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The TriTryp phosphatome: analysis of the protein phosphatase catalytic domains.

Brenchley R, Tariq H, McElhinney H, Szöor B, Huxley-Jones J, Stevens R, Matthews K, Tabernero L - BMC Genomics (2007)

Bottom Line: The prevalence of these neglected diseases results from a combination of poverty, inadequate prevention and difficult treatment.We found interesting differences with other eukaryotic genomes, such as the low proportion of tyrosine phosphatases and the expansion of the serine/threonine phosphatase family.These distinct traits may be exploited in the selection of suitable new targets for drug development to prevent transmission and spread of the diseases, taking advantage of the already extensive knowledge on protein phosphatase inhibitors.

View Article: PubMed Central - HTML - PubMed

Affiliation: Faculty of Life Sciences, Michael Smith, University of Manchester, M13 9PT, UK. Rachel.Brenchley@postgrad.manchester.ac.uk

ABSTRACT

Background: The genomes of the three parasitic protozoa Trypanosoma cruzi, Trypanosoma brucei and Leishmania major are the main subject of this study. These parasites are responsible for devastating human diseases known as Chagas disease, African sleeping sickness and cutaneous Leishmaniasis, respectively, that affect millions of people in the developing world. The prevalence of these neglected diseases results from a combination of poverty, inadequate prevention and difficult treatment. Protein phosphorylation is an important mechanism of controlling the development of these kinetoplastids. With the aim to further our knowledge of the biology of these organisms we present a characterisation of the phosphatase complement (phosphatome) of the three parasites.

Results: An ontology-based scan of the three genomes was used to identify 86 phosphatase catalytic domains in T. cruzi, 78 in T. brucei, and 88 in L. major. We found interesting differences with other eukaryotic genomes, such as the low proportion of tyrosine phosphatases and the expansion of the serine/threonine phosphatase family. Additionally, a large number of atypical protein phosphatases were identified in these species, representing more than one third of the total phosphatase complement. Most of the atypical phosphatases belong to the dual-specificity phosphatase (DSP) family and show considerable divergence from classic DSPs in both the domain organisation and sequence features.

Conclusion: The analysis of the phosphatome of the three kinetoplastids indicates that they possess orthologues to many of the phosphatases reported in other eukaryotes, including humans. However, novel domain architectures and unusual combinations of accessory domains, suggest distinct functional roles for several of the kinetoplastid phosphatases, which await further experimental exploration. These distinct traits may be exploited in the selection of suitable new targets for drug development to prevent transmission and spread of the diseases, taking advantage of the already extensive knowledge on protein phosphatase inhibitors.

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Phylogram of TriTryp PTPs. The phylogram of PTP catalytic domains includes TriTryp sequences and human, S. cerevisiae and A. thaliana as markers. Phosphatase domains are indicated by systematic gene IDs. Sequences are colour-coded by organism: blue for T. cruzi (Tc), T. brucei (Tb) and L. major (LmjF); red for human (Hs); brown for S. cerevisiae (Sc) and green for A. thaliana (At). Protein names replace Swiss-Prot IDs for some human, yeast and plant sequences. Results of the four phylogenetic methods are shown: bootstrap values > 70 are black for Neighbour-Joining, brown for Bayesian and purple for Maximum Parsimony. Asterisks (*) show Maximum Likelihood support.
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Figure 3: Phylogram of TriTryp PTPs. The phylogram of PTP catalytic domains includes TriTryp sequences and human, S. cerevisiae and A. thaliana as markers. Phosphatase domains are indicated by systematic gene IDs. Sequences are colour-coded by organism: blue for T. cruzi (Tc), T. brucei (Tb) and L. major (LmjF); red for human (Hs); brown for S. cerevisiae (Sc) and green for A. thaliana (At). Protein names replace Swiss-Prot IDs for some human, yeast and plant sequences. Results of the four phylogenetic methods are shown: bootstrap values > 70 are black for Neighbour-Joining, brown for Bayesian and purple for Maximum Parsimony. Asterisks (*) show Maximum Likelihood support.

Mentions: PTPs contain single polypeptide chains that form the catalytic domain and they are usually decorated with accessory subdomains (for example, SH2, Rhodanese, Ig, FN) critical for specific regulation or subcellular location [25,29]. PTPs are recognised by a highly conserved active-site motif, CX5R, necessary for a Cys-based mechanism of catalysis, assisted by a conserved Asp residue. The rest of the catalytic domain differs significantly between subfamilies. In addition to the classical PTPs a number of atypical phosphatases exist that lack catalytic activity (STYX or pseudophosphatases) [30]. All TriTryp PTPs identified have a single PTP domain (Figure 2) with the conserved active-site motif, CX5R, but with no extracellular regions or trans-membrane regions predicted, and without any additional recognisable regulatory or targeting domains commonly found in human PTPs. A sequence analysis shows that kinetoplastid PTPs fall into three separate groups (see Additional File 2) based on the conservation of the 10 landmark motifs known to be important for catalysis, substrate binding and maintenance of the three-dimensional fold characteristic of PTPs [25]. Group 1 contains the sequences that are the most similar to human phosphatase domains. A member of this group is present in L. major (LmPTP1) with an orthologous syntenic gene in T. cruzi (TcPTP1) (see Additional file 3). However, T. brucei lacks an orthologue of this protein, suggesting that it may have a role in intracellular parasitism. This is consistent with recent functional analysis of LmPTP1 demonstrating reduced virulence of amastigote forms upon genetic ablation [19]. Group 2 contains three proteins, TbPTP1, LmPTP2 and TcPTP2 (Note that, despite the nomenclature, TbPTP1 is not the orthologue of TcPTP1 and LmPTP1). We have recently characterised TbPTP1 as a tyrosine specific PTP with a critical role in controlling T. brucei differentiation [18]. These Group 2 PTPs lack motif 2 (DX2RVXL) in the phosphatase domain and contain up to six kinetoplastid-specific regions in both the pre-catalytic and catalytic domain of the protein. Distinct specific motifs are also found in Group 1 PTPs with slight sequence variations (see Additional file 4). The function of these regions is unknown but may be potentially important in substrate recognition or regulation. Group 3 (kinetoplastid-specific PTPs, kPTPs) sequences show the most interesting variations of the PTP domain with substitutions in most motifs and a deletion between motifs 7 and 8. Substitutions were detected in the structural motifs (motifs 2–7) of five hydrophobic residues-required for core stability-, by hydrophilic and basic residues. Altogether, these changes may have a considerable effect on the stability of the PTP domain and perhaps this is compensated by alternative folding arrangements or local conformational adjustments. These may become clear once structural information on these enzymes is available. Phylogenetic analysis of the PTP sequences (Figure 3) confirms the presence of three clades, which are distantly related to human, S. cerevisiae and A. thaliana PTPs.


The TriTryp phosphatome: analysis of the protein phosphatase catalytic domains.

Brenchley R, Tariq H, McElhinney H, Szöor B, Huxley-Jones J, Stevens R, Matthews K, Tabernero L - BMC Genomics (2007)

Phylogram of TriTryp PTPs. The phylogram of PTP catalytic domains includes TriTryp sequences and human, S. cerevisiae and A. thaliana as markers. Phosphatase domains are indicated by systematic gene IDs. Sequences are colour-coded by organism: blue for T. cruzi (Tc), T. brucei (Tb) and L. major (LmjF); red for human (Hs); brown for S. cerevisiae (Sc) and green for A. thaliana (At). Protein names replace Swiss-Prot IDs for some human, yeast and plant sequences. Results of the four phylogenetic methods are shown: bootstrap values > 70 are black for Neighbour-Joining, brown for Bayesian and purple for Maximum Parsimony. Asterisks (*) show Maximum Likelihood support.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2175518&req=5

Figure 3: Phylogram of TriTryp PTPs. The phylogram of PTP catalytic domains includes TriTryp sequences and human, S. cerevisiae and A. thaliana as markers. Phosphatase domains are indicated by systematic gene IDs. Sequences are colour-coded by organism: blue for T. cruzi (Tc), T. brucei (Tb) and L. major (LmjF); red for human (Hs); brown for S. cerevisiae (Sc) and green for A. thaliana (At). Protein names replace Swiss-Prot IDs for some human, yeast and plant sequences. Results of the four phylogenetic methods are shown: bootstrap values > 70 are black for Neighbour-Joining, brown for Bayesian and purple for Maximum Parsimony. Asterisks (*) show Maximum Likelihood support.
Mentions: PTPs contain single polypeptide chains that form the catalytic domain and they are usually decorated with accessory subdomains (for example, SH2, Rhodanese, Ig, FN) critical for specific regulation or subcellular location [25,29]. PTPs are recognised by a highly conserved active-site motif, CX5R, necessary for a Cys-based mechanism of catalysis, assisted by a conserved Asp residue. The rest of the catalytic domain differs significantly between subfamilies. In addition to the classical PTPs a number of atypical phosphatases exist that lack catalytic activity (STYX or pseudophosphatases) [30]. All TriTryp PTPs identified have a single PTP domain (Figure 2) with the conserved active-site motif, CX5R, but with no extracellular regions or trans-membrane regions predicted, and without any additional recognisable regulatory or targeting domains commonly found in human PTPs. A sequence analysis shows that kinetoplastid PTPs fall into three separate groups (see Additional File 2) based on the conservation of the 10 landmark motifs known to be important for catalysis, substrate binding and maintenance of the three-dimensional fold characteristic of PTPs [25]. Group 1 contains the sequences that are the most similar to human phosphatase domains. A member of this group is present in L. major (LmPTP1) with an orthologous syntenic gene in T. cruzi (TcPTP1) (see Additional file 3). However, T. brucei lacks an orthologue of this protein, suggesting that it may have a role in intracellular parasitism. This is consistent with recent functional analysis of LmPTP1 demonstrating reduced virulence of amastigote forms upon genetic ablation [19]. Group 2 contains three proteins, TbPTP1, LmPTP2 and TcPTP2 (Note that, despite the nomenclature, TbPTP1 is not the orthologue of TcPTP1 and LmPTP1). We have recently characterised TbPTP1 as a tyrosine specific PTP with a critical role in controlling T. brucei differentiation [18]. These Group 2 PTPs lack motif 2 (DX2RVXL) in the phosphatase domain and contain up to six kinetoplastid-specific regions in both the pre-catalytic and catalytic domain of the protein. Distinct specific motifs are also found in Group 1 PTPs with slight sequence variations (see Additional file 4). The function of these regions is unknown but may be potentially important in substrate recognition or regulation. Group 3 (kinetoplastid-specific PTPs, kPTPs) sequences show the most interesting variations of the PTP domain with substitutions in most motifs and a deletion between motifs 7 and 8. Substitutions were detected in the structural motifs (motifs 2–7) of five hydrophobic residues-required for core stability-, by hydrophilic and basic residues. Altogether, these changes may have a considerable effect on the stability of the PTP domain and perhaps this is compensated by alternative folding arrangements or local conformational adjustments. These may become clear once structural information on these enzymes is available. Phylogenetic analysis of the PTP sequences (Figure 3) confirms the presence of three clades, which are distantly related to human, S. cerevisiae and A. thaliana PTPs.

Bottom Line: The prevalence of these neglected diseases results from a combination of poverty, inadequate prevention and difficult treatment.We found interesting differences with other eukaryotic genomes, such as the low proportion of tyrosine phosphatases and the expansion of the serine/threonine phosphatase family.These distinct traits may be exploited in the selection of suitable new targets for drug development to prevent transmission and spread of the diseases, taking advantage of the already extensive knowledge on protein phosphatase inhibitors.

View Article: PubMed Central - HTML - PubMed

Affiliation: Faculty of Life Sciences, Michael Smith, University of Manchester, M13 9PT, UK. Rachel.Brenchley@postgrad.manchester.ac.uk

ABSTRACT

Background: The genomes of the three parasitic protozoa Trypanosoma cruzi, Trypanosoma brucei and Leishmania major are the main subject of this study. These parasites are responsible for devastating human diseases known as Chagas disease, African sleeping sickness and cutaneous Leishmaniasis, respectively, that affect millions of people in the developing world. The prevalence of these neglected diseases results from a combination of poverty, inadequate prevention and difficult treatment. Protein phosphorylation is an important mechanism of controlling the development of these kinetoplastids. With the aim to further our knowledge of the biology of these organisms we present a characterisation of the phosphatase complement (phosphatome) of the three parasites.

Results: An ontology-based scan of the three genomes was used to identify 86 phosphatase catalytic domains in T. cruzi, 78 in T. brucei, and 88 in L. major. We found interesting differences with other eukaryotic genomes, such as the low proportion of tyrosine phosphatases and the expansion of the serine/threonine phosphatase family. Additionally, a large number of atypical protein phosphatases were identified in these species, representing more than one third of the total phosphatase complement. Most of the atypical phosphatases belong to the dual-specificity phosphatase (DSP) family and show considerable divergence from classic DSPs in both the domain organisation and sequence features.

Conclusion: The analysis of the phosphatome of the three kinetoplastids indicates that they possess orthologues to many of the phosphatases reported in other eukaryotes, including humans. However, novel domain architectures and unusual combinations of accessory domains, suggest distinct functional roles for several of the kinetoplastid phosphatases, which await further experimental exploration. These distinct traits may be exploited in the selection of suitable new targets for drug development to prevent transmission and spread of the diseases, taking advantage of the already extensive knowledge on protein phosphatase inhibitors.

Show MeSH
Related in: MedlinePlus