Peculiarities of aminoacyl-tRNA synthetases from trypanosomatids

Abstract

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Trypanosoma brucei multi-aminoacyl-tRNA synthetase complex formation limits promiscuous tRNA proofreading

“…In plants, bacteria, and higher eukaryotes (metazoans), ProXp-ala domains are freestanding and edit mischarged Ala-tRNA Pro in trans . A BLAST search of Tb ProRS confirmed previous reports that only protozoans and fungi encode a ProXp-ala-ProRS fusion protein ( Ahel et al, 2003 ; Gowri et al, 2012 ; Parrot et al, 2021 ). Notably, many of the protists that encode a ProRS catalytic core with an appended ProXp-ala domain are human pathogens (i.e., P. falciparum, Leishmania ).…”

“…Bioinformatic analysis of Tb ProRS revealed that the INS-like NTD (residues 94–260) belongs to the ProXp-ala cluster of the INS superfamily ( Figure 1B ). The class II ARS consensus motifs and eukaryote-specific C-terminal zinc-binding domain are highly similar in sequence and structure to the ProRS domain of Homo sapiens EPRS ( Kuzmishin Nagy et al, 2020 ; Parrot et al, 2021 ; Vasu et al, 2021 ). The aminoacylation catalytic domain of Tb ProRS is separated from the appended ProXp-ala by a disordered linker (261–302).…”

“…The aminoacylation catalytic domain of Tb ProRS is separated from the appended ProXp-ala by a disordered linker (261–302). N-terminal to the ProXp-ala domain is a 93 amino acid region that AlphaFold2 predicts to be highly disordered—this sequence is predicted to be a mitochondrial-targeting sequence (MTS) ( Parrot et al, 2021 ). In plants, bacteria, and higher eukaryotes (metazoans), ProXp-ala domains are freestanding and edit mischarged Ala-tRNA Pro in trans .…”

Trypanosoma brucei multi-aminoacyl-tRNA synthetase complex formation limits promiscuous tRNA proofreading

“…In plants, bacteria, and higher eukaryotes (metazoans), ProXp-ala domains are freestanding and edit mischarged Ala-tRNA Pro in trans . A BLAST search of Tb ProRS confirmed previous reports that only protozoans and fungi encode a ProXp-ala-ProRS fusion protein ( Ahel et al, 2003 ; Gowri et al, 2012 ; Parrot et al, 2021 ). Notably, many of the protists that encode a ProRS catalytic core with an appended ProXp-ala domain are human pathogens (i.e., P. falciparum, Leishmania ).…”

“…Bioinformatic analysis of Tb ProRS revealed that the INS-like NTD (residues 94–260) belongs to the ProXp-ala cluster of the INS superfamily ( Figure 1B ). The class II ARS consensus motifs and eukaryote-specific C-terminal zinc-binding domain are highly similar in sequence and structure to the ProRS domain of Homo sapiens EPRS ( Kuzmishin Nagy et al, 2020 ; Parrot et al, 2021 ; Vasu et al, 2021 ). The aminoacylation catalytic domain of Tb ProRS is separated from the appended ProXp-ala by a disordered linker (261–302).…”

“…The aminoacylation catalytic domain of Tb ProRS is separated from the appended ProXp-ala by a disordered linker (261–302). N-terminal to the ProXp-ala domain is a 93 amino acid region that AlphaFold2 predicts to be highly disordered—this sequence is predicted to be a mitochondrial-targeting sequence (MTS) ( Parrot et al, 2021 ). In plants, bacteria, and higher eukaryotes (metazoans), ProXp-ala domains are freestanding and edit mischarged Ala-tRNA Pro in trans .…”

Quantitative analysis of C. elegans transcripts by Nanopore direct-cDNA sequencing reveals terminal hairpins in non trans-spliced mRNAs

“…Apart from the technical considerations, our observations raise the question of the functional significance of the presence of this stem-loop structure at the extremity of all C. elegans SL variants. It has been previously observed that potential stem-loop structures adjacent to the cap are widespread in the Spliced Leaders of phylogenetically divergent species although the sequence of the self-complementarity itself is not conserved 24 . We confirmed the same strand bias in Leishmania Tarentolae direct-cDNA sequencing experiments 24 , and it is likely that similar library behavior will extend to all species using trans -splicing.…”

Aminoacyl tRNA Synthetases: Implications of Structural Biology in Drug Development against Trypanosomatid Parasites

“…Even though the structures of HF-bound Pf ProRS and Hs ProRS are identical, there are substantial differences in the interaction of some of the residues such as Thr478, terminal phosphate group of AMPPNP, water molecule, etc., which suggest that inhibitors of Pf ProRS, like quinazolinone, might also inhibit trypanosomal ProRS. Both cytosolic and mitochondrial ProRS isoforms in Leishmania contain the Ybak/ProX domain at the N-terminus (Figure ), which is a prokaryotic-type editing domain and helps in the rectification of mischarged tRNAs. , …”

Trypanosoma brucei multi-aminoacyl-tRNA synthetase complex formation limits promiscuous tRNA proofreading

“…In plants, bacteria, and higher eukaryotes (metazoans), ProXp-ala domains are freestanding and edit mischarged Ala-tRNA Pro in trans . A BLAST search of Tb ProRS confirmed previous reports that only protozoans and fungi encode a ProXp-ala-ProRS fusion protein ( Ahel et al, 2003 ; Gowri et al, 2012 ; Parrot et al, 2021 ). Notably, many of the protists that encode a ProRS catalytic core with an appended ProXp-ala domain are human pathogens (i.e., P. falciparum, Leishmania ).…”

“…Bioinformatic analysis of Tb ProRS revealed that the INS-like NTD (residues 94–260) belongs to the ProXp-ala cluster of the INS superfamily ( Figure 1B ). The class II ARS consensus motifs and eukaryote-specific C-terminal zinc-binding domain are highly similar in sequence and structure to the ProRS domain of Homo sapiens EPRS ( Kuzmishin Nagy et al, 2020 ; Parrot et al, 2021 ; Vasu et al, 2021 ). The aminoacylation catalytic domain of Tb ProRS is separated from the appended ProXp-ala by a disordered linker (261–302).…”

“…The aminoacylation catalytic domain of Tb ProRS is separated from the appended ProXp-ala by a disordered linker (261–302). N-terminal to the ProXp-ala domain is a 93 amino acid region that AlphaFold2 predicts to be highly disordered—this sequence is predicted to be a mitochondrial-targeting sequence (MTS) ( Parrot et al, 2021 ). In plants, bacteria, and higher eukaryotes (metazoans), ProXp-ala domains are freestanding and edit mischarged Ala-tRNA Pro in trans .…”

Quantitative analysis of C. elegans transcripts by Nanopore direct-cDNA sequencing reveals terminal hairpins in non trans-spliced mRNAs

“…Apart from the technical considerations, our observations raise the question of the functional significance of the presence of this stem-loop structure at the extremity of all C. elegans SL variants. It has been previously observed that potential stem-loop structures adjacent to the cap are widespread in the Spliced Leaders of phylogenetically divergent species although the sequence of the self-complementarity itself is not conserved 24 . We confirmed the same strand bias in Leishmania Tarentolae direct-cDNA sequencing experiments 24 , and it is likely that similar library behavior will extend to all species using trans -splicing.…”

Aminoacyl tRNA Synthetases: Implications of Structural Biology in Drug Development against Trypanosomatid Parasites

“…Even though the structures of HF-bound Pf ProRS and Hs ProRS are identical, there are substantial differences in the interaction of some of the residues such as Thr478, terminal phosphate group of AMPPNP, water molecule, etc., which suggest that inhibitors of Pf ProRS, like quinazolinone, might also inhibit trypanosomal ProRS. Both cytosolic and mitochondrial ProRS isoforms in Leishmania contain the Ybak/ProX domain at the N-terminus (Figure ), which is a prokaryotic-type editing domain and helps in the rectification of mischarged tRNAs. , …”

Trypanosoma brucei multi-aminoacyl-tRNA synthetase complex formation limits promiscuous tRNA proofreading

“…In plants, bacteria, and higher eukaryotes (metazoans), ProXp-ala domains are freestanding and edit mischarged Ala-tRNA Pro in trans . A BLAST search of Tb ProRS confirmed previous reports that only protozoans and fungi encode a ProXp-ala-ProRS fusion protein ( Ahel et al, 2003 ; Gowri et al, 2012 ; Parrot et al, 2021 ). Notably, many of the protists that encode a ProRS catalytic core with an appended ProXp-ala domain are human pathogens (i.e., P. falciparum, Leishmania ).…”

“…Bioinformatic analysis of Tb ProRS revealed that the INS-like NTD (residues 94–260) belongs to the ProXp-ala cluster of the INS superfamily ( Figure 1B ). The class II ARS consensus motifs and eukaryote-specific C-terminal zinc-binding domain are highly similar in sequence and structure to the ProRS domain of Homo sapiens EPRS ( Kuzmishin Nagy et al, 2020 ; Parrot et al, 2021 ; Vasu et al, 2021 ). The aminoacylation catalytic domain of Tb ProRS is separated from the appended ProXp-ala by a disordered linker (261–302).…”

“…The aminoacylation catalytic domain of Tb ProRS is separated from the appended ProXp-ala by a disordered linker (261–302). N-terminal to the ProXp-ala domain is a 93 amino acid region that AlphaFold2 predicts to be highly disordered—this sequence is predicted to be a mitochondrial-targeting sequence (MTS) ( Parrot et al, 2021 ). In plants, bacteria, and higher eukaryotes (metazoans), ProXp-ala domains are freestanding and edit mischarged Ala-tRNA Pro in trans .…”

Quantitative analysis of C. elegans transcripts by Nanopore direct-cDNA sequencing reveals terminal hairpins in non trans-spliced mRNAs

“…Apart from the technical considerations, our observations raise the question of the functional significance of the presence of this stem-loop structure at the extremity of all C. elegans SL variants. It has been previously observed that potential stem-loop structures adjacent to the cap are widespread in the Spliced Leaders of phylogenetically divergent species although the sequence of the self-complementarity itself is not conserved 24 . We confirmed the same strand bias in Leishmania Tarentolae direct-cDNA sequencing experiments 24 , and it is likely that similar library behavior will extend to all species using trans -splicing.…”

Aminoacyl tRNA Synthetases: Implications of Structural Biology in Drug Development against Trypanosomatid Parasites

“…Even though the structures of HF-bound Pf ProRS and Hs ProRS are identical, there are substantial differences in the interaction of some of the residues such as Thr478, terminal phosphate group of AMPPNP, water molecule, etc., which suggest that inhibitors of Pf ProRS, like quinazolinone, might also inhibit trypanosomal ProRS. Both cytosolic and mitochondrial ProRS isoforms in Leishmania contain the Ybak/ProX domain at the N-terminus (Figure ), which is a prokaryotic-type editing domain and helps in the rectification of mischarged tRNAs. , …”