Modular Engineering of Biomass Degradation Pathways

Utilising datasheets for the informed automated design and build of a synthetic metabolic pathway

(2019) Kealan Exley et al.   Journal of Biological Engineering

Rewired cellular signaling coordinates sugar and hypoxic responses for anaerobic xylose fermentation in yeast

(2019) Kevin S. Myers et al.   PLoS Genetics

Engineering Zymomonas mobilis for Robust Cellulosic Ethanol Production

(2019) Juan Xia et al.   TRENDS IN BIOTECHNOLOGY

Establishing Synthesis Pathway-Host Compatibility via Enzyme Solubility

(2019) Sara A. Amin et al.   BIOTECHNOLOGY AND BIOENGINEERING

Everyone loves an underdog: metabolic engineering of the xylose oxidative pathway in recombinant microorganisms

(2018) Kris Niño G. Valdehuesa et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Promiscuous activities of heterologous enzymes lead to unintended metabolic rerouting in Saccharomyces cerevisiae engineered to assimilate various sugars from renewable biomass

(2018) Eun Ju Yun et al.   Biotechnology for Biofuels

EasyCloneYALI: CRISPR/Cas9-Based Synthetic Toolbox for Engineering of the Yeast Yarrowia lipolytica

(2018) Carina Holkenbrink et al.   Biotechnology Journal

Chemicals from lignin: an interplay of lignocellulose fractionation, depolymerisation, and upgrading

(2018) W. Schutyser et al.   CHEMICAL SOCIETY REVIEWS

Engineering yeast for utilization of alternative feedstocks

(2018) Allison Yaguchi et al.   CURRENT OPINION IN BIOTECHNOLOGY

Underground metabolism: network-level perspective and biotechnological potential

(2018) Richard A Notebaart et al.   CURRENT OPINION IN BIOTECHNOLOGY

Integrated analysis of isopentenyl pyrophosphate (IPP) toxicity in isoprenoid-producing Escherichia coli

(2018) Kevin W. George et al.   METABOLIC ENGINEERING

Refactoring the upper sugar metabolism of Pseudomonas putida for co-utilization of cellobiose, xylose, and glucose

(2018) Pavel Dvořák et al.   METABOLIC ENGINEERING

From lignin to nylon: Cascaded chemical and biochemical conversion using metabolically engineered Pseudomonas putida

(2018) Michael Kohlstedt et al.   METABOLIC ENGINEERING

Accelerating pathway evolution by increasing the gene dosage of chromosomal segments

(2018) Melissa Tumen-Velasquez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A semi-synthetic regulon enables rapid growth of yeast on xylose

(2018) Venkatesh Endalur Gopinarayanan et al.   Nature Communications

A promiscuous cytochrome P450 aromatic O-demethylase for lignin bioconversion

(2018) Sam J. B. Mallinson et al.   Nature Communications

Biochemical mechanisms determine the functional compatibility of heterologous genes

(2018) Andreas Porse et al.   Nature Communications

Characterization of Lignin Streams during Bionic Liquid-Based Pretreatment from Grass, Hardwood, and Softwood

(2018) Tanmoy Dutta et al.   ACS Sustainable Chemistry & Engineering

EasyCloneYALI: CRISPR/Cas9-Based Synthetic Toolbox for Engineering of the Yeast Yarrowia lipolytica

(2018) Carina Holkenbrink et al.   Biotechnology Journal

Rapid, parallel identification of pathways for catabolism of lignin-derived aromatic compounds in Novosphingobium aromaticivorans

(2018) Jacob H. Cecil et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Forecasting ethanol market volatility: new evidence from the corn implied volatility index

(2018) Anupam Dutta   Biofuels Bioproducts & Biorefining-Biofpr

The Metabolic Redox Regime of Pseudomonas putida Tunes Its Evolvability toward Novel Xenobiotic Substrates

(2018) Özlem Akkaya et al.   mBio

Catalytic Strategies Towards Lignin-Derived Chemicals

(2018) S. Van den Bosch et al.   Topics in Current Chemistry

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

(2018) Ryan J. Protzko et al.   Nature Communications

Lignin-first biomass fractionation: the advent of active stabilisation strategies

(2017) T. Renders et al.   Energy & Environmental Science

The crystal structure of a new O -demethylase from Sphingobium sp. strain SYK-6

(2017) Ayaka Harada et al.   FEBS Journal

Construction of a BioBrick™ compatible vector system for Rhodococcus

(2017) James Ellinger et al.   PLASMID

Bacterial catabolism of lignin-derived aromatics: New findings in a recent decade: Update on bacterial lignin catabolism

(2017) Naofumi Kamimura et al.   Environmental Microbiology Reports

Refactoring the Embden–Meyerhof–Parnas Pathway as a Whole of Portable GlucoBricks for Implantation of Glycolytic Modules in Gram-Negative Bacteria

(2017) Alberto Sánchez-Pascuala et al.   ACS Synthetic Biology

Application of Nonphosphorylative Metabolism as an Alternative for Utilization of Lignocellulosic Biomass

(2017) Maria K. McClintock et al.   Frontiers in Microbiology

Increasing the revenue from lignocellulosic biomass: Maximizing feedstock utilization

(2017) David Martin Alonso et al.   Science Advances

Improving heterologous membrane protein production in Escherichia coli by combining transcriptional tuning and codon usage algorithms

(2017) Nico J. Claassens et al.   PLoS One

A bacterial aromatic aldehyde dehydrogenase critical for the efficient catabolism of syringaldehyde

(2017) Naofumi Kamimura et al.   Scientific Reports

Combining Metabolic Engineering and Electrocatalysis: Application to the Production of Polyamides from Sugar

(2016) Miguel Suastegui et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Paving the Way for Lignin Valorisation: Recent Advances in Bioengineering, Biorefining and Catalysis

(2016) Roberto Rinaldi et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Engineered Microbial Production of 2-Pyrone-4,6-Dicarboxylic Acid from Lignin Residues for Use as an Industrial Platform Chemical

(2016) Yun Qian et al.   BioResources

Biological valorization of low molecular weight lignin

(2016) Omar Y. Abdelaziz et al.   BIOTECHNOLOGY ADVANCES

GroE chaperonins assisted functional expression of bacterial enzymes in Saccharomyces cerevisiae

(2016) Peng-Fei Xia et al.   BIOTECHNOLOGY AND BIOENGINEERING

Physicochemical and thermal properties of lignocellulosic fiber from sugar palm fibers: effect of treatment

(2016) Bushra Rashid et al.   CELLULOSE

Opportunities and challenges in biological lignin valorization

(2016) Gregg T Beckham et al.   CURRENT OPINION IN BIOTECHNOLOGY

New insights into the structure and composition of technical lignins: a comparative characterisation study

(2016) Sandra Constant et al.   GREEN CHEMISTRY

Engineering of an L-arabinose metabolic pathway in Rhodococcus jostii RHA1 for biofuel production

(2016) Xiaochao Xiong et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Tricin-lignins: occurrence and quantitation of tricin in relation to phylogeny

(2016) Wu Lan et al.   PLANT JOURNAL

Influence of Acidic (H3PO4) and Alkaline (NaOH) Additives on the Catalytic Reductive Fractionation of Lignocellulose

(2016) Tom Renders et al.   ACS Catalysis

Modular Optimization of a Hemicellulose-Utilizing Pathway in Corynebacterium glutamicum for Consolidated Bioprocessing of Hemicellulosic Biomass

(2016) Sung Sun Yim et al.   ACS Synthetic Biology

Total Utilization of Miscanthus Biomass, Lignin and Carbohydrates, Using Earth Abundant Nickel Catalyst

(2016) Hao Luo et al.   ACS Sustainable Chemistry & Engineering

Investigation of the Chemocatalytic and Biocatalytic Valorization of a Range of Different Lignin Preparations: The Importance of β-O-4 Content

(2016) Christopher S. Lancefield et al.   ACS Sustainable Chemistry & Engineering

Base-Catalyzed Depolymerization of Biorefinery Lignins

(2016) Rui Katahira et al.   ACS Sustainable Chemistry & Engineering

Current Understanding of the Correlation of Lignin Structure with Biomass Recalcitrance

(2016) Mi Li et al.   Frontiers in Chemistry

Combining C6 and C5 sugar metabolism for enhancing microbial bioconversion

(2015) Guo-Chang Zhang et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Catalytic depolymerisation of isolated lignins to fine chemicals using a Pt/alumina catalyst: part 1—impact of the lignin structure

(2015) Florent P. Bouxin et al.   GREEN CHEMISTRY

Towards lignin consolidated bioprocessing: simultaneous lignin depolymerization and product generation by bacteria

(2015) Davinia Salvachúa et al.   GREEN CHEMISTRY

Dynamic knockdown of E. coli central metabolism for redirecting fluxes of primary metabolites

(2015) Irene M. Brockman et al.   METABOLIC ENGINEERING

Simultaneous utilization of glucose and xylose via novel mechanisms in engineered Escherichia coli

(2015) Suk Min Kim et al.   METABOLIC ENGINEERING

Aromatic catabolic pathway selection for optimal production of pyruvate and lactate from lignin

(2015) Christopher W. Johnson et al.   METABOLIC ENGINEERING

New cofactor supports α,β-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition

(2015) Karl A. P. Payne et al.   NATURE

Syringyl lignin production in conifers: Proof of concept in a Pine tracheary element system

(2015) Armin Wagner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sustainable bio-ethanol production from agro-residues: A review

(2015) Anubhuti Gupta et al.   RENEWABLE & SUSTAINABLE ENERGY REVIEWS

A portable expression resource for engineering cross-species genetic circuits and pathways

(2015) Manish Kushwaha et al.   Nature Communications

The Functional Structure of Central Carbon Metabolism in Pseudomonas putida KT2440

(2014) Suresh Sudarsan et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Inverse metabolic engineering of Bacillus subtilis for xylose utilization based on adaptive evolution and whole-genome sequencing

(2014) Bo Zhang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

ccSOL omics: a webserver for solubility prediction of endogenous and heterologous expression in Escherichia coli

(2014) F. Agostini et al.   BIOINFORMATICS

Expression and Substrate Range of Streptomyces Vanillate Demethylase

(2014) Motohiro Nishimura et al.   BIOLOGICAL & PHARMACEUTICAL BULLETIN

The Implications of Lignocellulosic Biomass Chemical Composition for the Production of Advanced Biofuels

(2014) Nadav Sorek et al.   BIOSCIENCE

Targeted chemical upgrading of lignocellulosic biomass to platform molecules

(2014) J. S. Luterbacher et al.   GREEN CHEMISTRY

Phylogeny Poorly Predicts the Utility of a Challenging Horizontally Transferred Gene in Methylobacterium Strains

(2014) J. K. Michener et al.   JOURNAL OF BACTERIOLOGY

Enhancement of protocatechuate decarboxylase activity for the effective production of muconate from lignin-related aromatic compounds

(2014) Tomonori Sonoki et al.   JOURNAL OF BIOTECHNOLOGY

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

(2014) Luke N. Latimer et al.   METABOLIC ENGINEERING

Comparative engineering of Escherichia coli for cellobiose utilization: Hydrolysis versus phosphorolysis

(2014) Hyun-Dong Shin et al.   METABOLIC ENGINEERING

Lignin valorization through integrated biological funneling and chemical catalysis

(2014) J. G. Linger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lignin Valorization: Improving Lignin Processing in the Biorefinery

(2014) A. J. Ragauskas et al.   SCIENCE

Engineering redox balance through cofactor systems

(2014) Xiulai Chen et al.   TRENDS IN BIOTECHNOLOGY

Mechanical pretreatments of lignocellulosic biomass: towards facile and environmentally sound technologies for biofuels production

(2014) Abdellatif Barakat et al.   RSC Advances

Effective use of a horizontally-transferred pathway for dichloromethane catabolism requires post–transfer refinement

(2014) Joshua K Michener et al.   eLife

Characterizing the Promiscuity of LigAB, a Lignin Catabolite Degrading Extradiol Dioxygenase from Sphingomonas paucimobilis SYK-6

(2013) Kevin P. Barry et al.   BIOCHEMISTRY

Depolymerization of organosolv lignin to aromatic compounds over Cu-doped porous metal oxides

(2013) Katalin Barta et al.   GREEN CHEMISTRY

Quantification of Wheat Straw Lignin Structure by Comprehensive NMR Analysis

(2013) Jijiao Zeng et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Heterologous Expression of the Mevalonic Acid Pathway in Cyanobacteria Enhances Endogenous Carbon Partitioning to Isoprene

(2013) Fiona K. Bentley et al.   Molecular Plant

Acetylation of woody lignocellulose: significance and regulation

(2013) Prashant Mohan-Anupama Pawar et al.   Frontiers in Plant Science

The Bacillus BioBrick Box: generation and evaluation of essential genetic building blocks for standardized work with Bacillus subtilis

(2013) Jara Radeck et al.   Journal of Biological Engineering

The Entner-Doudoroff pathway empowersPseudomonas putida KT2440 with a high tolerance to oxidative stress

(2012) Max Chavarría et al.   ENVIRONMENTAL MICROBIOLOGY

Recent advances in engineering the central carbon metabolism of industrially important bacteria

(2012) Maria Papagianni   Microbial Cell Factories

Rethinking glycolysis: on the biochemical logic of metabolic pathways

(2012) Arren Bar-Even et al.   Nature Chemical Biology

The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes

(2012) Rafael Silva-Rocha et al.   NUCLEIC ACIDS RESEARCH

Identification and treatment of heme depletion attributed to overexpression of a lineage of evolved P450 monooxygenases

(2012) J. K. Michener et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inhibitory cross-talk upon introduction of a new metabolic pathway into an existing metabolic network

(2012) J. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ePathBrick: A Synthetic Biology Platform for Engineering Metabolic Pathways in E. coli

(2012) Peng Xu et al.   ACS Synthetic Biology

Xyloglucan and Its Biosynthesis

(2012) Olga A. Zabotina   Frontiers in Plant Science

Fungal arabinan and l-arabinose metabolism

(2011) Bernhard Seiboth et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Recent progress in consolidated bioprocessing

(2011) Daniel G Olson et al.   CURRENT OPINION IN BIOTECHNOLOGY

From biomass to feedstock: one-step fractionation of lignocellulose components by the selective organic acid-catalyzed depolymerization of hemicellulose in a biphasic system

(2011) Thorsten vom Stein et al.   GREEN CHEMISTRY

Pathways for degradation of lignin in bacteria and fungi

(2011) Timothy D. H. Bugg et al.   NATURAL PRODUCT REPORTS

Heterologous Expression of Membrane Proteins: Choosing the Appropriate Host

(2011) Florent Bernaudat et al.   PLoS One

Structural changes in switchgrass lignin and hemicelluloses during pretreatments by NMR analysis

(2011) Reichel Samuel et al.   POLYMER DEGRADATION AND STABILITY

Lignin content in natural Populus variants affects sugar release

(2011) M. H. Studer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BglBrick vectors and datasheets: A synthetic biology platform for gene expression

(2011) Taek Lee et al.   Journal of Biological Engineering

Towards Enhanced Galactose Utilization by Lactococcus lactis

(2010) A. R. Neves et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Isolation and characterisation of lactic acid bacterium for effective fermentation of cellobiose into optically pure homo l-(+)-lactic acid

(2010) Mohamed Ali Abdel-Rahman et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Simultaneous consumption of pentose and hexose sugars: an optimal microbial phenotype for efficient fermentation of lignocellulosic biomass

(2010) Jae-Han Kim et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Poplar as a feedstock for biofuels: A review of compositional characteristics

(2010) Poulomi Sannigrahi et al.   Biofuels Bioproducts & Biorefining-Biofpr

Chemical profiles of switchgrass

(2010) Zhoujian Hu et al.   BIORESOURCE TECHNOLOGY

Regioselective carboxylation of catechol by 3,4-dihydroxybenzoate decarboxylase of Enterobacter cloacae P

(2010) Toyokazu Yoshida et al.   BIOTECHNOLOGY LETTERS

Switchgrass as an energy crop for biofuel production: A review of its ligno-cellulosic chemical properties

(2010) Kasi David et al.   Energy & Environmental Science

Blueprints for Building Plant Cell Walls

(2010) M. McCann et al.   PLANT PHYSIOLOGY

Plant Cell Walls

(2010) K. Keegstra   PLANT PHYSIOLOGY

Engineered Saccharomyces cerevisiae capable of simultaneous cellobiose and xylose fermentation

(2010) S.-J. Ha et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Manufacturing Molecules Through Metabolic Engineering

(2010) J. D. Keasling   SCIENCE

Enhanced Enzymatic Hydrolysis of Lignocellulose by Optimizing Enzyme Complexes

(2009) Mingjia Zhang et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

Sugar transporters in efficient utilization of mixed sugar substrates: current knowledge and outlook

(2009) Toru Jojima et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Ethanol production from xylose in engineered Saccharomyces cerevisiae strains: current state and perspectives

(2009) Akinori Matsushika et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Chemical compositions of four switchgrass populations

(2009) Jinhua Yan et al.   BIOMASS & BIOENERGY

Xylose reductase from Pichia stipitis with altered coenzyme preference improves ethanolic xylose fermentation by recombinant Saccharomyces cerevisiae

(2009) Oskar Bengtsson et al.   Biotechnology for Biofuels

Dilute acid hydrolysis of lignocellulosic biomass

(2009) P. Lenihan et al.   CHEMICAL ENGINEERING JOURNAL

Native Lignin Structure ofMiscanthus x giganteusand Its Changes during Acetic and Formic Acid Fractionation

(2009) Juan José Villaverde et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Building outside of the box: iGEM and the BioBricks Foundation

(2009) Christina D Smolke   NATURE BIOTECHNOLOGY

Engineering for biofuels: exploiting innate microbial capacity or importing biosynthetic potential?

(2009) Hal Alper et al.   NATURE REVIEWS MICROBIOLOGY

Hydroxycinnamates in lignification

(2009) John Ralph   PHYTOCHEMISTRY REVIEWS

The Effects on Lignin Structure of Overexpression of Ferulate 5-Hydroxylase in Hybrid Poplar1

(2009) J. J. Stewart et al.   PLANT PHYSIOLOGY

Characterization of milled wood lignin and ethanol organosolv lignin from miscanthus

(2009) Roland El Hage et al.   POLYMER DEGRADATION AND STABILITY

Pectin, a versatile polysaccharide present in plant cell walls

(2009) Alphons G. J. Voragen et al.   STRUCTURAL CHEMISTRY

Engineering Pseudomonas putida S12 for Efficient Utilization of D-Xylose and L-Arabinose

(2008) J.-P. Meijnen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Refinement and standardization of synthetic biological parts and devices

(2008) Barry Canton et al.   NATURE BIOTECHNOLOGY

Carbon catabolite repression in bacteria: many ways to make the most out of nutrients

(2008) Boris Görke et al.   NATURE REVIEWS MICROBIOLOGY

Acid in ionic liquid: An efficient system for hydrolysis of lignocellulose

(2007) Changzhi Li et al.   GREEN CHEMISTRY