BACKGROUND
the oomycete genus phytophthora is comprised of over  <dig> species, most of which are plant pathogens  <cit> .
the most renowned and devastating species is p. infestans, which contributed to the potato famine in ireland, resulting in a million deaths through starvation, and the mass exodus of many more to other locations, principally in north america  <cit> .
the pathogen continues to blight modern agriculture and causes an annual loss in worldwide potato crops approaching $ <dig> billion  <cit> .
the economic damage has intensified research to increase our knowledge of this organism that has now been under investigation for more than  <dig> years.
the genome sequences of p. infestans, and two related species, p. sojae, causing soybean root and stem rot and p. ramorum, the sudden oak death pathogen, were recently determined  <cit> .
at  <dig>   <dig> and  <dig> megabases respectively, there is a considerable difference in the genome sizes of p. infestans, p. sojae and p. ramorum.
gene numbers among the three genomes are not drastically different and there is considerable co-linearity between them.
genome size expansion in p. infestans has mainly resulted from escalation in the number of repeat regions and transposons  <cit> .
analyses of phytophthora genomes have identified genes encoding proteins containing novel combinations of previously identified domains  <cit> .
in common with other organisms for which genome sequences have been elucidated, one protein category which is highly represented in the three phytophthora genomes is that of proteolytic enzymes  <cit> .
these protein hydrolases have a wide variety of roles in all organisms including nutrient provision, stress responses and cell death processes.
proteinases are categorised into a number of catalytic types, dependent on the nature of the nucleophile that participates in the catalytic reaction.
the merops database  classifies proteinases into clans which contain all the proteins that have arisen from a single evolutionary origin  <cit> .
a clan represents one or more families of proteinases that reveal their evolutionary relationship through similarities at the primary and 3d-structural levels.
our interests over many years have focussed on aspartic proteinases, which belong to the aa clan.
within this clan, most members reside in the a <dig> family and are related to the archetypal patriarch, pepsin, or in family a <dig> which encompasses proteinases from retroviruses including hiv  <cit> .
aps participate in a variety of physiological and pathological processes  <cit>  in vertebrates  while in plants aps have roles in senescence, stress responses and fertilization  <cit>  as well as in defence against pathogens  <cit> .
reciprocally, aps are deployed by pathogens to facilitate infection e.g.
hiv/aids  <cit> , thrush  and malaria  <cit> .
inhibitors targeted against hiv-proteinase are now in widespread use in therapy for treatment of hiv-infected individuals  <cit> .
recently it has been shown that one ap of plasmodium falciparum is an ideal target for development of therapeutic inhibitors to treat malaria  <cit> .
this ap is responsible for processing plasmodium effector proteins in a step that is crucial for their export into the host red blood cell, thereby reprogramming the host cell to meet the demands of the parasite.
with these examples serving to illustrate the reliance of both host and pathogens on ap activities, it was of considerable interest to establish and annotate the complement of aps encoded within the three phytophthora genomes, particularly since one of the major current subjects of oomycete research is on effectors that modulate host cell physiology and immune responses.
phytophthora effectors are small, secreted proteins that undergo translocation into host cells  <cit>  in a manner analogous to that for the plasmodium effectors  <cit> .
however, the components of the phytophthora translocation machinery remain to be identified.
here we describe the complete ap family of three phytophthora species and identify some of its members which may participate in effector translocation.
RESULTS
genome sequences of p. infestans , p. sojae and p. ramorum  were analysed for the presence of genes encoding putative pepsin-like aspartic proteinases as described in the methods.
pepsin-like aps from family a <dig> are typically produced in the form of a precursor, consisting of a signal peptide followed by a propart region that has to be excised from the zymogen polypeptide chain in order to generate the mature enzyme.
the mature enzyme region consists of two homologous catalytic domains, each of which provides a catalytic asp residue to the active site  <cit> .
each asp residue is located within the hallmark motif asp-thr/ser-gly, which is followed by a hydrophobic-hydrophobic-gly sequence, as exemplified by the family patriarch, pig pepsin .
together, these motifs form a structural feature known as a psi loop  <cit> .
a tyr residue is located at position  <dig>  in a β-hairpin loop which overlies the active site.
this residue is strictly conserved in all active pepsin-like aps and serves as a landmark residue that can be anticipated to be present in newly-identified ap sequences.
a number of other motifs and landmark residues  are present at characteristic locations along a <dig> family member polypeptides.
a total of  <dig> predicted protein sequences exhibiting some or all of these hallmark features and landmark residues were identified in p. infestans, with  <dig> and  <dig> entries detected in p. sojae and p. ramorum, respectively.
inspection of the sequences revealed that, in p. ramorum, gene model pr_ <dig> was erroneous due to incorrect assembly of the dna sequence in this region and gene model pr_ <dig>  present in a correctly assembled sequence, was a pseudogene lacking at least  <dig> residues of the n-terminus of a functional ap.
in p. sojae, the sequence encoded by gene ps_ <dig> was highly similar to aps but the two hallmark asp-thr/ser-gly motifs were replaced by asp-val-met and phe-thr-met respectively, such that the encoded protein could not possibly be active.
this entry, which lacked an orthologue in both p. infestans and p. ramorum, was thus considered also to be a pseudogene.
the above three gene models were thus excluded from further analyses.
the remaining  <dig> genes were the only ones consistently identified by repeated search using psi-blast  <cit>  or hmmer  <cit> , so that it would appear no further ap homologues are present within these three genomes.
these  <dig> gene models were analysed  and are further discussed in groups on the basis of orthology.
comparison of the orthologues from the three species revealed in a number of cases that the gene models, as originally annotated , were likely to be incorrect.
the wealth of information available on pepsin-like ap sequences  including the hallmark motifs/landmark residues described above, was applied together with available est and trace file data, to guide the final gene predictions for putative aps encoded in the three phytophthora genomes.
additional file  <dig> lists the gene models that required correction.
more than half of the original gene models annotated in the p. sojae and p. ramorum databases were correct, whilst almost all of the original entries for p. infestans were erroneous.
the annotation errors that were identified  included mis-identification  of the initiator met residue,  of intron presence/absence,  of the 5' and/or 3' splice junctions of introns as well as  sequence trace mis-reads or  trace mis-usage in assembly of the p. infestans sequence due to heterozygosity.
annotation errors in two p. infestans genes due to sequencing related issues were corrected by re-examination of original sequence trace files at ncbi and by re-sequencing relevant regions.
the corrected nucleotide sequences of these genes  are deposited in ncbi under accession numbers hm <dig> and hm <dig>  respectively.
for all gene models, the intron positions were verified by inspection of est information, if available, and by comparison with dna sequences of the orthologous gene in the other two species for the presence or absence of possible splice junctions at the equivalent nucleotide position.
the corrected gene models and their encoded polypeptides are summarised in table  <dig>  all corrections proposed for the p. infestans gene models were confirmed by available est data or by cloning and sequencing the cdna.
two of the three proposed corrected gene models for p. sojae  were confirmed by cloning and sequencing the cdna, while for the third , correction could not be confirmed as cdna amplification was unsuccessful.
corrections in p. ramorum gene models were not experimentally validated as this species has a quarantine status.
an initial insight into the expression patterns of these aps was obtained from microarray analysis of p. infestans genes using the genome-wide nimblegen array  <cit> .
consistent levels of expression were observed for each of the eleven piap genes during culture on different agar media and during infection on potato .
the number of introns and length of each polypeptide predicted by the database-annotated gene models  are depicted for the orthologues from p. infestans, p. sojae and p. ramorum set out in each row.
genes are presented as groups of orthologues.
the generic descriptors pxap1- <dig> are used to denote the respective encoded polypeptides.
the number of residues in each polypeptide is indicated.
the final protein sequences predicted for each of the  <dig> aps from the three phytophthora species are listed individually in additional file  <dig>  each of these sets of orthologous polypeptides was examined for the presence/absence of a signal peptide and a propart segment preceding the mature enzyme region.
these features are summarised in table  <dig>  the individual signal peptide/propart segment sequences for each of the  <dig> sets of orthologues are aligned in additional file  <dig>  in order to simplify the descriptions that follow, the identifiers pxap1- <dig> were assigned to each of these sets of orthologues.
except for pxap <dig>  the polypeptides continued beyond the conventional location of the c-terminus of an archetypal ap, as defined by the reference standard, pig pepsin .
each of the pxap <dig> - pxap <dig> polypeptides thus contained a c-terminal extension .
these extensions differed markedly in length and sequence  and could only be aligned with the sequences of their orthologue from the other phytophthora species, and not with any other sequence in the set of entries or with any archetypal ap.
only short extensions were present in the psap <dig> and prap <dig> polypeptides .
the c-terminal extensions for pxap <dig> and pxap <dig> - pxap <dig> were considerably longer and all contained at least one stretch of approximately  <dig> consecutive hydrophobic residues  which are predicted to provide a membrane-spanning segment.
thus, almost all the phytophthora aps  are predicted to be membrane-bound enzymes.
while it is not uncommon for individual aps from other species to be membrane-anchored in such a fashion , it is unprecedented for almost the entire ap complement of an organism to appear to be membrane-bound enzymes.
considerable experimental effort will need to be invested to establish whether all of these predicted polypeptides are indeed membrane-associated but in previous investigations, aps that have been predicted to contain a membrane-associated segment have always been proven by subsequent experimental investigations to be membrane-attached.
further consideration will be given to this aspect for the individual cases described below.
the sequences of the mature enzyme regions of each of the  <dig> sets of orthologues from the three phytophthora species were aligned and a phylogenetic tree was generated .
this resolved the pxap1- <dig> 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  and encode polypeptides with considerably different sequences  and, potentially, distinct activities.
each of the clades will be considered in turn.
archetypal pepsin-like aspartic proteinases
in clade  <dig> of the phylogenetic tree , three proteins designated piap <dig>  psap <dig> and prap <dig>  are encoded by orthologous single exon genes .
the pxap <dig> polypeptides  display all of the essential components i.e.
signal peptide, propart segment  and two-domain mature enzyme region , including all the necessary hallmark motifs and residues of archetypal pepsin-like aps described earlier .
these polypeptides are not extended at their c-terminus.
the phylogenetic analysis revealed that the three pxap <dig> polypeptides cluster closely with fungal aps  that are known to be located in the vacuole of the cell.
this subfamily, with saccharopepsin from s. cerevisiae as the parent member, is assigned the identifier a <dig>  in the merops database.
analyses of all sequenced fungal genomes has revealed that the only ap that is omnipresent is the vacuolar enzyme  <cit> .
thus, it seems likely that piap <dig>  psap <dig> and prap <dig> are the respective vacuolar aps from each phytophthora species.
piap <dig> has been produced in recombinant form and shown to have ap activity on haemoglobin .
the polypeptides of the pxap <dig> in clade  <dig>  are atypical in that they do not contain a signal peptide or a non-classical secretion signal .
this is highly unusual in aps although precedents have been observed in fungi including botrytis cinerea  <cit>  and in bacterial species of marine origin  <cit> .
it is not obvious how these polypeptides are able to become incorporated into a membrane through the  hydrophobic segment in their c-terminal extensions  when there is no signal peptide to mediate transfer into the endoplasmic reticulum.
experiments using fusion constructs with reporter proteins will be necessary to resolve this conundrum.
within clade  <dig>  five clusters  were resolved from one another .
more profound phylogenetic analysis  indicates that this clade forms a monophyletic clade with three entries from two filamentous fungi, i.e.
the zygomycetes rhizopus oryzae and phycomyces blakesleeanus.
pxap3-encoding genes were only detected in p. sojae and p. ramorum .
despite repeated searching, an orthologue of these two in p. infestans could not be detected.
the pxap <dig> genes are located in regions of co-linearity.
scrutiny of the five flanking genes  in the p. sojae and p. ramorum genomes revealed that orthologues are present in similar arrangement in p. infestans dna, however, on separate contigs.
the gap between the contigs corresponds to the likely location of the "missing" ap gene.
moreover, no unassembled reads were identified in p. infestans that matched psap <dig> or prap <dig> sequences.
the originally-annotated gene models for ps_ <dig> and pr_ <dig> both required considerable correction .
the 5'-splice donor site of the third intron in ps_ <dig> was identified to be a gc dinucleotide sequence.
this dinucleotide has been found to be used as the 5'-donor junction at low frequency  in a number of fungi  <cit>  but no information is available as yet on its use in oomycetes.
the amendments to the ps_ <dig> and pr_ <dig> gene models  resulted in predicted polypeptide sequences that contained both signal peptide and propart segments .
the sequences of the mature enzyme regions  showed a pairwise identity of 71%.
both polypeptides contained all three of the disulphide bonds that are common in vertebrate aps and they were only slightly extended at their c-terminal end relative to pepsin .
psap <dig> and prap <dig> can be predicted to display different substrate specificities.
the region between residues  <dig> and  <dig> is known conventionally as the "polyproline loop" and has been demonstrated to be a major determinant for substrate specificity  <cit> .
in prap <dig>  the sequence lgddlyw of this region has two extra  residues compared to the lsdd--w sequence of psap <dig> .
the presence of these two hydrophobic residues is likely to influence specificity.
like pxap <dig>  the pxap <dig> and pxap <dig> polypeptides from phytophthora contained the conventional ap segments of a signal peptide and propart , prior to the mature enzyme region .
each trio of polypeptides was also extended at its c-terminus but, whereas the extensions in pxap <dig> consisted of 136- <dig> residues with one putative membrane-spanning stretch, the pxap <dig> extensions were substantially longer .
indeed, the c-terminal extensions in piap <dig>  and its orthologues encompassed no less than seven potential transmembrane segments , an architecture highly reminiscent of the seven transmembrane stretches that constitute the super-family of g-protein coupled receptors   <cit> .
blast search using the sequence of the c-terminal extension of piap <dig> as query, identified the first non-self hit  as rpka, a g-protein coupled receptor family protein from dictyostelium discoideum  <cit> .
a  <dig> % similarity in a  <dig> amino acid overlap was calculated between the two sequences using smith-waterman analysis  <cit> .
the intriguing possibility thus arises that, in phytophthora species, a fusion protein is produced in which the n-terminal partner is an ap connected to a putative gpcr as the c-terminal component.
self-processing to release the ap component would generate the mature gpcr.
such a self-processing phenomenon is unprecedented, although receptors activated by extrinsic proteinases are well-documented  <cit> .
further investigations into the phytophthora ap-gpcr fusion-proteins would appear to be well-merited.
the final two sub-groups that were resolved within clade  <dig> consisted of pxap <dig> and pxap <dig> .
no orthologue was detected in p. sojae for the proteins piap <dig> and prap <dig>  encoded by pitg_ <dig> and pr_ <dig> .
the piap7- and prap7-encoding genes are located in co-linear orthologous regions of the p. infestans and p. ramorum genomes, as confirmed by the organization of flanking genes.
in p. sojae, the corresponding genomic region had a similar co-linearity arrangement with the exception of two missing genes, one of them in the region where an orthologous ap-encoding gene should have been located.
moreover, no unassembled reads were identified in p. sojae that matched the piap <dig> or prap <dig> sequences.
the simplest interpretation is that an ancestor of the pxap7-encoding gene was present in phytophthora, and deletion of the region resulted in loss of the orthologue in p. sojae, although it cannot be excluded that substitutions have accumulated to an extent that prevents recognition of the gene.
the pxap <dig> and pxap <dig> polypeptides showed an unusual variation in the component segments that constitute an archetypal ap in that a propart was absent .
in each case, the signal peptide  immediately precedes the mature enzyme region  which, in turn, is followed by a c-terminal extension .
as stated above, almost all pepsin-like aps are synthesised in the form of a precursor.
the propart segment makes a number of essential contributions, such as ensuring proper folding and intracellular sorting of the zymogen polypeptide, and facilitation of its activation into the mature enzyme form upon encountering the appropriate conditions  <cit> .
very recently, however, aps lacking a propart segment have been described from marine bacteria  <cit>  and fungi  <cit> , hence this unusual architecture of the pxap <dig> and pxap <dig> polypeptides in phytophthora species is not without precedent.
bace-like aspartic proteinases
the pxap <dig> and pxap <dig> polypeptides were resolved by the phylogenetic analysis into clade  <dig> .
these polypeptides also contained a signal peptide , the mature enzyme region  and a c-terminal extension  but they too lacked a propart , just like pxap <dig> and pxap <dig>
the phylogenetic analysis  revealed that these proteins cluster within clade  <dig> with human bace and its paralogue, bace <dig> .
the mature enzyme forms of bace/bace <dig> are initially synthesised in precursor forms that do contain propart segments.
while the presence of the propart has little effect on the intrinsic proteolytic activity, its inclusion at the n-terminus of probace/probace <dig> ensures much more rapid folding of the polypeptide than is observed when only the mature forms of each enzyme are produced .
bace and bace <dig> were among the first aps to be identified as having a c-terminal extension which ensured they were membrane-bound.
the mature enzyme regions  have hallmark features which distinguish a <dig> / <dig> subfamily members from classical aps such as pepsin.
among these are:  the highly-conserved trp <dig>  is replaced by ala and is itself relocated to a position  just downstream from the essential tyr <dig> residue on the β-hairpin loop that overhangs the active site cleft ,  disulphide bonds in characteristic locations that increase stability of the polypeptide.
these additional cys residues and the trp39ala replacement are all present in pxap <dig> and pxap <dig> proteins .
bace has been identified as the β-site alzheimer's precursor protein  cleaving enzyme  responsible for the cleavage that generates the free n-terminal end of the aβ peptide which plays a central role in alzheimer's disease  <cit> .
for almost a decade, bace has been the target of intense efforts to develop inhibitors to alleviate the dementia of alzheimer's disease.
genes encoding bace and its paralogue, bace <dig>  have been identified in species ranging from humans through elephant, opossum, armadillo, hedgehog, shrew, and fish, to platypus .
to the best of the authors' knowledge, the identification of pxap8-encoding genes from three phytophthora species provides the first indication that bace-like, membrane-bound aps may not be limited to the vertebrates.
intriguingly, the phytophthora genomes also contain genes encoding homologues of presenilin, nicastrin, anterior pharynx defective- <dig> and presenilin enhancer- <dig>  .
these are all components of the human γ-secretase complex which completes the proteolytic processing by releasing the aβ peptide at its c-terminal end from the alzheimer's precursor polypeptide  <cit> .
the presence of both β- and γ-secretase gene products in microbes such as phytophthora suggests that their function is not limited to the processing of a brain polypeptide related to alzheimer's disease.
these proteins therefore seem to be very ancient features that are conserved between oomycetes and vertebrates, and they have been coopted in vertebrate species to cleave the brain app polypeptide.
while the pxap <dig> polypeptides exhibited the hallmark characteristics of bace/bace <dig> subfamily members, the pxap <dig> proteins lacked one feature that is necessary for an ap to be active as an enzyme.
the tyr residue located at position  <dig>  is conserved in every pepsin-like ap that is known to be active, although it does not participate directly in the catalytic mechanism  <cit> .
in pxap <dig>  this tyr residue is replaced by phe  so the catalytic activity can be postulated to be compromised, at best.
a protein engineering study revealed that the replacement of tyr <dig> in a fungal ap by asn or phe permitted activity, albeit at a considerably reduced level, while all other replacements abolished activity  <cit> .
however, a number of catalytically-inactive aps have been reported previously, including the pregnancy-associated glycoproteins  found in the placenta of ungulates   <cit>  and perhaps most notably, the bla g <dig> protein  which is a predominant allergen from cockroach  <cit> .
the crystal structure of bla g <dig> shows that it has the fold and three-dimensional structure typical of pepsin-like aps  <cit> .
bla g <dig> and the pags from ovis aries and capra hircus all have a phe residue at position  <dig>  these three proteins have additional substitutions at the two active site dt/sg motifs, cementing their catalytic inactivity.
their function has been postulated to include roles in peptide-binding and presentation, but without cleavage.
if pxap <dig> should also prove to be catalytically ineffective, the active site will still be accessible for the binding of peptides that cannot undergo cleavage and so a role similar to the pags/bla g <dig> in peptide binding might be feasible.
this intriguing possibility is rendered all the more fascinating with the realisation that, in contrast to the pags/bla g <dig>  these phytophthora orthologues are likely to be membrane-bound through their c-terminal extensions  and might function as a novel type of surface receptor.
in this regard, it may well be noteworthy that the putative intracellular domain comprised of the residues downstream from the transmembrane segment in the c-terminal extension in pxap <dig> is considerably longer than its pxap <dig> counterpart .
neither of the c-terminal extensions, however, contains a discernible pfam domain or protein motif.
thus, all three phytophthora species may produce one catalytically-active bace-like enzyme  and one peptide-binding, membrane-bound enzymatically inactive paralogue with an intracellular extension of unknown function .
nepenthesin-like aspartic proteinases
the remaining three ap genes in each phytophthora genome , encoding polypeptides pxap <dig>  pxap <dig> and pxap <dig> cluster into clade  <dig> with representative aps from merops subfamily a1b including the patriarch of plant origin, nepenthesin, and plasmepsin v from plasmodium falciparum .
the pxap <dig> -  <dig> polypeptides contrast with their pxap <dig> -  <dig> counterparts in having the archetypal ap architecture of a signal peptide followed by a propart , a mature enzyme region , terminating with c-terminal extensions .
pxap <dig> -  <dig> differed, however, from all of the other phytophthora aps  in having a small extra segment inserted  in the region just upstream from tyr <dig> .
no less than seven cys residues are present between residues  <dig> -  <dig>  with a further three cys residues  conserved at characteristic locations elsewhere in the mature enzyme regions of the nine phytophthora aps in clade  <dig>  together, these cys residues are likely to form five specific disulphide bridges, paired as indicated in figure  <dig>  this arrangement of disulphide bridges has been deduced from biochemical analyses of the aps of plant origin  <cit>  that cluster with pxap <dig> -  <dig> in clade  <dig>  indeed, most of the aps in plants  <cit>  contain these cys residues as well as the insert and they are grouped into subfamily a1b in the merops database.
the plant aps identified in clade  <dig> are readily distinguished on the basis of their functional activity from one another and from others that are not included here for the sake of brevity, such as the nucellins , regulators of the degradation of nucellar cells after ovule fertilisation  <cit> , and the chloroplast nucleoids dna-binding  proteinase  which catalyses the degradation of rubisco in senescent leaves  <cit> .
nepenthesins  are extracellular enzymes secreted by the carnivorous plant, nepenthes, to digest its prey  <cit>  while cdr <dig> of arabidopsis plays a crucial role in activating resistance of arabidopsis against microbial pathogens  <cit> .
overexpression of cdr <dig> leads to constitutive disease resistance, while gene silencing compromises resistance.
the cdr <dig> gene product is suggested to release an as yet unidentified peptide that activates a signalling cascade to induce disease resistance in a salicylate-dependent manner  <cit> .
recombinant cdr <dig> protein has been produced in e. coli and shown to be active as an ap in a dimeric form  <cit> .
two intermolecular disulphide bonds were proposed to be responsible for the covalent association of the two polypeptide chains in the proteolytically-active homodimer  <cit> .
the cys residues involved in the homodimer formation are highlighted in figure  <dig> by a star ().
cys residues are present at identical locations within pxap <dig> , suggesting that this enzyme may also function as a homodimer.
in contrast, pxap <dig> is devoid of cysteine residues in this region and so, based on this criterion, should function as a monomer.
pxap <dig> does contain two cysteine residues but at different positions within this region of the polypeptide .
whether these remain as free cysteines or are involved in disulphide bonds, intra- or inter-molecular, requires experimental investigation.
one feature does serve to distinguish between the plant aps and the nine pxap <dig> -  <dig> polypeptides clustered in clade  <dig> .
most plant aps do not have c-terminal extensions .
in contrast, all nine of the oomycete pxap <dig> -  <dig> polypeptides do have c-terminal extensions, ensuring that all are membrane-bound enzymes .
in addition to plant aps, plasmepsin v was resolved into clade  <dig>  as the entry most closely associated with the pxap <dig> -  <dig> polypeptides.
plasmepsin v is one of ten aps encoded within the genome of plasmodium falciparum  <cit> , the causative agent of malaria.
this enzyme  has a c-terminal extension with a hydrophobic stretch  that results in its anchoring as a membrane-bound polypeptide  <cit> .
very recently, plasmepsin v has been demonstrated to be the  proteinase responsible for processing the precursors of plasmodium effector proteins at the pexel motif ; this step is essential for the translocation of these polypeptides into the host red blood cell  <cit> .
the malaria parasite exports hundreds of such effector proteins across the parasitophorous vacuolar membrane into the human red blood cell, thereby reprogramming the host cell to meet the needs of the parasite.
plasmepsin v is conserved in plasmodium species but is not produced in vertebrates susceptible to parasitic infection and thus serves as a target enzyme against which to develop inhibitors as novel therapeutic agents for treatment of malaria.
intriguingly, phytophthora species also secrete effector proteins that are important in modulating host defence and cell death mechanisms and many such effector proteins contain the internal sequence motif rxlr, similar to the plasmodium pexel motif  <cit> .
phytophthora effector proteins are secreted after removal of their signal peptide, giving rise to a polypeptide that contains in its n-terminal region the rxlr-containing domain which is essential for subsequent delivery into the plant cell  <cit> .
it is tempting to consider that a phytophthora effector precursor might undergo further processing to remove the rxlr domain, thereby releasing the mature, biologically active effector domain.
the similarities described above between plasmepsin v and its pxap <dig>  pxap <dig> and pxap <dig> orthologues in phytophthora suggests a conserved biological role.
by analogy to the role of plasmepsin v in processing of plasmodium effector proteins  <cit> , one or more of its phytophthora orthologues may reside in the translocon and act in the processing of phytophthora effector precursors.
there are obvious structural and genetic differences between the secretion mechanisms of the two parasites.
the genome sequences of phytophthora species lack genes homologous to the translocon complex components identified in plasmodium  <cit> .
nevertheless, our hypothesis invites experimental investigation into targeting these particular aps in phytophthora as a pathogenic achilles heel through which the devastating losses from infection by phytophthora might be reduced.
CONCLUSIONS
one of the twelve pepsin-like aps encoded within the genomes of the three phytophthora species is predicted to be produced as an unprecedented fusion protein with a putative g-protein coupled receptor as the c-terminal partner.
the other aps appear to be related to existing enzymes from other species that have already been documented.
these include the vacuolar enzyme, and somewhat more unexpectedly, bace/bace2-like aps in an active and likely inactive form akin to the bla g2/pag proteins, and plasmepsin v-like enzymes.
whether the latter are functional homologs of their plasmodium counterpart, operating in the processing of rxlr-type effector proteins during transit to the plant cell, would appear to be worthy of immediate experimental investigation given the high level of current interest in this topic.
elucidation of the physiological roles of the aps identified here offers highly fertile areas ripe for examination.
the significant revision of the erroneous gene models and the detailed annotation presented here should be highly beneficial in facilitating future experimental design.

 the oomycete genus phytophthora is comprised of over species, most of which are plant pathogens. the most renowned and devastating species is p. infestans, which contributed to the potato famine in ireland, resulting in a million deaths through starvation, and the mass exodus of many more to other locations, principally in north america. the pathogen continues to blight modern agriculture and causes an annual loss in worldwide potato crops approaching $ billion. the economic damage has intensified research to increase our knowledge of this organism that has now been under investigation for more than years. the genome sequences of p. infestans, and two related species, p. sojae, causing soybean root and stem rot and p. ramorum, the sudden oak death pathogen, were recently determined. at and megabases respectively, there is a considerable difference in the genome sizes of p. infestans, p. sojae and p. ramorum. gene numbers among the three genomes are not drastically different and there is considerable co-linearity between them. genome size expansion in p. infestans has mainly resulted from escalation in the number of repeat regions and transposons. analyses of phytophthora genomes have identified genes encoding proteins containing novel combinations of previously identified domains. in common with other organisms for which genome sequences have been elucidated, one protein category which is highly represented in the three phytophthora genomes is that of proteolytic enzymes. these protein hydrolases have a wide variety of roles in all organisms including nutrient provision, stress responses and cell death processes. proteinases are categorised into a number of catalytic types, dependent on the nature of the nucleophile that participates in the catalytic reaction. the merops database classifies proteinases into clans which contain all the proteins that have arisen from a single evolutionary origin. a clan represents one or more families of proteinases that reveal their evolutionary relationship through similarities at the primary and 3d-structural levels. our interests over many years have focussed on aspartic proteinases, which belong to the aa clan. within this clan, most members reside in the a family and are related to the archetypal patriarch, pepsin, or in family a which encompasses proteinases from retroviruses including hiv. aps participate in a variety of physiological and pathological processes in vertebrates while in plants aps have roles in senescence, stress responses and fertilization as well as in defence against pathogens. reciprocally, aps are deployed by pathogens to facilitate infection e.g. hiv/aids, thrush and malaria. inhibitors targeted against hiv-proteinase are now in widespread use in therapy for treatment of hiv-infected individuals. recently it has been shown that one ap of plasmodium falciparum is an ideal target for development of therapeutic inhibitors to treat malaria. this ap is responsible for processing plasmodium effector proteins in a step that is crucial for their export into the host red blood cell, thereby reprogramming the host cell to meet the demands of the parasite. with these examples serving to illustrate the reliance of both host and pathogens on ap activities, it was of considerable interest to establish and annotate the complement of aps encoded within the three phytophthora genomes, particularly since one of the major current subjects of oomycete research is on effectors that modulate host cell physiology and immune responses. phytophthora effectors are small, secreted proteins that undergo translocation into host cells in a manner analogous to that for the plasmodium effectors. however, the components of the phytophthora translocation machinery remain to be identified. here we describe the complete ap family of three phytophthora species and identify some of its members which may participate in effector translocation.  genome sequences of p. infestans, p. sojae and p. ramorum were analysed for the presence of genes encoding putative pepsin-like aspartic proteinases as described in the methods. pepsin-like aps from family a are typically produced in the form of a precursor, consisting of a signal peptide followed by a propart region that has to be excised from the zymogen polypeptide chain in order to generate the mature enzyme. the mature enzyme region consists of two homologous catalytic domains, each of which provides a catalytic asp residue to the active site. each asp residue is located within the hallmark motif asp-thr/ser-gly, which is followed by a hydrophobic-hydrophobic-gly sequence, as exemplified by the family patriarch, pig pepsin. together, these motifs form a structural feature known as a psi loop. a tyr residue is located at position in a β-hairpin loop which overlies the active site. this residue is strictly conserved in all active pepsin-like aps and serves as a landmark residue that can be anticipated to be present in newly-identified ap sequences. a number of other motifs and landmark residues are present at characteristic locations along a family member polypeptides. a total of predicted protein sequences exhibiting some or all of these hallmark features and landmark residues were identified in p. infestans, with and entries detected in p. sojae and p. ramorum, respectively. inspection of the sequences revealed that, in p. ramorum, gene model pr_ was erroneous due to incorrect assembly of the dna sequence in this region and gene model pr_ present in a correctly assembled sequence, was a pseudogene lacking at least residues of the n-terminus of a functional ap. in p. sojae, the sequence encoded by gene ps_ was highly similar to aps but the two hallmark asp-thr/ser-gly motifs were replaced by asp-val-met and phe-thr-met respectively, such that the encoded protein could not possibly be active. this entry, which lacked an orthologue in both p. infestans and p. ramorum, was thus considered also to be a pseudogene. the above three gene models were thus excluded from further analyses. the remaining genes were the only ones consistently identified by repeated search using psi-blast or hmmer, so that it would appear no further ap homologues are present within these three genomes. these gene models were analysed and are further discussed in groups on the basis of orthology. comparison of the orthologues from the three species revealed in a number of cases that the gene models, as originally annotated, were likely to be incorrect. the wealth of information available on pepsin-like ap sequences including the hallmark motifs/landmark residues described above, was applied together with available est and trace file data, to guide the final gene predictions for putative aps encoded in the three phytophthora genomes. additional file lists the gene models that required correction. more than half of the original gene models annotated in the p. sojae and p. ramorum databases were correct, whilst almost all of the original entries for p. infestans were erroneous. the annotation errors that were identified included mis-identification of the initiator met residue, of intron presence/absence, of the 5' and/or 3' splice junctions of introns as well as sequence trace mis-reads or trace mis-usage in assembly of the p. infestans sequence due to heterozygosity. annotation errors in two p. infestans genes due to sequencing related issues were corrected by re-examination of original sequence trace files at ncbi and by re-sequencing relevant regions. the corrected nucleotide sequences of these genes are deposited in ncbi under accession numbers hm and hm respectively. for all gene models, the intron positions were verified by inspection of est information, if available, and by comparison with dna sequences of the orthologous gene in the other two species for the presence or absence of possible splice junctions at the equivalent nucleotide position. the corrected gene models and their encoded polypeptides are summarised in table all corrections proposed for the p. infestans gene models were confirmed by available est data or by cloning and sequencing the cdna. two of the three proposed corrected gene models for p. sojae were confirmed by cloning and sequencing the cdna, while for the third, correction could not be confirmed as cdna amplification was unsuccessful. corrections in p. ramorum gene models were not experimentally validated as this species has a quarantine status. an initial insight into the expression patterns of these aps was obtained from microarray analysis of p. infestans genes using the genome-wide nimblegen array. consistent levels of expression were observed for each of the eleven piap genes during culture on different agar media and during infection on potato. the number of introns and length of each polypeptide predicted by the database-annotated gene models are depicted for the orthologues from p. infestans, p. sojae and p. ramorum set out in each row. genes are presented as groups of orthologues. the generic descriptors pxap1- are used to denote the respective encoded polypeptides. the number of residues in each polypeptide is indicated. the final protein sequences predicted for each of the aps from the three phytophthora species are listed individually in additional file each of these sets of orthologous polypeptides was examined for the presence/absence of a signal peptide and a propart segment preceding the mature enzyme region. these features are summarised in table the individual signal peptide/propart segment sequences for each of the sets of orthologues are aligned in additional file in order to simplify the descriptions that follow, the identifiers pxap1- were assigned to each of these sets of orthologues. except for pxap the polypeptides continued beyond the conventional location of the c-terminus of an archetypal ap, as defined by the reference standard, pig pepsin. each of the pxap - pxap polypeptides thus contained a c-terminal extension. these extensions differed markedly in length and sequence and could only be aligned with the sequences of their orthologue from the other phytophthora species, and not with any other sequence in the set of entries or with any archetypal ap. only short extensions were present in the psap and prap polypeptides. the c-terminal extensions for pxap and pxap - pxap were considerably longer and all contained at least one stretch of approximately consecutive hydrophobic residues which are predicted to provide a membrane-spanning segment. thus, almost all the phytophthora aps are predicted to be membrane-bound enzymes. while it is not uncommon for individual aps from other species to be membrane-anchored in such a fashion, it is unprecedented for almost the entire ap complement of an organism to appear to be membrane-bound enzymes. considerable experimental effort will need to be invested to establish whether all of these predicted polypeptides are indeed membrane-associated but in previous investigations, aps that have been predicted to contain a membrane-associated segment have always been proven by subsequent experimental investigations to be membrane-attached. further consideration will be given to this aspect for the individual cases described below. the sequences of the mature enzyme regions of each of the sets of orthologues from the three phytophthora species were aligned and a phylogenetic tree was generated. this resolved the pxap1- 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 and encode polypeptides with considerably different sequences and, potentially, distinct activities. each of the clades will be considered in turn. archetypal pepsin-like aspartic proteinases in clade of the phylogenetic tree, three proteins designated piap psap and prap are encoded by orthologous single exon genes. the pxap polypeptides display all of the essential components i.e. signal peptide, propart segment and two-domain mature enzyme region, including all the necessary hallmark motifs and residues of archetypal pepsin-like aps described earlier. these polypeptides are not extended at their c-terminus. the phylogenetic analysis revealed that the three pxap polypeptides cluster closely with fungal aps that are known to be located in the vacuole of the cell. this subfamily, with saccharopepsin from s. cerevisiae as the parent member, is assigned the identifier a in the merops database. analyses of all sequenced fungal genomes has revealed that the only ap that is omnipresent is the vacuolar enzyme. thus, it seems likely that piap psap and prap are the respective vacuolar aps from each phytophthora species. piap has been produced in recombinant form and shown to have ap activity on haemoglobin. the polypeptides of the pxap in clade are atypical in that they do not contain a signal peptide or a non-classical secretion signal. this is highly unusual in aps although precedents have been observed in fungi including botrytis cinerea and in bacterial species of marine origin. it is not obvious how these polypeptides are able to become incorporated into a membrane through the hydrophobic segment in their c-terminal extensions when there is no signal peptide to mediate transfer into the endoplasmic reticulum. experiments using fusion constructs with reporter proteins will be necessary to resolve this conundrum. within clade five clusters were resolved from one another. more profound phylogenetic analysis indicates that this clade forms a monophyletic clade with three entries from two filamentous fungi, i.e. the zygomycetes rhizopus oryzae and phycomyces blakesleeanus. pxap3-encoding genes were only detected in p. sojae and p. ramorum. despite repeated searching, an orthologue of these two in p. infestans could not be detected. the pxap genes are located in regions of co-linearity. scrutiny of the five flanking genes in the p. sojae and p. ramorum genomes revealed that orthologues are present in similar arrangement in p. infestans dna, however, on separate contigs. the gap between the contigs corresponds to the likely location of the "missing" ap gene. moreover, no unassembled reads were identified in p. infestans that matched psap or prap sequences. the originally-annotated gene models for ps_ and pr_ both required considerable correction. the 5'-splice donor site of the third intron in ps_ was identified to be a gc dinucleotide sequence. this dinucleotide has been found to be used as the 5'-donor junction at low frequency in a number of fungi but no information is available as yet on its use in oomycetes. the amendments to the ps_ and pr_ gene models resulted in predicted polypeptide sequences that contained both signal peptide and propart segments. the sequences of the mature enzyme regions showed a pairwise identity of 71%. both polypeptides contained all three of the disulphide bonds that are common in vertebrate aps and they were only slightly extended at their c-terminal end relative to pepsin. psap and prap can be predicted to display different substrate specificities. the region between residues and is known conventionally as the "polyproline loop" and has been demonstrated to be a major determinant for substrate specificity. in prap the sequence lgddlyw of this region has two extra residues compared to the lsdd--w sequence of psap. the presence of these two hydrophobic residues is likely to influence specificity. like pxap the pxap and pxap polypeptides from phytophthora contained the conventional ap segments of a signal peptide and propart, prior to the mature enzyme region. each trio of polypeptides was also extended at its c-terminus but, whereas the extensions in pxap consisted of 136- residues with one putative membrane-spanning stretch, the pxap extensions were substantially longer. indeed, the c-terminal extensions in piap and its orthologues encompassed no less than seven potential transmembrane segments, an architecture highly reminiscent of the seven transmembrane stretches that constitute the super-family of g-protein coupled receptors. blast search using the sequence of the c-terminal extension of piap as query, identified the first non-self hit as rpka, a g-protein coupled receptor family protein from dictyostelium discoideum. a % similarity in a amino acid overlap was calculated between the two sequences using smith-waterman analysis. the intriguing possibility thus arises that, in phytophthora species, a fusion protein is produced in which the n-terminal partner is an ap connected to a putative gpcr as the c-terminal component. self-processing to release the ap component would generate the mature gpcr. such a self-processing phenomenon is unprecedented, although receptors activated by extrinsic proteinases are well-documented. further investigations into the phytophthora ap-gpcr fusion-proteins would appear to be well-merited. the final two sub-groups that were resolved within clade consisted of pxap and pxap. no orthologue was detected in p. sojae for the proteins piap and prap encoded by pitg_ and pr_. the piap7- and prap7-encoding genes are located in co-linear orthologous regions of the p. infestans and p. ramorum genomes, as confirmed by the organization of flanking genes. in p. sojae, the corresponding genomic region had a similar co-linearity arrangement with the exception of two missing genes, one of them in the region where an orthologous ap-encoding gene should have been located. moreover, no unassembled reads were identified in p. sojae that matched the piap or prap sequences. the simplest interpretation is that an ancestor of the pxap7-encoding gene was present in phytophthora, and deletion of the region resulted in loss of the orthologue in p. sojae, although it cannot be excluded that substitutions have accumulated to an extent that prevents recognition of the gene. the pxap and pxap polypeptides showed an unusual variation in the component segments that constitute an archetypal ap in that a propart was absent. in each case, the signal peptide immediately precedes the mature enzyme region which, in turn, is followed by a c-terminal extension. as stated above, almost all pepsin-like aps are synthesised in the form of a precursor. the propart segment makes a number of essential contributions, such as ensuring proper folding and intracellular sorting of the zymogen polypeptide, and facilitation of its activation into the mature enzyme form upon encountering the appropriate conditions. very recently, however, aps lacking a propart segment have been described from marine bacteria and fungi, hence this unusual architecture of the pxap and pxap polypeptides in phytophthora species is not without precedent. bace-like aspartic proteinases the pxap and pxap polypeptides were resolved by the phylogenetic analysis into clade. these polypeptides also contained a signal peptide, the mature enzyme region and a c-terminal extension but they too lacked a propart, just like pxap and pxap the phylogenetic analysis revealed that these proteins cluster within clade with human bace and its paralogue, bace. the mature enzyme forms of bace/bace are initially synthesised in precursor forms that do contain propart segments. while the presence of the propart has little effect on the intrinsic proteolytic activity, its inclusion at the n-terminus of probace/probace ensures much more rapid folding of the polypeptide than is observed when only the mature forms of each enzyme are produced. bace and bace were among the first aps to be identified as having a c-terminal extension which ensured they were membrane-bound. the mature enzyme regions have hallmark features which distinguish a / subfamily members from classical aps such as pepsin. among these are: the highly-conserved trp is replaced by ala and is itself relocated to a position just downstream from the essential tyr residue on the β-hairpin loop that overhangs the active site cleft, disulphide bonds in characteristic locations that increase stability of the polypeptide. these additional cys residues and the trp39ala replacement are all present in pxap and pxap proteins. bace has been identified as the β-site alzheimer's precursor protein cleaving enzyme responsible for the cleavage that generates the free n-terminal end of the aβ peptide which plays a central role in alzheimer's disease. for almost a decade, bace has been the target of intense efforts to develop inhibitors to alleviate the dementia of alzheimer's disease. genes encoding bace and its paralogue, bace have been identified in species ranging from humans through elephant, opossum, armadillo, hedgehog, shrew, and fish, to platypus. to the best of the authors' knowledge, the identification of pxap8-encoding genes from three phytophthora species provides the first indication that bace-like, membrane-bound aps may not be limited to the vertebrates. intriguingly, the phytophthora genomes also contain genes encoding homologues of presenilin, nicastrin, anterior pharynx defective- and presenilin enhancer-. these are all components of the human γ-secretase complex which completes the proteolytic processing by releasing the aβ peptide at its c-terminal end from the alzheimer's precursor polypeptide. the presence of both β- and γ-secretase gene products in microbes such as phytophthora suggests that their function is not limited to the processing of a brain polypeptide related to alzheimer's disease. these proteins therefore seem to be very ancient features that are conserved between oomycetes and vertebrates, and they have been coopted in vertebrate species to cleave the brain app polypeptide. while the pxap polypeptides exhibited the hallmark characteristics of bace/bace subfamily members, the pxap proteins lacked one feature that is necessary for an ap to be active as an enzyme. the tyr residue located at position is conserved in every pepsin-like ap that is known to be active, although it does not participate directly in the catalytic mechanism. in pxap this tyr residue is replaced by phe so the catalytic activity can be postulated to be compromised, at best. a protein engineering study revealed that the replacement of tyr in a fungal ap by asn or phe permitted activity, albeit at a considerably reduced level, while all other replacements abolished activity. however, a number of catalytically-inactive aps have been reported previously, including the pregnancy-associated glycoproteins found in the placenta of ungulates and perhaps most notably, the bla g protein which is a predominant allergen from cockroach. the crystal structure of bla g shows that it has the fold and three-dimensional structure typical of pepsin-like aps. bla g and the pags from ovis aries and capra hircus all have a phe residue at position these three proteins have additional substitutions at the two active site dt/sg motifs, cementing their catalytic inactivity. their function has been postulated to include roles in peptide-binding and presentation, but without cleavage. if pxap should also prove to be catalytically ineffective, the active site will still be accessible for the binding of peptides that cannot undergo cleavage and so a role similar to the pags/bla g in peptide binding might be feasible. this intriguing possibility is rendered all the more fascinating with the realisation that, in contrast to the pags/bla g these phytophthora orthologues are likely to be membrane-bound through their c-terminal extensions and might function as a novel type of surface receptor. in this regard, it may well be noteworthy that the putative intracellular domain comprised of the residues downstream from the transmembrane segment in the c-terminal extension in pxap is considerably longer than its pxap counterpart. neither of the c-terminal extensions, however, contains a discernible pfam domain or protein motif. thus, all three phytophthora species may produce one catalytically-active bace-like enzyme and one peptide-binding, membrane-bound enzymatically inactive paralogue with an intracellular extension of unknown function. nepenthesin-like aspartic proteinases the remaining three ap genes in each phytophthora genome, encoding polypeptides pxap pxap and pxap cluster into clade with representative aps from merops subfamily a1b including the patriarch of plant origin, nepenthesin, and plasmepsin v from plasmodium falciparum. the pxap - polypeptides contrast with their pxap - counterparts in having the archetypal ap architecture of a signal peptide followed by a propart, a mature enzyme region, terminating with c-terminal extensions. pxap - differed, however, from all of the other phytophthora aps in having a small extra segment inserted in the region just upstream from tyr. no less than seven cys residues are present between residues - with a further three cys residues conserved at characteristic locations elsewhere in the mature enzyme regions of the nine phytophthora aps in clade together, these cys residues are likely to form five specific disulphide bridges, paired as indicated in figure this arrangement of disulphide bridges has been deduced from biochemical analyses of the aps of plant origin that cluster with pxap - in clade indeed, most of the aps in plants contain these cys residues as well as the insert and they are grouped into subfamily a1b in the merops database. the plant aps identified in clade are readily distinguished on the basis of their functional activity from one another and from others that are not included here for the sake of brevity, such as the nucellins, regulators of the degradation of nucellar cells after ovule fertilisation, and the chloroplast nucleoids dna-binding proteinase which catalyses the degradation of rubisco in senescent leaves. nepenthesins are extracellular enzymes secreted by the carnivorous plant, nepenthes, to digest its prey while cdr of arabidopsis plays a crucial role in activating resistance of arabidopsis against microbial pathogens. overexpression of cdr leads to constitutive disease resistance, while gene silencing compromises resistance. the cdr gene product is suggested to release an as yet unidentified peptide that activates a signalling cascade to induce disease resistance in a salicylate-dependent manner. recombinant cdr protein has been produced in e. coli and shown to be active as an ap in a dimeric form. two intermolecular disulphide bonds were proposed to be responsible for the covalent association of the two polypeptide chains in the proteolytically-active homodimer. the cys residues involved in the homodimer formation are highlighted in figure by a star (). cys residues are present at identical locations within pxap, suggesting that this enzyme may also function as a homodimer. in contrast, pxap is devoid of cysteine residues in this region and so, based on this criterion, should function as a monomer. pxap does contain two cysteine residues but at different positions within this region of the polypeptide. whether these remain as free cysteines or are involved in disulphide bonds, intra- or inter-molecular, requires experimental investigation. one feature does serve to distinguish between the plant aps and the nine pxap - polypeptides clustered in clade. most plant aps do not have c-terminal extensions. in contrast, all nine of the oomycete pxap - polypeptides do have c-terminal extensions, ensuring that all are membrane-bound enzymes. in addition to plant aps, plasmepsin v was resolved into clade as the entry most closely associated with the pxap - polypeptides. plasmepsin v is one of ten aps encoded within the genome of plasmodium falciparum, the causative agent of malaria. this enzyme has a c-terminal extension with a hydrophobic stretch that results in its anchoring as a membrane-bound polypeptide. very recently, plasmepsin v has been demonstrated to be the proteinase responsible for processing the precursors of plasmodium effector proteins at the pexel motif; this step is essential for the translocation of these polypeptides into the host red blood cell. the malaria parasite exports hundreds of such effector proteins across the parasitophorous vacuolar membrane into the human red blood cell, thereby reprogramming the host cell to meet the needs of the parasite. plasmepsin v is conserved in plasmodium species but is not produced in vertebrates susceptible to parasitic infection and thus serves as a target enzyme against which to develop inhibitors as novel therapeutic agents for treatment of malaria. intriguingly, phytophthora species also secrete effector proteins that are important in modulating host defence and cell death mechanisms and many such effector proteins contain the internal sequence motif rxlr, similar to the plasmodium pexel motif. phytophthora effector proteins are secreted after removal of their signal peptide, giving rise to a polypeptide that contains in its n-terminal region the rxlr-containing domain which is essential for subsequent delivery into the plant cell. it is tempting to consider that a phytophthora effector precursor might undergo further processing to remove the rxlr domain, thereby releasing the mature, biologically active effector domain. the similarities described above between plasmepsin v and its pxap pxap and pxap orthologues in phytophthora suggests a conserved biological role. by analogy to the role of plasmepsin v in processing of plasmodium effector proteins, one or more of its phytophthora orthologues may reside in the translocon and act in the processing of phytophthora effector precursors. there are obvious structural and genetic differences between the secretion mechanisms of the two parasites. the genome sequences of phytophthora species lack genes homologous to the translocon complex components identified in plasmodium. nevertheless, our hypothesis invites experimental investigation into targeting these particular aps in phytophthora as a pathogenic achilles heel through which the devastating losses from infection by phytophthora might be reduced.  one of the twelve pepsin-like aps encoded within the genomes of the three phytophthora species is predicted to be produced as an unprecedented fusion protein with a putative g-protein coupled receptor as the c-terminal partner. the other aps appear to be related to existing enzymes from other species that have already been documented. these include the vacuolar enzyme, and somewhat more unexpectedly, bace/bace2-like aps in an active and likely inactive form akin to the bla g2/pag proteins, and plasmepsin v-like enzymes. whether the latter are functional homologs of their plasmodium counterpart, operating in the processing of rxlr-type effector proteins during transit to the plant cell, would appear to be worthy of immediate experimental investigation given the high level of current interest in this topic. elucidation of the physiological roles of the aps identified here offers highly fertile areas ripe for examination. the significant revision of the erroneous gene models and the detailed annotation presented here should be highly beneficial in facilitating future experimental design. 
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. one of the twelve phytophthora aps is an unprecedented fusion protein with a putative g-protein coupled receptor as the c-terminal partner. 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 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. 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. annotation of phytophthora aps would provide invaluable information for studies into their roles in the physiology of phytophthora species and interactions with their hosts. pepsin-like aspartic proteinases are produced in a wide variety of species and contain conserved motifs and landmark residues. 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. nine of the original gene models in the p. infestans database and several in p. sojae and p. ramorum were erroneous. gene models were corrected on the basis of est data, consistent positioning of introns between orthologues and conservation of hallmark motifs. the significant revision of gene models and detailed annotation presented here should significantly facilitate experimental design. of the sub-families, several contained an unconventional architecture, as they either lacked a signal peptide or a propart region. phylogenetic analysis resolved the phytophthora aps into clades. genomes of phytophthora infestans, p. sojae and p. ramorum contain 11- genes encoding aps. indeed, elucidation of the physiological roles of the aps identified here offers areas for future study.
 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 are produced in a wide variety of species 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.  genomes of phytophthora infestans, p. sojae and p. ramorum contain 11- genes encoding aps. nine of the original gene models in the p. infestans database and several in p. sojae and p. ramorum 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 clades. of the 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.  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. 