Figure 5
Pseudo-motifs in representative candidate fungal tRNase ZLs. The top panel shows alignment for pseudo substrate recognition and catalytic motifs found in tRNase ZLs from S. cerevisiae (SceTrz1) [19], A. gossypii (AgoTrz1), C. albicans (CalTrz1), A. nidulans (AniTrz1), C. immitis (CimTrz1), S. sclerotiorum (SscTrz1), P. tritici-repentis (PtrTrz1), N. crassa (NcrTrz1), F. graminearum (FgrTrz1), C. elegans (CelTrz1)[56], D. melanogaster (DmeTrz1) [54], A. thaliana (AthTrz4) [13] and humans (HsaTrz2) [9]. The bottom panel shows alignment for the corresponding conserved motifs in tRNase Zs from B. subtilis (BsuTrz1) [55], Archaeoglobus fulgidus (ArcTrz1; accession no. NP_069772), Halobacterium salinarum (HalTrz1; accession no. NP_280881), Methanosarcina acetivorans (MacTrz1; accession no. NP_617924), Enterococcus faecalis (EfaTrz1; accession no.NP_815399), Lactococcus lactis subsp (LlaTrz1; accession no. NP_266786), Nanoarchaeum equitans (NeqTrz1; accession no. NP_963358), Methanococcus maripaludis (MmaTrz1; accession no. NP_988026) and Pyrococcus abyssi (PabTrz1; accession no. NP_126781). The pseudo-PxKxRN loops of C. elegans and human tRNase ZLs are not included since they are indiscernible. The candidate fungal tRNase ZLs are defined in Additional file 1. GenBank accession numbers that are not listed in Additional file 1 are indicated. The alignment was extended to include surrounding regions to illustrate the further homology revealed by searching the Conserved Domain database (CDD), which could aid in the identification of pseudo-motifs. Similar or identical amino acid residues are shaded as described in the legend to Figure 2. The positions of amino acid residues of the D. melanogaster tRNase ZL critical for catalytic efficiency [30, 31] are indicated by asterisk.