title: Quantitative design of regulatory elements based on high-precision strength prediction using artificial neural network.
abstract: Accurate and controllable regulatory elements such as promoters and ribosome binding sites (RBSs) are indispensable tools to quantitatively regulate gene expression for rational pathway engineering. Therefore, de novo designing regulatory elements is brought back to the forefront of synthetic biology research. Here we developed a quantitative design method for regulatory elements based on strength prediction using artificial neural network (ANN). One hundred mutated Trc promoter & RBS sequences, which were finely characterized with a strength distribution from 0 to 3.559 (relative to the strength of the original sequence which was defined as 1), were used for model training and test. A precise strength prediction model, NET90_19_576, was finally constructed with high regression correlation coefficients of 0.98 for both model training and test. Sixteen artificial elements were in silico designed using this model. All of them were proved to have good consistency between the measured strength and our desired strength. The functional reliability of the designed elements was validated in two different genetic contexts. The designed parts were successfully utilized to improve the expression of BmK1 peptide toxin and fine-tune deoxy-xylulose phosphate pathway in Escherichia coli. Our results demonstrate that the methodology based on ANN model can de novo and quantitatively design regulatory elements with desired strengths, which are of great importance for synthetic biology applications.
authors.affiliation: Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
authors.forename: Hailin
authors.initials: H
authors.lastname: Meng
authors.forename: Jianfeng
authors.initials: J
authors.lastname: Wang
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Xiong
authors.forename: Feng
authors.initials: F
authors.lastname: Xu
authors.forename: Guoping
authors.initials: G
authors.lastname: Zhao
authors.forename: Yong
authors.initials: Y
authors.lastname: Wang
mesh_terms: D000818:Animals; D003198:Computer Simulation; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D005818:Genetic Engineering; D008957:Models, Genetic; D016571:Neural Networks, Computer; D011401:Promoter Regions, Genetic; D011994:Recombinant Proteins / Q000235:genetics / Q000378:metabolism; D015203:Reproducibility of Results; D012604:Scorpion Venoms / Q000235:genetics* / Q000378:metabolism; D012605:Scorpions; D014994:Xylose / Q000031:analogs & derivatives / Q000378:metabolism
chemical_list: C418407:KBT toxin, Buthus martensii; D011994:Recombinant Proteins; D012604:Scorpion Venoms; C492551:deoxyxylulose phosphate; D014994:Xylose
references.citation: Subcell Biochem. 2012;64:181-201
references.pmid: 23080251
references.citation: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W126-31
references.pmid: 17439967
references.citation: PLoS Biol. 2007 Sep;5(9):e229
references.pmid: 17713988
references.citation: BMC Bioinformatics. 2010 Oct 07;11 Suppl 6:S21
references.pmid: 20946605
references.citation: Nucleic Acids Res. 1987 Mar 11;15(5):2343-61
references.pmid: 3550697
references.citation: Vaccine. 2007 Feb 19;25(9):1634-46
references.pmid: 17145123
references.citation: PLoS Comput Biol. 2011 Sep;7(9):e1002157
references.pmid: 21935350
references.citation: Nat Biotechnol. 2008 Jul;26(7):787-93
references.pmid: 18612302
references.citation: Nat Biotechnol. 2009 Oct;27(10):946-50
references.pmid: 19801975
references.citation: Nat Biotechnol. 2003 Jul;21(7):796-802
references.pmid: 12778056
references.citation: Appl Environ Microbiol. 1998 Jan;64(1):82-7
references.pmid: 9435063
references.citation: Bioinformatics. 2005 Apr 1;21(7):1062-8
references.pmid: 15513998
references.citation: J Biol Eng. 2009 Mar 20;3:4
references.pmid: 19298678
references.citation: Bioinformatics. 2010 Oct 15;26(20):2633-4
references.pmid: 20702394
references.citation: Biotechnol Appl Biochem. 2007 May;47(Pt 1):1-9
references.pmid: 17432953
references.citation: J Bacteriol. 1994 Oct;176(19):5999-6006
references.pmid: 7523360
references.citation: Metab Eng. 2012 May;14(3):223-32
references.pmid: 22037345
references.citation: Appl Environ Microbiol. 2011 Jun;77(11):3600-8
references.pmid: 21498769
references.citation: Pharm Res. 1993 Feb;10(2):165-70
references.pmid: 8456062
references.citation: FEBS J. 2011 Mar;278(5):729-39
references.pmid: 21205203
references.citation: PLoS One. 2012;7(3):e33279
references.pmid: 22442681
references.citation: Nucleic Acids Res. 1992 Jul 11;20(13):3471-7
references.pmid: 1630917
references.citation: Proc Natl Acad Sci U S A. 2005 Sep 6;102(36):12678-83
references.pmid: 16123130
references.citation: BMC Genomics. 2007 Oct 17;8:374
references.pmid: 17941982
references.citation: Cancer Lett. 2010 May 28;291(2):158-66
references.pmid: 19906483
references.citation: Biotechnol Lett. 2008 Jan;30(1):23-9
references.pmid: 17701272
references.citation: Nucleic Acids Res. 1991 Apr 11;19(7):1593-9
references.pmid: 2027766
references.citation: Genome Res. 2004 Jun;14(6):1188-90
references.pmid: 15173120
references.citation: Nucleic Acids Res. 1994 Jun 11;22(11):2158-65
references.pmid: 8029027
references.citation: Comput Biol Med. 2011 Oct;41(10):946-59
references.pmid: 21880310
references.citation: Genes Genet Syst. 2009 Dec;84(6):425-30
references.pmid: 20228580
references.citation: Nat Biotechnol. 2012 May 20;30(6):521-30
references.pmid: 22609971
references.citation: J Pharm Biomed Anal. 2000 Jun;22(5):717-27
references.pmid: 10815714
references.citation: BMC Biotechnol. 2007 Jun 18;7:34
references.pmid: 17572914
references.citation: Biotechnol Lett. 2011 Jul;33(7):1309-17
references.pmid: 21424168
references.citation: Genet Mol Biol. 2011 Apr;34(2):353-60
references.pmid: 21734842
references.citation: Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):2854-9
references.pmid: 20133665
references.citation: Nucleic Acids Res. 1992 Aug 25;20(16):4331-8
references.pmid: 1508724
references.citation: Bioinformatics. 2004 Aug 4;20 Suppl 1:i63-8
references.pmid: 15262782
references.citation: Annu Int Conf IEEE Eng Med Biol Soc. 2008;2008:1355-8
references.pmid: 19162919