Table 1.
Peroxisomal targeting signals in orthologues of SidI, SidH and SidF
| SidI | SidH | SidF | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Organism | Accession | PTS | Score (PTS1) | Accession | PTS | Score (PTS1) | Accession | PTS | Score (PTS1) | |
| Eurotiomycetes | Aspergillus fumigatus | XP_753087.1 | RLQQTLSHL | – | XP_748661.1 | SKL | 10.8 | XP_748660.1 | AKL | 7.5 |
| Neosartorya fischeri | XP_001264038.1 | RLQQTLSHL | – | XP_001259092.1 | SKL | 10.5 | XP_001259091.1 | AKL | 7.5 | |
| Aspergillus niger | XP_001390954.1 | RLQQTLSHF | – | XP_001390237.1 | SKL | 9.6 | XP_001390236.1 | AKL | 6.9 | |
| Aspergillus clavatus | XP_001268556.1 | RLQQTLSHL | – | XP_001273567.1 | SNL | 9.3 | XP_001273568.1 | AKL | 7.3 | |
| Aspergillus oryzae | XP_001821069.1 | RLQQTLSHI | – | XP_001826764.1 | SNL | 5.4 | XP_001826765.1 | AKL | 5.2 | |
| Penicillium chrysogenum | XP_002569340.1 | RLQQTLSHV | – | XP_002565937.1 | SKL | 8.1 | XP_002565938.1 | AKL | 6.9 | |
| Aspergillus nidulans | XP_658213.1 | RLQQTLSHL | – | XP_663839.1 | SNLd | 5.9 | XP_663838.1 | AKL | 7.7 | |
| Ajellomyces capsulatus | EEH02760.1 | RLQQTLNHI | – | EEH07298.1 | SKL | 12.4 | XP_001536540.1 | SKL | 14.0 | |
| Talaromyces stipitatus | XP_002484634 | RLQQTQRHI | – | XP_002486020.1 | SKL | 8.4 | XP_002486021.1 | AKL | 6.9 | |
| Leotiomycetes | Botryotinia fuckeliana | XP_001546797.1 | PKLa | 13.5 | XP_001551006 | SKL | 9.1 | XP_001551005.1 | PKLa | 6.5 |
| Sclerotinia sclerotiorum | XP_001585101.1 | PKL | 12.7 | XP_001594442.1 | SKLb | 9.1 | XP_001594441.1 | AKL | 6.9 | |
| Sordariomycetes | Neurospora crassa | XP_959826.1 | SKL | 6.2 | XP_962600.1 | SKL | 6.3 | XP_959825.1 | PKL | 6.5 |
| Gibberella zeae | XP_384509.1 | SKL | 3.7 | XP_383922.1 | SKL | 10.4 | XP_383921.1 | PKL | 2.2 | |
| Podospora anserina | XP_001905332.1 | AKL | 12.6 | XP_003437360.1 | SKL | 8.6 | XP_001905331.1 | PKL | 8.0 | |
| Chaetomium globosum | XP_001226170.1 | AKL | 0.0 | XP_001227399.1 | SKL | 8.6 | XP_001227400.1 | AKL | 6.9 | |
| Magnaporthe oryzae | EHA55987 | AKL | 10.1 | EHA47011.1 | SKL | 9.3 | XP_362759.1 | PKL | 8.2 | |
| Dothideomycetes | Phaeosphaeria nodorum | XP_001804551.1 | RLNQTLLQIc | – | XP_001790987.1 | SKL | 11.7 | XP_001804552.1 | ARL | 8.5 |
| Basidiomycota | Ustilago maydis | XP_760950.1 | – | – | XP_757580.1 Fer4 | – | – | XP_757579.1 Fer5 | – | – |
Updated genome data from Botrytis cinerea strain B05.10 with the locus tag B0510_2726 (SidI) and B0510_7543 (SidF) reveal gene products containing a PTS1 (PKL). http://www.broadinstitute.org/annotation/genome/botrytis_cinerea/FeatureSearch
The annotated gene is organized in four exons, whereas all other orthologues have two. Manual reannotating of the intron/exon structure increased the sequence similarity to its orthologues and led to a PTS1-containing C-terminus (EWYPRLVKSPNFAEGIQAYVDKRPPKWVNSKL).
The correct start codon is most likely 414 bp upstream and in frame of the annotated start, which leads to a gene product with higher similarity to its orthologues and contains the quoted PTS2.
The deposited sequence most likely contains a sequencing error leading to a false C-terminus. Contig 1.106, which was used for gene assembly, misses in contrast to contig 1.107 a cytosine after nt 745 of the cds. Correction of the sequence generated a C-terminus showing 80% identity with A. fumigatus SidH (EEASSALVDEWYPKLIAGENFHEGVKAFVEKRQPRWRASNL).
Variants of the classical PTS1 SKL sequence such as –ARL, –AKL or –PKL were shown to be functional peroxisomal targeting signals in human, yeast and Penicillium chrysogenum (Amery et al., 1998; Kiel et al., 2009). The PTS1 scores of proteins were obtained using the PTS1-predictor program http://mendel.imp.ac.at/mendeljsp/sat/pts1/PTS1predictor.jsp (Neuberger et al., 2003). Positive scores indicate high probability of peroxisomal targeting, sequences with scores < −10 are unlikely to function as PTS1, and motifs with scores in between have unclear function. PTS2 motifs were identified using the PTS2 finder http://www.peroxisomedb.org/diy_PTS2.html, which does not provide reliability scores.