DOI: 10.5061/dryad.2br48
title: Data from: Evolution and diversification of the organellar release factor family

description: Translation termination is accomplished by proteins of the Class I release
 factor family (RF) that recognize stop codons and catalyze the ribosomal
 release of the newly synthesized peptide. Bacteria have two canonical RFs:
 RF1 recognizes UAA and UAG, RF2 recognizes UAA and UGA. Despite that these
 2 release factor proteins are sufficient for de facto translation
 termination, the eukaryotic organellar RF protein family, which has
 evolved from bacterial release factors, has expanded considerably,
 comprising multiple subfamilies, most of which have not been functionally
 characterized or formally classified. Here we integrate multiple sources
 of information to analyze the remarkable differentiation of the RF family
 among organelles. We document the origin, phylogenetic distribution and
 sequence structure features of the mitochondrial and plastidial release
 factors: mtRF1a, mtRF1, mtRF2a, mtRF2b, mtRF2c, ICT1, C12orf65, pRF1 and
 pRF2, and review published relevant experimental data. The canonical
 release factors (mtRF1a, mtRF2a, pRF1 and pRF2) and ICT1 are derived from
 bacterial ancestors, while the others have resulted from gene duplications
 of another release factor. These new RF family members have all lost one
 or more specific motifs relevant for bona fide release factor function but
 are mostly targeted to the same organelle as their ancestor. We also
 characterize the subset of canonical release factor proteins that bear
 non-classical PxT/SPF tripeptide motifs, and provide a
 molecular-model-based rationale for their retained ability to recognize
 stop codons. Finally we analyze the co-evolution of canonical RFs with the
 organellar genetic code. Although the RF presence in an organelle and its
 stop codon usage tend to co-evolve, we find three taxa that encode an RF2
 without using UGA stop codons, and one reverse scenario, where mamiellales
 green algae use UGA stop codons in their mitochondria without having a
 mitochondrial type RF2. For the latter we put forward a “stop-codon
 re-invention” hypothesis that involves the retargeting of the plastid
 release factor to the mitochondrion.
description: RF1 subfamily alignment
 (mtRF1a, mtRF1 and pRF1)Fasta multiple sequence
 alignment of Release Factor 1 proteins. Sequences were retrieved from
 GenBank nr database using PSI-BLAST. The alignment was obtained with
 ClustalW (v2.0.10), and 60% of the gaps was removed with BMGE (v1.0). The
 alignment was visually inspected and manually adjusted to accuratly align
 all functionally characterized domains and sequence motifs. Fasta multiple
 sequence alignment of Release Factor 2 proteins. Sequences were retrieved
 from GenBank nr database using PSI-BLAST. The alignment was obtained with
 ClustalW (v2.0.10), and 60% of the gaps was removed with BMGE (v1.0). The
 alignment was visually inspected and manually adjusted to accuratly align
 all functionally characterized domains and sequence motifs. Each sequence
 header contains the species name, the identity of each protein and, for
 bacterial species, the bacterial group they belong to. The numbers present
 in the header are not meaningful.mtrf1a_mtrf1_prf1.bmge60gapRemoved.aln.fastaRF2 subfamily alignment (mtrf2a, mtrf2b, mtrf2c, prf2)Fasta multiple sequence alignment of Release Factor 2 proteins. Sequences were retrieved from GenBank nr database using PSI-BLAST. The alignment was obtained with ClustalW (v2.0.10), and 60% of the gaps was removed with BMGE (v1.0). The alignment was visually inspected and manually adjusted to accuratly align all functionally characterized domains and sequence motifs. Each sequence header contains the species name, the identity of each protein and, for bacterial species, the bacterial group they belong to. The numbers present in the header are not meaningful.mtrf2c_mtrf2a_prf2_mtrf2b.bmge60gapRemoved.aln.fastaEukaryotic Complete Release Factor family alignment (RF1, RF2, ICT1, C12orf65)Fasta multiple sequence alignment of all eukaryotic Release Factor proteins. Sequences were retrieved from GenBank nr database using PSI-BLAST. These were aligned through profile to profile sequential alignment of the individual subfamilies’ alignments using ClustalW (v2.0.10) followed by one last round of alignment refinement with Muscle’s refine option. Finally, the whole RF family alignment was inspected and manually adjusted. No gaps were removed. Each sequence header contains the species name and the identity of each protein.rf1_rf2_ict1_c12orf65-EukOnly.full-seqs.aln.fasta