A Synthetic Reaction Cascade Implemented by Colocalization of Two Proteins within Catalytically Active Inclusion Bodies.

In nature, enzymatic reaction cascades, i.e., realized in metabolic networks, operate with unprecedented efficacy, with the reactions often being spatially and temporally orchestrated. The principle of "learning from nature" has in recent years inspired the setup of synthetic reaction cascades combining biocatalytic reaction steps to artificial cascades. Hereby, the spatial organization of multiple enzymes, e.g., by coimmobilization, remains a challenging task, as currently no generic principles are available that work for every enzyme. We here present a tunable, genetically programmed coimmobilization strategy that relies on the fusion of a coiled-coil domain as aggregation inducing-tag, resulting in the formation of catalytically active inclusion body coimmobilizates (Co-CatIBs). Coexpression and coimmobilization was proven using two fluorescent proteins, and the strategy was subsequently extended to two enzymes, which enabled the realization of an integrated enzymatic two-step cascade for the production of (1 R,2 R)-1-phenylpropane-1,2-diol (PPD), a precursor of the calicum channel blocker diltiazem. In particular, the easy production and preparation of Co-CatIBs, readily yielding a biologically produced enzyme immobilizate renders the here presented strategy an interesting alternative to existing cascade immobilization techniques.

[1]  Y. Rhee,et al.  Controlled Localization of Functionally Active Proteins to Inclusion Bodies Using Leucine Zippers , 2014, PloS one.

[2]  J. Turkenburg,et al.  Structures of Alcohol Dehydrogenases from Ralstonia and Sphingobium spp. Reveal the Molecular Basis for Their Recognition of ‘Bulky–Bulky’ Ketones , 2014, Topics in Catalysis.

[3]  M. L. Ferreira,et al.  Cross-linked enzyme aggregates (CLEAs) of selected lipases: a procedure for the proper calculation of their recovered activity , 2013, AMB Express.

[4]  R. Tsien,et al.  green fluorescent protein , 2020, Catalysis from A to Z.

[5]  Julia Frunzke,et al.  Construction of Recombinant Pdu Metabolosome Shells for Small Molecule Production in Corynebacterium glutamicum. , 2017, ACS synthetic biology.

[6]  F. Studier,et al.  Protein production by auto-induction in high density shaking cultures. , 2005, Protein expression and purification.

[7]  Vera D. Jäger,et al.  Catalytically-active inclusion bodies-Carrier-free protein immobilizates for application in biotechnology and biomedicine. , 2017, Journal of biotechnology.

[8]  Wolfgang Wiechert,et al.  Spatiotemporal microbial single‐cell analysis using a high‐throughput microfluidics cultivation platform , 2015, Cytometry. Part A : the journal of the International Society for Analytical Cytology.

[9]  G. Schneider,et al.  Rational Protein Design of ThDP‐Dependent Enzymes—Engineering Stereoselectivity , 2008, Chembiochem : a European journal of chemical biology.

[10]  R. Tsien,et al.  Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein , 2004, Nature Biotechnology.

[11]  François Taddei,et al.  Asymmetric segregation of protein aggregates is associated with cellular aging and rejuvenation , 2008, Proceedings of the National Academy of Sciences.

[12]  Soo-Jin Yeom,et al.  Leucine zipper-mediated targeting of multi-enzyme cascade reactions to inclusion bodies in Escherichia coli for enhanced production of 1-butanol. , 2017, Metabolic engineering.

[13]  Faisal A. Aldaye,et al.  Organization of Intracellular Reactions with Rationally Designed RNA Assemblies , 2011, Science.

[14]  Shuxiong Chen,et al.  Enzyme Engineering for In Situ Immobilization , 2016, Molecules.

[15]  Teruyuki Nagamune,et al.  Supramolecular protein assembly supports immobilization of a cytochrome P450 monooxygenase system as water-insoluble gel , 2015, Scientific Reports.

[16]  J. Cui,et al.  A Simple Technique of Preparing Stable CLEAs of Phenylalanine Ammonia Lyase Using Co-aggregation with Starch and Bovine Serum Albumin , 2013, Applied Biochemistry and Biotechnology.

[17]  R. Sheldon,et al.  Cross‐Linked Aggregates of the Hydroxynitrile Lyase from Manihot esculenta: Highly Active and Robust Biocatalysts , 2006 .

[18]  Kevin W Eliceiri,et al.  NIH Image to ImageJ: 25 years of image analysis , 2012, Nature Methods.

[19]  Vincent Noireaux,et al.  A vesicle bioreactor as a step toward an artificial cell assembly. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Christof M Niemeyer,et al.  Assembly and purification of enzyme-functionalized DNA origami structures. , 2015, Angewandte Chemie.

[21]  H. Hess,et al.  Proximity does not contribute to activity enhancement in the glucose oxidase–horseradish peroxidase cascade , 2016, Nature Communications.

[22]  R. Kammerer,et al.  Crystal structure of a naturally occurring parallel right-handed coiled coil tetramer , 2001, Nature Structural Biology.

[23]  Martina Pohl,et al.  Characterization of benzaldehyde lyase from Pseudomonas fluorescens: A versatile enzyme for asymmetric C-C bond formation. , 2006, Bioorganic chemistry.

[24]  B. Narasimhan,et al.  Multienzyme Immobilization and Colocalization on Nanoparticles Enabled by DNA Hybridization , 2015 .

[25]  M. Kantam,et al.  A trifunctional catalyst for one-pot synthesis of chiral diols via Heck coupling-N-oxidation-asymmetric dihydroxylation: application for the synthesis of diltiazem and taxol side chain. , 2003, The Journal of organic chemistry.

[26]  Wolfgang Marquardt,et al.  Mechanistic kinetic model for symmetric carboligations using benzaldehyde lyase , 2008, Biotechnology and bioengineering.

[27]  T. Funatsu,et al.  Kinetic study of de novo chromophore maturation of fluorescent proteins. , 2011, Analytical biochemistry.

[28]  Vassilios Ioannidis,et al.  ExPASy: SIB bioinformatics resource portal , 2012, Nucleic Acids Res..

[29]  Sumitra Datta,et al.  Enzyme immobilization: an overview on techniques and support materials , 2012, 3 Biotech.

[30]  A. Guiseppi-Elie,et al.  Enzyme microgels in packed-bed bioreactors with downstream amperometric detection using microfabricated interdigitated microsensor electrode arrays. , 2001, Biotechnology and bioengineering.

[31]  Ellen M. Quardokus,et al.  MicrobeJ, a tool for high throughput bacterial cell detection and quantitative analysis , 2016, Nature Microbiology.

[32]  M. Reuss,et al.  High-cell-density fermentation for production of L-N-carbamoylase using an expression system based on the Escherichia coli rhaBAD promoter. , 2001, Biotechnology and bioengineering.

[33]  G. Cannon,et al.  Halothiobacillus neapolitanus Carboxysomes Sequester Heterologous and Chimeric RubisCO Species , 2008, PloS one.

[34]  Zhanglin Lin,et al.  Formation of active inclusion bodies induced by hydrophobic self-assembling peptide GFIL8 , 2015, Microbial Cell Factories.

[35]  Karl-Erich Jaeger,et al.  Exchange of single amino acids at different positions of a recombinant protein affects metabolic burden in Escherichia coli , 2015, Microbial Cell Factories.

[36]  J. Rose,et al.  Forizymes – functionalised artificial forisomes as a platform for the production and immobilisation of single enzymes and multi-enzyme complexes , 2016, Scientific Reports.

[37]  R Vicuña,et al.  Benzaldehyde lyase, a novel thiamine PPi-requiring enzyme, from Pseudomonas fluorescens biovar I , 1989, Journal of bacteriology.

[38]  J. Betton,et al.  Formation of active inclusion bodies in the periplasm of Escherichia coli , 2006, Molecular microbiology.

[39]  Roger A Sheldon,et al.  A new, mild cross‐linking methodology to prepare cross‐linked enzyme aggregates , 2004, Biotechnology and bioengineering.

[40]  K. Jaeger,et al.  Fusion of a Coiled‐Coil Domain Facilitates the High‐Level Production of Catalytically Active Enzyme Inclusion Bodies , 2016 .

[41]  Marco W Fraaije,et al.  Coupled reactions by coupled enzymes: alcohol to lactone cascade with alcohol dehydrogenase–cyclohexanone monooxygenase fusions , 2017, Applied Microbiology and Biotechnology.

[42]  Nathan C Shaner,et al.  A guide to choosing fluorescent proteins , 2005, Nature Methods.

[43]  J. Büchs,et al.  Parallel online multi‐wavelength (2D) fluorescence spectroscopy in each well of a continuously shaken microtiter plate , 2016, Biotechnology journal.

[44]  Yan Chen,et al.  Chromophore maturation and fluorescence fluctuation spectroscopy of fluorescent proteins in a cell-free expression system. , 2012, Analytical biochemistry.

[45]  Bernd Nidetzky,et al.  Fusion to a pull‐down domain: a novel approach of producing Trigonopsis variabilisD‐amino acid oxidase as insoluble enzyme aggregates , 2007, Biotechnology and bioengineering.

[46]  Se Hyeon Park,et al.  Cadaverine Production by Using Cross-Linked Enzyme Aggregate of Escherichia coli Lysine Decarboxylase. , 2017, Journal of microbiology and biotechnology.

[47]  R. Bischoff,et al.  Covalent immobilization of a flavoprotein monooxygenase via its flavin cofactor. , 2016, Enzyme and microbial technology.

[48]  Bochu Wang,et al.  Immobilized multienzymatic systems for catalysis of cascade reactions , 2016 .

[49]  Zhoutong Sun,et al.  Whole-Cell-Catalyzed Multiple Regio- and Stereoselective Functionalizations in Cascade Reactions Enabled by Directed Evolution. , 2016, Angewandte Chemie.

[50]  M. M. Bradford A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. , 1976, Analytical biochemistry.

[51]  Fernando López-Gallego,et al.  Co‐immobilized Phosphorylated Cofactors and Enzymes as Self‐Sufficient Heterogeneous Biocatalysts for Chemical Processes , 2016, Angewandte Chemie.

[52]  R. Tsien,et al.  Partitioning of Lipid-Modified Monomeric GFPs into Membrane Microdomains of Live Cells , 2002, Science.

[53]  Jochen Wachtmeister,et al.  Whole‐Cell Teabag Catalysis for the Modularisation of Synthetic Enzyme Cascades in Micro‐Aqueous Systems , 2014 .

[54]  Joachim Goedhart,et al.  Bright monomeric red fluorescent protein with an extended fluorescence lifetime , 2007, Nature Methods.

[55]  Enzyme fusion for whole-cell biotransformation of long-chain sec-alcohols into esters , 2015, Applied Microbiology and Biotechnology.

[56]  Dörte Rother,et al.  (Chemo)enzymatic cascades - Nature's synthetic strategy transferred to the laboratory , 2015 .

[57]  Yifei Zhang,et al.  Enhanced Activity of Immobilized or Chemically Modified Enzymes , 2015 .

[58]  Michael Mueller,et al.  Structure and mechanism of the ThDP‐dependent benzaldehyde lyase from Pseudomonas fluorescens , 2005, The FEBS journal.

[59]  A Miyawaki,et al.  Dynamic and quantitative Ca2+ measurements using improved cameleons. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[60]  R. Sheldon,et al.  Cross-linked enzyme aggregates: a simple and effective method for the immobilization of penicillin acylase. , 2000, Organic letters.

[61]  Jeff Hasty,et al.  Rational engineering of synthetic microbial systems: from single cells to consortia. , 2018, Current opinion in microbiology.

[62]  W. Kroutil,et al.  Biochemical characterization of an alcohol dehydrogenase from Ralstonia sp. , 2013, Biotechnology and bioengineering.

[63]  Brian F. Pfleger,et al.  Transcription control engineering and applications in synthetic biology , 2017, Synthetic and systems biotechnology.

[64]  W. Kroutil,et al.  Stereoselective synthesis of bulky 1,2-diols with alcohol dehydrogenases , 2012 .