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Evolution and diversification of the organellar release factor family.

Duarte I, Nabuurs SB, Magno R, Huynen M - Mol. Biol. Evol. (2012)

Bottom Line: The canonical release factors (mtRF1a, mtRF2a, pRF1, and pRF2) and ICT1 are derived from bacterial ancestors, whereas the others have resulted from gene duplications of another release factor.Although the RF presence in an organelle and its stop codon usage tend to coevolve, 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 reinvention" hypothesis that involves the retargeting of the plastid release factor to the mitochondrion.

View Article: PubMed Central - PubMed

Affiliation: Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.

ABSTRACT
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 two 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, whereas 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 nonclassical PxT/SPF tripeptide motifs and provide a molecular-model-based rationale for their retained ability to recognize stop codons. Finally, we analyze the coevolution of canonical RFs with the organellar genetic code. Although the RF presence in an organelle and its stop codon usage tend to coevolve, 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 reinvention" hypothesis that involves the retargeting of the plastid release factor to the mitochondrion.

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Molecular modeling of the noncanonical PxT motif from Caenorhabditis elegans’ mtRF1a. (A) Hydrogen bonding interaction between the first nucleotide of the UAA stop codon (U1) and the threonine of the PxT motif (labeled Thr) of the reading head of RF1 in the Thermus thermophilus crystal structure (PBD entry 3D5A [Laurberg et al. 2008]). (B) Molecular model of the reading head conformation in the C. elegans RF1. The asparagine of the PxN motif is capable of making a similar hydrogen bonding interaction to the first nucleotide of the stop codon as a result of a two amino acid deletion in the recognition loop. The first two stop codon nucleotides (U1 and U2) are shown in green in both panels.
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mss157-F6: Molecular modeling of the noncanonical PxT motif from Caenorhabditis elegans’ mtRF1a. (A) Hydrogen bonding interaction between the first nucleotide of the UAA stop codon (U1) and the threonine of the PxT motif (labeled Thr) of the reading head of RF1 in the Thermus thermophilus crystal structure (PBD entry 3D5A [Laurberg et al. 2008]). (B) Molecular model of the reading head conformation in the C. elegans RF1. The asparagine of the PxN motif is capable of making a similar hydrogen bonding interaction to the first nucleotide of the stop codon as a result of a two amino acid deletion in the recognition loop. The first two stop codon nucleotides (U1 and U2) are shown in green in both panels.

Mentions: To better understand the retained functionality of this alternative loop conformation, we have built a molecular model of C. elegans’ mtRF1a (with its PVN motif and shorter recognition loop). To do so, we used T. thermophilus’ crystal structure of RF1 bound to a ribosome with a UAA stop codon in the A-site (fig. 6A). Our model clearly shows that, despite the shortened recognition loop, the tripeptide’s asparagine (N) is still able to make the crucial hydrogen bonding interaction to the first nucleotide of the stop codon (fig. 6B), just like the threonine in the canonical PxT motif, which determines selectivity over other nucleotides (Korostelev et al. 2008; Laurberg et al. 2008).Fig. 6.


Evolution and diversification of the organellar release factor family.

Duarte I, Nabuurs SB, Magno R, Huynen M - Mol. Biol. Evol. (2012)

Molecular modeling of the noncanonical PxT motif from Caenorhabditis elegans’ mtRF1a. (A) Hydrogen bonding interaction between the first nucleotide of the UAA stop codon (U1) and the threonine of the PxT motif (labeled Thr) of the reading head of RF1 in the Thermus thermophilus crystal structure (PBD entry 3D5A [Laurberg et al. 2008]). (B) Molecular model of the reading head conformation in the C. elegans RF1. The asparagine of the PxN motif is capable of making a similar hydrogen bonding interaction to the first nucleotide of the stop codon as a result of a two amino acid deletion in the recognition loop. The first two stop codon nucleotides (U1 and U2) are shown in green in both panels.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3472500&req=5

mss157-F6: Molecular modeling of the noncanonical PxT motif from Caenorhabditis elegans’ mtRF1a. (A) Hydrogen bonding interaction between the first nucleotide of the UAA stop codon (U1) and the threonine of the PxT motif (labeled Thr) of the reading head of RF1 in the Thermus thermophilus crystal structure (PBD entry 3D5A [Laurberg et al. 2008]). (B) Molecular model of the reading head conformation in the C. elegans RF1. The asparagine of the PxN motif is capable of making a similar hydrogen bonding interaction to the first nucleotide of the stop codon as a result of a two amino acid deletion in the recognition loop. The first two stop codon nucleotides (U1 and U2) are shown in green in both panels.
Mentions: To better understand the retained functionality of this alternative loop conformation, we have built a molecular model of C. elegans’ mtRF1a (with its PVN motif and shorter recognition loop). To do so, we used T. thermophilus’ crystal structure of RF1 bound to a ribosome with a UAA stop codon in the A-site (fig. 6A). Our model clearly shows that, despite the shortened recognition loop, the tripeptide’s asparagine (N) is still able to make the crucial hydrogen bonding interaction to the first nucleotide of the stop codon (fig. 6B), just like the threonine in the canonical PxT motif, which determines selectivity over other nucleotides (Korostelev et al. 2008; Laurberg et al. 2008).Fig. 6.

Bottom Line: The canonical release factors (mtRF1a, mtRF2a, pRF1, and pRF2) and ICT1 are derived from bacterial ancestors, whereas the others have resulted from gene duplications of another release factor.Although the RF presence in an organelle and its stop codon usage tend to coevolve, 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 reinvention" hypothesis that involves the retargeting of the plastid release factor to the mitochondrion.

View Article: PubMed Central - PubMed

Affiliation: Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.

ABSTRACT
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 two 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, whereas 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 nonclassical PxT/SPF tripeptide motifs and provide a molecular-model-based rationale for their retained ability to recognize stop codons. Finally, we analyze the coevolution of canonical RFs with the organellar genetic code. Although the RF presence in an organelle and its stop codon usage tend to coevolve, 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 reinvention" hypothesis that involves the retargeting of the plastid release factor to the mitochondrion.

Show MeSH