TABLE 2.
Summary of Giardia SNARE localization
Subcellular localization of Giardia SNAREs determined by IFA was compared with the predicted localization determined by FASTA, HMMPfam, and HHPRED. To determine the closest orthologous gene for each Giardia SNARE protein, FASTA searches were performed with standard parameters on the UniProtKB/Swiss-Prot data base. The homology of the SNARE domain to the HMMs defined in Kloepper et al. (21) allowed us to predict the localization for each SNARE protein using HMMPfam. By using HHPRED and HHSENSER, the subcellular localization of the closest homologous KOG entry for each Giardia SNARE was analyzed. Subcellular localization was experimentally determined by IFA using organelle markers for each compartment. Presumed intracellular sites are as follows: NE (nuclear envelope), ER, GA (Golgi apparatus), TGN, PVs, VC (vacuolar compartment), ESVs, PM (plasma membrane).
| gSNARE | Accession GL50803_ | FASTA | HMM | HHPRED | IFA localization in non-encysting cells | IFA localization in encysting cells |
|---|---|---|---|---|---|---|
| gQa1 | 7,309 | EC | PM | PM | PVs | PVs/ESVs |
| gQa2 | 3,869 | TGN | TGN | GA/EC | NE/ER | NE/ER/ESVs |
| gQa3 | 96,994 | PM | PM | PM | NE/small vesicles/PVs/PM | small vesicles/PVs/PM |
| gQa4 | 11,220 | ER | ER | ER | NE/ER/vesicles | NE/ER/ESVs |
| gQa5 | 10,803 | VC | PM | EC | PVs/PM | PVs/PM/ESVs |
| gQb1 | 16,054 | EC | TGN | ER/EC | Vesicles | Vesicles |
| gQb2 | 17,464 | GA | GA | GA | Vesicles | Vesicles |
| gQb3 | 5,161 | ER | ER | ER/EC | Mitosomes | Mitosomes |
| gQb4 | 5,785 | No hit | EC | ER/EC | PVs/PM | PVs/PM |
| gQb5 | 10,315 | EC | TGN | ER/EC | NE/ER | NE/ER/ESVs |
| gQc1 | 5,927 | PM | EC | EC | PVs/PM | PVs/PM |
| gQc2 | 7,590 | VC | ER | EC | PVs/PM | PVs/PM |
| gQc3 | 10,013 | PM | EC | PM | ER/vesicles | Vesicles |
| gQc4 | 19,509 | GA/ER-GA | EC | EC | PVs/PM | PVs/PM/ESVs |
| gR1 | 9,489 | ER | GA | ER | NE/ER | NE/ER/ESVs |
| gR2 | 7,306 | GA/ER-GA | GA | GA/ER-GA | NE/ER cytoplasm | NE/ER/cytoplasm ESVs |
| gR3 | 14,469 | TGN/EC | EC | EC | PM | PM |