title: Classification of the adenylation and acyl-transferase activity of NRPS and PKS systems using ensembles of substrate specific hidden Markov models.
abstract: There is a growing interest in the Non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs) of microbes, fungi and plants because they can produce bioactive peptides such as antibiotics. The ability to identify the substrate specificity of the enzyme's adenylation (A) and acyl-transferase (AT) domains is essential to rationally deduce or engineer new products. We here report on a Hidden Markov Model (HMM)-based ensemble method to predict the substrate specificity at high quality. We collected a new reference set of experimentally validated sequences. An initial classification based on alignment and Neighbor Joining was performed in line with most of the previously published prediction methods. We then created and tested single substrate specific HMMs and found that their use improved the correct identification significantly for A as well as for AT domains. A major advantage of the use of HMMs is that it abolishes the dependency on multiple sequence alignment and residue selection that is hampering the alignment-based clustering methods. Using our models we obtained a high prediction quality for the substrate specificity of the A domains similar to two recently published tools that make use of HMMs or Support Vector Machines (NRPSsp and NRPS predictor2, respectively). Moreover, replacement of the single substrate specific HMMs by ensembles of models caused a clear increase in prediction quality. We argue that the superiority of the ensemble over the single model is caused by the way substrate specificity evolves for the studied systems. It is likely that this also holds true for other protein domains. The ensemble predictor has been implemented in a simple web-based tool that is available at http://www.cmbi.ru.nl/NRPS-PKS-substrate-predictor/.
authors: Center for Molecular and Biomolecular Informatics, Nijmegen Center for Molecular Life Sciences, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands.
authors: Barzan I
authors: BI
authors: Khayatt
authors: Lex
authors: L
authors: Overmars
authors: Roland J
authors: RJ
authors: Siezen
authors: Christof
authors: C
authors: Francke
mesh_terms: D000217:Acyltransferases / Q000378:metabolism*; D000249:Adenosine Monophosphate / Q000378:metabolism; D020134:Catalytic Domain; D008390:Markov Chains; D009713:Nucleotidyltransferases / Q000378:metabolism*; D046908:Peptide Biosynthesis, Nucleic Acid-Independent / Q000502:physiology*; D048630:Polyketide Synthases / Q000737:chemistry* / Q000378:metabolism; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D013379:Substrate Specificity; D060388:Support Vector Machine
chemical_list: D000249:Adenosine Monophosphate; D048630:Polyketide Synthases; D000217:Acyltransferases; D009713:Nucleotidyltransferases
references: J Biol Chem. 1995 Jun 2;270(22):12961-4
references: 7768883
references: J Mol Biol. 2007 May 18;368(5):1500-17
references: 17400247
references: Mol Biosyst. 2011 May;7(5):1549-63
references: 21365089
references: Microb Biotechnol. 2008 Jul;1(4):275-82
references: 21261848
references: Nucleic Acids Res. 2012 Jan;40(Database issue):D71-5
references: 22102590
references: Chem Biol. 1999 Jan;6(1):31-41
references: 9889147
references: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W405-13
references: 15215420
references: J Org Chem. 2009 Sep 4;74(17):6416-20
references: 19711990
references: Mol Microbiol. 1992 Sep;6(18):2743-4
references: 1447981
references: Mol Microbiol. 2008 Oct;70(2):445-61
references: 18942174
references: FEBS Lett. 1997 Sep 15;414(3):532-6
references: 9323029
references: BMC Bioinformatics. 2007 Sep 03;8:327
references: 17764579
references: BMC Bioinformatics. 2007 Mar 08;8:83
references: 17346331
references: Curr Opin Chem Biol. 2012 Apr;16(1-2):117-23
references: 22342766
references: Nucleic Acids Res. 2012 Jan;40(Database issue):D48-53
references: 22144687
references: Mol Biol Evol. 2005 Oct;22(10):2027-39
references: 15958783
references: Angew Chem Int Ed Engl. 2012 Jan 27;51(5):1256-60
references: 22213143
references: Nucleic Acids Res. 2005 Oct 12;33(18):5799-808
references: 16221976
references: Curr Opin Chem Biol. 2011 Feb;15(1):22-31
references: 21111667
references: Chem Biol. 1999 Aug;6(8):493-505
references: 10421756
references: Nat Prod Rep. 2007 Oct;24(5):1073-109
references: 17898898
references: Nat Prod Rep. 2007 Dec;24(6):1225-44
references: 18033577
references: Curr Opin Chem Biol. 2001 Oct;5(5):525-34
references: 11578925
references: J Biotechnol. 2009 Mar 10;140(1-2):13-7
references: 19297688
references: Chembiochem. 2008 Apr 14;9(6):826-48
references: 18357594
references: Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14558-63
references: 19666480
references: Bioinformatics. 2004 Feb 12;20(3):426-7
references: 14960472
references: Toxins (Basel). 2010 Oct;2(10):2359-410
references: 22069558
references: BMC Bioinformatics. 2007 Nov 22;8:460
references: 18034891
references: Annu Rev Microbiol. 2004;58:453-88
references: 15487945
references: Mol Microbiol. 1993 May;8(5):821-31
references: 8355609
references: Angew Chem Int Ed Engl. 2009;48(26):4688-716
references: 19514004
references: Proc Natl Acad Sci U S A. 2009 Jul 28;106(30):12295-300
references: 19590008
references: Bioinformatics. 2012 Feb 1;28(3):426-7
references: 22130593
references: Trends Biochem Sci. 1998 Oct;23(10):403-5
references: 9810230
references: Chem Biol. 2000 Mar;7(3):211-24
references: 10712928
references: Genome Res. 2004 Jun;14(6):1188-90
references: 15173120
references: BMC Bioinformatics. 2009 Jun 16;10:185
references: 19531248
references: J Am Chem Soc. 2011 Apr 6;133(13):4746-9
references: 21391603
references: Nucleic Acids Res. 2011 Jul;39(Web Server issue):W362-7
references: 21558170
references: EMBO J. 1997 Jul 16;16(14):4174-83
references: 9250661
references: Methods Enzymol. 2009;458:181-217
references: 19374984
references: J Mol Biol. 2003 Apr 25;328(2):335-63
references: 12691745
references: Chem Rev. 2005 Feb;105(2):715-38
references: 15700962
references: Bioinformatics. 1998;14(9):755-63
references: 9918945
references: Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4595-600
references: 18250311
references: Nucleic Acids Res. 2010 Jul;38(Web Server issue):W487-96
references: 20444870
references: Mol Biosyst. 2009 Jan;5(1):77-90
references: 19081934
references: Antimicrob Agents Chemother. 1997 Sep;41(9):1904-9
references: 9303382
references: Appl Microbiol Biotechnol. 2012 Oct;96(1):61-7
references: 22854892
references: Chem Rev. 1997 Nov 10;97(7):2651-2674
references: 11851476
references: Microbiology (Reading). 2004 Jun;150(Pt 6):1629-1636
references: 15184549
references: Science. 2004 Mar 19;303(5665):1805-10
references: 15031493
references: Nature. 2007 Aug 16;448(7155):755-6
references: 17700681
references: Curr Opin Chem Biol. 2005 Oct;9(5):447-58
references: 16107321
references: Nucleic Acids Res. 2005 Jan 20;33(2):511-8
references: 15661851