Development of a formaldehyde biosensor with application to synthetic methylotrophy.

Abstract:

:Formaldehyde is a prevalent environmental toxin and a key intermediate in single carbon metabolism. The ability to monitor formaldehyde concentration is, therefore, of interest for both environmental monitoring and for metabolic engineering of native and synthetic methylotrophs, but current methods suffer from low sensitivity, complex workflows, or require expensive analytical equipment. Here we develop a formaldehyde biosensor based on the FrmR repressor protein and cognate promoter of Escherichia coli. Optimization of the native repressor binding site and regulatory architecture enabled detection at levels as low as 1 µM. We then used the sensor to benchmark the in vivo activity of several NAD-dependent methanol dehydrogenase (Mdh) variants, the rate-limiting enzyme that catalyzes the first step of methanol assimilation. In order to use this biosensor to distinguish individuals in a mixed population of Mdh variants, we developed a strategy to prevent cross-talk by using glutathione as a formaldehyde sink to minimize intercellular formaldehyde diffusion. Finally, we applied this biosensor to balance expression of mdh and the formaldehyde assimilation enzymes hps and phi in an engineered E. coli strain to minimize formaldehyde build-up while also reducing the burden of heterologous expression. This biosensor offers a quick and simple method for sensitively detecting formaldehyde, and has the potential to be used as the basis for directed evolution of Mdh and dynamic formaldehyde control strategies for establishing synthetic methylotrophy.

journal_name

Biotechnol Bioeng

authors

Woolston BM,Roth T,Kohale I,Liu DR,Stephanopoulos G

doi

10.1002/bit.26455

subject

Has Abstract

pub_date

2018-01-01 00:00:00

pages

206-215

issue

1

eissn

0006-3592

issn

1097-0290

journal_volume

115

pub_type

杂志文章
  • Effect of Vitreoscilla hemoglobin expression on growth and specific tissue plasminogen activator productivity in recombinant chinese hamster ovary cells.

    abstract::Previous studies suggest that secretion of cloned proteins synthesized by recombinant Chinese hamster ovary (CHO) cells can be adenosine triphosphate (ATP) limited. Other research indicates that the presence of cloned Vitreoscilla hemoglobin (VHb) enhances ATP production in oxygen-limited Escherichia coli. To evaluate...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260441114

    authors: Pendse GJ,Bailey JE

    更新日期:1994-12-01 00:00:00

  • Relationship between mass transfer coefficient and liquid flow velocity in heterogenous biofilms using microelectrodes and confocal microscopy.

    abstract::The relationship between local mass transfer coefficient and fluid velocity in heterogenous biofilms was investigated by combining microelectrodes and confocal scanning laser microscopy (CSLM). The biofilms were grown for up to 7 days and consisted of cell clusters separated by interstitial channels. Mass transfer coe...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/(SICI)1097-0290(19971220)56:6<681::AID-BIT

    authors: Stoodley P,Yang S,Lappin-Scott H,Lewandowski Z

    更新日期:1997-12-20 00:00:00

  • Photo inactivation of virus particles in microfluidic capillary systems.

    abstract::It has long been established that UVC light is a very effective method for inactivating pathogens in a fluid, yet the application of UVC irradiation to modern biotechnological processes is limited by the intrinsic short penetration distance of UVC light in optically dense protein solutions. This experimental and numer...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.25912

    authors: Ren Y,Crump CM,Mackley MM,Li Puma G,Reis NM

    更新日期:2016-07-01 00:00:00

  • Identification and CRISPR/Cas9 Inactivation of the C1s Protease Responsible for Proteolysis of Recombinant Proteins Produced in CHO Cells.

    abstract::Proteolysis associated with recombinant protein expression in Chinese Hamster Ovary (CHO) cells has hindered the development of biologics including HIV vaccines. When expressed in CHO cells, the recombinant HIV envelope protein, gp120, undergoes proteolytic clipping by a serine protease at a key epitope recognized by ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.27016

    authors: Li SW,Yu B,Byrne G,Wright M,O'Rourke S,Mesa K,Berman PW

    更新日期:2019-09-01 00:00:00

  • Single pass tangential flow filtration to debottleneck downstream processing for therapeutic antibody production.

    abstract::As the therapeutic monoclonal antibody (mAb) market continues to grow, optimizing production processes is becoming more critical in improving efficiencies and reducing cost-of-goods in large-scale production. With the recent trends of increasing cell culture titers from upstream process improvements, downstream capaci...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.24377

    authors: Dizon-Maspat J,Bourret J,D'Agostini A,Li F

    更新日期:2012-04-01 00:00:00

  • Fermentation and isolation of C10-deacetylase for the production of 10-deacetylbaccatin III from baccatin III.

    abstract::10-Deacetylabaccatin III (10 DAB), an important precursor for paclitaxel semisynthesis, is enhanced in yew extracts using C10-deacetylase and C13-deacylase enzymes.(4) C10-deacetylase is an intracellular enzyme produced by the fermentation of a soil microorganism, Nocardioides luteus (SC 13912). During the fermentatio...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260480518

    authors: Nanduri VB,Hanson RL,Laporte TL,Ko RY,Patel RN,Szarka LJ

    更新日期:1995-12-05 00:00:00

  • Temperature and oxygen level determine N2 O respiration activities of heterotrophic N2 O-reducing bacteria: Biokinetic study.

    abstract::Nitrous oxide (N2 O), a potent greenhouse gas, is reduced to N2 gas by N2 O-reducing bacteria (N2 ORB), a process which represents an N2 O sink in natural and engineered ecosystems. The N2 O sink activity by N2 ORB depends on temperature and O2 exposure, yet the specifics are not yet understood. This study explores th...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.27654

    authors: Zhou Y,Suenaga T,Qi C,Riya S,Hosomi M,Terada A

    更新日期:2020-12-11 00:00:00

  • Fluorescence-based sensing system for copper using genetically engineered living yeast cells.

    abstract::A whole cell-based optical sensing system for copper was developed based on Saccharomyces cerevisiae cells harboring plasmid pYEX-GFPuv. The basis of this system was the ability of the transcriptional activator protein Ace1 present in S. cerevisiae to control the expression of the reporter protein, GFPuv. When copper ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.20331

    authors: Shetty RS,Deo SK,Liu Y,Daunert S

    更新日期:2004-12-05 00:00:00

  • Kinetic and thermal characteristics of enzyme-graft copolymers.

    abstract::The characteristics of horseradish peroxidase (HRP) immobilized onto Sepharose by a photochemical-initiated graft copolymerization are presented. Active copolymers were synthesized using different amounts of glycidylmethacrylate (GMA), bisacryloylpiperazine (BAP), or 1,3,5-hexhydrotriacryloyl-(s)-triazine (HTsT) as fu...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260250310

    authors: Cremonesi P,D'Angiuro L

    更新日期:1983-03-01 00:00:00

  • Maximizing neotissue growth kinetics in a perfusion bioreactor: An in silico strategy using model reduction and Bayesian optimization.

    abstract::In regenerative medicine, computer models describing bioreactor processes can assist in designing optimal process conditions leading to robust and economically viable products. In this study, we started from a (3D) mechanistic model describing the growth of neotissue, comprised of cells, and extracellular matrix, in a...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.26500

    authors: Mehrian M,Guyot Y,Papantoniou I,Olofsson S,Sonnaert M,Misener R,Geris L

    更新日期:2018-03-01 00:00:00

  • Redox control bioreactor: a unique biological water processor.

    abstract::The redox control bioreactor (RCB) is a new hollow fiber membrane bioreactor (HFMBR) design in which oxygen and hydrogen gases are provided simultaneously through separate arrays of juxtaposed hollow fiber (HF) membranes. This study applied the RCB for completely autotrophic conversion of ammonia to N(2) through nitri...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.21617

    authors: Smith DP,Rector T,Reid-Black K,Hummerick M,Strayer R,Birmele M,Roberts MS,Garland JL

    更新日期:2008-03-01 00:00:00

  • A multi-pronged investigation into the effect of glucose starvation and culture duration on fed-batch CHO cell culture.

    abstract::In this study, omics-based analysis tools were used to explore the effect of glucose starvation and culture duration on monoclonal antibody (mAb) production in fed-batch CHO cell culture to gain better insight into how these parameters can be controlled to ensure optimal mAb productivity and quality. Titer and N-glyco...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.25620

    authors: Fan Y,Jimenez Del Val I,Müller C,Lund AM,Sen JW,Rasmussen SK,Kontoravdi C,Baycin-Hizal D,Betenbaugh MJ,Weilguny D,Andersen MR

    更新日期:2015-10-01 00:00:00

  • Generation of stable, high-producing CHO cell lines by lentiviral vector-mediated gene transfer in serum-free suspension culture.

    abstract::Lentivirus-derived vectors (LVs) were studied for the generation of stable recombinant Chinese hamster ovary (CHO) cell lines. Stable pools and clones expressing the enhanced green fluorescent protein (eGFP) were selected via fluorescence-activated cell sorting (FACS). For comparison, cell pools and cell lines were al...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.22968

    authors: Oberbek A,Matasci M,Hacker DL,Wurm FM

    更新日期:2011-03-01 00:00:00

  • Reactive oxygen species induced by shear stress mediate cell death in Bacillus subtilis.

    abstract::Exposure of Bacillus subtilis to a shear rate of 1,482/s leads to a rapid loss of cell viability after 10 h of growth. Biochemical and molecular evidences provided below strongly suggest that cell death under high shear results from an apoptosis-like process similar to that described in eukaryotes, with activation of ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.20835

    authors: Sahoo S,Rao KK,Suraishkumar GK

    更新日期:2006-05-05 00:00:00

  • Rhamnolipid production by Pseudomonas aeruginosa under denitrification: effects of limiting nutrients and carbon substrates.

    abstract::Being biosurfactants, rhamnolipids create severe foaming when produced in aerobic Pseudomonas aeruginosa fermentation. The necessary reduction of aeration causes oxygen limitation and restricts cell and product concentrations. In this study, we evaluate the new strategy of rhamnolipid production under denitrification ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/1097-0290(20010105)72:1<25::aid-bit4>3.0.c

    authors: Chayabutra C,Wu J,Ju LK

    更新日期:2001-01-05 00:00:00

  • Optimization of amorphadiene synthesis in bacillus subtilis via transcriptional, translational, and media modulation.

    abstract::Genetically engineered microbes have been intensively investigated as a means for the cost-effective production of isoprenoids. Bacillus subtilis is a promising microbial host for this purpose because of its fast growth rate and GRAS (generally regarded as safe) status. To date, development of this host has been impai...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.24900

    authors: Zhou K,Zou R,Zhang C,Stephanopoulos G,Too HP

    更新日期:2013-09-01 00:00:00

  • Local direction change of surface gliding microtubules.

    abstract::In vitro gliding assay, microtubule translocation by kinesin motor proteins on a surface, has been used as an engineering tool in analyte detection, molecular cargo transport, and other applications. Although controlling the moving direction is often necessary to realize these applications, current direction control m...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.26933

    authors: Li F,Pan J,Choi JH

    更新日期:2019-05-01 00:00:00

  • Zonal rate model for axial and radial flow membrane chromatography, part II: model-based scale-up.

    abstract::Membrane chromatography (MC) systems are finding increasing use in downstream processing trains for therapeutic proteins due to the unique mass-transfer characteristics they provide. As a result, there is increased need for model-based methods to scale-up MC units using data collected on a scaled-down unit. Here, a st...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.25217

    authors: Ghosh P,Lin M,Vogel JH,Choy D,Haynes C,von Lieres E

    更新日期:2014-08-01 00:00:00

  • Application of continuous zone electrophoresis to preparative separation of proteins.

    abstract::A comprehensive study of the application of continuous zone electrophoresis to preparative separation of proteins in free solution is presented. First, the influence of electric field strength, buffer residence time in the chamber, sample flow rate, and sample concentration on separation resolution and throughput were...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260420707

    authors: Nath S,Schütte H,Hustedt H,Deckwer WD

    更新日期:1993-09-20 00:00:00

  • Bcl-xL expression interferes with the effects of L-glutamine supplementation on hybridoma cultures.

    abstract::While feeding protocols and ectopic expression of anti-apoptotic genes have been used to improve the viability of hybridoma cell lines, the effect of the expression levels of survival genes on the behavior of hybridomas following nutrient supplementation is unknown. In this study, we compared the behavior of the Sp2/0...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.10467

    authors: Charbonneau JR,Furtak T,Lefebvre J,Gauthier ER

    更新日期:2003-02-05 00:00:00

  • Itaconic acid production from glycerol using Escherichia coli harboring a random synonymous codon-substituted 5'-coding region variant of the cadA gene.

    abstract::Aspergillus terreus cadA, encoding cis-aconitate decarboxylase, is an essential gene for itaconic acid (IA) biosynthesis, but it is primarily expressed as insoluble aggregates in most industrial hosts. This has been a hurdle for the development of recombinant strategies for IA production. Here, we created a library of...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.25914

    authors: Jeon HG,Cheong DE,Han Y,Song JJ,Choi JH

    更新日期:2016-07-01 00:00:00

  • A gaussian model for substrates of entangled cross-linked poly(ethylene glycol) in biomedical applications.

    abstract::Cells usually spread on a synthetic substrate through bonds between receptors and chemical groups on the substrate (ligands). Therefore, it is valuable to study the effects of the average number density of these chemical groups and the average distance between them to model and predict the cell behavior. Poly(ethylene...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.22889

    authors: Eskandari M,Brey E,Cinar A

    更新日期:2011-02-01 00:00:00

  • Chemically stabilized trypsin used in dipeptide synthesis.

    abstract::Bovine pancreatic trypsin was treated with ethylene glycol bis(succinic acid N-hydroxysuccinimide ester). Approximately 8 of 14 lysines per trypsin molecule were modified. This derivative (EG trypsin) was more stable than native between 30 degrees and 70 degrees C: T50 values were 59 degrees C and 46 degrees C, respec...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:

    authors: Murphy A,O Fágáin C

    更新日期:1998-05-20 00:00:00

  • Oxygen transfer in animal cell culture medium.

    abstract::Both k(L)a and k(L) measurements were carried out by an unsteady state technique at impeller speeds ranging from 1.6 to 5.8 s(-1) in a mechanically agitated animal cell culture vessel of working volume 1.5 L. Checks were made that the time constant of the oxygen electrode was negligible compared to the time for aerati...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260300307

    authors: Lavery M,Nienow AW

    更新日期:1987-08-20 00:00:00

  • Effect of methanol feeding strategies on production and yield of recombinant mouse endostatin from Pichia pastoris.

    abstract::Pichia pastoris, a methylotrophic yeast, is an efficient producer of recombinant proteins in which the heterologous gene is under the control of the methanol-induced AOX1 promoter. Hence, the accepted production procedure has two phases: In the first phase, the yeast utilizes glycerol and biomass is accumulated; in th...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.10587

    authors: Trinh LB,Phue JN,Shiloach J

    更新日期:2003-05-20 00:00:00

  • Increasing cell-free gene expression yields from linear templates in Escherichia coli and Vibrio natriegens extracts by using DNA-binding proteins.

    abstract::In crude extract-based cell-free protein synthesis (CFPS), DNA templates are transcribed and translated into functional proteins. Although linear expression templates (LETs) are less laborious and expensive to generate, plasmid templates are often desired over polymerase chain reaction-generated LETs due to increased ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.27538

    authors: Zhu B,Gan R,Cabezas MD,Kojima T,Nicol R,Jewett MC,Nakano H

    更新日期:2020-08-20 00:00:00

  • Yield stress of pretreated corn stover suspensions using magnetic resonance imaging.

    abstract::Cellulose fibers in water form networks that give rise to an apparent yield stress, especially at high solids contents. Measuring the yield stress and correlating it with fiber concentration is important for the biomass and pulp industries. Understanding how the yield stress behaves at high solids concentrations is cr...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.23197

    authors: Lavenson DM,Tozzi EJ,McCarthy MJ,Powell RL

    更新日期:2011-10-01 00:00:00

  • Interactions between animal cells and gas bubbles: The influence of serum and pluronic F68 on the physical properties of the bubble surface.

    abstract::We describe a method by which the degree of bubble saturation can be determined by measuring the velocity of single bubbles at different heights from the bubble source in pure water containing increasing concentrations of surfactants. The highest rising velocities were measured in pure water. Addition of surfactants c...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260430603

    authors: Jordan M,Eppenberger HM,Sucker H,Widmer F,Einsele A

    更新日期:1994-03-15 00:00:00

  • The response of a bioelectrochemical cell with Saccharomyces cerevisiae metabolizing glucose under various fermentation conditions.

    abstract::Working conditions of a biochemical fuel cell formed by an oxygen cathode and a platinum bioanode in a Saccharomyces cerevisiae suspension metabolizing glucose are described. The biocell response in terms of bioanode potential and current drainage under different fermentation conditions is reported. A kinetic equation...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260171011

    authors: Videla HA,Arvía AJ

    更新日期:1975-10-01 00:00:00

  • Effects of short elastin-like peptides on filamentous particles and their transition behavior.

    abstract::While elastin-like polypeptides and peptides (ELPs) have been used for various stimulus-responsive applications, details of their switching remain unclear. We therefore constructed a novel series of filamentous phage particles displaying a high surface density of short ELPs. The surface display of ELPs did not disrupt...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.24854

    authors: Hathorne AP,Bermudez H

    更新日期:2013-07-01 00:00:00