Supporting data for the manuscript: Chaudhari et al., Synthesis cost is a hidden driver of convergent amino acid composition in plastid ribosomal proteins. List of contents:Data S1 Sequence alignments of all surveyed plastid and nuclear genes in Orobanchaceae, Geraniaceae, Fabaceae, and Caryophyllaceae. These genes included the plastid-encoded plastid ribosome genes (CpPRP), nuclear-encoded plastid-targeted ribosomal proteins (NuPRP), nuclear-encoded plastid-targeted non-ribosomal proteins (NuCpOT), and nuclear-encoded cytosolic ribosomal proteins (NuCyRP). The RNA editing sites of plastid genes were predicted using PREPACT v3 and masked using a custom Python script. The N-terminal peptides of nuclear-encoded plastid-targeted genes were predicted using TargetP v2.0 and trimmed. Data S2 Changes in protein folding stability estimated by ELASPIC2. Protein stability was measured by changes in free energy of protein folding (ΔΔG) using the deep learning powered tool ELASPIC. Pairwise comparisons were performed between 1) observed natural protein pairs (e.g., one Cymbarieae species and a closely related outgroup) and 2) reconstructed ancestral proteins with artificial mutations (e.g., reconstructed ancestral protein of Cymbarieae with introduced R→K mutations).
Arnav Chaudhari, Palash Sethi, Yvemirca Vilbrun et al.· Zenodo (CERN European Organi...· 0 citations
Supporting data for the manuscript: Chaudhari et al., Synthesis cost is a hidden driver of convergent amino acid composition in plastid ribosomal proteins. List of contents:Data S1 Sequence alignments of all surveyed plastid and nuclear genes in Orobanchaceae, Geraniaceae, Fabaceae, and Caryophyllaceae. These genes included the plastid-encoded plastid ribosome genes (CpPRP), nuclear-encoded plastid-targeted ribosomal proteins (NuPRP), nuclear-encoded plastid-targeted non-ribosomal proteins (NuCpOT), and nuclear-encoded cytosolic ribosomal proteins (NuCyRP). The RNA editing sites of plastid genes were predicted using PREPACT v3 and masked using a custom Python script. The N-terminal peptides of nuclear-encoded plastid-targeted genes were predicted using TargetP v2.0 and trimmed. Data S2 Changes in protein folding stability estimated by ELASPIC2. Protein stability was measured by changes in free energy of protein folding (ΔΔG) using the deep learning powered tool ELASPIC. Pairwise comparisons were performed between 1) observed natural protein pairs (e.g., one Cymbarieae species and a closely related outgroup) and 2) reconstructed ancestral proteins with artificial mutations (e.g., reconstructed ancestral protein of Cymbarieae with introduced R→K mutations).
Arnav Chaudhari, Palash Sethi, Yvemirca Vilbrun et al.· Zenodo (CERN European Organi...· 0 citations