Challenges and opportunities in biological funneling of heterogeneous and toxic substrates beyond lignin

RND efflux pumps in Gram-negative bacteria; regulation, structure and role in antibiotic resistance

(2020) Abigail L Colclough et al.   Future Microbiology

Metabolic engineering of Escherichia coli for the utilization of ethanol

(2020) Yujin Cao et al.   Journal of Biological Research-Thessaloniki

Recent Advances of CRISPR/Cas9-Based Genetic Engineering and Transcriptional Regulation in Industrial Biology

(2020) Shangjie Zhang et al.   Frontiers in Bioengineering and Biotechnology

Reverse engineering of fatty acid-tolerant Escherichia coli identifies design strategies for robust microbial cell factories

(2020) Yingxi Chen et al.   METABOLIC ENGINEERING

Deletion of genomic islands in the Pseudomonas putida KT2440 genome can create an optimal chassis for synthetic biology applications

(2020) Peixin Liang et al.   Microbial Cell Factories

An engineered PET depolymerase to break down and recycle plastic bottles

(2020) V. Tournier et al.   NATURE

Outer membrane vesicles catabolize lignin-derived aromatic compounds in Pseudomonas putida KT2440

(2020) Davinia Salvachúa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improved bacterial recombineering by parallelized protein discovery

(2020) Timothy M. Wannier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants

(2020) Russell T. Walton et al.   SCIENCE

Analysis of chemical characteristics of lignite upgrading wastewater and its agricultural utilization

(2020) Huifen Zhang et al.   WATER SCIENCE AND TECHNOLOGY

Multifunctional SEVA shuttle vectors for actinomycetes and Gram‐negative bacteria

(2020) Coral García‐Gutiérrez et al.   MicrobiologyOpen

Distillery Stillage: Characteristics, Treatment, and Valorization

(2020) Wioleta Mikucka et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

Engineering microbial pathways for production of bio-based chemicals from lignocellulosic sugars: current status and perspectives

(2020) Jean Marie Francois et al.   Biotechnology for Biofuels

Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors

(2020) Andrew V. Anzalone et al.   NATURE BIOTECHNOLOGY

A decade of advances in transposon-insertion sequencing

(2020) Amy K. Cain et al.   NATURE REVIEWS GENETICS

Synthetic microbial communities of heterotrophs and phototrophs facilitate sustainable growth

(2020) Cristal Zuñiga et al.   Nature Communications

Fatty Acid and Alcohol Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing

(2020) Mitchell G. Thompson et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Valorizing a hydrothermal liquefaction aqueous phase through co-production of chemicals and lipids using the oleaginous yeast Yarrowia lipolytica

(2020) Lauren T. Cordova et al.   BIORESOURCE TECHNOLOGY

Characterization and engineering of a two-enzyme system for plastics depolymerization

(2020) Brandon C. Knott et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial Genetic Engineering by Means of Recombineering for Reverse Genetics

(2020) Ursula Fels et al.   Frontiers in Microbiology

Machine learning for metabolic engineering: A review

(2020) Christopher E. Lawson et al.   METABOLIC ENGINEERING

Bioprospecting of native efflux pumps to enhance furfural tolerance in ethanologenic Escherichia coli

(2019) Gavin Kurgan et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Accelerated genome engineering of Pseudomonas putida by I-Sce I―mediated recombination and CRISPR-Cas9 counterselection

(2019) Nicolas T. Wirth et al.   Microbial Biotechnology

Recent advances in lignin valorization with bacterial cultures: microorganisms, metabolic pathways, and bio-products

(2019) Zhaoxian Xu et al.   Biotechnology for Biofuels

Removal of aromatic inhibitors produced from lignocellulosic hydrolysates by Acinetobacter baylyi ADP1 with formation of ethanol by Kluyveromyces marxianus

(2019) Anita Singh et al.   Biotechnology for Biofuels

A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action

(2019) Jason H. Yang et al.   CELL

Drying and depolymerization technologies of Zhaotong lignite: A review

(2019) Zhan-Ku Li et al.   FUEL PROCESSING TECHNOLOGY

Evaluation of small organic acids present in fast pyrolysis bio‐oil from lignocellulose as feedstocks for bacterial bioconversion

(2019) Stefanie Arnold et al.   Global Change Biology Bioenergy

Reactive Enamines and Imines In Vivo: Lessons from the RidA Paradigm

(2019) Andrew J. Borchert et al.   TRENDS IN BIOCHEMICAL SCIENCES

Machine and deep learning meet genome-scale metabolic modeling

(2019) Guido Zampieri et al.   PLoS Computational Biology

Protein post-translational modifications in bacteria

(2019) Boris Macek et al.   NATURE REVIEWS MICROBIOLOGY

Metabolite Repair Enzymes Control Metabolic Damage in Glycolysis

(2019) Guido T. Bommer et al.   TRENDS IN BIOCHEMICAL SCIENCES

Bacterial microcompartments: catalysis-enhancing metabolic modules for next generation metabolic and biomedical engineering

(2019) Henning Kirst et al.   BMC BIOLOGY

Horizontal transfer of a pathway for coumarate catabolism unexpectedly inhibits purine nucleotide biosynthesis

(2019) Dan M. Close et al.   MOLECULAR MICROBIOLOGY

SEVA 3.0: an update of the Standard European Vector Architecture for enabling portability of genetic constructs among diverse bacterial hosts

(2019) Esteban Martínez-García et al.   NUCLEIC ACIDS RESEARCH

Hidden resources in the Escherichia coli genome restore PLP synthesis and robust growth after deletion of the essential gene pdxB

(2019) Juhan Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adaptive laboratory evolution of tolerance to dicarboxylic acids in Saccharomyces cerevisiae

(2019) Rui Pereira et al.   METABOLIC ENGINEERING

The Escherichia coli transcriptome mostly consists of independently regulated modules

(2019) Anand V. Sastry et al.   Nature Communications

Mixed carbon substrates: a necessary nuisance or a missed opportunity?

(2019) Nian Liu et al.   CURRENT OPINION IN BIOTECHNOLOGY

CRISPR-Enabled Tools for Engineering Microbial Genomes and Phenotypes

(2018) Katia Tarasava et al.   Biotechnology Journal

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

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

Thermochemical wastewater valorization via enhanced microbial toxicity tolerance

(2018) Lahiru N. Jayakody et al.   Energy & Environmental Science

Dynamic metabolic control: towards precision engineering of metabolism

(2018) Di Liu et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

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

(2018) Michael Kohlstedt et al.   METABOLIC ENGINEERING

Engineering E. coli for simultaneous glucose–xylose utilization during methyl ketone production

(2018) Xi Wang et al.   Microbial Cell Factories

Metabolic engineering of Corynebacterium glutamicum for the production of cis, cis-muconic acid from lignin

(2018) Judith Becker et al.   Microbial Cell Factories

Perturbation of the metabolic network in Salmonella enterica reveals cross-talk between coenzyme A and thiamine pathways

(2018) Dustin C. Ernst et al.   PLoS One

Dynamic allocation of orthogonal ribosomes facilitates uncoupling of co-expressed genes

(2018) Alexander P. S. Darlington et al.   Nature Communications

CRISPR-Enabled Tools for Engineering Microbial Genomes and Phenotypes

(2018) Katia Tarasava et al.   Biotechnology Journal

Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non-traditional microorganisms

(2018) Patricia Calero et al.   Microbial Biotechnology

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

Bacterial contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing

(2018) Roland C. Wilhelm et al.   ISME Journal

Multi-omic elucidation of aromatic catabolism in adaptively evolved Rhodococcus opacus

(2018) William R. Henson et al.   METABOLIC ENGINEERING

Mutant phenotypes for thousands of bacterial genes of unknown function

(2018) Morgan N. Price et al.   NATURE

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

(2018) Özlem Akkaya et al.   mBio

Lipid metabolism of phenol-tolerant Rhodococcus opacus strains for lignin bioconversion

(2018) William R. Henson et al.   Biotechnology for Biofuels

Valorization of Food and Agricultural Waste: A Step Towards Greener Future

(2018) Priyanka Rao et al.   CHEMICAL RECORD

Textile dye wastewater characteristics and constituents of synthetic effluents: a critical review

(2018) D. A. Yaseen et al.   International Journal of Environmental Science and Technology

Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions

(2018) Xihui Xu et al.   ISME Journal

Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow

(2018) Elizabeth Brunk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enabling genetic analysis of diverse bacteria with Mobile-CRISPRi

(2018) Jason M. Peters et al.   Nature Microbiology

Engineering Escherichia coli membrane phospholipid head distribution improves tolerance and production of biorenewables

(2017) Zaigao Tan et al.   METABOLIC ENGINEERING

Cofactor engineering to regulate NAD+/NADH ratio with its application to phytosterols biotransformation

(2017) Liqiu Su et al.   Microbial Cell Factories

Extending the Host Range of Bacteriophage Particles for DNA Transduction

(2017) Ido Yosef et al.   MOLECULAR CELL

Biotechnological Perspectives of Pyrolysis Oil for a Bio-Based Economy

(2017) Stefanie Arnold et al.   TRENDS IN BIOTECHNOLOGY

Programming mRNA decay to modulate synthetic circuit resource allocation

(2017) Ophelia S. Venturelli et al.   Nature Communications

Characterization and Catalytic Upgrading of Aqueous Stream Carbon from Catalytic Fast Pyrolysis of Biomass

(2017) Anne K. Starace et al.   ACS Sustainable Chemistry & Engineering

Base-Catalyzed Depolymerization of Solid Lignin-Rich Streams Enables Microbial Conversion

(2017) Alberto Rodriguez et al.   ACS Sustainable Chemistry & Engineering

Metabolite Damage and Metabolite Damage Control in Plants

(2016) Andrew D. Hanson et al.   Annual Review of Plant Biology

Engineering Cellular Metabolism

(2016) Jens Nielsen et al.   CELL

Opportunities and challenges in biological lignin valorization

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

Engineering membrane and cell-wall programs for tolerance to toxic chemicals: Beyond solo genes

(2016) Nicholas R Sandoval et al.   CURRENT OPINION IN MICROBIOLOGY

Multidrug efflux pumps of Gram-positive bacteria

(2016) Bryan D. Schindler et al.   DRUG RESISTANCE UPDATES

Microbial mutualism dynamics governed by dose-dependent toxicity of cross-fed nutrients

(2016) Breah LaSarre et al.   ISME Journal

A critical review on textile wastewater treatments: Possible approaches

(2016) Chandrakant R. Holkar et al.   JOURNAL OF ENVIRONMENTAL MANAGEMENT

Comparative transcriptomics elucidates adaptive phenol tolerance and utilization in lipid-accumulatingRhodococcus opacusPD630

(2016) Aki Yoneda et al.   NUCLEIC ACIDS RESEARCH

Machine Learning for High-Throughput Stress Phenotyping in Plants

(2016) Arti Singh et al.   TRENDS IN PLANT SCIENCE

Aqueous Stream Characterization from Biomass Fast Pyrolysis and Catalytic Fast Pyrolysis

(2016) Brenna A. Black et al.   ACS Sustainable Chemistry & Engineering

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

Better together: engineering and application of microbial symbioses

(2015) Stephanie G Hays et al.   CURRENT OPINION IN BIOTECHNOLOGY

Metabolic pathway balancing and its role in the production of biofuels and chemicals

(2015) J Andrew Jones et al.   CURRENT OPINION IN BIOTECHNOLOGY

Product based evaluation of pyrolysis of food waste and its digestate

(2015) Suraj Adebayo Opatokun et al.   ENERGY

Adipic acid production from lignin

(2015) Derek R. Vardon et al.   Energy & Environmental Science

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

(2015) Davinia Salvachúa et al.   GREEN CHEMISTRY

Bacterial microcompartments: widespread prokaryotic organelles for isolation and optimization of metabolic pathways

(2015) Thomas A. Bobik et al.   MOLECULAR MICROBIOLOGY

Programming Bacteriophages by Swapping Their Specificity Determinants

(2015) Moran G. Goren et al.   TRENDS IN MICROBIOLOGY

Waste paper for recycling: Overview and identification of potentially critical substances

(2015) Kostyantyn Pivnenko et al.   WASTE MANAGEMENT

Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons

(2015) Kelly M. Wetmore et al.   mBio

Plastic waste as a novel substrate for industrial biotechnology

(2015) Nick Wierckx et al.   Microbial Biotechnology

Engineering of Pseudomonas taiwanensis VLB120 for Constitutive Solvent Tolerance and Increased Specific Styrene Epoxidation Activity

(2014) Jan Volmer et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Conversion of post consumer polyethylene to the biodegradable polymer polyhydroxyalkanoate

(2014) Maciej W. Guzik et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Removing environmental organic pollutants with bioremediation and phytoremediation

(2014) Jun Won Kang   BIOTECHNOLOGY LETTERS

Recent advances in the reconstruction of metabolic models and integration of omics data

(2014) Rajib Saha et al.   CURRENT OPINION IN BIOTECHNOLOGY

Pseudomonas 2.0: genetic upgrading of P. putida KT2440 as an enhanced host for heterologous gene expression

(2014) Esteban Martínez-García et al.   Microbial Cell Factories

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

Engineering alcohol tolerance in yeast

(2014) F. H. Lam et al.   SCIENCE

Catalytic Fast Pyrolysis: A Review

(2013) Theodore Dickerson et al.   Energies

The metabolic cost of flagellar motion inPseudomonas putida KT2440

(2013) Esteban Martínez-García et al.   ENVIRONMENTAL MICROBIOLOGY

Metabolite damage and its repair or pre-emption

(2013) Carole L Linster et al.   Nature Chemical Biology

Development of a bioprocess to convert PET derived terephthalic acid and biodiesel derived glycerol to medium chain length polyhydroxyalkanoate

(2012) Shane T. Kenny et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

The future of metabolic engineering and synthetic biology: Towards a systematic practice

(2012) Vikramaditya G. Yadav et al.   METABOLIC ENGINEERING

Development of a Method for Markerless Gene Deletion in Pseudomonas putida

(2011) Nadja Graf et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Solvent tolerance in Gram-negative bacteria

(2011) Ana Segura et al.   CURRENT OPINION IN BIOTECHNOLOGY

Complete Genome Sequence of Sphingobium sp. Strain SYK-6, a Degrader of Lignin-Derived Biaryls and Monoaryls

(2011) E. Masai et al.   JOURNAL OF BACTERIOLOGY

A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: From biofuels and chemicals, to biocatalysis and bioremediation

(2010) Sergios A. Nicolaou et al.   METABOLIC ENGINEERING

Characterization of lignin monomers in low rank coal humic acids using the derivatization/reductive cleavage method

(2010) Laurent Grasset et al.   ORGANIC GEOCHEMISTRY

Addressing the role of the extrusion pump-bearing pGRT1 plasmid in toluene biodegradation by Pseudomonas putida DOT-T1E under real case scenarios

(2009) M. Hernandez et al.   WATER SCIENCE AND TECHNOLOGY

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

(2008) Boris Görke et al.   NATURE REVIEWS MICROBIOLOGY