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The aspartic proteinase family of three Phytophthora species.

Kay J, Meijer HJ, ten Have A, van Kan JA - BMC Genomics (2011)

Bottom Line: Unexpectedly, however, the oomycetes were found to have both active and probably-inactive forms of an AP similar to vertebrate BACE, the enzyme responsible for initiating the processing cascade that generates the Aβ peptide central to Alzheimer's Disease.Since the translocation of Phytophthora effector proteins is currently a topic of intense research activity, the identification in Phytophthora of potential functional homologues of plasmepsin V would appear worthy of investigation.The significant revision of gene models and detailed annotation presented here should significantly facilitate experimental design.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK.

ABSTRACT

Background: Phytophthora species are oomycete plant pathogens with such major social and economic impact that genome sequences have been determined for Phytophthora infestans, P. sojae and P. ramorum. Pepsin-like aspartic proteinases (APs) are produced in a wide variety of species (from bacteria to humans) and contain conserved motifs and landmark residues. APs fulfil critical roles in infectious organisms and their host cells. Annotation of Phytophthora APs would provide invaluable information for studies into their roles in the physiology of Phytophthora species and interactions with their hosts.

Results: Genomes of Phytophthora infestans, P. sojae and P. ramorum contain 11-12 genes encoding APs. Nine of the original gene models in the P. infestans database and several in P. sojae and P. ramorum (three and four, respectively) were erroneous. Gene models were corrected on the basis of EST data, consistent positioning of introns between orthologues and conservation of hallmark motifs. Phylogenetic analysis resolved the Phytophthora APs into 5 clades. Of the 12 sub-families, several contained an unconventional architecture, as they either lacked a signal peptide or a propart region. Remarkably, almost all APs are predicted to be membrane-bound.

Conclusions: One of the twelve Phytophthora APs is an unprecedented fusion protein with a putative G-protein coupled receptor as the C-terminal partner. The others appear to be related to well-documented enzymes from other species, including a vacuolar enzyme that is encoded in every fungal genome sequenced to date. Unexpectedly, however, the oomycetes were found to have both active and probably-inactive forms of an AP similar to vertebrate BACE, the enzyme responsible for initiating the processing cascade that generates the Aβ peptide central to Alzheimer's Disease. The oomycetes also encode enzymes similar to plasmepsin V, a membrane-bound AP that cleaves effector proteins of the malaria parasite Plasmodium falciparum during their translocation into the host red blood cell. Since the translocation of Phytophthora effector proteins is currently a topic of intense research activity, the identification in Phytophthora of potential functional homologues of plasmepsin V would appear worthy of investigation. Indeed, elucidation of the physiological roles of the APs identified here offers areas for future study. The significant revision of gene models and detailed annotation presented here should significantly facilitate experimental design.

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Alignment of the mature enzyme regions of the PxAP3 - 7 predicted polypeptides with pig pepsin. The numbering system is that of pig pepsin (PepA_PIG) and other details are as described in the legend to Figure 2. The polyproline loop regions of PsAP3 and PrAP3, discussed in the text, are highlighted by a dotted box ().
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Figure 3: Alignment of the mature enzyme regions of the PxAP3 - 7 predicted polypeptides with pig pepsin. The numbering system is that of pig pepsin (PepA_PIG) and other details are as described in the legend to Figure 2. The polyproline loop regions of PsAP3 and PrAP3, discussed in the text, are highlighted by a dotted box ().

Mentions: The sequences of the mature enzyme regions of each of the 12 sets of orthologues from the three Phytophthora species were aligned and a phylogenetic tree was generated (Figure 1). This resolved the PxAP1-12 sequences into five clades that are related to well-documented APs from other species. Each Phytophthora species is thus equipped with an AP gene family, the members of which have distinct gene organisations (Table 3) and encode polypeptides with considerably different sequences (Figures 2, 3, 4, 5) and, potentially, distinct activities. Each of the clades will be considered in turn.


The aspartic proteinase family of three Phytophthora species.

Kay J, Meijer HJ, ten Have A, van Kan JA - BMC Genomics (2011)

Alignment of the mature enzyme regions of the PxAP3 - 7 predicted polypeptides with pig pepsin. The numbering system is that of pig pepsin (PepA_PIG) and other details are as described in the legend to Figure 2. The polyproline loop regions of PsAP3 and PrAP3, discussed in the text, are highlighted by a dotted box ().
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3116508&req=5

Figure 3: Alignment of the mature enzyme regions of the PxAP3 - 7 predicted polypeptides with pig pepsin. The numbering system is that of pig pepsin (PepA_PIG) and other details are as described in the legend to Figure 2. The polyproline loop regions of PsAP3 and PrAP3, discussed in the text, are highlighted by a dotted box ().
Mentions: The sequences of the mature enzyme regions of each of the 12 sets of orthologues from the three Phytophthora species were aligned and a phylogenetic tree was generated (Figure 1). This resolved the PxAP1-12 sequences into five clades that are related to well-documented APs from other species. Each Phytophthora species is thus equipped with an AP gene family, the members of which have distinct gene organisations (Table 3) and encode polypeptides with considerably different sequences (Figures 2, 3, 4, 5) and, potentially, distinct activities. Each of the clades will be considered in turn.

Bottom Line: Unexpectedly, however, the oomycetes were found to have both active and probably-inactive forms of an AP similar to vertebrate BACE, the enzyme responsible for initiating the processing cascade that generates the Aβ peptide central to Alzheimer's Disease.Since the translocation of Phytophthora effector proteins is currently a topic of intense research activity, the identification in Phytophthora of potential functional homologues of plasmepsin V would appear worthy of investigation.The significant revision of gene models and detailed annotation presented here should significantly facilitate experimental design.

View Article: PubMed Central - HTML - PubMed

Affiliation: School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK.

ABSTRACT

Background: Phytophthora species are oomycete plant pathogens with such major social and economic impact that genome sequences have been determined for Phytophthora infestans, P. sojae and P. ramorum. Pepsin-like aspartic proteinases (APs) are produced in a wide variety of species (from bacteria to humans) and contain conserved motifs and landmark residues. APs fulfil critical roles in infectious organisms and their host cells. Annotation of Phytophthora APs would provide invaluable information for studies into their roles in the physiology of Phytophthora species and interactions with their hosts.

Results: Genomes of Phytophthora infestans, P. sojae and P. ramorum contain 11-12 genes encoding APs. Nine of the original gene models in the P. infestans database and several in P. sojae and P. ramorum (three and four, respectively) were erroneous. Gene models were corrected on the basis of EST data, consistent positioning of introns between orthologues and conservation of hallmark motifs. Phylogenetic analysis resolved the Phytophthora APs into 5 clades. Of the 12 sub-families, several contained an unconventional architecture, as they either lacked a signal peptide or a propart region. Remarkably, almost all APs are predicted to be membrane-bound.

Conclusions: One of the twelve Phytophthora APs is an unprecedented fusion protein with a putative G-protein coupled receptor as the C-terminal partner. The others appear to be related to well-documented enzymes from other species, including a vacuolar enzyme that is encoded in every fungal genome sequenced to date. Unexpectedly, however, the oomycetes were found to have both active and probably-inactive forms of an AP similar to vertebrate BACE, the enzyme responsible for initiating the processing cascade that generates the Aβ peptide central to Alzheimer's Disease. The oomycetes also encode enzymes similar to plasmepsin V, a membrane-bound AP that cleaves effector proteins of the malaria parasite Plasmodium falciparum during their translocation into the host red blood cell. Since the translocation of Phytophthora effector proteins is currently a topic of intense research activity, the identification in Phytophthora of potential functional homologues of plasmepsin V would appear worthy of investigation. Indeed, elucidation of the physiological roles of the APs identified here offers areas for future study. The significant revision of gene models and detailed annotation presented here should significantly facilitate experimental design.

Show MeSH
Related in: MedlinePlus