Research progress of multi-enzyme complexes based on the design of scaffold protein

Abstract

•	The strategies of compartmentalization and substrate channel for organisms to manipulate multi-enzyme reactions are reviewed.
•	The discovered enzyme cascade reactions related to scaffold proteins are summarized.
•	The influence of linkers on fusion proteins and their possible mechanisms are highlighted and prospected.

Keywords

Enzyme cascades / Substrate channel / Scaffold protein / Fusion protein / Linker

References

[1] Amet N, Lee H-F, Shen W-C. Insertion of the designed helical linker led to increased expression of Tf-Based fusion proteins. Pharm Res, 2009, 26(3): 523-528.

[2] Arai R. Design of helical linkers for fusion proteins and protein-based nanostructures. Methods Enzymol, 2021, 647: 209-230.

[3] Arai R, Ueda H, Kitayama A, Kamiya N, Nagamune T. Design of the linkers which effectively separate domains of a bifunctional fusion protein. Protein Eng, 2001, 14(8): 529-532.

[4] Arai R, Wriggers W, Nishikawa Y, Nagamune T, Fujisawa T. Conformations of variably linked chimeric proteins evaluated by synchrotron X-ray small-angle scattering. Proteins, 2004, 57(4): 829-838.

[5] Argos P. An investigation of oligopeptides linking domains in protein tertiary structures and possible candidates for general gene fusion. J Mol Biol, 1990, 211(4): 943-958.

[6] Arunachalam J, Kanagasabai V, Gautham N. Protein structure prediction using mutually orthogonal Latin squares and a genetic algorithm. Biochem Biophys Res Commun, 2006, 342(2): 424-433.

[7] Ataka K, Pieribone VA. A genetically targetable fluorescent probe of channel gating with rapid kinetics. Biophys J , 2002, 82: 509-516.

[8] Avalos JL, Fink GR, Stephanopoulos G. Compartmentalization of metabolic pathways in yeast mitochondria improves the production of branched-chain alcohols. Nat Biotechnol, 2013, 31(4): 335-341.

[9] Barton GJ. Protein secondary structure prediction. Curr Opin Struct Biol, 1995, 5(3): 372-376.

[10] Bayer EA, Morag E, Lamed R. The cellulosome—a treasure-trove for biotechnology. Trends Biotechnol, 1994, 12(9): 379-386.

[11] Bayer E-A, Belaich J-P, Shoham Y, Lamed R. The cellulosomes: multienzyme machines for degradation of plant cell wall polysaccharides. Annu Rev Microbiol, 2004, 58: 521-554.

[12] Bayer E-A, Lamed R, White B-A, Flint H-J. From cellulosomes to cellulosomics. Chem Rec, 2008, 8(6): 364-377.

[13] Beeckmans S, V.D.E., Kanarek L. . Immobilized enzymes as tools for the demonstration of metabolon formation. A Short Overview J Mol Recognit, 1993, 6(4): 195-204.

[14] Black GW, Hazlewood GP, Xue GP, Orpin CG, Gilbert HJ. Xylanase B from Neocallimastix patriciarum contains a non-catalytic 455-residue linker sequence comprised of 57 repeats of an octapeptide. Biochem J, 1994

[15] Boonyakida J, Khoris IM, Nasrin F, Park EY. Improvement of modular protein display efficiency in SpyTag-implemented norovirus-like particles. Biomacromol, 2023, 24(1): 308-318.

[16] Bouin A, Zhang C, Lindley ND, Truan G, Lautier T. Exploring linker's sequence diversity to fuse carotene cyclase and hydroxylase for zeaxanthin biosynthesis. Metab Eng Commun, 2023, 16.

[17] Buddingh' BC, v.H.J. . Artificial cells: synthetic compartments with life-like functionality and adaptivity. Acc Chem Res, 2017, 50(4): 769-777.

[18] Bule P, Alves V-D, Leitao A, Ferreira L-M-A, Bayer E-A, Smith S-P, Gilbert H-J, Najmudin S, Fontes C-M-G-A. Single binding mode integration of hemicellulose-degrading enzymes via adaptor scaffoldins in Ruminococcus flavefaciens Cellulosome. J Biol Chem, 2016, 291(52): 26658-26669.

[19] Bülow L, M.K. . Multienzyme systems obtained by gene fusion. Trends Biotechnol, 1991, 9(7): 226-231.

[20] Cai Y, Zhou S, Jin Z, Wei H, Shang L, Deng J, . Reengineering of albumin-fused cocaine hydrolase CocH1 (TV-1380) to prolong its biological half-life. AAPS J, 2019, 22(1): 5.

[21] Cai Y, Wang M, Xiao X, Liang B, Fan S, Zheng Z, . A membraneless starch/O-2 biofuel cell based on bacterial surface regulable displayed sequential enzymes of glucoamylase and glucose dehydrogenase. Biosens Bioelectron, 2022, 207.

[22] Cavaco-Paulo A, Morgado J, Andreaus J, Kilburn D. Interactions of cotton with CBD peptides. Enzyme Microb Technol, 1999, 25(8–9): 639-643.

[23] Chen X, Zaro JL, Shen WC. Fusion protein linkers: property, design and functionality. Adv Drug Deliv Rev, 2013, 65(10): 1357-1369.

[24] Chen H, Wu B, Zhang T, Jia J, Lu J, Chen Z, . Effect of linker length and flexibility on the Clostridium thermocellum esterase displayed on Bacillus subtilis spores. Appl Biochem Biotechnol, 2017, 182(1): 168-180.

[25] Chen X, Chen X, Zhu L, Liu W, Jiang L. Efficient production of inulo-oligosaccharides from inulin by exo- and endo-inulinase co-immobilized onto a self-assembling protein scaffold. Int J Biol Macromol, 2022, 210: 588-599.

[26] Chi CN, Bach A, Stromgaard K, Gianni S, Jemth P. Ligand binding by PDZ domains. BioFactors, 2012, 38(5): 338-348.

[27] Crasto CJ, Feng JA. LINKER :a program to generate linker sequences for fusion proteins. Protein Eng, 2000, 13(5): 309-312.

[28] Deng D, Meng Q, Li Z, Ma R, Yang Y, Wang Z, . Enzyme-inspired assembly: incorporating multivariate interactions to optimize the Host-Guest configuration for high-speed enantioselective catalysis. ACS Appl Mater Interfaces, 2020, 12(42): 47966-47974.

[29] Dietmann S, Aguilar D, Mader M, Oesterheld M, Ruepp A, Stuempflen V, . Resources and tools for investigating biomolecular networks in mammals. Curr Pharm Des, 2006, 12(29): 3723-3734.

[30] Dueber JE, Wu GC, Malmirchegini GR, Moon TS, Petzold CJ, Ullal AV, . Synthetic protein scaffolds provide modular control over metabolic flux. Nat Biotechnol, 2009, 27(8): 753-759.

[31] Espinoza-Fonseca LM, Wong-Ramirez C, Trujillo-Ferrara JG. Tyr74 is essential for the formation, stability and function of Plasmodium falciparum triosephosphate isomerase dimer. Arch Biochem Biophys, 2010, 494(1): 46-57.

[32] Evans JS, Levine BA, Trayer IP, Dorman CJ, Higgins CF. Sequence-imposed structural constraints in the TonB protein of E coli. FEBS Lett, 1986, 208(2): 211-216.

[33] Fan J, Huang L, Sun J, Qiu Y, Zhou J, Shen Y. Strategy for linker selection to enhance refolding and bioactivity of VAS-TRAIL fusion protein based on inclusion body conformation and activity. J Biotechnol, 2015, 209: 16-22.

[34] Fierobe H-P, Mechaly A, Tardif C, Belaich A, Lamed R, Shoham Y, Belaich J-P, Bayer E-A. Design and production of active cellulosome chimeras. Selective incorporation of dockerin-containing enzymes into defined functional complexes. J Biol Chem, 2001

[35] Freitas AI, Domingues L, Aguiar TQ. Tag-mediated single-step purification and immobilization of recombinant proteins toward protein-engineered advanced materials. J Adv Res, 2022, 36: 249-264.

[36] Gall FL, Reusch U, Little M, Kipriyanov SM. Effect of linker sequences between the antibody variable domains on the formation, stability and biological activity of a bispecific tandem diabody. Protein Eng Des Sel, 2004, 17(4): 357-366.

[37] Geck MK, Kirsch JF. A novel, definitive test for substrate channeling illustrated with the aspartate aminotransferase/malate dehydrogenase system. Biochemistry, 1999, 38(25): 8032-8037.

[38] George RA, Jaap H. An analysis of protein domain linkers: their classification and role in protein folding. Protein Eng, 2002, 15(11): 871-879.

[39] Gokhale RS, Khosla C. Role of linkers in communication between protein modules. Curr Opin Chem Biol, 2000, 4(1): 22-27.

[40] Guntas G, Ostermeier M. Creation of an allosteric enzyme by domain insertion. J Mol Biol, 2004, 336(1): 263-273.

[41] Haimovitz R, Barak Y, Morag E, Voronov-Goldman M, Shoham Y, Lamed R, . Cohesin-dockerin microarray: Diverse specificities between two complementary families of interacting protein modules. Proteomics, 2010, 8(5): 968-979.

[42] Henrik Pettersson GP. Kinetics of the coupled reaction catalysed by a fusion protein of L-galactosidase and galactose dehydrogenase. Biochim Biophys Acta, 2001, 1549(2): 155-160.

[43] Hernandez K, Fernandez-Lafuente R. Control of protein immobilization: coupling immobilization and site-directed mutagenesis to improve biocatalyst or biosensor performance. Enzyme Microb Technol, 2011, 48(2): 107-122.

[44] Hirakawa H, Nagamune T. A branched fusion P450 system containing CYP119. J Biosci Bioeng, 2009, 108: S100-S101.

[45] Hong SY, Lee JS, Cho KM, Math RK, Kim YH, Hong SJ, . Assembling a novel bifunctional cellulase-xylanase from Thermotoga maritima by end-to-end fusion. Biotechnol Lett, 2006, 28(22): 1857-1862.

[46] Hong LZ, Xue QY, Chong X, Yang W, Xiang HX, Zhi ML. Increasing the homogeneity, stability and activity of human serum albumin and interferon-alpha2b fusion protein by linker engineering. Protein Expr Purif, 2008, 61(1): 73-77.

[47] Hu BB, Zhu MJ. Reconstitution of cellulosome: research progress and its application in biorefinery. Biotechnol Appl Biochem, 2019, 66(5): 720-730.

[48] Hu W, Feng L, Yang X, Zhen L, Xia H, Li G, . A flexible peptide linker enhances the immunoreactivity of two copies HBsAg preS1 (21–47) fusion protein. J Biotechnol, 2004, 107(1): 83-90.

[49] Huang Z-L, Zhang C, Wu X, Su N, Xing X. Recent progress in fusion enzyme design and applications. Chin J Biotechnol, 2012, 28(04): 393-409.

[50] Huang Z, Zhang C, Xing XH. Design and construction of chimeric linker library with controllable flexibilities for precision protein engineering. Methods Enzymol, 2021, 647: 23-49.

[51] Huston JS, Levinson D, Mudgett-Hunter M, Tai MS, Novotný J, Margolies MN, Ridge RJ, Bruccoleri RE, Haber E, Crea R, . Protein engineering of antibody binding sites recovery of specific activity in an anti-digoxin single-chain Fv analogue produced in Escherichia coli. Proc Natl Acad Sci USA, 1988, 85(16): 5879-5883.

[52] Idan O, Hess H. Origins of activity enhancement in enzyme cascades on scaffolds. ACS Nano, 2013, 7(10): 8658-8665.

[53] Igor T, Jerry P, Greenberg S, . 600 ps Molecular dynamics reveals stable substructures and flexible hinge points in cAMP dependent protein kinase. Biopolymers, 1999, 50(5): 513-524.

[54] Iturrate L, Sanchez-Moreno I, Doyaguez E-G, Garcia-Junceda E. Substrate channelling in an engineered bifunctional aldolase/kinase enzyme confers catalytic advantage for C-C bond formation. Chem Commun, 2009, 13(13): 1721-1723.

[55] Ivarsson M, Prenkert M, Cheema A, Wretenberg P, Andjelkov N. Mussel adhesive protein as a promising alternative to fibrin for scaffold fixation during cartilage repair surgery. Cartilage, 2021

[56] James P, Philip K, Daniel C, . Inhibition of human cyp1a2 oxidation of 5,6-dimethyl-xanthenone-4-acetic acid by acridines: a molecular modelling study. Clin Exp Pharmacol Physiol, 2005, 32(8): 633-639.

[57] Jia L, Minamihata K, Ichinose H, Tsumoto K, Kamiya N. Polymeric SpyCatcher scaffold enables bioconjugation in a ratio-controllable manner. Biotechnol J, 2017

[58] Jiang Y, Zhang X-Y, Yuan H, Huang D, Wang R, Liu H, Wang T. Research progress and the biotechnological applications of multienzyme complex. Appl Microbiol Biotechnol, 2021, 105(5): 1759-1777.

[59] Jones DT. Progress in protein structure prediction. Curr Opin Struct Biol, 1997, 7(3): 377-387.

[60] Kabiri M, Tafaghodi M, Saberi MR, Moghadam M, Rezaee SA, Sankian M. Separation of the epitopes in a multi-epitope chimera: helical or flexible linkers. Protein Pept Lett, 2020, 27(7): 604-613.

[61] Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 2006, 22(17): 2577-2637.

[62] Kajiwara K, Aoki W, Koike N, Ueda M. Development of a yeast cell surface display method using the SpyTag/SpyCatcher system. Sci Rep, 2021, 11(1): 11059.

[63] Kang W, Ma T, Liu M, Qu J, Liu Z, Zhang H, . Modular enzyme assembly for enhanced cascade biocatalysis and metabolic flux. Nat Commun, 2019, 10(1): 4248.

[64] Karle IL, Banerjee A, Balaram P. Design of two-helix motifs in peptides: crystal structure of a system of linked helices of opposite chirality and a model helix-linker peptide. Fold Des, 1997, 2(4): 203-210.

[65] Karp M, Oker-Blom C. A streptavidin-luciferase fusion protein: comparisons and applications. Biomol Eng, 1999, 16(1–4): 101-104.

[66] Kavoosi M, Creagh A-L, Kilburn D-G, Haynes C-A. Strategy for selecting and characterizing linker peptides for CBM9-tagged fusion proteins expressed in Escherichia coli. Biotechnol Bioeng, 2007, 98(3): 599-610.

[67] Khobragade TP, Sarak S, Pagar AD, Jeon H, Giri P, Yun H. Synthesis of sitagliptin intermediate by a multi-enzymatic cascade system using lipase and transaminase with benzylamine as an amino donor. Front Bioeng Biotechnol, 2021, 9.

[68] Komarala EP, Neethinathan CSS, Kokkiligadda S, Mariyappan K, Yoo SS, Yoo PJ, . DNA Scaffolds with manganese Oxide/Oxyhydroxide nanoparticles for highly stable supercapacitance electrodes. Acs Appl Nano Mat, 2022, 5(7): 8902-8912.

[69] Kossmann C, Ma S, Clemmensen LS, Stromgaard K. Chemical Synthesis of PDZ Domains. Methods Mol Biol, 2021, 2256: 193-216.

[70] Kulsharova G, Dimov N, Marques MPC, Szita N, Baganz F. Simplified immobilisation method for histidine-tagged enzymes in poly(methyl methacrylate) microfluidic devices. N Biotechnol, 2018, 47: 31-38.

[71] Lamed R, Setter E, Kenig R, Bayer E. Cellulosome: a discrete cell surface organelle of Clostridium thermocellum which exhibits separate antigenic, cellulose-binding and various cellulolytic activities. Biotechnol Bioeng Symp, 1983, 13: 163-181.

[72] Li G, Huang Z, Zhang C, Dong BJ, Guo RH, Yue HW, . Construction of a linker library with widely controllable flexibility for fusion protein design. Appl Microbiol Biotechnol, 2016, 100(1): 215-225.

[73] Li ZH, Wang J, Li YX, Liu XW, Yuan Q. Self-assembled DNA nanomaterials with highly programmed structures and functions. Mater Chem Front, 2018, 2(3): 423-436.

[74] Lin J-L, Palomec L, Wheeldon I. Design and analysis of enhanced catalysis in scaffolded multienzyme cascade reactions. Acs Catal, 2014, 4(2): 505-511.

[75] Lu P, Feng MG. Bifunctional enhancement of a beta-glucanase-xylanase fusion enzyme by optimization of peptide linkers. Appl Microbiol Biotechnol, 2008, 79(4): 579-587.

[76] Ma S, Wu J, Hu H, Mu Y, Zhang L, Zhao Y, . Novel fusion peptides deliver exosomes to modify injectable thermo-sensitive hydrogels for bone regeneration. Mater Today Bio, 2022, 13.

[77] Maeda Y, Ueda H, Hara T, Kazami J, Kawano G, Suzuki E, . Expression of a bifunctional chimeric protein A-Vargula hilgendorfii luciferase in mammalian cells. Biotechniques, 1996, 20(1): 116-121.

[78] Maeda Y, Ueda H, Kazami J, Kawano G, Suzuki E, Nagamune T. Engineering of functional chimeric protein G-Vargula luciferase. Anal Biochem, 1997, 249(2): 147-152.

[79] Maki M, Leung K-T, Qin W. The prospects of cellulase-producing bacteria for the bioconversion of lignocellulosic biomass. Int J Biol Sci, 2009, 5(5): 500-516.

[80] Malin G, Janne L, Stuart D, Teeri TT, Karl H, Mats M. Stable linker peptides for a cellulose-binding domain-lipase fusion protein expressed in Pichia pastoris. Protein Eng, 2001, 9: 711-715.

[81] Mechaly A, Fierobe H-P, Belaich A, Belaich J-P, Lamed R, Shoham Y, Bayer E-A. Cohesin-dockerin interaction in cellulosome assembly: a single hydroxyl group of a dockerin domain distinguishes between nonrecognition and high affinity recognition. J Biol Chem, 2001, 276(13): 9883-9888.

[82] Meng DD, Ying Y, Chen XH, Lu M, Ning K, Wang LS, . Distinct roles for carbohydrate-binding modules of glycoside hydrolase 10 (GH10) and GH11 xylanases from Caldicellulosiruptor sp. strain F32 in thermostability and catalytic efficiency. Appl Environ Microbiol, 2015, 81(6): 2006-2014.

[83] Meng D, Wu R, Wang J, Zhu Z, You C. Acceleration of cellodextrin phosphorolysis for bioelectricity generation from cellulosic biomass by integrating a synthetic two-enzyme complex into an in vitro synthetic enzymatic biosystem. Biotechnol Biofuels, 2019, 12: 267.

[84] Meng DD, Wang J, You C. The properties of the linker in a mini-scaffoldin influence the catalytic efficiency of scaffoldin-mediated enzyme complexes. Enzyme Microb Technol, 2020, 133.

[85] Mojgan K, A., Louise, Creagh, Douglas, , . Strategy for selecting and characterizing linker peptides for CBM9-tagged fusion proteins expressed in Escherichia coli. Biotechnol Bioeng, 2007, 98(3): 599-610.

[86] Moon TS, Dueber JE, Shiue E, Prather KL. Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli. Metab Eng, 2010, 12(3): 298-305.

[87] Muller J, Niemeyer CM. DNA-directed assembly of artificial multienzyme complexes. Biochem Biophys Res Commun, 2008, 377(1): 62-67.

[88] Nakata E, Dinh H, Nguyen TM, Morii T. DNA binding adaptors to assemble proteins of interest on DNA scaffold. Methods Enzymol, 2019, 617: 287-322.

[89] Nguyen TM, Nakata E, Saimura M, Dinh H, Morii T. Design of modular protein tags for orthogonal covalent bond formation at specific DNA sequences. J Am Chem Soc, 2017, 139(25): 8487-8496.

[90] Nobuhide Doi HY. Design of generic biosensors based on green fluorescent proteins with allosteric sites by directed evolution. FEBS Lett, 1999, 453(3): 305-307.

[91] Park SH, Finkelstein G, LaBean TH. Stepwise self-assembly of DNA tile lattices using dsDNA bridges. J Am Chem Soc, 2008, 130(1): 40-41.

[92] Park SY, Lytton-Jean AKR, Lee B, Weigand S, Schatz GC, Mirkin CA. DNA-programmable nanoparticle crystallization. Nature, 2008, 451(7178): 553-556.

[93] Pham TA, Berrin JG, Record E, To KA, Sigoillot JC. Hydrolysis of softwood by Aspergillus mannanase: Role of a carbohydrate-binding module. J Biotechnol, 2010, 148(4): 163-170.

[94] Pham VD, Somasundaram S, Lee SH, Park SJ, Hong SH. Redirection of metabolic flux into novel gamma-aminobutyric acid production pathway by introduction of synthetic scaffolds strategy in Escherichia Coli. Appl Biochem Biotechnol, 2016, 178(7): 1315-1324.

[95] Quin MB, Wallin KK, Zhang G, Schmidt-Dannert C. Spatial organization of multi-enzyme biocatalytic cascades. Org Biomol Chem, 2017, 15(20): 4260-4271.

[96] Rademacher N, Kuropka B, Kunde SA, Wahl MC, Freund C, Shoichet SA. Intramolecular domain dynamics regulate synaptic MAGUK protein interactions. Elife, 2019, 8.

[97] Rapali P, Mitteau R, Braun C, Massoni-Laporte A, Unlu C, Bataille L, . Scaffold-mediated gating of Cdc42 signalling flux. Elife, 2017, 6.

[98] Ren R, Mayer BJ, Cicchetti P, Baltimore D. Identification of a ten-amino acid proline-rich SH3 binding site. Science, 1993, 259(5098): 1157-1161.

[99] Ribeiro LF, Amarelle V, Ribeiro LFC, Guazzaroni ME. Converting a periplasmic binding protein into a synthetic biosensing switch through domain insertion. Biomed Res Int, 2019, 2019: 4798793.

[100] Ricca E, Brucher B, Schrittwieser JH. Multi-enzymatic cascade reactions: overview and perspectives. Adv Synth Catalysis, 2011, 353(13): 2239-2262.

[101] Rinker S, Ke YG, Liu Y, Chhabra R, Yan H. Self-assembled DNA nanostructures for distance-dependent multivalent ligand-protein binding. Nat Nanotechnol, 2008, 3(7): 418-422.

[102] Robinson CR, Sauer RT. Optimizing the stability of single-chain proteins by linker length and composition mutagenesis. Proc Natl Acad Sci USA, 1998, 95(11): 5929-5934.

[103] Różycki B, Cieplak M. Stiffness of the C-terminal disordered linker affects the geometry of the active site in endoglucanase Cel8A. Mol Biosyst, 2016, 12(12): 3589-3599.

[104] Ruan R, Jin P, Zhang L, Wang C, Chen C, Ding W, . Peptide-chaperone-directed transdermal protein delivery requires energy. Mol Pharm, 2014, 11(11): 4015-4022.

[105] Saksela K, Permi P. SH3 domain ligand binding: What's the consensus and where's the specificity?. FEBS Lett, 2012, 586(17): 2609-2614.

[106] Schoffelen S, Hest JV. Chemical approaches for the construction of multi-enzyme reaction systems. Curr Opin Struct Biol, 2013, 23(4): 613-621.

[107] Schoffelen S, van Hest JCM. Multi-enzyme systems: bringing enzymes together in vitro. Soft Matter, 2012, 8(6): 1736-1746.

[108] Seras-Franzoso J, Peebo K, Garcia-Fruitos E, Vazquez E, Rinas U, Villaverde A. Improving protein delivery of fibroblast growth factor-2 from bacterial inclusion bodies used as cell culture substrates. Acta Biomater, 2014, 10(3): 1354-1359.

[109] Shamriz S, Ofoghi H, Moazami N. Effect of linker length and residues on the structure and stability of a fusion protein with malaria vaccine application. Comput Biol Med, 2016, 76: 24-29.

[110] Sheng YY, Zhou K, Liu L, Wu HC. A nanopore sensing assay resolves cascade reactions in a multienzyme system. Angew Chem Int Ed Engl, 2022, 61(20

[111] Shi J, Wu Y, Zhang S, Tian Y, Yang D, Jiang Z. Bioinspired construction of multi-enzyme catalytic systems. Chem Soc Rev, 2018, 47(12): 4295-4313.

[112] Simmel FC. Three-dimensional nanoconstruction with DNA. Angew Chem Int Ed Engl, 2008, 47(32): 5884-5887.

[113] Smith S-P, Bayer E-A, Czjzek M. Continually emerging mechanistic complexity of the multi-enzyme cellulosome complex. Curr Opin Struct Biol, 2017, 44: 151-160.

[114] Song HY, Kim DR, Lee KI, Hwang IT. A new bi-modular endo-β-1,4-xylanase KRICT PX-3 from whole genome sequence of Paenibacillus terrae HPL-003. Enzyme Microb Tech, 2014, 54(1): 1-7.

[115] Spivey HO, Ovádi J. Substrate channeling. Methods Enzymol, 1999, 19(2): 306-321.

[116] Srere PA. Complexes of sequential metabolic enzymes. Annu Rev Biochem, 1987, 56(1): 89-124.

[117] Srour B, Gervason S, Hoock MH, Monfort B, Want K, Larkem D, . Iron insertion at the assembly site of the ISCU scaffold protein is a conserved process initiating Fe-S cluster biosynthesis. J Am Chem Soc, 2022, 144(38): 17496-17515.

[118] Sun X, Tang X, Wang Q, Chen P, Hill P, Fang B, . Fusion expression of bifunctional enzyme complex for luciferin-recycling to enhance the luminescence imaging. J Photochem Photobiol B, 2018, 185: 66-72.

[119] Sun C, Li G, Li H, Lyu Y, Yu S, Zhou J. Enhancing Flavan-3-ol biosynthesis in Saccharomyces cerevisiae. J Agric Food Chem, 2021, 69(43): 12763-12772.

[120] Sun X, Yuan Y, Chen Q, Nie S, Guo J, Ou Z, . Metabolic pathway assembly using docking domains from type I cis-AT polyketide synthases. Nat Commun, 2022, 13(1): 5541.

[121] Sutherland AR, Alam MK, Geyer CR. Post-translational assembly of protein parts into complex devices by using SpyTag/SpyCatcher protein ligase. ChemBioChem, 2019, 20(3): 319-328.

[122] Sweetlove LJ, Fernie AR. The role of dynamic enzyme assemblies and substrate channelling in metabolic regulation. Nat Commun, 2018, 9(1): 2136.

[123] Takagi M, Hashida S, Goldstein MA, Doi RH. The hydrophobic repeated domain of the Clostridium cellulovorans cellulose-binding protein (CbpA) has specific interactions with endoglucanases. J Bacteriol, 1993, 175(21): 7119-7122.

[124] Takahashi S, Kishi K, Hiraga R, Hayashi K, Mamada Y, Oshige M, . A new method for immobilization of His-Tagged proteins with the application of low-frequency AC electric field. Sensors, 2018, 18(3): 784.

[125] Tokatlidis K, D.P., Béguin P, . Properties conferred on Clostridium thermocellum endoglucanase CelC by grafting the duplicated segment of endoglucanase CelD. Protein Eng, 1993, 6(8): 947-952.

[126] Trinh R, Gurbaxani B, Morrison SL, Seyfzadeh M. Optimization of codon pair use within the (GGGGS)₃ linker sequence results in enhanced protein expression. Mol Immunol, 2004, 40(10): 717-722.

[127] Tsitkov, S.a.H., H, . Design principles for a compartmentalized enzyme cascade reaction. ACS Catal, 2019, 9(3): 2432-2439.

[128] Turner SL, Russell GC, Williamson MP, Guest JR. Restructuring an interdomain linker in the dihydrolipoamide acetyltransferase component of the pyruvate dehydrogenase complex of Escherichia coli. Protein Eng, 1993, 6(1): 101-108.

[129] Ullah J, Chen HY, Vastermark A, Jia JR, Wu BG, Ni Z, . Impact of orientation and flexibility of peptide linkers on T-maritima lipase Tm1350 displayed on Bacillus subtilis spores surface using CotB as fusion partner. World J Microbiol Biotechnol, 2017, 33(9): 166.

[130] Vanderstraeten J, Briers Y. Synthetic protein scaffolds for the colocalisation of co-acting enzymes. Biotechnol Adv, 2020, 44.

[131] Vera A-M, Galera-Prat A, Wojciechowski M, Rozycki B, Laurents D-V, Carrion-Vazquez M, Cieplak M, Tinnefeld P. Cohesin-dockerin code in cellulosomal dual binding modes and its allosteric regulation by proline isomerization. Structure, 2021, 29(6): 587-597.

[132] Viswanathan R, Labadie GR, Poulter CD. Regioselective covalent immobilization of catalytically active glutathione S-Transferase on glass slides. Bioconjug Chem, 2013, 24(4): 571-577.

[133] Voelker AE, Viswanathan R. Synthesis of a suite of bioorthogonal glutathione S-Transferase substrates and their enzymatic incorporation for protein immobilization. J Org Chem, 2013, 78(19): 9647-9658.

[134] Wang Y, Yu O. Synthetic scaffolds increased resveratrol biosynthesis in engineered yeast cells. J Biotechnol, 2012, 157(1): 258-260.

[135] Wang XF, Guo TL, Chen JH, Li XF, Zhou YQ, Pan ZY. Covalent and selective immobilization of GST fusion proteins with fluorophosphonate-based probes. Chem Commun, 2018, 54(37): 4661-4664.

[136] Wang J, Lu Y, Cheng P, Zhang C, Tang L, Du L, . Construction of bi-enzyme self-assembly clusters based on SpyCatcher/SpyTag for the efficient biosynthesis of (R)-Ethyl 2-hydroxy-4-phenylbutyrate. Biomolecules, 2023, 13(1): 91.

[137] Wang X, Jiang Y, Liu H, Zhang X, Yuan H, Huang D, . In vitro assembly of the trehalose bi-enzyme complex with artificial scaffold protein. Front Bioeng Biotechnol, 2023, 11: 1251298.

[138] Weizmann Y, Braunschweig AB, Wilner OI, Cheglakov Z, Willner I. A polycatenated DNA scaffold for the one-step assembly of hierarchical nanostructures. Proc Natl Acad Sci USA, 2008, 105(14): 5289-5294.

[139] Wheeldon I, Minteer S-D, Banta S, Barton S-C, Atanassov P, Sigman M. Substrate channelling as an approach to cascade reactions. Nat Chem, 2016, 8(4): 299-309.

[140] Whitaker WR, Dueber JE. Metabolic pathway flux enhancement by synthetic protein scaffolding. Methods Enzymol, 2011, 497: 447-468.

[141] Wilner OI, Weizmann Y, Gill R, Lioubashevski O, Freeman R, Willner I. Enzyme cascades activated on topologically programmed DNA scaffolds. Nat Nanotechnol, 2009, 4(4): 249-254.

[142] Winfree E, Liu F, Wenzler LA, Seeman NC. Design and self-assembly of two-dimensional DNA crystals. Nature, 1998, 394(6693): 539-544.

[143] Wong LS, Thirlway J, Micklefield J. Direct site-selective covalent protein immobilization catalyzed by a phosphopantetheinyl transferase. J Am Chem Soc, 2008, 130(37): 12456-12464.

[144] Wriggers W, Chakravarty S, Jennings P-A. Control of protein functional dynamics by peptide linkers. Biopolymers, 2005, 80(6): 736-746.

[145] Wu F, Minteer S. Krebs cycle metabolon: structural evidence of substrate channeling revealed by cross-linking and mass spectrometry. Angew Chem Int Ed Engl, 2015, 54(6): 1851-1854.

[146] Yanase T, Okuda-Shimazaki J, Asano R, Ikebukuro K, Sode K, Tsugawa W. Development of a versatile method to construct direct electron transfer-type enzyme complexes employing SpyCatcher/SpyTag System. Int J Mol Sci, 2023, 24(3): 1837.

[147] Yang GG, Xu XY, Ding Y, Cui QQ, Wang Z, Zhang QY, . Linker length affects expression and bioactivity of the onconase fusion protein in Pichia pastoris. Genet Mol Res, 2015, 14(4): 19360-19370.

[148] You C, Myung S, Zhang Y-H. Facilitated substrate channeling in a self-assembled trifunctional enzyme complex. Angew Chem Int Ed Engl, 2012, 51(35): 8787-8790.

[149] Yun B, Shen WC. Improving the oral efficacy of recombinant granulocyte colony-stimulating factor and transferrin fusion protein by spacer optimization. Pharm Res, 2006, 23(9): 2116-2121.

[150] Zhang Y-H. Substrate channeling and enzyme complexes for biotechnological applications. Biotechnol Adv, 2011, 29(6): 715-725.

[151] Zhang YF, Hess H. Toward rational design of high-efficiency enzyme cascades. Acs Catal, 2017, 7(9): 6018-6027.

[152] Zhao HL, Yao XQ, Xue C, Wang Y, Xiong XH, Liu ZM. Increasing the homogeneity, stability and activity of human serum albumin and interferon-alpha2b fusion protein by linker engineering. Protein Expr Purif, 2008, 61(1): 73-77.

[153] Zhong X, Ma Y, Zhang X, Zhang J, Wu B, Hollmann F, . More efficient enzymatic cascade reactions by spatially confining enzymes via the SpyTag/SpyCatcher technology. Mol Catalysis, 2022

[154] Zhou Y, Guo T, Tang G, Wu H, Wong NK, Pan Z. Site-selective protein immobilization by covalent modification of GST fusion proteins. Bioconjug Chem, 2014, 25(11): 1911-1915.

[155] Zverlov V-V, Klupp M, Krauss J, Schwarz W-H. Mutations in the scaffoldin gene, cipA, of Clostridium thermocellum with impaired cellulosome formation and cellulose hydrolysis: Insertions of a new transposable element, IS1447, and implications for cellulase synergism on crystalline cellulose. J Bacteriol, 2008, 190(12): 4321-4327.

Funding

Innovative Research Group Project of the National Natural Science Foundation of China(32001632)

Key Technology Research and Development Program of Shandong(2022CXGC010506)

Natural Science Foundation of Shandong Province(ZR2020QB041)

Foundation of Qilu University of Technology of Cultivating Subject for Biology and Biochemistry (No. 202003)

State Key Laboratory of Biobased Material and Green Papermaking, Qilu University of Technology(No. ZZ20200136)

Key Research and Development Program of Zibo(2021XCYF0085)