Enzymatic protein switches built from paralogous input domains.

Abstract:

:Protein switches have a variety of potential applications in biotechnology and medicine that motivate efforts to accelerate their development. Switches can be built by the proper fusion of two proteins with the prerequisite input and output functions. However, the exact fusion geometry for switch creation, which typically involves insertion of one protein domain into the other, is difficult to predict. Based on our previous work developing protein switches using periplasmic binding proteins as input domains, we wondered whether there are "hot spots" for insertion of output domains and successful switch creation within this class of proteins. Here we describe directed evolution experiments that identified switches in which TEM-1 beta-lactamase (BLA) is inserted into the class I periplasmic binding proteins ribose binding protein (RBP), glucose binding protein (GBP), and xylose binding protein (XBP). Although some overlap in sites for successful switch insertion could be found among the paralogs, successful switches at these sites required different linkers between the domains and different circular permutations of the BLA protein. Our data suggests that sites for successful switch creation are not easily transferable between paralogs. Furthermore, by comparison to a previous study in which switches were created by inserting a xylanase into XBP, we find no correlation between insertion sites when using two different output domains. We conclude that the switch property likely depends on the precise molecular details of the fusions and cannot be easily predicted from some overall general structural property of the fusion topology.

journal_name

Biotechnol Bioeng

authors

Tullman J,Nicholes N,Dumont MR,Ribeiro LF,Ostermeier M

doi

10.1002/bit.25852

subject

Has Abstract

pub_date

2016-04-01 00:00:00

pages

852-8

issue

4

eissn

0006-3592

issn

1097-0290

journal_volume

113

pub_type

杂志文章
  • Simulation of growth and detachment in biofilm systems under defined hydrodynamic conditions.

    abstract::Detachment from biofilms was evaluated using a mixed culture biofilm grown on primary wastewater in a tube reactor. The growth of biofilms and the detachment of biomass from biofilms are strongly influenced by hydrodynamic conditions. In a long-term study, three biofilms were cultivated in a biofilm tube reactor. The ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.10503

    authors: Horn H,Reiff H,Morgenroth E

    更新日期:2003-03-05 00:00:00

  • Application of high throughput pretreatment and co-hydrolysis system to thermochemical pretreatment. Part 2: Dilute alkali.

    abstract::High throughput pretreatment (HTPH) and enzymatic hydrolysis systems are now vital for screening large numbers of biomass samples to investigate biomass recalcitrance over various pretreatment and enzymatic hydrolysis conditions. Although hydrothermal pretreatment is currently being employed in most high throughput ap...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.24951

    authors: Li H,Gao X,Demartini JD,Kumar R,Wyman CE

    更新日期:2013-11-01 00:00:00

  • Hydrodynamic characteristics of immobilized cell beads in a liquid-solid fluidized-bed bioreactor.

    abstract::This study examined the hydrodynamic characteristics of a liquid-solid fluidized-bed bioreactor using elastic particles (PVA gel beads) of various diameters as carriers. The drag coefficient-Reynolds number, velocity-voidage, and expansion index-Reynolds number relationships observed during fluidization of PVA gel bea...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.10710

    authors: Wu JY,Chen KC,Chen CT,Hwang SC

    更新日期:2003-09-05 00:00:00

  • Theory and applications of unstructured growth models: Kinetic and energetic aspects.

    abstract::Microbial kinetics and energetics are discussed in connection with the formulation of unstructured growth models. The development of microbial energetics and the use of macroscopic methods in the study of microbial growth are briefly evaluated. The general approach to the modelling of microbial growth has been critica...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260251202

    authors: Esener AA,Roels JA,Kossen NW

    更新日期:1983-12-01 00:00:00

  • Use of exogenous specialised bacteria in the biological detoxification of a dump site-polychlorobiphenyl-contaminated soil in slurry phase conditions

    abstract::The possibility of biologically detoxifying a contaminated soil from an Italian dump site containing about 1500 mg/kg (in dry soil) of polychlorinated biphenyls was studied in the laboratory in this work. The soil, which contained indigenous aerobic bacteria capable of growing on biphenyl or on monochlorobenzoic acids...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/(sici)1097-0290(19990720)64:2<240::aid-bit

    authors: Fava F,Bertin L

    更新日期:1999-07-20 00:00:00

  • Yeast suspension filtration: flux enhancement using an upward gas/liquid slug flow-application to continuous alcoholic fermentation with cell recycle.

    abstract::This study deals with the use of an upward gas/liquid slug flow to reduce tubular mineral membrane fouling. The injection of air into the feedstream is designed to create hydrodynamic conditions that destabilize the cake layer over the membrane surface inside the filtration module complex. Experimental study was carri...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/(sici)1097-0290(19980405)58:1<47::aid-bit5

    authors: Mercier M,Maranges C,Fonade C,Lafforgue-Delorme C

    更新日期:1998-04-05 00:00:00

  • Improvement of the production of GFPuv-beta1,3-N-acetylglucosaminyltransferase 2 fusion protein using a molecular chaperone-assisted insect-cell-based expression system.

    abstract::A stable Tn-5B1-4 insect cell line co-expressing the recombinant GFPuv-beta1,3-N-acetylglucosaminyltransferase 2 (GFPuv-beta3GnT2) protein fused to a melittin signal sequence with a lectin-like molecular chaperone, human calnexin (hCNX) or human calreticulin (hCRT), was constructed. The expression of either of these m...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.20362

    authors: Kato T,Murata T,Usui T,Park EY

    更新日期:2005-02-20 00:00:00

  • Coculture of genetically transformed roots and shoots for synthesis, translocation, and biotransformation of secondary metabolites.

    abstract::Genetically transformed shooty teratomas of Atropa belladonna and a Duboisia leichhardtii x D. myoporoides hybrid were studied for biotransformation of tropane alkaloids in shake flasks and bioreactors. Although de novo synthesis of hyoscyamine and scopolamine was limited, shoots of both species were able to transloca...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/(SICI)1097-0290(19960305)49:5<481::AID-BIT

    authors: Subroto MA,Kwok KH,Hamill JD,Doran PM

    更新日期:1996-03-05 00:00:00

  • Toxicity of terpenes to spores and mycelium of Penicillium digitatum.

    abstract::Spores, although often considered metabolically inert, catalyze a variety of reactions. The use of spores instead of mycelium for bioconversions has several advantages. In this paper, we describe the difference in susceptibility of mycelium and spores against toxic substrates and products. A higher resistance of spore...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.10435

    authors: Wolken WA,Tramper J,van der Werf MJ

    更新日期:2002-12-20 00:00:00

  • Steric hindrance of growth of filamentous fungi in solid substrate fermentation of wheat straw.

    abstract::Cellulolytic fungi, such as Trichoderma reesei, T. lignorum, and Chaetomium cellulolyticum reach a low packing density of mycelia when grown on straw under conditions of solid substrate fermentation. The low packing density is shown to be caused partially by the geometric limitation of the growth of mycelia in the sub...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260271209

    authors: Laukevics JJ,Apsite AF,Viesturs US,Tengerdy RP

    更新日期:1985-12-01 00:00:00

  • H(2) photoproduction by batch culture of Anabaena variabilis ATCC 29413 and its mutant PK84 in a photobioreactor.

    abstract::Hydrogen production by Anabaena variabilis ATCC 29413 and of its mutant PK84, grown in batch cultures, was studied in a photobioreactor. The highest volumetric H(2) production rates of native and mutant strains were found in cultures grown at gradually increased irradiation. The native strain evolved H(2) only under a...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/(sici)1097-0290(19990920)64:6<709::aid-bit

    authors: Tsygankov AA,Borodin VB,Rao KK,Hall DO

    更新日期:1999-09-20 00:00:00

  • A low shear stress modular bioreactor for connected cell culture under high flow rates.

    abstract::A generic "system on a plate" modular multicompartmental bioreactor array which enables microwell protocols to be transferred directly to the bioreactor modules, without redesign of cell culture experiments or protocols is described. The modular bioreactors are simple to assemble and use and can be easily compared wit...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.22671

    authors: Mazzei D,Guzzardi MA,Giusti S,Ahluwalia A

    更新日期:2010-05-01 00:00:00

  • A cell-free platform for rapid synthesis and testing of active oligosaccharyltransferases.

    abstract::Protein glycosylation, or the attachment of sugar moieties (glycans) to proteins, is important for protein stability, activity, and immunogenicity. However, understanding the roles and regulations of site-specific glycosylation events remains a significant challenge due to several technological limitations. These limi...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.26502

    authors: Schoborg JA,Hershewe JM,Stark JC,Kightlinger W,Kath JE,Jaroentomeechai T,Natarajan A,DeLisa MP,Jewett MC

    更新日期:2018-03-01 00:00:00

  • Physiological response of Clostridium carboxidivorans during conversion of synthesis gas to solvents in a gas-fed bioreactor.

    abstract::Clostridium carboxidivorans P7 is one of three microbial catalysts capable of fermenting synthesis gas (mainly CO, CO(2) , and H(2) ) to produce the liquid biofuels ethanol and butanol. Gasification of feedstocks to produce synthesis gas (syngas), followed by microbial conversion to solvents, greatly expands the diver...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.24549

    authors: Ukpong MN,Atiyeh HK,De Lorme MJ,Liu K,Zhu X,Tanner RS,Wilkins MR,Stevenson BS

    更新日期:2012-11-01 00:00:00

  • Determination of diffusion coefficients of proteins in stationary phases by frontal chromatography.

    abstract::A strategy to determine effective diffusion coefficients of proteins in chromatographic gels is presented in this article. An experimental methodology based on frontal liquid chromatography was combined with a numerical methodology based on a mathematical model describing the chromatographic process including the extr...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.20738

    authors: Kempe H,Persson P,Axelsson A,Nilsson B,Zacchi G

    更新日期:2006-03-05 00:00:00

  • Infrared picosecond laser for perforation of single plant cells.

    abstract::The functional analysis of plant cells at the cellular and subcellular levels requires novel technologies for the directed manipulation of individual cells. In this report, we demonstrate the use of an infrared (1,064 nm) picosecond laser for the perforation of tobacco cell protoplasts. A single pulse was sufficient t...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.21549

    authors: Schinkel H,Jacobs P,Schillberg S,Wehner M

    更新日期:2008-01-01 00:00:00

  • Determination of the baculovirus transducing titer in mammalian cells.

    abstract::Baculovirus has emerged as a promising vector for in vivo or ex vivo gene therapy. To date, the infectious titer and multiplicity of infection (MOI) based on the ability of baculovirus to infect insect cells are commonly adopted to indicate the virus dosage. However, the infectious titer and MOI do not reliably repres...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.20749

    authors: Chan ZR,Lai CW,Lee HP,Chen HC,Hu YC

    更新日期:2006-02-20 00:00:00

  • General theory of determining intraparticle active immobilized enzyme distribution and rate parameters.

    abstract::A general theory is presented in this article for determining the intrinsic rate constants for the main reaction and deactivation reaction, the effective diffusivity of the substrate, and the active enzyme distribution within porous solid supports from deactivation study of a continuous stirred-basket reactor (CSBR). ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260330805

    authors: Hossain MM,Do DD

    更新日期:1989-03-01 00:00:00

  • Development of a new bioprocess scheme using frozen seed train intermediates to initiate CHO cell culture manufacturing campaigns.

    abstract::Agility to schedule and execute cell culture manufacturing campaigns quickly in a multi-product facility will play a key role in meeting the growing demand for therapeutic proteins. In an effort to shorten campaign timelines, maximize plant flexibility and resource utilization, we investigated the initiation of cell c...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.24808

    authors: Seth G,Hamilton RW,Stapp TR,Zheng L,Meier A,Petty K,Leung S,Chary S

    更新日期:2013-05-01 00:00:00

  • High-level production and covalent immobilization of Providencia rettgeri penicillin G acylase (PAC) from recombinant Pichia pastoris for the development of a novel and stable biocatalyst of industrial applicability.

    abstract::A complete, integrated process for the production of an innovative formulation of penicillin G acylase from Providencia rettgeri(rPAC(P.rett))of industrial applicability is reported. In order to improve the yield of rPAC, the clone LN5.5, carrying four copies of pac gene integrated into the genome of Pichia pastoris, ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.20728

    authors: Senerovic L,Stankovic N,Spizzo P,Basso A,Gardossi L,Vasiljevic B,Ljubijankic G,Tisminetzky S,Degrassi G

    更新日期:2006-02-05 00:00:00

  • Non-invasive online detection of microbial lysine formation in stirred tank bioreactors by using calorespirometry.

    abstract::Non-invasive methods for online monitoring of biotechnological processes without compromising the integrity of the reactor system are very important to generate continuous data. Even though calorimetry has been used in conventional biochemical analysis for decades, it has not yet been specifically applied for online d...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.24815

    authors: Regestein L,Maskow T,Tack A,Knabben I,Wunderlich M,Lerchner J,Büchs J

    更新日期:2013-05-01 00:00:00

  • Modelling Xanthomonas campestris batch fermentations in a bubble column.

    abstract::Rate and yield expressions relating to biomass and xanthan formation and to nitrogen, glucose, and oxygen consumption were established for Xanthomonas campestris batch fermentations in a bubble column. Microbial growth was described by the logistic rate equation, characterized by a maximum specific growth rate mu(M) =...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260330404

    authors: Pons A,Dussap CG,Gros JB

    更新日期:1989-01-20 00:00:00

  • Kinetic, dynamic, and pathway studies of glycerol metabolism by Klebsiella pneumoniae in anaerobic continuous culture: IV. Enzymes and fluxes of pyruvate metabolism.

    abstract::The activities of pyruvate kinase (PK), pyruvate: formate-lyase (PFL), pyruvate dehydrogenase (PDH), and citrate synthase (CS) involved in the anaerobic glycerol conversion by Klebsiella pneumoniae were studied in continuous culture under conditions of steady states and sustained oscillations. Both the in vitro and in...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:

    authors: Menzel K,Ahrens K,Zeng A,Deckwer W

    更新日期:1998-12-05 00:00:00

  • Quantification of cell culture factors affecting recombinant protein yields in baculovirus-infected insect cells.

    abstract::An experimental study was undertaken to quantify the effects of infection cell density, medium condition, and surface aeration on recombinant protein yields in insect cells. In the absence of surface aeration and fresh medium, insect cells generated higher product yields (on a per cell basis) when infected with recomb...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260390605

    authors: Lindsay DA,Betenbaugh MJ

    更新日期:1992-03-15 00:00:00

  • Novel application of oxygen-transferring membranes to improve anaerobic wastewater treatment.

    abstract::Anaerobic biological wastewater treatment has numerous advantages over conventional aerobic processes; anaerobic biotechnologies, however, still have a reputation for low-quality effluents and operational instabilities. In this study, anaerobic bioreactors were augmented with an oxygen-transferring membrane to improve...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.20219

    authors: Kappell AS,Semmens MJ,Novak PJ,LaPara TM

    更新日期:2005-02-20 00:00:00

  • Organic solvents strip water off enzymes.

    abstract::Exchange of enzyme-bound H(2)O with T(2)O in aqueous solution followed by freeze drying provided tritiated water bound to chymotrypsin, subtilisin Carlsberg, and horseradish peroxidase. The desorption of T(2)O from these enzymes suspended in various organic solvents showed that all three enzymes lost enzyme-bound wate...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260390405

    authors: Gorman LA,Dordick JS

    更新日期:1992-02-20 00:00:00

  • Tissue-specific biomass recalcitrance in corn stover pretreated with liquid hot-water: SEM imaging (part 2).

    abstract::In the first part of our work, we combined compositional analysis, pretreatment and enzyme hydrolysis for fractionated pith, rind, and leaf tissues from a hybrid stay-green corn, in order to identify the role of structural characteristics on enzyme hydrolysis of cell walls. Hydrolysis experiments coupled with chemical...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.23335

    authors: Zeng M,Ximenes E,Ladisch MR,Mosier NS,Vermerris W,Huang CP,Sherman DM

    更新日期:2012-02-01 00:00:00

  • A flow injection flow cytometry system for on-line monitoring of bioreactors.

    abstract::For direct and on-line study of the physiological states of cell cultures, a robust flow injection system has been designed and interfaced with flow cytometry (FI-FCM). The core of the flow injection system includes a microchamber designed for sample processing. The design of this microchamber allows not only an accur...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/(sici)1097-0290(19990305)62:5<609::aid-bit

    authors: Zhao R,Natarajan A,Srienc F

    更新日期:1999-03-05 00:00:00

  • Gelatin interpenetration in poly N-isopropylacrylamide network reduces the compressive modulus of the scaffold: A property employed to mimic hepatic matrix stiffness.

    abstract::The progression of liver disease from normal to cirrhotic state is characterized by modulation of the stiffness of the extracellular matrix (ECM). Mimicking this modulation in vitro scaffold could provide a better insight into hepatic cell behavior. In this study, interpenetrating poly(N-isopropylacrylamide-co-gelatin...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.27218

    authors: Sarkar J,Kamble SC,Patil R,Kumar A,Gosavi SW

    更新日期:2020-02-01 00:00:00

  • Lipase activity in vesicular systems: characterization of candida cylindracea lipase and its activity in polymerizable dialkylammonium surfactant vesicles.

    abstract::Lipase from Candida cylindracea (CCL) was incorporated into polymerizable positively charged dialkylammonium bromide surfactant vesicles. The enzyme was incorporated by the use of the dehydration-rehydration method or by incubation. In the latter case, trapping efficiencies of up to 100% could be obtained. Activities ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260420207

    authors: Mosmuller EW,Franssen MC,Engbersen JF

    更新日期:1993-06-20 00:00:00