Table 1.
Clades and genomes analyzed, with statistics on CIF estimation gene sets.
Fig 1.
tRNA gene cluster size distribution for Trypanosoma, Leishmania, and other TriTrypDB version 41 genomes.
Green labels at tops of stacks show percentages of total tRNA genes in clusters of given length. Numbers within each bar show frequencies of gene clusters of that length.
Fig 2.
Density plots of gene-finder scores according to source of detection.
Fig 3.
Conserved divergence of parasite tRNAAla CIFs across eight phylogenetic clades of Leishmania and Trypanosoma.
Evolutionary divergence of trypanosomes relative to Leishmania major increases clockwise from Leishmania major.
Fig 4.
Conserved divergence of parasite tRNAThr CIFs across eight phylogenetic clades of Leishmania and Trypanosoma.
Evolutionary divergence of trypanosomes relative to Leishmania major increases clockwise from Leishmania major.
Fig 5.
Adenine function logos for humans and four clades of Leishmania.
Complete single-site function logo results are shown in S24–S31 Figs. The total height of a stack of letters at any site quantifies the information potentially gained about the functional type of a tRNA by a tRNA-binding protein if it recognizes the specific feature corresponding to that site and logo, for example Adenine at Sprinzl coordinate 16 (or some modification that biosynthetically depends on A16) in the case of the left-most boxed site. The letters within each stack symbolize functional types of tRNAs, wherein IUPAC one-letter amino acid codes represent elongator tRNA aminoacylation identities and “X” symbolizes initiator tRNAs. The relative heights of letters within each stack quantifies the over-representation of tRNA functional types carrying that feature relative to the background frequency determined by gene frequencies of functional types (as calculated through the normalized log-odds).
Fig 6.
Function logos for tRNA Class-Informative Base-Pairs and Class-Informative Mis-Pairs in humans.
The meanings of letters, stack heights and letter heights are all the same as in Fig 5.
Fig 7.
Function logos for tRNA Class-Informative Base-Pairs and Class-Informative Mis-Pairs in the L. major clade.
The meanings of letters, stack heights and letter heights are all the same as in Fig 5.
Fig 8.
Function logos for tRNA Class-Informative Base-Pairs and Class-Informative Mis-Pairs in the American Trypanosoma clade.
The meanings of letters, stack heights and letter heights are all the same as in Fig 5.
Fig 9.
Identification of Leishmania major AlaRS inhibitors.
A) Workflow to identify aminoacylation inhibitors (details described in Methods). B) Representative image of the MNP chemical screen. The spot boxed in red is an example of a predicted inhibitor depicted by the decrease in signal intensity. DMSO positive control (+). C) Three of the four identified inhibitors prevented the accumulation of Ala-tRNAAla formation, 1428B was a false-positive result from our preliminary screen. D) The three identified inhibitors perturbed L. major AlaRS activation (black) but had no effect on human AlaRS (gray). The relative amino acid activation is plotted relative to the DMSO control. Error bars indicate the standard deviation of three replicates.
Fig 10.
Identification of Leishmania major ThrRS inhibitors.
A) The MNP library was re-screened at the highest concentrations to qualitatively identify Lm ThrRS aminoacylation inhibitors. Plate IDs reference the position within the original library and not library IDs. B) Eight inhibitors were qualitatively identified from the preliminary screen. Two of the candidates did not inhibit aminoacylation (black), two inhibited at ~50% activity (gray), and four inhibited at greater than 25% (white).C) All four active inhibitors continued to perturb aminoacylation over a time course experiment. Error bars indicate the standard deviation of three replicates.
Fig 11.
Leishmania major and Trypanosoma cruzi AlaRS have conserved tRNA identity elements.
A) CIF Divergence Models for tRNAAla in Leishmania major and Trypanosoma cruzi B) The three identified Lm AlaRS inhibitors also have activity against the Tc AlaRS enzyme. Error bars indicate the standard deviation of three replicates.