Identification, Characterization, and Application of a Highly Sensitive Lactam Biosensor from Pseudomonas putida

Thompson, Mitchell G.; Pearson, Allison N.; Barajas, Jesus F.; Cruz-Morales, Pablo; Sedaghatian, Nima; Costello, Zak; Garber, Megan E.; Incha, Matthew R.; Valencia, Luis E.; Baidoo, Edward K.; Martin, Hector Garcia; Mukhopadhyay, Aindrila; Keasling, Jay D.

doi:10.1021/acssynbio.9b00292

Title: Identification, Characterization, and Application of a Highly Sensitive Lactam Biosensor from Pseudomonas putida

Journal Article · 15 December 2019 · ACS Synthetic Biology

DOI: https://doi.org/10.1021/acssynbio.9b00292 · OSTI ID:1782137

Thompson, Mitchell G. ^[1]; Pearson, Allison N. ^[2]; Barajas, Jesus F. ^[3]; Cruz-Morales, Pablo ^[4]; Sedaghatian, Nima ^[2]; Costello, Zak ^[5]; Garber, Megan E. ^[6]; Incha, Matthew R. ^[1]; Valencia, Luis E. ^[7]; Baidoo, Edward K. ^[2];

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Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Systems & Engineering Div.; Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology
Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Systems & Engineering Div.
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Systems & Engineering Div.; USDOE Agile BioFoundry, Emeryville, CA (United States)
Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Systems & Engineering Div.; Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology; Instituto Tecnologico y de Estudios superiores de Monterrey, Monterrey (Mexico). Centro de Biotecnologia FEMSA
Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Systems & Engineering Div.; Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology; USDOE Agile BioFoundry, Emeryville, CA (United States)
Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Systems & Engineering Div.; Univ. of California, Berkeley, CA (United States). Comparative Biochemistry Graduate Group
Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Systems & Engineering Div.; Univ. of California, Berkeley, CA (United States). Joint Program in Bioengineering
Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Systems & Engineering Div.; Univ. of California, Berkeley, CA (United States). Dept. of Plant and Microbial Biology; USDOE Agile BioFoundry, Emeryville, CA (United States); Basque Center for Applied Mathematics (BCAM), Bilbao (Spain)
Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States). Biological Systems & Engineering Div.; Univ. of California, Berkeley, CA (United States). Joint Program in Bioengineering; Univ. of California, Berkeley, CA (United States). Dept. of Chemical and Biomolecular Engineering; Technical Univ. of Denmark, Lyngby (Denmark). Novo Nordisk Foundation Center for Biosustainability; Shenzhen Univ. (China)

Caprolactam is an important polymer precursor to nylon traditionally derived from petroleum and produced on a scale of 5 million tons per year. Current biological pathways for the production of caprolactam are inefficient with titers not exceeding 2 mg/L, necessitating novel pathways for its production. As development of novel metabolic routes often require thousands of designs and result in low product titers, a highly sensitive biosensor for the final product has the potential to rapidly speed up development times. Here we report a highly sensitive biosensor for valerolactam and caprolactam from Pseudomonas putida KT2440 which is > 1000 × more sensitive to an exogenous ligand than previously reported sensors. Manipulating the expression of the sensor oplR (PP_3516) substantially altered the sensing parameters, with various vectors showing K_d values ranging from 700 nM (79.1 μg/L) to 1.2 mM (135.6 mg/L). Our most sensitive construct was able to detect in vivo production of caprolactam above background at~6 μg/L. The high sensitivity and range of OplR is a powerful tool toward the development of novel routes to the biological synthesis of caprolactam.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Energy Efficiency and Renewable Energy (EERE)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1782137

Journal Information:: ACS Synthetic Biology, Journal Name: ACS Synthetic Biology Journal Issue: 1 Vol. 9; ISSN 2161-5063

Publisher:: American Chemical Society (ACS)Copyright Statement

Country of Publication:: United States

Language:: English

References (40)

Biochemical Characterization of β-Amino Acid Incorporation in Fluvirucin B ₂ Biosynthesis Barajas, Jesus F.; Zargar, Amin; Pang, Bo ChemBioChem, Vol. 19, Issue 13 https://doi.org/10.1002/cbic.201800169	journal	May 2018
Characterization of the caprolactam degradation pathway in Pseudomonas jessenii using mass spectrometry-based proteomics Otzen, Marleen; Palacio, Cyntia; Janssen, Dick B. Applied Microbiology and Biotechnology, Vol. 102, Issue 15 https://doi.org/10.1007/s00253-018-9073-7	journal	May 2018
Nitrile-inducible gene expression in mycobacteria Pandey, Amit K.; Raman, Sahadevan; Proff, Rose Tuberculosis, Vol. 89, Issue 1 https://doi.org/10.1016/j.tube.2008.07.007	journal	January 2009
The Acinetobacter sp. chnB promoter together with its cognate positive regulator ChnR is an attractive new candidate for metabolic engineering applications in bacteria Steigedal, Magnus; Valla, Svein Metabolic Engineering, Vol. 10, Issue 2 https://doi.org/10.1016/j.ymben.2007.08.002	journal	March 2008
Metabolic engineering of Escherichia coli for the production of four-, five- and six-carbon lactams Chae, Tong Un; Ko, Yoo-Sung; Hwang, Kyu-Sang Metabolic Engineering, Vol. 41 https://doi.org/10.1016/j.ymben.2017.04.001	journal	May 2017
Production of nonnatural straight-chain amino acid 6-aminocaproate via an artificial iterative carbon-chain-extension cycle Cheng, Jie; Hu, Ge; Xu, Yanqin Metabolic Engineering, Vol. 55 https://doi.org/10.1016/j.ymben.2019.06.009	journal	September 2019
Structural Insights into Anthranilate Priming during Type II Polyketide Biosynthesis Jackson, David R.; Tu, Stephanie S.; Nguyen, MyChi ACS Chemical Biology, Vol. 11, Issue 1 https://doi.org/10.1021/acschembio.5b00500	journal	November 2015
Metabolic Engineering toward Sustainable Production of Nylon-6 Turk, Stefan C. H. J.; Kloosterman, Wigard P.; Ninaber, Dennis K. ACS Synthetic Biology, Vol. 5, Issue 1 https://doi.org/10.1021/acssynbio.5b00129	journal	November 2015
Development of a Transcription Factor-Based Lactam Biosensor Zhang, Jingwei; Barajas, Jesus F.; Burdu, Mehmet ACS Synthetic Biology, Vol. 6, Issue 3 https://doi.org/10.1021/acssynbio.6b00136	journal	November 2016
Application of an Acyl-CoA Ligase from Streptomyces aizunensis for Lactam Biosynthesis Zhang, Jingwei; Barajas, Jesus F.; Burdu, Mehmet ACS Synthetic Biology, Vol. 6, Issue 5 https://doi.org/10.1021/acssynbio.6b00372	journal	February 2017
Development of Transcription Factor-Based Designer Macrolide Biosensors for Metabolic Engineering and Synthetic Biology Kasey, Christian M.; Zerrad, Mounir; Li, Yiwei ACS Synthetic Biology, Vol. 7, Issue 1 https://doi.org/10.1021/acssynbio.7b00287	journal	August 2017
Artificial Caprolactam-Specific Riboswitch as an Intracellular Metabolite Sensor Jang, Sungyeon; Jang, Sungho; Im, Dae-Kyun ACS Synthetic Biology, Vol. 8, Issue 6 https://doi.org/10.1021/acssynbio.8b00452	journal	May 2019
Ring-closure reactions. 22. Kinetics of cyclization of diethyl (.omega.-bromoalkyl)malonates in the range of 4- to 21-membered rings. Role of ring strain Casadei, Maria Antonietta; Galli, Carlo; Mandolini, Luigi Journal of the American Chemical Society, Vol. 106, Issue 4 https://doi.org/10.1021/ja00316a039	journal	February 1984
NHC-Catalyzed Intramolecular Redox Amidation for the Synthesis of Functionalized Lactams Thai, Karen; Wang, Li; Dudding, Travis Organic Letters, Vol. 12, Issue 24 https://doi.org/10.1021/ol102536s	journal	December 2010
j5 DNA Assembly Design Automation Software Hillson, Nathan J.; Rosengarten, Rafael D.; Keasling, Jay D. ACS Synthetic Biology, Vol. 1, Issue 1, p. 14-21 https://doi.org/10.1021/sb2000116	journal	December 2011
Enzymatic assembly of DNA molecules up to several hundred kilobases Gibson, Daniel G.; Young, Lei; Chuang, Ray-Yuan Nature Methods, Vol. 6, Issue 5, p. 343-345 https://doi.org/10.1038/nmeth.1318	journal	April 2009
ModelFinder: fast model selection for accurate phylogenetic estimates Kalyaanamoorthy, Subha; Minh, Bui Quang; Wong, Thomas K. F. Nature Methods, Vol. 14, Issue 6 https://doi.org/10.1038/nmeth.4285	journal	May 2017
Pooled CRISPR interference screening enables genome-scale functional genomics study in bacteria with superior performance Wang, Tianmin; Guan, Changge; Guo, Jiahui Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-04899-x	journal	June 2018
A synthetic microbial biosensor for high-throughput screening of lactam biocatalysts Yeom, Soo-Jin; Kim, Moonjeong; Kwon, Kil Koang Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-018-07488-0	journal	November 2018
Mutant phenotypes for thousands of bacterial genes of unknown function Price, Morgan N.; Wetmore, Kelly M.; Waters, R. Jordan Nature, Vol. 557, Issue 7706 https://doi.org/10.1038/s41586-018-0124-0	journal	May 2018
Pestalactams A–C: novel caprolactams from the endophytic fungus Pestalotiopsis sp. Davis, Rohan A.; Carroll, Anthony R.; Andrews, Katherine T. Organic & Biomolecular Chemistry, Vol. 8, Issue 8 https://doi.org/10.1039/b924169h	journal	January 2010
Design of a "green" one-step catalytic production of -caprolactam (precursor of nylon-6) Thomas, J. M.; Raja, R. Proceedings of the National Academy of Sciences, Vol. 102, Issue 39 https://doi.org/10.1073/pnas.0506907102	journal	September 2005
Differential plasmid rescue from transgenic mouse DNAs into Escherichia coli methylation-restriction mutants. Grant, S. G.; Jessee, J.; Bloom, F. R. Proceedings of the National Academy of Sciences, Vol. 87, Issue 12 https://doi.org/10.1073/pnas.87.12.4645	journal	June 1990
Transcriptional regulation of the Rhodococcus rhodochrous J1 nitA gene encoding a nitrilase. Komeda, H.; Hori, Y.; Kobayashi, M. Proceedings of the National Academy of Sciences, Vol. 93, Issue 20 https://doi.org/10.1073/pnas.93.20.10572	journal	October 1996
Actinobacteria phylogenomics, selective isolation from an iron oligotrophic environment and siderophore functional characterization, unveil new desferrioxamine traits Cruz-Morales, Pablo; Ramos-Aboites, Hilda E.; Licona-Cassani, Cuauhtémoc FEMS Microbiology Ecology, Vol. 93, Issue 9 https://doi.org/10.1093/femsec/fix086	journal	July 2017
MEME: discovering and analyzing DNA and protein sequence motifs Bailey, T. L.; Williams, N.; Misleh, C. Nucleic Acids Research, Vol. 34, Issue Web Server https://doi.org/10.1093/nar/gkl198	journal	July 2006
Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools Ham, T. S.; Dmytriv, Z.; Plahar, H. Nucleic Acids Research, Vol. 40, Issue 18 https://doi.org/10.1093/nar/gks531	journal	June 2012
Synthetic biosensors for precise gene control and real-time monitoring of metabolites Rogers, Jameson K.; Guzman, Christopher D.; Taylor, Noah D. Nucleic Acids Research, Vol. 43, Issue 15 https://doi.org/10.1093/nar/gkv616	journal	July 2015
AraC protein, regulation of the l-arabinose operon in Escherichia coli , and the light switch mechanism of AraC action Schleif, Robert FEMS Microbiology Reviews, Vol. 34, Issue 5 https://doi.org/10.1111/j.1574-6976.2010.00226.x	journal	September 2010
Identification of a Transcriptional Activator (ChnR) and a 6-Oxohexanoate Dehydrogenase (ChnE) in the Cyclohexanol Catabolic Pathway in Acinetobacter sp. Strain NCIMB 9871 and Localization of the Genes That Encode Them Iwaki, Hiroaki; Hasegawa, Yoshie; Teraoka, Masahiro Applied and Environmental Microbiology, Vol. 65, Issue 11 https://doi.org/10.1128/AEM.65.11.5158-5162.1999	journal	November 1999
In Vivo DNA-Binding and Oligomerization Properties of the Shigella flexneri AraC-Like Transcriptional Regulator VirF as Identified by Random and Site-Specific Mutagenesis Porter, Megan E.; Dorman, Charles J. Journal of Bacteriology, Vol. 184, Issue 2 https://doi.org/10.1128/JB.184.2.531-539.2002	journal	January 2002
Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons Wetmore, Kelly M.; Price, Morgan N.; Waters, Robert J. mBio, Vol. 6, Issue 3, Article No. e00306-15 https://doi.org/10.1128/mBio.00306-15	journal	May 2015
Massively Parallel Fitness Profiling Reveals Multiple Novel Enzymes in Pseudomonas putida Lysine Metabolism Thompson, Mitchell G.; Blake-Hedges, Jacquelyn M.; Cruz-Morales, Pablo mBio, Vol. 10, Issue 3 https://doi.org/10.1128/mBio.02577-18	journal	May 2019
High-Throughput Metabolic Engineering: Advances in Small-Molecule Screening and Selection Dietrich, Jeffrey A.; McKee, Adrienne E.; Keasling, Jay D. Annual Review of Biochemistry, Vol. 79, Issue 1 https://doi.org/10.1146/annurev-biochem-062608-095938	journal	June 2010
Development of a broad-host synthetic biology toolbox for ralstonia eutropha and its application to engineering hydrocarbon biofuel production Bi, Changhao; Su, Peter; Müller, Jana Microbial Cell Factories, Vol. 12, Issue 1 https://doi.org/10.1186/1475-2859-12-107	journal	January 2013
DeviceEditor visual biological CAD canvas Chen, Joanna; Densmore, Douglas; Ham, Timothy S. Journal of Biological Engineering, Vol. 6, Issue 1 https://doi.org/10.1186/PREACCEPT-1967068768635731	journal	January 2012
Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P. PLoS Computational Biology, Vol. 3, Issue 9 https://doi.org/10.1371/journal.pcbi.0030175	journal	September 2007
A One Pot, One Step, Precision Cloning Method with High Throughput Capability Engler, Carola; Kandzia, Romy; Marillonnet, Sylvestre PLoS ONE, Vol. 3, Issue 11, Article No. e3647 https://doi.org/10.1371/journal.pone.0003647	journal	November 2008
Validating regulatory predictions from diverse bacteria with mutant fitness data Sagawa, Shiori; Price, Morgan N.; Deutschbauer, Adam M. PLOS ONE, Vol. 12, Issue 5 https://doi.org/10.1371/journal.pone.0178258	journal	May 2017
A rapid methods development workflow for high-throughput quantitative proteomic applications Chen, Yan; Vu, Jonathan; Thompson, Mitchell G. PLOS ONE, Vol. 14, Issue 2 https://doi.org/10.1371/journal.pone.0211582	journal	February 2019

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