certain catalytic RNA sequences have properties that would enable interpretation of divalent cation levels in their environment. By assaying the responsiveness of two variants of the Tetrahymena ribozyme to the Ca(2+) ion as a sign for the more catalytically useful Mg(2+) ion, we show an empirical proof-of-principle that interpretation can be an evolvable trait in RNA, often suggested as a model system for early life. In particular we demonstrate that in vitro, the wild-type version of the Tetrahymena ribozyme is not interpretive, in that it cannot use Ca(2+) as a sign for Mg(2+). Yet a variant of this sequence containing five mutations that alter its ability to utilize the Ca(2+) ion engenders a strong interpretive characteristic in this RNA.

Conclusions: We have shown that RNA molecules in a test tube can meet the minimum criteria for the evolution of interpretive behaviour in regards to their responses to divalent metal ion concentrations in their environment. Interpretation in RNA molecules provides a property entirely dependent on natural physico-chemical interactions, but capable of shaping the evolutionary trajectory of macromolecules, especially in the earliest stages of life's history.

Show MeSH
Related in: MedlinePlus