Fig 1.
A: Amino acid distribution in the hydrophobic regions of signal peptides. B: left: AF2 predicted structures with different combinations between SRP54 proteins and signal peptides from L. infantum and S. cerevisiae (G. Euk.: Generic Eukaryotic, Kineto: Kinetoplastid, Signal p: Signal peptide). Pdb models used: signal_sacs2_sc.pdb, signal_sacs2_lei.pdb, signal_leiin_sc.pdb. signal_leiin_lei.pdb (structures are available in the S1 Structures). C: Energy (free enthalpy) calculation results from different combinations of SRP54 and signal peptides D: Receiver Operating Characteristics (ROC) of the Leishmania specific signal peptide prediction method (LeiSig) E: Signal peptide predictions on 5 Leishmania species with different approaches.
Fig 2.
A: Comparison of the sequence logos of all known or predicted KDEL-like motifs of five eukaryotes from different lineages show its conservation. B: This original K/H/RDEL consensus is altered in kinetoplastids, mostly yielding peptides ending in DL. C: Superimposed protein models show that the gatekeeper loop of the ER retrieval receptor (KDEL receptor) of kinetoplastids differs from other eukaryotes, clashing with the main chain of an incoming, canonical KDEL peptide (pdb:6I6H) in case of all examined parasitic species, but not in the free-living Bodo saltans. D: HADDOCK models show that the long gatekeeper loop forces the ligands of the Leishmania receptor to take a different main chain conformation than in the mammalian KDEL receptor. E: Recognizing the altered consensus of receptors allows the identification of conserved families of kinetoplastid ER-resident proteins including newly-identified protein groups (Blue bars show the presence of KDEL-like peptide-containing orthologs, while light blue bars indicate homologous proteins without KDEL).
Fig 3.
A: Our evolutionary model of ATG8 protein groups in Leishmaniinae. For each paralog, the surface mutations expected to block LIR binding are shown in red, while the novel invariant surface is in orange. The small structural figures show matching protein surfaces from the same angle. Predicted ATG4 cleavage sites (P-4 to P-1) for each protein group are exemplified by a sequence written in gray below each group name. B: The ATG8A, ATG8B and ATG8C genes are typically found in two tandem arrays within leishmanial genomes but their copy numbers vary highly across species. C: The preserved LIR peptide-binding ability of ATG8 proteins is illustrated by a simulated model between this protein and a Leishmania LIR motif model peptide, similar to the ones seen in conserved autophagy apparatus proteins ATG2, ATG3 and ATG4 (frequency logos from proteins in group Discoba written below). D: The simulated complexes between ATG8 and the enzyme ATG4.2 and between ATG8C and ATG4.2 are highly similar and betray a potential existence of a LIR-equivalent motif for atypical ATG8s.
Table 1.
Select Leishmania infantum proteins with likely functional LIR motifs and the evolutionary conservation of the motifs.
Motif cores are bolded and underlined.