title: The aspartic proteinase family of three Phytophthora species.
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.
authors: School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK.
authors: John
authors: J
authors: Kay
authors: Harold J G
authors: HJ
authors: Meijer
authors: Arjen
authors: A
authors: ten Have
authors: Jan A L
authors: JA
authors: van Kan
references: Mol Plant Microbe Interact. 2006 Dec;19(12):1337-47
references: 17153918
references: Annu Rev Biophys Biomol Struct. 1998;27:249-84
references: 9646869
references: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W390-3
references: 15215417
references: J Mol Biol. 1990 Jul 5;214(1):199-222
references: 2115088
references: Plant Cell. 1997 Sep;9(9):1673-82
references: 9338968
references: Gene. 1995 Jul 4;159(2):193-7
references: 7622048
references: Genomics. 2006 Mar;87(3):338-47
references: 16406724
references: Biochem J. 2004 Jul 1;381(Pt 1):295-306
references: 15035659
references: Nature. 1999 Dec 2;402(6761):537-40
references: 10591214
references: J Biol Chem. 2007 Oct 26;282(43):31358-65
references: 17650510
references: Protein Pept Lett. 2009;16(2):121-31
references: 19200034
references: Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22
references: 19920124
references: Science. 1999 Oct 22;286(5440):735-41
references: 10531052
references: Fungal Genet Biol. 2010 Jan;47(1):53-65
references: 19853057
references: Bioinformatics. 2001 Jul;17(7):646-53
references: 11448883
references: Plant Cell. 2008 Jul;20(7):1728-30
references: 18647825
references: Trends Parasitol. 2001 Nov;17(11):532-7
references: 11872398
references: J Mol Biol. 2000 Sep 8;302(1):205-17
references: 10964570
references: BMC Genomics. 2009 Sep 16;10:437
references: 19758436
references: Am J Respir Crit Care Med. 2002 Feb 1;165(3):391-7
references: 11818327
references: Plant Cell. 2008 Jul;20(7):1930-47
references: 18621946
references: Curr Biol. 2007 May 15;17(10):892-7
references: 17481898
references: Nature. 2010 Feb 4;463(7281):627-31
references: 20130643
references: Cell Microbiol. 2009 Jan;11(1):13-20
references: 18783481
references: Mol Biochem Parasitol. 2005 Oct;143(2):183-91
references: 16024107
references: Nature. 2009 Jun 18;459(7249):945-9
references: 19536257
references: Nat Struct Mol Biol. 2010 Feb;17(2):151-8
references: 20062056
references: Biochimie. 2008 Feb;90(2):243-59
references: 17980477
references: Protein Sci. 1998 Apr;7(4):815-36
references: 9568890
references: Science. 2006 Sep 1;313(5791):1261-6
references: 16946064
references: Nature. 2005 Aug 25;436(7054):1113-8
references: 16121172
references: Eur J Biochem. 2004 Jun;271(11):2067-75
references: 15153096
references: BMC Bioinformatics. 2007 Nov 22;8:460
references: 18034891
references: J Mol Biol. 2005 Apr 29;348(2):433-44
references: 15811379
references: EMBO J. 2004 Feb 25;23(4):980-8
references: 14765119
references: Plant Physiol Biochem. 2008 Jul;46(7):724-9
references: 18514539
references: Syst Biol. 2003 Oct;52(5):696-704
references: 14530136
references: Mol Plant Microbe Interact. 2006 Dec;19(12):1295-301
references: 17153913
references: Protein Eng. 1996 Oct;9(10):869-75
references: 8931126
references: AIDS. 1998 Sep 10;12(13):1611-8
references: 9764779
references: Curr Opin Plant Biol. 2008 Aug;11(4):373-9
references: 18511334
references: Bioinformatics. 1998;14(9):755-63
references: 9918945
references: EMBO J. 1999 Apr 1;18(7):1723-9
references: 10202136
references: Microbes Infect. 2002 Nov;4(13):1369-77
references: 12443902
references: N Biotechnol. 2009 Jun;25(5):318-24
references: 19491047
references: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references: 9254694
references: J Mol Biol. 1981 Mar 25;147(1):195-7
references: 7265238
references: Chem Rev. 2002 Dec;102(12):4431-58
references: 12475196
references: Nature. 2009 Sep 17;461(7262):393-8
references: 19741609
references: J Biol Chem. 2001 Mar 30;276(13):10366-73
references: 11266439
references: Mol Plant Pathol. 2009 Nov;10(6):795-803
references: 19849785
references: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W380-2
references: 15215415
references: Curr Opin Hematol. 2007 May;14(3):230-5
references: 17414212
references: Nucleic Acids Res. 2010 Jan;38(Database issue):D227-33
references: 19892822
references: Plant Mol Biol. 1997 Dec;35(6):821-31
references: 9426602
references: PLoS One. 2009 Jul 02;4(7):e6133
references: 19582169
references: Nature. 2010 Feb 4;463(7281):632-6
references: 20130644