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The cofactor challenge in synthetic methylotrophy: bioengineering and industrial applications

CURRENT OPINION IN BIOTECHNOLOGY (2023)

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Signal Peptide Efficiency: From High-Throughput Data to Prediction and Explanation

Stefano Grasso et al.

Summary: The passage of proteins across biological membranes via the Sec pathway is a universally conserved process with critical functions. Estimating the impact of physicochemical signal peptide features on protein secretion levels was achieved through a high-throughput assay and machine learning model. The results allow for quantifying feature importance and predicting protein secretion levels, providing a versatile tool for signal peptide design and evaluation.

ACS SYNTHETIC BIOLOGY (2023)

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Article Chemistry, Multidisciplinary

Renewable methanol production from green hydrogen and captured CO2: A techno-economic assessment

Stefano Sollai et al.

Summary: This paper presents a pre-feasibility study on a power-to-fuel plant configuration for the production of renewable methanol. The study utilizes green hydrogen and captured carbon dioxide as raw materials. A comprehensive process model is developed to simulate the plant sections and the overall system. The economic analysis indicates that the technology is currently not competitive, but expected to become competitive in the future with the implementation of new European policies.

JOURNAL OF CO2 UTILIZATION (2023)

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Article Biotechnology & Applied Microbiology

Paving the way for synthetic C1-Metabolism in Pseudomonas putida through the reductive glycine pathway

Lyon Bruinsma et al.

Summary: In this study, the carbon metabolism of the industrially important bacterium Pseudomonas putida was engineered to utilize one-carbon compounds such as methanol, formate, and CO2 as sustainable microbial feedstocks for the production of chemicals and fuels. The functionality of the C1-assimilation module was demonstrated and successfully extended to include methanol and CO2. This research lays the foundation for further engineering P. putida as a sustainable and versatile cell factory that can utilize formate, methanol, and CO2 as sole feedstocks.

METABOLIC ENGINEERING (2023)

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Review Engineering, Chemical

Engineering the native methylotrophs for the bioconversion of methanol to value-added chemicals: current status and future perspectives

Jing Wang et al.

Summary: Methanol is becoming popular as a fermentation feedstock for large-scale bioproduction. Native methylotrophs, which can use methanol as the sole carbon and energy source, are ideal hosts for methanol bioconversion. This review discusses the natural methanol utilization pathways in native methylotrophs, the synthetic biology tools developed for engineering them, and strategies for improving their methanol utilization efficiency. Additionally, representative examples of engineering native methylotrophs to produce value-added products from methanol are summarized, as well as the major challenges and potential solutions for using native methylotrophs in methanol-based biomanufacturing.

GREEN CHEMICAL ENGINEERING (2023)

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Review Chemistry, Medicinal

Pyrroloquinoline Quinone Chemistry, Biology, and Biosynthesis

Geoffrey A. Cordell et al.

Summary: This review presents aspects of the chemistry, biology, biosynthesis, and commercial production of the widely distributed and essential redox factor PQQ methoxatin, as well as some applications. The understanding of its biosynthesis at the genomic level is an ongoing process.

CHEMICAL RESEARCH IN TOXICOLOGY (2022)

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Article Biotechnology & Applied Microbiology

Carbon-negative production of acetone and isopropanol by gas fermentation at industrial pilot scale

Fungmin Eric Liew et al.

Summary: We have developed a carbon-negative fermentation route for producing acetone and isopropanol from waste gas, which fixes carbon and has a negative carbon footprint. By engineering acetogens, we achieved sustainable, high-efficiency, high-selectivity chemicals production.

NATURE BIOTECHNOLOGY (2022)

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Article Biochemistry & Molecular Biology

eQuilibrator 3.0: a database solution for thermodynamic constant estimation

Moritz E. Beber et al.

Summary: eQuilibrator is a database of biochemical equilibrium constants and Gibbs free energies, which has recently been updated and now includes a new Python-based interface with many new features and improvements. These enhancements will make thermodynamic modeling more accessible and facilitate the integration of eQuilibrator into other software platforms.

NUCLEIC ACIDS RESEARCH (2022)

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Article Agricultural Engineering

Towards new carbon-neutral food systems: Combining carbon capture and utilization with microbial protein production

L. Van Peteghem et al.

Summary: Alternative protein sources, such as microbial protein (MP), are being considered to reduce the environmental impact of food production. This study proposes the use of Carbon Capture and Utilization (CCU) to drive heterotrophic MP production. By comparing different MP production routes and their metabolic pathways, the potential of this concept as a carbon-neutral food or feed production process is evaluated. Acetate and ethanol are found to be the most beneficial substrates for the integrated CCU-to-MP process.

BIORESOURCE TECHNOLOGY (2022)

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Review Biochemical Research Methods

Synthetic or natural? Metabolic engineering for assimilation and valorization of methanol

Patrick A. Sanford et al.

Summary: Recent metabolic engineering efforts to import C1 catabolic pathways into non-methylotrophic bacteria have led to synthetic strains growing on methanol, but their growth rates and product yields are still inferior to native methylotrophs. Moreover, the development of genetic engineering tools has made native C1 utilizers more tractable, raising the question of whether it is better to use an engineered strain or a native host for the microbial assimilation of C1 substrates.

CURRENT OPINION IN BIOTECHNOLOGY (2022)

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Review Microbiology

Employing methylotrophs for a green economy: one-carbon to fuel them all and through metabolism redesign them

Alekhya Govindaraju et al.

Summary: This article addresses recent advances in microbial platforms, focusing on the development of bacterial methylotrophic platforms. These platforms have the potential to revolutionize industrial energy production, mitigate resource shortages, and reduce waste and pollution by enabling the reuse of products and materials at their highest value.

CURRENT OPINION IN MICROBIOLOGY (2022)

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Review Biotechnology & Applied Microbiology

Development and application of CRISPR-based genetic tools in Bacillus species and Bacillus phages

Yafeng Song et al.

Summary: The CRISPR system, developed as a precise and efficient genome editing tool, has been widely applied in various research fields including biotechnology and medical sciences. This review focuses on the advancements and applications of the CRISPR system in Bacillus subtilis and other Bacillus species, as well as potential strategies for further improvement and future directions for rendering Bacillus species cell factories more effective and powerful.

JOURNAL OF APPLIED MICROBIOLOGY (2022)

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Article Biochemistry & Molecular Biology

The TonB-dependent uptake of pyrroloquinoline-quinone (PQQ) and secretion of gluconate by Escherichia coli K-12

Klaus Hantke et al.

Summary: Escherichia coli takes up glucose through the phosphotransferase system (PTS), but requires external supply of PQQ to activate glucose dehydrogenase (Gcd). PqqU acts as a transporter for PQQ through the outer membrane and protects the cells from phage infection. PQQ allows E. coli to activate Gcd even at low concentrations, and E. coli can also secrete gluconate under phosphate limiting conditions.

MOLECULAR MICROBIOLOGY (2022)

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Article Multidisciplinary Sciences

Generation of an Escherichia coli strain growing on methanol via the ribulose monophosphate cycle

Philipp Keller et al.

Summary: This study reports the conversion of Escherichia coli into a synthetic methylotroph that can assimilate methanol via the ribulose monophosphate cycle. The methylotrophic E. coli strain optimizes methanol oxidation by upregulating an improved methanol dehydrogenase, increasing ribulose monophosphate cycle activity, channeling carbon flux through the Entner-Doudoroff pathway, and downregulating tricarboxylic acid cycle enzymes. This research lays the foundation for the efficient utilization of methanol as a carbon and energy resource.

NATURE COMMUNICATIONS (2022)

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Article Multidisciplinary Sciences

Methanol biotransformation toward high-level production of fatty acid derivatives by engineering the industrial yeast Pichia pastoris

Peng Cai et al.

Summary: Methanol-based biorefinery is a promising strategy for achieving carbon neutrality goals. This study successfully rewired the global metabolism of Pichia pastoris to efficiently produce free fatty acids and fatty alcohols from methanol.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)

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Article Endocrinology & Metabolism

Rescuing yeast from cell death enables overproduction of fatty acids from sole methanol

Jiaoqi Gao et al.

Summary: This study demonstrates that engineering the production of free fatty acids from methanol can lead to cell death and decreased phospholipid levels, but cell growth can be restored through adaptive laboratory evolution. Inactivating certain genes preserves cell survival by restoring phospholipid metabolism. By manipulating metabolic pathways, high-level production of free fatty acids from methanol can be achieved. The prevention of methanol-associated toxicity is linked to lipid metabolism and methanol tolerance.

NATURE METABOLISM (2022)

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Article Biotechnology & Applied Microbiology

Metabolic engineering ofPichia pastorisfor malic acid production from methanol

Feng Guo et al.

Summary: The study demonstrates the application of rational design and gene regulation in engineeringP. pastoristo produce malic acid from sole methanol, achieving a significant increase in malic acid yield through optimization of accumulation modules and gene knockouts. The results provide important guidance and reference for metabolic engineering ofP. pastoristo produce value-added chemicals.

BIOTECHNOLOGY AND BIOENGINEERING (2021)

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Article Biochemistry & Molecular Biology

Biosensor-Based Directed Evolution of Methanol Dehydrogenase from Lysinibacillus xylanilyticus

Thien-Kim Le et al.

Summary: The study focused on the direct evolution of Mdh from Lysinibacillus xylanilyticus using a transcriptional factor-based biosensor, leading to the isolation of mutants with high catalytic activity at very low methanol concentrations. These mutants showed significant improvements in methanol conversion efficiency and have the potential to be used in engineering synthetic methylotrophy and enhancing methanol conversion to various useful products.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

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Review Biochemistry & Molecular Biology

Bioinorganic insights of the PQQ-dependent alcohol dehydrogenases

Pedro D. Sarmiento-Pavia et al.

Summary: PQQ-dependent enzymes are mainly found in different types of bacteria and are classified into three main groups based on their structural features. The discovery of lanthanide-dependent enzymes has expanded our understanding of the natural role of these enzymes.

JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY (2021)

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Review Biotechnology & Applied Microbiology

Methanol Dehydrogenases as a Key Biocatalysts for Synthetic Methylotrophy

Thien-Kim Le et al.

Summary: One-carbon (C1) chemicals can serve as potential building blocks for cheap and sustainable resources, which can be converted into various products or pharmaceutical precursors through biological and chemical processes. Among these, methanol is considered a biorenewable platform feedstock, converting almost all bioresources into methanol through syngas conversion for the production of fuels and chemicals.

FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY (2021)

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Review Biochemistry & Molecular Biology

Pyrroloquinoline-Quinone Is More Than an Antioxidant: A Vitamin-like Accessory Factor Important in Health and Disease Prevention

Karen R. Jonscher et al.

Summary: Pyrroloquinoline quinone (PQQ) is associated with biological processes such as mitochondriogenesis, reproduction, growth, and aging, and can attenuate clinically relevant dysfunctions related to ischemia, inflammation, and lipotoxicity. As an enzymatic cofactor or accessory factor, PQQ modulates lactate acid and other dehydrogenases to enhance NAD+-dependent sirtuin activity and mediate mitochondrial functions.

BIOMOLECULES (2021)

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Article Multidisciplinary Sciences

Photovoltaic-driven microbial protein production can use land and sunlight more efficiently than conventional crops

Dorian Leger et al.

Summary: The translation discusses the increasing pressure on the environment due to population growth and changes in dietary patterns, emphasizing the need for a revolution in the way natural resources are harnessed. It also highlights the potential of cultivating microbial biomass to produce single-cell protein (SCP) for protein-rich feed and food supplements, and the lack of quantitative comparison between traditional agriculture and photovoltaic-driven SCP systems.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)

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Article Energy & Fuels

Urgent need for post-growth climate mitigation scenarios

Jason Hickel et al.

Summary: Post-growth approaches may offer an easier path to achieving rapid mitigation and improving social outcomes compared to traditional growth-based scenarios. Climate modellers should explore these alternatives to traditional economic growth assumptions.

NATURE ENERGY (2021)

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Article Biochemistry & Molecular Biology

Understanding the chemistry of the artificial electron acceptors PES, PMS, DCPIP and Wurster's Blue in methanol dehydrogenase assays

Berenice Jahn et al.

JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY (2020)

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Article Biochemistry & Molecular Biology

Growth of E. coli on formate and methanol via the reductive glycine pathway

Seohyoung Kim et al.

NATURE CHEMICAL BIOLOGY (2020)

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An energy-auxotrophEscherichia coliprovides an in vivo platform for assessing NADH regeneration systems

Sebastian Wenk et al.

BIOTECHNOLOGY AND BIOENGINEERING (2020)

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Converting Escherichia coli to a Synthetic Methylotroph Growing Solely on Methanol

Frederic Y-H Chen et al.

CELL (2020)

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NATURE COMMUNICATIONS (2020)

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Production of 2-keto-L-gulonic acid by metabolically engineered Escherichia coli

Weizhu Zeng et al.

BIORESOURCE TECHNOLOGY (2020)

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Review Chemistry, Multidisciplinary

Transforming the carbon economy: challenges and opportunities in the convergence of low-cost electricity and reductive CO2 utilization

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ENERGY & ENVIRONMENTAL SCIENCE (2020)

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Phage-Assisted Evolution of Bacillus methanolicus Methanol Dehydrogenase 2

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ACS SYNTHETIC BIOLOGY (2019)

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NATURE CATALYSIS (2019)

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Editorial Material Biology

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

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BMC BIOLOGY (2019)

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A two-component protease in Methylorubrum extorquens with high activity toward the peptide precursor of the redox cofactor pyrroloquinoline quinone

Ana M. Martins et al.

JOURNAL OF BIOLOGICAL CHEMISTRY (2019)

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Review Chemistry, Physical

Artificial Multienzyme Scaffolds: Pursuing in Vitro Substrate Channeling with an Overview of Current Progress

Gregory A. Ellis et al.

ACS CATALYSIS (2019)

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Engineering thermal stability and solvent tolerance of the soluble quinoprotein PedE from Pseudomonas putida KT2440 with a heterologous whole-cell screening approach

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MICROBIAL BIOTECHNOLOGY (2018)

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The role of dynamic enzyme assemblies and substrate channelling in metabolic regulation

Lee J. Sweetlove et al.

NATURE COMMUNICATIONS (2018)

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The Pyrroloquinoline-Quinone-Dependent Pyranose Dehydrogenase from Coprinopsis cinerea Drives Lytic Polysaccharide Monooxygenase Action

Aniko Varnai et al.

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Identification of dimethylamine monooxygenase in marine bacteria reveals a metabolic bottleneck in the methylated amine degradation pathway

Ian Lidbury et al.

ISME JOURNAL (2017)

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Functional Role of Lanthanides in Enzymatic Activity and Transcriptional Regulation of Pyrroloquinoline Quinone-Dependent Alcohol Dehydrogenases in Pseudomonas putida KT2440

Matthias Wehrmann et al.

MBIO (2017)

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Characterization of membrane-bound dehydrogenases of Gluconobacter oxydans 621H using a new system for their functional expression

Markus Mientus et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2017)

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Biochemical and structural characterization of quinoprotein aldose sugar dehydrogenase from Thermus thermophilus HJ6: Mutational analysis of Tyr156 in the substrate-binding site

Han-Woo Kim et al.

ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS (2016)

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O2-independent demethylation of trimethylamine N-oxide by Tdm of Methylocella silvestris

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FEBS JOURNAL (2016)

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Lanthanide-Dependent Regulation of Methanol Oxidation Systems in Methylobacterium extorquens AM1 and Their Contribution to Methanol Growth

Huong N. Vu et al.

JOURNAL OF BACTERIOLOGY (2016)

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Scaffoldless engineered enzyme assembly for enhanced methanol utilization

J. Vincent Price et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

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Crystal Structure of Alcohol Oxidase from Pichia pastoris

Christian Koch et al.

PLOS ONE (2016)

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Arren Bar-Even et al.

BIOCHEMISTRY (2015)

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Review Biochemical Research Methods

Synthetic methylotrophy: engineering the production of biofuels and chemicals based on the biology of aerobic methanol utilization

William B. Whitaker et al.

CURRENT OPINION IN BIOTECHNOLOGY (2015)

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A Novel Pyrroloquinoline Quinone-Dependent 2-Keto-D-Glucose Dehydrogenase from Pseudomonas aureofaciens

Kiwamu Umezawa et al.

JOURNAL OF BACTERIOLOGY (2015)

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Folate in demethylation: The crystal structure of the rat dimethylglycine dehydrogenase complexed with tetrahydrofolate

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BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH (2014)

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Characterization of membrane-bound dehydrogenases from Gluconobacter oxydans 621H via whole-cell activity assays using multideletion strains

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APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2013)

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How Escherichia coli Tolerates Profuse Hydrogen Peroxide Formation by a Catabolic Pathway

Sripriya Ravindra Kumar et al.

JOURNAL OF BACTERIOLOGY (2013)

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The molecular mechanisms and physiological consequences of oxidative stress: lessons from a model bacterium

James A. Imlay

NATURE REVIEWS MICROBIOLOGY (2013)

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Distribution and Properties of the Genes Encoding the Biosynthesis of the Bacterial Cofactor, Pyrroloquinoline Quinone

Yao-Qing Shen et al.

BIOCHEMISTRY (2012)

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Review Microbiology

Modularity of methylotrophy, revisited

Ludmila Chistoserdova

ENVIRONMENTAL MICROBIOLOGY (2011)

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Molecular structure and gene analysis of Ce3+-induced methanol dehydrogenase of Bradyrhizobium sp MAFF211645

Nanung Agus Fitriyanto et al.

JOURNAL OF BIOSCIENCE AND BIOENGINEERING (2011)

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Alcohol dehydrogenase of acetic acid bacteria: structure, mode of action, and applications in biotechnology

Toshiharu Yakushi et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2010)

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Solving corrosion problems in biofuels industry

E. Torsner

CORROSION ENGINEERING SCIENCE AND TECHNOLOGY (2010)

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Channeling and conformational changes in the heterotetrameric sarcosine oxidase from Corynebacterium sp. U-96

Tomotaka Moriguchi et al.

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Export of functional Streptomyces coelicolor alditol oxidase to the periplasm or cell surface of Escherichia coli and its application in whole-cell biocatalysis

Edwin van Bloois et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2009)

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Article Biochemistry & Molecular Biology

An Internal Reaction Chamber in Dimethylglycine Oxidase Provides Efficient Protection from Exposure to Toxic Formaldehyde

Tewes Tralau et al.

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Microcompartments for B12-dependent 1,2-propanediol degradation provide protection from DNA and cellular damage by a reactive metabolic intermediate

Edith M. Sampson et al.

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Bacillus methanolicus:: a candidate for industrial production of amino acids from methanol at 50°C

Trygve Brautaset et al.

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On oxygen limitation in a whole cell biocatalytic Baeyer-Villiger oxidation process

Christopher V. F. Baldwin et al.

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Soluble aldose sugar dehydrogenase from Escherichia coli -: A highly exposed active site conferring broad substrate specificity

Stacey M. Southall et al.

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Article Biochemistry & Molecular Biology

Channelling and formation of 'active' formaldehyde in dimethylglycine oxidase

D Leys et al.

EMBO JOURNAL (2003)

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Review Biochemistry & Molecular Biology

Pyrroloquinoline quinone (PQQ) and quinoprotein enzymes

C Anthony

ANTIOXIDANTS & REDOX SIGNALING (2001)

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