phosphoglycerate kinase

Phosphoglycerate kinase

The cytosolic and glycosomal phosphoglycerate kinase (PGK) isoenzymes from trypanosomatids are very similar to each other and differ essentially only in the presence of a peroxisome targeting signal (PTS1) at the C-terminus of the glycosomal enzyme. The trypanosomatid PGKs are clearly distinct from all other eukaryotic homologues, including those of the protists such as the ciliates and the apicomplexan Plasmodium, in that they lack an 11 amino-acid long insertion found in all other eukaryotic sequences (see Figure). Moreover, in a previous phylogenetic analysis (Adje et al., 1998) they clustered robustly together with the prokaryotic sequences and had as their nearest neighbour the enzymes from cyanobacteria and chloroplasts of plants.

Further details of the analysis

The T. brucei glycosomal PGK was compared with the SwissProt database indexed at European Bioinformatics Institute (EBI, Hinxton UK) on 28 July 2001 and having 99162 entries, using the NCBI BLASTP program and the BLOSUM 62 matrix (http://www2.ebi.ac.uk/blastall/). Click here to inspect the BLASTP output file.

The best E values (0 to e-154) were obtained with itself (PGKC_TRYBB) and with the other trypanosomatid sequences, followed by the PGKs from Clostridium acetobutylicum (PGK_CLOAB), Thermotoga maritima (PGKT_THEMA)and wheat (PGKY_WHEAT). The top 100 sequences from the blastp output were aligned using the "RunDBClustalW" option in the BLASTP output. The ClustalW alignment is availabe here for inspection. The positions with gaps were removed and the alignment containing 100 sequences with 157 positions was transformed to Phylip format and used for the creation of a bootstrapped neighbor-joining and maximum likelihood tree.

Maximum likelihood mapping as implemented in PUZZLE version 4.0.1. indicated the presence in the dataset of a weak phylogenetic signal (7% star-like quartets and 88.1% of the quartet trees were well-resolved). Four-cluster likelihood mapping was used to ask the question as to whether the trypanosomatids could cluster with either the protozoan (b), the other eukaryotes (d) or the chloroplast/cyanobacterial (c) clade. Seventy-six percent of quartet trees favoured grouping of trypanosomatids with the cyanobacteria and chloroplast sequences, only 11% was in favour of their grouping with the other protists and 9% favoured grouping with all other eukaryotes.

The trypanosomatid PGKs are clearly distinct from all other eukaryotic homologues, including those of the protists such as the ciliates Tetrahymena and Euplotes and the apicomplexan Plasmodium, in that they lack an 11 amino-acid long insertion found in all other eukaryotic sequences (Figure).

In the NJ tree (pdf format) the trypanosomatids clustered together with the prokaryotes, but there was no significant bootstrap support for a specific clustering with cyanobacterial or chloroplasts sequences. However, there was also no bootstrap support for any relative order of branching in this part of the tree which in this region was highly star-like. However, the trypanosomatid clade was well separated from the eukaryotic clade, which included all the non-trypanosomatid protists of which the grouping was highly robust (99% bootstrap support).

Conclusion:

The trypanosomatid PGK sequences are of prokaryotic origin and not related to those of other protozoa. Their clustering together with the prokaryotes suggests that the trypanosomatid PGKs originated by horizontal transfer involving the acquisition of a bacterial type PGK, possibly from a cyanobacterium.