Full Text Journal Articles by
Author John E Dueber

Advertisement

Find full text journal articles






Peroxisome compartmentalization of a toxic enzyme improves alkaloid production.

Parbir S Grewal, Jennifer A Samson, Jordan J Baker, Brian Choi, John E Dueber,

Eukaryotic cells compartmentalize metabolic pathways in organelles to achieve optimal reaction conditions and avoid crosstalk with cytosolic factors. We found that cytosolic expression of norcoclaurine synthase (NCS), the enzyme that catalyzes the first committed reaction in benzylisoquinoline alkaloid biosynthesis, is toxic in Saccharomyces cerevisiae and, consequently, restricts (S)-reticuline production. We ... Read more >>

Nat Chem Biol (Nature chemical biology)
[2020, :]

Cited: 0 times

View full text PDF listing >>



Exploration of Acetylation as a Base-Labile Protecting Group in Escherichia coli for an Indigo Precursor.

Luke N Latimer, Zachary N Russ, James Lucas, John E Dueber,

Biochemical protecting groups are observed in natural metabolic pathways to control reactivity and properties of chemical intermediates; similarly, they hold promise as a tool for metabolic engineers to achieve the same goals. Protecting groups come with costs: lower yields from carbon, metabolic load to the production host, deprotection catalyst costs ... Read more >>

ACS Synth Biol (ACS synthetic biology)
[2020, 9(10):2775-2783]

Cited: 0 times

View full text PDF listing >>



Advertisement

Targeted Diversification in the S. cerevisiae Genome with CRISPR-Guided DNA Polymerase I.

Connor J Tou, David V Schaffer, John E Dueber,

New technologies to target nucleotide diversification in vivo are promising enabling strategies to perform directed evolution for engineering applications and forward genetics for addressing biological questions. Recently, we reported EvolvR-a system that employs CRISPR-guided Cas9 nickases fused to nick-translating, error-prone DNA polymerases to diversify targeted genomic loci-in E. coli. As CRISPR-Cas9 ... Read more >>

ACS Synth Biol (ACS synthetic biology)
[2020, 9(7):1911-1916]

Cited: 0 times

View full text PDF listing >>



A yeast platform for high-level synthesis of tetrahydroisoquinoline alkaloids.

Michael E Pyne, Kaspar Kevvai, Parbir S Grewal, Lauren Narcross, Brian Choi, Leanne Bourgeois, John E Dueber, Vincent J J Martin,

The tetrahydroisoquinoline (THIQ) moiety is a privileged substructure of many bioactive natural products and semi-synthetic analogs. Plants manufacture more than 3,000 THIQ alkaloids, including the opioids morphine and codeine. While microbial species have been engineered to synthesize a few compounds from the benzylisoquinoline alkaloid (BIA) family of THIQs, low product ... Read more >>

Nat Commun (Nature communications)
[2020, 11(1):3337]

Cited: 0 times

View full text PDF listing >>



Publisher Correction: Modular and tunable biological feedback control using a de novo protein switch.

Andrew H Ng, Taylor H Nguyen, Mariana Gómez-Schiavon, Galen Dods, Robert A Langan, Scott E Boyken, Jennifer A Samson, Lucas M Waldburger, John E Dueber, David Baker, Hana El-Samad,

An amendment to this paper has been published and can be accessed via a link at the top of the paper. ... Read more >>

Nature (Nature)
[2020, 579(7798):E8]

Cited: 0 times

View full text PDF listing >>



Genomewide and Enzymatic Analysis Reveals Efficient d-Galacturonic Acid Metabolism in the Basidiomycete Yeast Rhodosporidium toruloides.

Ryan J Protzko, Christina A Hach, Samuel T Coradetti, Magdalena A Hackhofer, Sonja Magosch, Nils Thieme, Gina M Geiselman, Adam P Arkin, Jeffrey M Skerker, John E Dueber, J Philipp Benz,

Biorefining of renewable feedstocks is one of the most promising routes to replace fossil-based products. Since many common fermentation hosts, such as Saccharomyces cerevisiae, are naturally unable to convert many component plant cell wall polysaccharides, the identification of organisms with broad catabolism capabilities represents an opportunity to expand the range ... Read more >>

mSystems (mSystems)
[2019, 4(6):]

Cited: 1 time

View full text PDF listing >>



Modular and tunable biological feedback control using a de novo protein switch.

Andrew H Ng, Taylor H Nguyen, Mariana Gómez-Schiavon, Galen Dods, Robert A Langan, Scott E Boyken, Jennifer A Samson, Lucas M Waldburger, John E Dueber, David Baker, Hana El-Samad,

De novo-designed proteins1-3 hold great promise as building blocks for synthetic circuits, and can complement the use of engineered variants of natural proteins4-7. One such designer protein-degronLOCKR, which is based on 'latching orthogonal cage-key proteins' (LOCKR) technology8-is a switch that degrades a protein of interest in vivo upon induction by ... Read more >>

Nature (Nature)
[2019, 572(7768):265-269]

Cited: 1 time

View full text PDF listing >>



De novo design of bioactive protein switches.

Robert A Langan, Scott E Boyken, Andrew H Ng, Jennifer A Samson, Galen Dods, Alexandra M Westbrook, Taylor H Nguyen, Marc J Lajoie, Zibo Chen, Stephanie Berger, Vikram Khipple Mulligan, John E Dueber, Walter R P Novak, Hana El-Samad, David Baker,

Allosteric regulation of protein function is widespread in biology, but is challenging for de novo protein design as it requires the explicit design of multiple states with comparable free energies. Here we explore the possibility of designing switchable protein systems de novo, through the modulation of competing inter- and intramolecular ... Read more >>

Nature (Nature)
[2019, 572(7768):205-210]

Cited: 4 times

View full text PDF listing >>



Engineering Saccharomyces cerevisiae for co-utilization of D-galacturonic acid and D-glucose from citrus peel waste.

Ryan J Protzko, Luke N Latimer, Ze Martinho, Elise de Reus, Tanja Seibert, J Philipp Benz, John E Dueber,

Pectin-rich biomasses, such as citrus peel and sugar beet pulp, hold promise as inexpensive feedstocks for microbial fermentations as enzymatic hydrolysis of their component polysaccharides can be accomplished inexpensively to yield high concentrations of fermentable sugars and D-galacturonic acid (D-galUA). In this study, we tackle a number of challenges associated ... Read more >>

Nat Commun (Nature communications)
[2018, 9(1):5059]

Cited: 3 times

View full text PDF listing >>



CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window.

Shakked O Halperin, Connor J Tou, Eric B Wong, Cyrus Modavi, David V Schaffer, John E Dueber,

The capacity to diversify genetic codes advances our ability to understand and engineer biological systems1,2. A method for continuously diversifying user-defined regions of a genome would enable forward genetic approaches in systems that are not amenable to efficient homology-directed oligonucleotide integration. It would also facilitate the rapid evolution of biotechnologically ... Read more >>

Nature (Nature)
[2018, 560(7717):248-252]

Cited: 25 times

View full text PDF listing >>



Correction to: Identification and characterization of a galacturonic acid transporter from Neurospora crassa and its application for Saccharomyces cerevisiae fermentation processes.

J Philipp Benz, Ryan J Protzko, Jonas M S Andrich, Stefan Bauer, John E Dueber, Chris R Somerville,

[This corrects the article DOI: 10.1186/1754-6834-7-20.]. ... Read more >>

(Biotechnology for biofuels)
[2017, 10:287]

Cited: 0 times

View full text PDF listing >>



Bioproduction of a betalain color palette in Saccharomyces cerevisiae.

Parbir S Grewal, Cyrus Modavi, Zachary N Russ, Nicholas C Harris, John E Dueber,

Betalains are a family of natural pigments found exclusively in the plant order Caryophyllales. All members of this chemical family are biosynthesized through the common intermediate betalamic acid, which is capable of spontaneously condensing with various primary and secondary amines to produce betalains. Of particular interest is the red-violet betanin, ... Read more >>

Metab Eng (Metabolic engineering)
[2018, 45:180-188]

Cited: 11 times

View full text PDF listing >>



Iterative optimization of xylose catabolism in Saccharomyces cerevisiae using combinatorial expression tuning.

Luke N Latimer, John E Dueber,

A common challenge in metabolic engineering is rapidly identifying rate-controlling enzymes in heterologous pathways for subsequent production improvement. We demonstrate a workflow to address this challenge and apply it to improving xylose utilization in Saccharomyces cerevisiae. For eight reactions required for conversion of xylose to ethanol, we screened enzymes for ... Read more >>

Biotechnol. Bioeng. (Biotechnology and bioengineering)
[2017, 114(6):1301-1309]

Cited: 2 times

View full text PDF listing >>



Application of a Palladium-Catalyzed C-H Functionalization/Indolization Method to Syntheses of cis-Trikentrin A and Herbindole B.

Raul A Leal, Caroline Bischof, Youjin V Lee, Shota Sawano, Christopher C McAtee, Luke N Latimer, Zachary N Russ, John E Dueber, Jin-Quan Yu, Richmond Sarpong,

We describe herein formal syntheses of the indole alkaloids cis-trikentrin A and herbindole B from a common meso-hydroquinone intermediate prepared by a ruthenium-catalyzed [2+2+1+1] cycloaddition that has not been used previously in natural product synthesis. Key steps include a sterically demanding Buchwald-Hartwig amination as well as a unique C(sp(3) )-H amination/indole formation. ... Read more >>

Angew Chem Int Ed Engl (Angewandte Chemie (International ed. in English))
[2016, 55(39):11824-11828]

Cited: 2 times

View full text PDF listing >>



Microbial Factories for the Production of Benzylisoquinoline Alkaloids.

Lauren Narcross, Elena Fossati, Leanne Bourgeois, John E Dueber, Vincent J J Martin,

Benzylisoquinoline alkaloids (BIAs) are a family of ∼2500 alkaloids with both potential and realized pharmaceutical value, including most notably the opiates such as codeine and morphine. Only a few BIAs accumulate readily in plants, which limits the pharmaceutical potential of the family. Shifting BIA production to microbial sources could provide ... Read more >>

Trends Biotechnol. (Trends in biotechnology)
[2016, 34(3):228-241]

Cited: 15 times

View full text PDF listing >>



A Barcoding Strategy Enabling Higher-Throughput Library Screening by Microscopy.

Robert Chen, Harneet S Rishi, Vladimir Potapov, Masaki R Yamada, Vincent J Yeh, Thomas Chow, Celia L Cheung, Austin T Jones, Terry D Johnson, Amy E Keating, William C DeLoache, John E Dueber,

Dramatic progress has been made in the design and build phases of the design-build-test cycle for engineering cells. However, the test phase usually limits throughput, as many outputs of interest are not amenable to rapid analytical measurements. For example, phenotypes such as motility, morphology, and subcellular localization can be readily ... Read more >>

ACS Synth Biol (ACS synthetic biology)
[2015, 4(11):1205-1216]

Cited: 7 times

View full text PDF listing >>



Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds.

Jesse G Zalatan, Michael E Lee, Ricardo Almeida, Luke A Gilbert, Evan H Whitehead, Marie La Russa, Jordan C Tsai, Jonathan S Weissman, John E Dueber, Lei S Qi, Wendell A Lim,

Eukaryotic cells execute complex transcriptional programs in which specific loci throughout the genome are regulated in distinct ways by targeted regulatory assemblies. We have applied this principle to generate synthetic CRISPR-based transcriptional programs in yeast and human cells. By extending guide RNAs to include effector protein recruitment sites, we construct ... Read more >>

Cell (Cell)
[2015, 160(1-2):339-350]

Cited: 304 times

View full text PDF listing >>



A Highly Characterized Yeast Toolkit for Modular, Multipart Assembly.

Michael E Lee, William C DeLoache, Bernardo Cervantes, John E Dueber,

Saccharomyces cerevisiae is an increasingly attractive host for synthetic biology because of its long history in industrial fermentations. However, until recently, most synthetic biology systems have focused on bacteria. While there is a wealth of resources and literature about the biology of yeast, it can be daunting to navigate and ... Read more >>

ACS Synth Biol (ACS synthetic biology)
[2015, 4(9):975-986]

Cited: 109 times

View full text PDF listing >>



An enzyme-coupled biosensor enables (S)-reticuline production in yeast from glucose.

William C DeLoache, Zachary N Russ, Lauren Narcross, Andrew M Gonzales, Vincent J J Martin, John E Dueber,

Benzylisoquinoline alkaloids (BIAs) are a diverse family of plant-specialized metabolites that include the pharmaceuticals codeine and morphine and their derivatives. Microbial synthesis of BIAs holds promise as an alternative to traditional crop-based manufacturing. Here we demonstrate the production of the key BIA intermediate (S)-reticuline from glucose in Saccharomyces cerevisiae. To ... Read more >>

Nat. Chem. Biol. (Nature chemical biology)
[2015, 11(7):465-471]

Cited: 89 times

View full text PDF listing >>



Avoidance of truncated proteins from unintended ribosome binding sites within heterologous protein coding sequences.

Weston R Whitaker, Hanson Lee, Adam P Arkin, John E Dueber,

Genetic sequences ported into non-native hosts for synthetic biology applications can gain unexpected properties. In this study, we explored sequences functioning as ribosome binding sites (RBSs) within protein coding DNA sequences (CDSs) that cause internal translation, resulting in truncated proteins. Genome-wide prediction of bacterial RBSs, based on biophysical calculations employed ... Read more >>

ACS Synth Biol (ACS synthetic biology)
[2015, 4(3):249-257]

Cited: 7 times

View full text PDF listing >>



Design and implementation of a biomolecular concentration tracker.

Victoria Hsiao, Emmanuel L C de los Santos, Weston R Whitaker, John E Dueber, Richard M Murray,

As a field, synthetic biology strives to engineer increasingly complex artificial systems in living cells. Active feedback in closed loop systems offers a dynamic and adaptive way to ensure constant relative activity independent of intrinsic and extrinsic noise. In this work, we use synthetic protein scaffolds as a modular and ... Read more >>

ACS Synth Biol (ACS synthetic biology)
[2015, 4(2):150-161]

Cited: 9 times

View full text PDF listing >>



Selection of chromosomal DNA libraries using a multiplex CRISPR system.

Owen W Ryan, Jeffrey M Skerker, Matthew J Maurer, Xin Li, Jordan C Tsai, Snigdha Poddar, Michael E Lee, Will DeLoache, John E Dueber, Adam P Arkin, Jamie H D Cate,

The directed evolution of biomolecules to improve or change their activity is central to many engineering and synthetic biology efforts. However, selecting improved variants from gene libraries in living cells requires plasmid expression systems that suffer from variable copy number effects, or the use of complex marker-dependent chromosomal integration strategies. ... Read more >>

Elife (eLife)
[2014, 3:]

Cited: 65 times

View full text PDF listing >>



Employing a combinatorial expression approach to characterize xylose utilization in Saccharomyces cerevisiae.

Luke N Latimer, Michael E Lee, Daniel Medina-Cleghorn, Rebecca A Kohnz, Daniel K Nomura, John E Dueber,

Fermentation of xylose, a major constituent of lignocellulose, will be important for expanding sustainable biofuel production. We sought to better understand the effects of intrinsic (genotypic) and extrinsic (growth conditions) variables on optimal gene expression of the Scheffersomyces stipitis xylose utilization pathway in Saccharomyces cerevisiae by using a set of ... Read more >>

Metab Eng (Metabolic engineering)
[2014, 25:20-29]

Cited: 33 times

View full text PDF listing >>



Cell-free protein synthesis: search for the happy middle.

Zachary N Russ, John E Dueber,

Cell-free protein synthesis (CFPS) is a versatile technique gaining popularity because it allows researchers access to on-demand production of proteins. This Commentary by Zachary Russ and John Dueber discusses the latest research article by Rui Gan and Michael Jewett, which reports a convenient and cost-effective methodology for the preparation of ... Read more >>

Biotechnol J (Biotechnology journal)
[2014, 9(5):593-594]

Cited: 1 time

View full text PDF listing >>



Identification and characterization of a galacturonic acid transporter from Neurospora crassa and its application for Saccharomyces cerevisiae fermentation processes.

J Philipp Benz, Ryan J Protzko, Jonas Ms Andrich, Stefan Bauer, John E Dueber, Chris R Somerville,

BACKGROUND:Pectin-rich agricultural wastes potentially represent favorable feedstocks for the sustainable production of alternative energy and bio-products. Their efficient utilization requires the conversion of all major constituent sugars. The current inability of the popular fermentation host Saccharomyces cerevisiae to metabolize the major pectic monosaccharide D-galacturonic acid (D-GalA) significantly hampers these efforts. ... Read more >>

(Biotechnology for biofuels)
[2014, 7(1):20]

Cited: 25 times

View full text PDF listing >>



Advertisement

Disclaimer
1.0433 s