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Open Access Research article

Describing the structural robustness landscape of bacterial small RNAs

Guillermo Rodrigo13* and Mario A Fares12

Author Affiliations

1 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

2 Department of Genetics, Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin, Ireland

3 Institute of Systems and Synthetic Biology, Genopole, Université d' Évry Val d' Essonne, CNRS, 91034 Évry Paris, France

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BMC Evolutionary Biology 2012, 12:52  doi:10.1186/1471-2148-12-52

Published: 13 April 2012

Additional files

Additional file 1:

Figure S1 Histograms of the structural properties for the bacterial sncRNAs.

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Additional file 2:

Figure S2 Plasticity modulates variability in robustness. Scatter plots between the intrinsic distance (d0) and the standard deviations of the distances between structures after one (Δd1) or two mutations (Δd2) or environmental changes (Δde) for the bacterial sncRNAs.

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Additional file 3:

Figure S3 Dependence of evolvability on structural properties. Relationship scheme between plasticity (P), epistasis (E), mutational robustness (Rm), and evolvability for bacterial sncRNAs.

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Additional file 4:

Figure S4. Average effect of the location (relative distance) of mutations on epistasis using a large set of artificial sncRNAs.

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Additional file 5:

Figure S5 Robustness and neutral evolution. 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. One iteration corresponds to one mutation.

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Additional file 6:

Figure S6 Mutational versus environmental robustness. Scatter plot between mutational (Rm) and environmental (Re) robustness for the bacterial sncRNAs, showing the gene name of the three frontier elements (genes rydC, C0664 and ssrA).

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Additional file 7:

Figure S7 Correlation between mutational and environmental robustness. Scatter plot between the z-scores for environmental and mutational robustness (Re and Rm), relative to sample III.

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Additional file 8:

Figure S8 Effect of environmental stability on robustness. (a) Mutational and (b) environmental robustness (Rm and Re) of gene ffs for different bacteria (Buchnera aphidicola, Mycoplasma genitalium, Vibrio fischeri, Escherichia coli, Salmonella enterica, Citrobacter koseri, Serratia proteamaculans, and Pseudomonas putida). * denotes statistical significance in a one-tailed z-test with (a) P-value = 0.059 and (b) P-value = 0.041. When including into the analysis 15 more strains of E. coli with different ffs sequences, we obtained (a) P-value = 0.005 and (b) P-value = 0.017.

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Additional file 9:

Figure S9 Length correlates with stability and functionality. Scatter plots between length (L) and free energy of the ensemble (G) and degree of functionality (V) for the bacterial sncRNAs (G in Kcal/mol).

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Additional file 10:

Figure S10 Plasticity does not correlate with functionality. Scatter plot between degree of functionality (V) and plasticity (P) for the bacterial sncRNAs.

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Additional file 11:

Table S1 Sequences for the small non-coding RNAs (sncRNAs) obtained from the genome of the bacterium Escherichia coli K12 MG1655.

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Additional file 12:

Table S2 Structural properties for the bacterial sncRNAs. These are length (L), free energy of the thermodynamic ensemble (G), degree of functionality (V), plasticity (P), mutational robustness (Rm), epistasis (E), and environmental robustness (Re).

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Additional file 13:

Table S3 Statistical significance analysis results. Z-scores for plasticity (P), mutational robustness (Rm), environmental robustness (Re), and epistasis (E), for each sncRNA and relative to sample III.

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Additional file 14:

Table S4 Effect of random sample of sequences on robustness. Sample I accounts for sequences obtained from inverse folding routines. Sequences of sample II were subsequently randomized by introducing neutral mutations (which not change the structure). Sequences of sample III were randomized by introducing neutral mutations and neutral pairs of mutations and compensatory mutations (for nucleotides in a stem). Using z-scores, we show the percentage of sncRNAs that are robust (z > 0) and significantly robust (zc = 1.64, P-value = 0.05).

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