☆ 4.7 Review

Unleashing the capacity of Rhodococcus for converting lignin into lipids

BIOTECHNOLOGY ADVANCES (2024)

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Article Energy & Fuels

Lignin to polyhydroxyalkanoate bioprocessing by novel strain of Pseudomonas monteilii

Pornkamol Unrean et al.

Summary: This study optimized a fed-batch process using lignin-rich black liquor as carbon source for the production of polyhydroxyalkanoate (PHA). The optimized feeding profiles and C:N ratio significantly enhanced the lignin conversion efficiency and PHA synthesis.

BIOMASS CONVERSION AND BIOREFINERY (2023)

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Article Biochemical Research Methods

Development and Application of Whole-Cell Biosensors for the Detection of Gallic Acid

Ingrida Kutraite et al.

Summary: This study reports the characterization of a transcription factor-based inducible system that responds to gallic acid in a dose-dependent manner. The activation of this system requires gallate dioxygenase activity and the effector molecule is identified as an intermediate of gallic acid metabolism. Furthermore, the applicability of the P. putida-based biosensor is demonstrated by detecting and measuring gallic acid in tea leaf extracts.

ACS SYNTHETIC BIOLOGY (2023)

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Article Green & Sustainable Science & Technology

Chemical recycling ofa lignin-based non-isocyanate polyurethane foam

James Sternberg et al.

Summary: The plastic waste crisis requires new polymers designed for recycling. Lignin, found in woody biomass, is a promising biobased source due to its aromatic nature. However, the reactivity and heterogeneous structure of lignin pose challenges for its use in polymers and designing recycling solutions. A chemical recycling technique is demonstrated here to depolymerize lignin and produce a recycled precursor that can be reused in non-isocyanate polyurethane foams. The closed-loop recycling process of lignin-derived foam shows a pathway towards a circular economy.

NATURE SUSTAINABILITY (2023)

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Review Biotechnology & Applied Microbiology

Folding of heterologous proteins in bacterial cell factories: Cellular mechanisms and engineering strategies

Yixin Rong et al.

Summary: The expression of correctly folded and functional heterologous proteins is crucial in biotechnological production processes. Bacterial platform organisms like E. coli are commonly used due to their proven suitability at an industrial scale, but can suffer from protein aggregation and low functional protein levels. This review explores cellular mechanisms influencing protein folding and expression across different organisms, and discusses experimental methods to improve protein folding, such as codon optimization and chaperone co-production.

BIOTECHNOLOGY ADVANCES (2023)

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Article Biochemical Research Methods

A High-Quality Genome-Scale Model for Rhodococcus opacus Metabolism

Garrett W. Roell et al.

Summary: Researchers have developed the first genome-scale model of R. opacus PD630, called iGR1773, based on its genomic sequence and associated data. The model can predict the growth rate and metabolic fluxes of R. opacus, and can also be used to predict the utilization patterns of aromatic compounds. This model is important for computational strain design in metabolic engineering.

ACS SYNTHETIC BIOLOGY (2023)

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Article Engineering, Environmental

Towards jet fuel from technical lignins: Feedstock-catalyst-product interactions revealed during catalytic hydrogenolysis

Matthew S. Kollman et al.

Summary: The one-pot conversion of technical lignins to jet fuel is limited by the recondensation of unstable intermediates. A two-stage process involving reductive depolymerization and oligomers upgrading may increase yield. This study focuses on the initial depolymerization of industrially relevant lignins and explores the effects of feedstocks, catalysts, and process conditions on product composition. Hydrogen and temperature synergistically suppress coking during pine kraft depolymerization, while ruthenium and zinc are effective catalysts for converting hardwood kraft lignin to oligomers suitable for upgrading to jet fuel-range hydrocarbons.

CHEMICAL ENGINEERING JOURNAL (2023)

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Article Biochemistry & Molecular Biology

Bioconversion of Homogeneous Linear C-Lignin to Polyhydroxyalkanoates

Zhi-Min Zhao et al.

Summary: This study investigated the bioconversion of homogeneous linear catechyl lignin (C-lignin) to polyhydroxyalkanoates (PHA) for the first time. C-lignins from different sources showed variations in molecular structures. Nonetherified catechol units were consumed during fermentation. C2 lignin, with a lower weight-average molecular weight compared to C1, exhibited superior bioconversion performance.

BIOMACROMOLECULES (2023)

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Article Agricultural Engineering

Microbial valorization of lignin: Prospects and challenges

R. Reshmy et al.

Summary: Lignin, the second most prevalent biomaterial, can be valorized using bacteria to produce valuable products. Challenges include product separation and purification difficulties, as well as methods to enhance lignin decomposition.

BIORESOURCE TECHNOLOGY (2022)

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Article Engineering, Environmental

High-solid ethylenediamine pretreatment to fractionate new lignin streams from lignocellulosic biomass

Li Xu et al.

Summary: The study utilized a high-solid ethylenediamine pretreatment method to develop a new aminolignin with high aqueous solubility and minimal condensed structures. Unique amination reactions introduced hydrophilic amine and amide groups into lignin substructures, enhancing lignin processability. This solid-state EDA pretreatment holds promise for improving lignin's solubility and minimizing condensation, potentially advancing lignin-first biomass fractionation.

CHEMICAL ENGINEERING JOURNAL (2022)

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Review Biochemical Research Methods

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

Andrew J. Borchert et al.

Summary: Advancements in microbial metabolism understanding and manipulation have led to the utilization of engineered biological systems for a sustainable energy and materials economy. While metabolic engineering primarily focuses on carbohydrates, opportunities exist to extract value from heterogeneous and toxic waste streams through biological funneling, presenting new challenges.

CURRENT OPINION IN BIOTECHNOLOGY (2022)

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Review Microbiology

Microbial assimilation of lignin-derived aromatic compounds and conversion to value-added products

Christopher C. Azubuike et al.

Summary: Lignin is a plentiful and sustainable source of aromatic compounds that can be converted to valuable products through microbial conversion. However, the current conversion processes have low yields, and further research is needed to achieve viable conversion processes.

CURRENT OPINION IN MICROBIOLOGY (2022)

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Article Chemistry, Multidisciplinary

An integrated process for the valorization of corn stover promoted by NaCl in a GVL/H2O system

Yiping Luo et al.

Summary: An integrated green process for the valorization of corn stover was developed using NaCl in GVL/H2O. NaCl enhanced the extraction of hemicellulose and lignin, as well as the degradation of hemicellulose to small molecular products. It also promoted the cleavage of chemical bonds in lignin and decarboxylation reactions, resulting in lower molecular weight oligomers and monophenols. The salt effects of NaCl allowed for in situ separation of liquid products, and the cellulose-rich solid residues were activated to produce high performance activated carbon. The process has great potential for pollution control in industrial processes.

GREEN CHEMISTRY (2022)

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Article Environmental Sciences

The ss-ketoadipate pathway of Acinetobacter baumannii is involved in complement resistance and affects resistance against aromatic antibiotics

Jennifer Breisch et al.

Summary: In this study, it was found that Acinetobacter baumannii adapts to the human host through the ss-ketoadipate pathway and this pathway is associated with antibiotic resistance.

ENVIRONMENTAL MICROBIOLOGY REPORTS (2022)

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Review Energy & Fuels

Perspectives on Fully Synthesized Sustainable Aviation Fuels: Direction and Opportunities

Stephen Kramer et al.

Summary: The aviation sector is working towards reducing greenhouse gas emissions by developing reduced carbon aviation fuels. While current aircraft are designed around petroleum-based aviation kerosene, the industry aims to qualify and approve synthesized aviation fuel components. These components are not necessarily interchangeable with traditional aviation fuels and must be blended within approved limits for commercial aviation use. The sector also seeks to move towards using 100% synthesized aviation fuels that meet sustainability criteria. However, the development and assessment of these fuels will be separate from technical performance evaluations.

FRONTIERS IN ENERGY RESEARCH (2022)

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Review Biotechnology & Applied Microbiology

Adaptive laboratory evolution principles and applications in industrial biotechnology

Maria Mavrommati et al.

Summary: Adaptive laboratory evolution (ALE) is an innovative approach that generates microbial strains with desired characteristics through the implementation of natural selection rules. ALE has been applied to various microorganisms to improve their performance and investigate the genetic background of evolution, showing promising applications.

BIOTECHNOLOGY ADVANCES (2022)

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Article Agricultural Engineering

Cosolvent enhanced lignocellulosic fractionation tailoring lignin chemistry and enhancing lignin bioconversion

Zhi-Min Zhao et al.

Summary: This study fully evaluated the bioconversion performance of CELF lignin for the first time and found that it outperforms other technical lignins in terms of carboxylic acid OH content, molecular weight, and linkages. Rhodococcus opacus PD630 cell count and lipid yield were significantly improved with CELF lignin compared to ethanol organosolv lignin and kraft lignin. Principal component analysis indicated that more carboxylic acid groups and lower molecular weight contributed to the enhanced bioconversion performance of CELF lignin.

BIORESOURCE TECHNOLOGY (2022)

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Review Engineering, Environmental

Catalytic lignin valorisation by depolymerisation, hydrogenation, demethylation and hydrodeoxygenation: Mechanism, chemical reaction kinetics and transport phenomena

Tina Rocnik et al.

Summary: This review focuses on the mechanism, chemical reaction kinetics, and transport phenomena of lignin depolymerisation, as well as the recently introduced aspects in the field of lignin chemistry. It also discusses the modeling of heat and mass transfer during lignin depolymerisation and upgrade.

CHEMICAL ENGINEERING JOURNAL (2022)

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Article Energy & Fuels

Ex-situ catalytic pyrolysis of lignin using lignin-carbon catalyst combined with HZSM-5 to improve the yield of high-quality liquid fuels

Huiyan Zhang et al.

Summary: The ex-situ catalytic pyrolysis of lignin using LC catalysts combined with HZSM-5 can enhance the aromatic yield. LC catalysts prepared under optimal conditions show excellent depolymerization performance for both lignin and biomass. The total aromatic yield is significantly improved by using the optimal LC catalyst combined with HZSM-5, and LC catalysts have good renewability.

FUEL (2022)

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Article Biochemistry & Molecular Biology

Structural characterization of lignin and lignin-carbohydrate complex (LCC) of sesame hull

Meng-Ke He et al.

Summary: In this study, lignin and lignin-carbohydrate complex (LCC) from sesame hulls were investigated to explore dehulling techniques. The results showed that rhamnose and glucose were the major components in lignin and LCC fractions. Bjo center dot rkman LCC had the largest molecular weight, MWL had the smallest molecular weight, and LCC-AcOH had the largest polydispersity index. The study also revealed the presence of a new type of lignin (C-type lignin) and identified the major lignin-linked bonds in different fractions.

INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES (2022)

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Article Multidisciplinary Sciences

Highly stable and tunable peptoid/hemin enzymatic mimetics with natural peroxidase-like activities

Tengyue Jian et al.

Summary: By developing self-assembled peptoid/hemin nanomaterials, a class of peroxidase mimetics with tunable catalytic activity and high stability is created, showing highly modulable catalytic activities towards lignin depolymerization. These catalysts are highly stable and efficient in lignin depolymerization.

NATURE COMMUNICATIONS (2022)

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Article Chemistry, Multidisciplinary

Biodegradation of Lignin into Low-Molecular-Weight Oligomers by Multicopper Laccase-Mimicking Nanozymes of the Cu/GMP Complex at Room Temperature

Yingying Yang et al.

Summary: A facile strategy using Cu/GMP catalyst to degrade lignin at room temperature and atmospheric pressure was reported, resulting in high yield of lignin oligomers. Moreover, these oligomers exhibited positive effects on the oxidative stability of canola oil biodiesel, showing potential to replace expensive antioxidants.

ACS SUSTAINABLE CHEMISTRY & ENGINEERING (2022)

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Article Chemistry, Multidisciplinary

Enhancing Lignin Dispersion and Bioconversion by Eliminating Thermal Sterilization

Zhi-Min Zhao et al.

Summary: This study introduces a strategy to eliminate thermal sterilization, which significantly enhances the dispersion of lignin in aqueous fermentation media. This promotes lignin bioconversion efficiently.

ACS SUSTAINABLE CHEMISTRY & ENGINEERING (2022)

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Article Biochemistry & Molecular Biology

Low-Molecular-Weight Lignin Recovery with Nanofiltration in the Kraft Pulping Process

Mariona Battestini Vives et al.

Summary: This study evaluates the use of nanofiltration for the separation and concentration of low-molecular-weight lignin from ultrafiltration permeate. The results show that nanofiltration process can produce a concentrated lignin fraction.

MEMBRANES (2022)

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Review Biotechnology & Applied Microbiology

Current status, challenges and prospects for lignin valorization by using Rhodococcus sp.

Wankui Jiang et al.

Summary: This review evaluates the potential of Rhodococcus sp. as a cell factory for lignin biotransformation, focusing on its abilities in phenol tolerance, lignin depolymerization, and lignin-derived aromatic hydrocarbon metabolism. The detailed metabolic mechanism and bioproducts spectrum of lignin biotransformation by Rhodococcus sp. will be comprehensively discussed. Additionally, available molecular tools for lignin conversion and possible directions for future lignin biotransformation will be reviewed.

BIOTECHNOLOGY ADVANCES (2022)

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Review Biotechnology & Applied Microbiology

Bacterial conversion routes for lignin valorization

He Liu et al.

Summary: Lignin, as a renewable aromatic resource, shows promise for the production of value-added products. This article provides a systematic overview of bacterial lignin valorization and highlights the potential of cascaded conversion routes for upgrading lignin into value-added products.

BIOTECHNOLOGY ADVANCES (2022)

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Review Biotechnology & Applied Microbiology

Creative biological lignin conversion routes toward lignin valorization

Zhi-Hua Liu et al.

Summary: Lignin, as the largest renewable aromatic resource, shows potential for sustainable production of chemicals, fuels, and materials. The review presents biological lignin conversion routes (BLCRs) that offer opportunities for lignin valorization through biological funneling and aromatic bioconversion pathways, enabling a lignocellulose-based bioeconomy.

TRENDS IN BIOTECHNOLOGY (2022)

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Article Chemistry, Physical

Continuous hydrodeoxygenation of lignin to jet-range aromatic hydrocarbons

Michael L. Stone et al.

Summary: This study reports a continuous, two-stage catalytic process using molybdenum carbide to convert lignin into aromatic hydrocarbons. The results show high selectivity and carbon recovery. Tier a fuel property testing indicates that the lignin-derived aromatic compounds may have performance advantages over conventional jet fuel aromatic compounds.

JOULE (2022)

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Review Chemistry, Multidisciplinary

Lignin for energy applications - state of the art, life cycle, technoeconomic analysis and future trends

Anne Beaucamp et al.

Summary: Lignin, a by-product of papermaking and biofuel industries, is a valuable sustainable polymer suitable for high value energy applications. This review discusses lignin chemistry, extraction techniques, and important chemistries for emerging energy applications.

GREEN CHEMISTRY (2022)

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Article Biotechnology & Applied Microbiology

A CRISPR/Cas9-based single-stranded DNA recombineering system for genome editing of Rhodococcus opacus PD630

Youxiang Liang et al.

Summary: The failure of conventional CRISPR/Cas9 technologies in Rhodococcus opacus was mainly due to the cytotoxicity of Cas9 and the deficiency in pathways for repairing DNA double-strand breaks. An efficient single-stranded DNA recombineering system coupled with CRISPR/Cas9 counter-selection was successfully developed for rapid and scarless editing of the R. opacus genome. This novel tool enabled gene disruption, base mutation, and simultaneous disruption of double genes, with editing efficiencies ranging from 22% to 100%.

SYNTHETIC AND SYSTEMS BIOTECHNOLOGY (2021)

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Editorial Material Biotechnology & Applied Microbiology

Promoting Lignin Valorization by Coping with Toxic C1 Byproducts

Zhihui Zhang et al.

Summary: Methanol and formaldehyde, toxic C1 compounds generated during lignin bioconversion, can be detoxified and assimilated by methylotrophs to produce useful metabolites and cell biomass. Constructing integrated biosystems shows promise for utilizing toxic C1 byproducts and promoting lignin valorization.

TRENDS IN BIOTECHNOLOGY (2021)

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Article Biotechnology & Applied Microbiology

Metabolic engineering of Rhodococcus jostii RHA1 for production of pyridine-dicarboxylic acids from lignin

Edward M. Spence et al.

Summary: Genetic modification of Rhodococcus jostii RHA1 led to higher titres of pyridine-2,4-dicarboxylic acid and pyridine-2,5-dicarboxylic acid bioproducts from lignin breakdown, through insertion of specific genes on expression vectors. Enhanced lignin degradation and increased productivity were observed, demonstrating the potential for improved bioproduct production through genetic engineering.

MICROBIAL CELL FACTORIES (2021)

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Article Chemistry, Physical

Reductive Catalytic Fractionation of Flax Shive over Ru/C Catalysts

Aleksandr S. Kazachenko et al.

Summary: This study presents reductive catalytic fractionation (RCF) of flax shive in ethanol and isopropanol using a bifunctional catalyst (Ru/C) and molecular hydrogen at elevated temperatures, resulting in solvolytic depolymerization of lignin and hemicelluloses. The catalytic hydrogenation effectively stabilizes lignin intermediates, preventing repolymerization reactions and producing a lignin fraction with high depolymerization degree. Bifunctional catalysts Ru/C significantly increase the conversion and yield of monophenolic compounds in the hydrogenation of flax shive.

CATALYSTS (2021)

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Review Agricultural Engineering

Valorization of volatile fatty acids derived from low-cost organic waste for lipogenesis in oleaginous microorganisms-A review

Alok Patel et al.

Summary: Volatile fatty acids, generated during anaerobic digestion of organic waste, have emerged as a renewable feedstock for microbial oil production. This review discusses the metabolic pathways enabling lipogenesis from volatile fatty acids and strategies to enhance lipid accumulation by tuning the ratios of volatile fatty acids in oleaginous microorganisms.

BIORESOURCE TECHNOLOGY (2021)

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Article Green & Sustainable Science & Technology

Hydrothermal carbonization and liquefaction for sustainable production of hydrochar and aromatics

Yang Cao et al.

Summary: This article critically reviews the recent advances in hydrothermal carbonization and liquefaction technologies for the sustainable production of hydrochar and aromatics from different biomass wastes. The importance of identifying the physical and chemical properties of feedstock, as well as the science-informed design and optimization of operational parameters, are crucial for the selective production of valueadded chemicals and multifunctional hydrochar. Current limitations and original perspectives for advancing hydrothermal processing of biomass towards carbon-efficient resource utilization and circular economy in future applications are identified and discussed in this review.

RENEWABLE & SUSTAINABLE ENERGY REVIEWS (2021)

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Review Biotechnology & Applied Microbiology

Depolymerization and conversion of lignin to value-added bioproducts by microbial and enzymatic catalysis

Caihong Weng et al.

Summary: Lignin, the most abundant renewable aromatic compound in nature, is hindered by its intrinsic heterogeneity and recalcitrance; bioprocessing with microbial and enzymatic catalysis offers an efficient method for lignin depolymerization and conversion into value-added bioproducts.

BIOTECHNOLOGY FOR BIOFUELS (2021)

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Article Green & Sustainable Science & Technology

Investigation of correlation between chemical composition and properties of biodiesel using principal component analysis (PCA) and artificial neural network (ANN)

M. Jahirul et al.

Summary: This study used principal component analysis and artificial intelligence models to investigate the impact of biodiesel chemical composition on its properties. By utilizing experimental data and literature information, the study established a model to show the complex multi-dimensional correlation between biodiesel properties and chemical composition.

RENEWABLE ENERGY (2021)

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Article Chemistry, Multidisciplinary

Synthesis of High-Density Components of Jet Fuel from Lignin-Derived Aromatics via Alkylation and Subsequent Hydrodeoxygenation

Jing Bai et al.

Summary: High-density polycyclic alkanes prepared from lignocellulose biomass are synthesized using lignin-derived phenol and benzyl acetate, followed by hydrodeoxygenation reaction over a Pd/C catalyst. The HDO products show high density and heating values, with perhydrofluorene and dicyclohexylmethane as dominant components. This strategy provides a potential alternative to fossil fuels.

ACS SUSTAINABLE CHEMISTRY & ENGINEERING (2021)

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Review Biotechnology & Applied Microbiology

Genetic toolkits for engineering Rhodococcus species with versatile applications

Youxiang Liang et al.

Summary: Rhodococcus species have diverse catabolic activities and strong adaptive capabilities, making them widely used in various biotechnological applications. However, their engineering is challenging due to lack of universal molecular tools and low transformation efficiency. Future trends in Rhodococcus engineering include the adaptation and optimization of synthetic and systems biology tools for improved applications and research.

BIOTECHNOLOGY ADVANCES (2021)

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Article Materials Science, Paper & Wood

Metal-alkali catalytic valorization of lignocellulose towards aromatics and small molecular alcohols and acids in a holistic approach

Wei Lv et al.

Summary: This work developed an approach for the complete catalytic conversion of woody biomass into valuable products, including lignin-derived aromatics and (semi-)cellulose-derived small molecular alcohols. By using a mixed solvent system and metal-alkaline catalysts, the depolymerization and transformation of lignocellulose were achieved, providing a versatile valorization strategy for biomass catalysis.

CELLULOSE (2021)

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Article Agricultural Engineering

Revealing the topochemical and structural changes of poplar lignin during a two-step hydrothermal pretreatment combined with alkali extraction

Shao-Chao Sun et al.

Summary: This study successfully extracted lignin with high yield and ultra-high purity from poplar using a combined method of hydrothermal pretreatment and alkali extraction. Confocal Raman microscopy analysis revealed that lignin was preferentially delignified in the secondary wall and compound middle lamella, then throughout the entire morphological regions of the cell wall. NMR results showed that the cleavage of beta-O-4 linkages was the dominant reaction, leading to an increase in phenolic hydroxyl groups, a decrease in molecular weight, and heterogeneity of the isolated lignin.

INDUSTRIAL CROPS AND PRODUCTS (2021)

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Article Biochemistry & Molecular Biology

1-Ethyl-3-methylimidazolium acetate ionic liquid as simple and efficient catalytic system for the oxidative depolymerization of alkali lignin

Wenbo Li et al.

Summary: The oxidative depolymerization of alkali lignin in the [C(2)C(1)im]OAc system under mild conditions was successful, with the addition of water further improving reaction efficiency. The system allowed for the breakdown of specific inter-unit linkages of lignin, resulting in residual lignin with low molecular weight and narrow polydispersity index. The [C(2)C(1)im]OAc-based system proved to be a simple and efficient catalytic system for lignin oxidative depolymerization.

INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES (2021)

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Article Chemistry, Multidisciplinary

Techno-economic analysis and life cycle assessment of a biorefinery utilizing reductive catalytic fractionation

Andrew W. Bartling et al.

Summary: Reductive catalytic fractionation (RCF) is a promising method to fractionate lignocellulose and convert lignin to a narrow product slate. Analyses of techno-economic, life cycle assessment, and air emissions are crucial for guiding research towards commercialization, with a focus on cost and sustainability considerations.

ENERGY & ENVIRONMENTAL SCIENCE (2021)

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Article Chemistry, Multidisciplinary

An eco-friendly biomass pretreatment strategy utilizing reusable enzyme mimicking nanoparticles for lignin depolymerization and biofuel production

Rajiv Chandra Rajak et al.

Summary: A nanoparticle mediated pretreatment strategy has been developed to specifically depolymerize lignin from lignocellulosic biomass, leaving solid residues rich in carbohydrates while releasing fermentable sugars for biofuel production.

GREEN CHEMISTRY (2021)

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Article Chemistry, Multidisciplinary

Elucidating the mechanisms of enhanced lignin bioconversion by an alkali sterilization strategy

Zhi-Min Zhao et al.

Summary: Alkali sterilization effectively enhances the dispersion and fermentation performance of lignin substrates, improving bioconversion efficiency. Changes in particle size and molecular structure of lignin after alkali sterilization, including the generation of more hydrophilic carboxyl groups, reduction in molecular weight, and narrowing molar-mass dispersity, promote Rhodococcus opacus PD630 cell growth and metabolism, leading to increased lignin degradation and lipid production.

GREEN CHEMISTRY (2021)

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Review Chemistry, Multidisciplinary

Guidelines for performing lignin-first biorefining

Mahdi M. Abu-Omar et al.

Summary: The valorisation of lignin is crucial for the economic viability of the lignocellulosic biorefining industry. The lignin-first biorefining approach, which considers lignin valorisation in the design phase, has been shown to make the fullest use of lignocellulose. Despite the diverse approaches to reporting and analyzing results from lignin-first methods, we propose guidelines for analyzing critical data in order to facilitate direct comparisons between studies.

ENERGY & ENVIRONMENTAL SCIENCE (2021)

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Review Biotechnology & Applied Microbiology

Addressing uncertainty in genome-scale metabolic model reconstruction and analysis

David B. Bernstein et al.

Summary: The reconstruction and analysis of genome-scale metabolic models is a powerful systems biology approach, but limited by multiple heterogeneous sources of uncertainty that are difficult to quantify. A unified formal characterization of these uncertainties through probabilistic approaches and ensemble modeling will facilitate convergence towards consistent reconstruction pipelines, improved data integration algorithms, and more accurate assessment of predictive capacity.

GENOME BIOLOGY (2021)

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Article Energy & Fuels

Enzymatic demethylation of Kraft lignin for lignin-based phenol-formaldehyde resin applications

Balaji Venkatesagowda et al.

BIOMASS CONVERSION AND BIOREFINERY (2020)

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Article Environmental Sciences

Metalloporphyrin as a Biomimetic Catalyst for the Catalytic Oxidative Degradation of Lignin to Produce Aromatic Monomers

Jinfeng Xie et al.

WASTE AND BIOMASS VALORIZATION (2020)

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Article Environmental Sciences

Adaptation mechanisms of Rhodococcus sp. CNS16 under different temperature gradients: Physiological and transcriptome

Chen Wang et al.

CHEMOSPHERE (2020)

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Article Multidisciplinary Sciences

A sustainable wood biorefinery for low-carbon footprint chemicals production

Yuhe Liao et al.

SCIENCE (2020)

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Article Chemistry, Physical

Low temperature catalytic conversion of oligomers derived from lignin in pubescens on Pd/NbOPO4

Qianying Fang et al.

APPLIED CATALYSIS B-ENVIRONMENTAL (2020)

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Article Biotechnology & Applied Microbiology

Mechanism of the oxidative stress-mediated increase in lipid accumulation by the bacterium, R. opacus PD630: Experimental analysis and genome-scale metabolic modeling

Archanaa Sundararaghavan et al.

BIOTECHNOLOGY AND BIOENGINEERING (2020)

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Article Chemistry, Multidisciplinary

Preparation of Highly Reactive Lignin by Ozone Oxidation: Application as Surfactants with Antioxidant and Anti-UV Properties

Chen Shi et al.

ACS SUSTAINABLE CHEMISTRY & ENGINEERING (2020)

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Review Chemistry, Multidisciplinary

Emerging Strategies for Modifying Lignin Chemistry to Enhance Biological Lignin Valorization

Zhi-Min Zhao et al.

CHEMSUSCHEM (2020)

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The Hydroxyquinol Degradation Pathway in Rhodococcus jostii RHA1 and Agrobacterium Species Is an Alternative Pathway for Degradation of Protocatechuic Acid and Lignin Fragments

Edward M. Spence et al.

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Review Biochemical Research Methods

Bioconversion of renewable feedstocks by Rhodococcus opacus

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CURRENT OPINION IN BIOTECHNOLOGY (2020)

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Ethylenediamine Enhances Ionic Liquid Pretreatment Performance at High Solid Loading

Li Xu et al.

ACS SUSTAINABLE CHEMISTRY & ENGINEERING (2020)

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Review Biotechnology & Applied Microbiology

Biotechnology of Rhodococcus for the production of valuable compounds

Martina Cappelletti et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2020)

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Article Biochemistry & Molecular Biology

i-Propylammonium Lead Chloride Based Perovskite Photocatalysts for Depolymerization of Lignin Under UV Light

Samia Kausar et al.

MOLECULES (2020)

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Article Chemistry, Multidisciplinary

Non-catalytic oxidative depolymerization of lignin in perfluorodecalin to produce phenolic monomers

Parinaz Hafezisefat et al.

GREEN CHEMISTRY (2020)

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Article Biotechnology & Applied Microbiology

Discovery of potential pathways for biological conversion of poplar wood into lipids by co-fermentation of Rhodococci strains

Xiaolu Li et al.

BIOTECHNOLOGY FOR BIOFUELS (2019)

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Article Energy & Fuels

Transformation of Ammonia Fiber Expansion (AFEX) corn stover lignin into microbial lipids by Rhodococcus opacus

Zening Wang et al.

FUEL (2019)

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Article Multidisciplinary Sciences

Constructing a synthetic pathway for acetylcoenzyme A from one-carbon through enzyme design

Xiaoyun Lu et al.

NATURE COMMUNICATIONS (2019)

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Review Biotechnology & Applied Microbiology

A field of dreams: Lignin valorization into chemicals, materials, fuels, and health-care products

Judith Becker et al.

BIOTECHNOLOGY ADVANCES (2019)

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Article Biotechnology & Applied Microbiology

New insights into the genome of Rhodococcus ruber strain Chol-4

Govinda Guevara et al.

BMC GENOMICS (2019)

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Article Biochemistry & Molecular Biology

C1 Compound Biosensors: Design, Functional Study, and Applications

Jin-Young Lee et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2019)

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Article Biotechnology & Applied Microbiology

Biomass and lipid production by Rhodococcus opacus PD630 in molasses-based media with and without osmotic-stress

Maythee Saisriyoot et al.

JOURNAL OF BIOTECHNOLOGY (2019)

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Review Green & Sustainable Science & Technology

Identifying and creating pathways to improve biological lignin valorization

Zhi-Hua Liu et al.

RENEWABLE & SUSTAINABLE ENERGY REVIEWS (2019)

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Article Chemistry, Multidisciplinary

Mechanism-Guided Design of Highly Efficient Protein Secretion and Lipid Conversion for Biomanufacturing and Biorefining

Shangxian Xie et al.

ADVANCED SCIENCE (2019)

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Article Energy & Fuels

Highly Efficient Lignin Depolymerization via Effective Inhibition of Condensation during Polyoxometalate-Mediated Oxidation

Weisheng Yang et al.

ENERGY & FUELS (2019)

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Article Thermodynamics

Effect of synthetic and food waste-derived volatile fatty acids on lipid accumulation in Rhodococcus sp. YHY01 and the properties of produced biodiesel

Shashi Kant Bhatia et al.

ENERGY CONVERSION AND MANAGEMENT (2019)

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Article Engineering, Environmental

Construction of an Escherichia coli strain to degrade phenol completely with two modified metabolic modules

Bo Wang et al.

JOURNAL OF HAZARDOUS MATERIALS (2019)

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Article Multidisciplinary Sciences

Enabling microbial syringol conversion through structure-guided protein engineering

Melodie M. Machovina et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)

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Article Engineering, Environmental

Valorization of food-waste hydrolysate by Lentibacillus salarius NS12IITR for the production of branched chain fatty acid enriched lipid with potential application as a feedstock for improved biodiesel

Noopur Singh et al.

WASTE MANAGEMENT (2019)

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Article Biochemical Research Methods

Construction of Genetic Logic Gates Based on the T7 RNA Polymerase Expression System in Rhodococcus opacus PD630

Drew M. DeLorenzo et al.

ACS SYNTHETIC BIOLOGY (2019)

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Article Agricultural Engineering

A clean and green approach for odd chain fatty acids production in Rhodococcus sp. YHY01 by medium engineering

Shashi Kant Bhatia et al.

BIORESOURCE TECHNOLOGY (2019)

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Article Energy & Fuels

Depolymerization of Lignin over a Ni-Pd Bimetallic Catalyst Using Isopropanol as an in Situ Hydrogen Source

Bingxing Jiang et al.

ENERGY & FUELS (2019)

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Article Chemistry, Multidisciplinary

Electrochemical Aminoxyl-Mediated Oxidation of Primary Alcohols in Lignin to Carboxylic Acids: Polymer Modification and Depolymerization

Mohammad Rafiee et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2019)

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Article Agricultural Engineering

Bioconversion of barley straw lignin into biodiesel using Rhodococcus sp. YHY01

Shashi Kant Bhatia et al.

BIORESOURCE TECHNOLOGY (2019)

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Review Biotechnology & Applied Microbiology

Genome analysis and -omics approaches provide new insights into the biodegradation potential of Rhodococcus

Jessica Zampolli et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2019)

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Article Agricultural Engineering

Lipid production from corn stover by a cost-efficient system featuring ammonium carbonate-steam explosion and recirculating enzymatic hydrolysis

Hui Xu et al.

BIOMASS & BIOENERGY (2019)

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Article Microbiology

Characterization and Transcriptional Regulation of n-Alkane Hydroxylase Gene Cluster of Rhodococcus jostii RHA1

Namiko Gibu et al.

MICROORGANISMS (2019)

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Article Chemistry, Multidisciplinary

Dual Function Lewis Acid Catalyzed Depolymerization of Industrial Corn Stover Lignin into Stable Monomeric Phenols

Kakasaheb Y. Nandiwale et al.

ACS SUSTAINABLE CHEMISTRY & ENGINEERING (2019)

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Article Biotechnology & Applied Microbiology

Whole gene transcriptomic analysis of PCB/biphenyl degrading Rhodococcus jostii RHA1

Shazwana Sha'arani et al.

JOURNAL OF GENERAL AND APPLIED MICROBIOLOGY (2019)

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Article Biochemistry & Molecular Biology

Membrane Separation of the Base-Catalyzed Depolymerization of Black Liquor Retentate for Low-Molecular-Mass Compound Production

Kena Li et al.

MEMBRANES (2019)

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Article Agricultural Engineering

A review on microbial lipids as a potential biofuel

Sara A. Shields-Menard et al.

BIORESOURCE TECHNOLOGY (2018)

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Article Biotechnology & Applied Microbiology

Combinatorial pretreatment and fermentation optimization enabled a record yield on lignin bioconversion

Zhi-Hua Liu et al.

BIOTECHNOLOGY FOR BIOFUELS (2018)

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Review Chemistry, Multidisciplinary

Bright Side of Lignin Depolymerization: Toward New Platform Chemicals

Zhuohua Sun et al.

CHEMICAL REVIEWS (2018)

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Review Chemistry, Multidisciplinary

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

W. Schutyser et al.

CHEMICAL SOCIETY REVIEWS (2018)

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Article Environmental Sciences

Toxicity evaluation of lignocellulose-derived phenolic inhibitors on Saccharomyces cerevisiae growth by using the QSTR method

Jinju Hou et al.

CHEMOSPHERE (2018)

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Article Chemistry, Multidisciplinary

Efficient conversion of lignin into a water-soluble polymer by a chelator-mediated Fenton reaction: optimization of H2O2 use and performance as a dispersant

Michael S. Kent et al.

GREEN CHEMISTRY (2018)

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Article Multidisciplinary Sciences

A promiscuous cytochrome P450 aromatic O-demethylase for lignin bioconversion

Sam J. B. Mallinson et al.

NATURE COMMUNICATIONS (2018)

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Article Chemistry, Multidisciplinary

Integrated production of bio-jet fuel containing lignin-derived arenes via lipid deoxygenation

Yijian Lu et al.

CHEMICAL COMMUNICATIONS (2018)

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Article Biotechnology & Applied Microbiology

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

William R. Henson et al.

METABOLIC ENGINEERING (2018)

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Article Chemistry, Multidisciplinary

A Coenzyme-Free Biocatalyst for the Value-Added Utilization of Lignin-Derived Aromatics

Jun Ni et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2018)

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Article Chemistry, Multidisciplinary

Synergistic maximization of the carbohydrate output and lignin processability by combinatorial pretreatment

Zhi-Hua Liu et al.

GREEN CHEMISTRY (2017)

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Review Chemistry, Multidisciplinary

Lignin transformations for high value applications: towards targeted modifications using green chemistry

S. Gillet et al.

GREEN CHEMISTRY (2017)

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Article Biotechnology & Applied Microbiology

The effects of model aromatic lignin compounds on growth and lipid accumulation of Rhodococcus rhodochrous

Sara A. Shields-Menard et al.

INTERNATIONAL BIODETERIORATION & BIODEGRADATION (2017)

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Article Biochemistry & Molecular Biology

Modification of oil palm fronds lignin by incorporation of m-cresol for improving structural and antioxidant properties

Nurul Atiqah Sa'don et al.

INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES (2017)

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Article Biotechnology & Applied Microbiology

Rewiring neutral lipids production for the de novo synthesis of wax esters in Rhodococcus opacus PD630

Mariana P. Lanfranconi et al.

JOURNAL OF BIOTECHNOLOGY (2017)

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Article Biochemistry & Molecular Biology

Co-fermentation of lignocellulose-based glucose and inhibitory compounds for lipid synthesis by Rhodococcus jostii RHA1

Zhu Chen et al.

PROCESS BIOCHEMISTRY (2017)

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Review Green & Sustainable Science & Technology

Biological valorization strategies for converting lignin into fuels and chemicals

Zhu Chen et al.

RENEWABLE & SUSTAINABLE ENERGY REVIEWS (2017)

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Article Biochemical Research Methods

Development of Chemical and Metabolite Sensors for Rhodococcus opacus PD630

Drew M. DeLorenzo et al.

ACS SYNTHETIC BIOLOGY (2017)

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Article Chemistry, Multidisciplinary

Lipid Production from Dilute Alkali Corn Stover Lignin by Rhodococcus Strains

Yucai He et al.

ACS SUSTAINABLE CHEMISTRY & ENGINEERING (2017)

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Article Chemistry, Multidisciplinary

Advanced Chemical Design for Efficient Lignin Bioconversion

Shangxian Xie et al.

ACS SUSTAINABLE CHEMISTRY & ENGINEERING (2017)

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Article Chemistry, Physical

The Ni-Mo/γ-Al2O3 catalyzed hydrodeoxygenation of FAME to aviation fuel

Meng Wang et al.

CATALYSIS COMMUNICATIONS (2017)

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Article Chemistry, Analytical

Enhancement of the peroxidase-like activity of cerium-doped ferrite nanoparticles for colorimetric detection of H2O2 and glucose

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ANALYTICAL METHODS (2017)

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Article Biotechnology & Applied Microbiology

Rapid metabolic analysis of Rhodococcus opacus PD630 via parallel 13C-metabolite fingerprinting

Whitney D. Hollinshead et al.

BIOTECHNOLOGY AND BIOENGINEERING (2016)

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Article Biotechnology & Applied Microbiology

Enhanced lipid production by Rhodosporidium toruloides using different fed-batch feeding strategies with lignocellulosic hydrolysate as the sole carbon source

Qiang Fei et al.

BIOTECHNOLOGY FOR BIOFUELS (2016)

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Review Chemistry, Multidisciplinary

Lignin Valorization through Catalytic Lignocellulose Fractionation: A Fundamental Platform for the Future Biorefinery

Maxim V. Galkin et al.

CHEMSUSCHEM (2016)

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Review Biochemical Research Methods

Opportunities and challenges in biological lignin valorization

Gregg T. Beckham et al.

CURRENT OPINION IN BIOTECHNOLOGY (2016)

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Article Chemistry, Multidisciplinary

Systems biology-guided biodesign of consolidated lignin conversion

Lu Lin et al.

GREEN CHEMISTRY (2016)

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Article Chemistry, Multidisciplinary

Synergistic enzymatic and microbial lignin conversion

Cheng Zhao et al.

GREEN CHEMISTRY (2016)

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Article Biotechnology & Applied Microbiology

Rhodococcus opacus B4: a promising bacterium for production of biofuels and biobased chemicals

Ana Rita Castro et al.

AMB EXPRESS (2016)

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Article Biotechnology & Applied Microbiology

Microbial lipid production by oleaginous Rhodococci cultured in lignocellulosic autohydrolysates

Zhen Wei et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2015)

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Article Biochemistry & Molecular Biology

In vitro reconstitution of the catabolic reactions catalyzed by PcaHG, PcaB, and PcaL: the protocatechuate branch of the β-ketoadipate pathway in Rhodococcus jostii RHA1

Tomoya Yamanashi et al.

BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY (2015)

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Review Biotechnology & Applied Microbiology

Can laccases catalyze bond cleavage in lignin?

Line Munk et al.

BIOTECHNOLOGY ADVANCES (2015)

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Article Chemistry, Multidisciplinary

Bioconversion of oxygen-pretreated Kraft lignin to microbial lipid with oleaginous Rhodococcus opacus DSM 1069

Zhen Wei et al.

GREEN CHEMISTRY (2015)

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Article Chemistry, Multidisciplinary

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

Davinia Salvachua et al.

GREEN CHEMISTRY (2015)

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Article Biotechnology & Applied Microbiology

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

Christopher W. Johnson et al.

METABOLIC ENGINEERING (2015)

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Article Biochemistry & Molecular Biology

Pyrolysis Oil-Based Lipid Production as Biodiesel Feedstock by Rhodococcus opacus

Zhen Wei et al.

APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY (2015)

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Article Biotechnology & Applied Microbiology

Overexpression of a phosphatidic acid phosphatase type 2 leads to an increase in triacylglycerol production in oleaginous Rhodococcus strains

Martin A. Hernandez et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2015)

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Article Multidisciplinary Sciences

Optimizing Polychlorinated Biphenyl Degradation by Flavonoid-Induced Cells of the Rhizobacterium Rhodococcus erythropolis U23A

Thi Thanh My Pham et al.

PLOS ONE (2015)

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Article Engineering, Environmental

Simultaneous lipid production and dairy wastewater treatment using Rhodococcus opacus in a batch bioreactor for potential biodiesel application

Sanjay Kumar et al.

JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING (2015)

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Article Multidisciplinary Sciences

Improving fatty acids production by engineering dynamic pathway regulation and metabolic control

Peng Xu et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)

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Article Biochemistry & Molecular Biology

Breaking Down Lignin to High-Value Chemicals: The Conversion of Lignocellulose to Vanillin in a Gene Deletion Mutant of Rhodococcus jostii RHA1

Paul D. Sainsbury et al.

ACS CHEMICAL BIOLOGY (2013)

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Article Biotechnology & Applied Microbiology

The atf2 gene is involved in triacylglycerol biosynthesis and accumulation in the oleaginous Rhodococcus opacus PD630

Martin A. Hernandez et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2013)

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Review Biotechnology & Applied Microbiology

Engineering of NADPH regenerators in Escherichia coli for enhanced biotransformation

Won-Heong Lee et al.

APPLIED MICROBIOLOGY AND BIOTECHNOLOGY (2013)

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Article Agricultural Engineering

Sugarcane bagasse degradation and characterization of three white-rot fungi

Xiu Qin Dong et al.

BIORESOURCE TECHNOLOGY (2013)

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Review Biochemical Research Methods

Microbial production of fatty acid-derived fuels and chemicals

Rebecca M. Lennen et al.

CURRENT OPINION IN BIOTECHNOLOGY (2013)

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Article Chemistry, Multidisciplinary

Lignin to lipid bioconversion by oleaginous Rhodococci

Matyas Kosa et al.

GREEN CHEMISTRY (2013)

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Article Biotechnology & Applied Microbiology

Vanillin Catabolism in Rhodococcus jostii RHA1

Hao-Ping Chen et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2012)

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Review Biotechnology & Applied Microbiology

Biotechnological opportunities with the β-ketoadipate pathway

Tyrone Wells et al.

TRENDS IN BIOTECHNOLOGY (2012)

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Article Biochemistry & Molecular Biology

Identification of DypB from Rhodococcus jostii RHA1 as a Lignin Peroxidase

Mark Ahmad et al.

BIOCHEMISTRY (2011)

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Review Biochemistry & Molecular Biology

Pathways for degradation of lignin in bacteria and fungi

Timothy D. H. Bugg et al.

NATURAL PRODUCT REPORTS (2011)

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Review Microbiology

Microbial degradation of aromatic compounds - from one strategy to four

Georg Fuchs et al.

NATURE REVIEWS MICROBIOLOGY (2011)

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Article Genetics & Heredity

Comparative and Functional Genomics of Rhodococcus opacus PD630 for Biofuels Development

Jason W. Holder et al.

PLOS GENETICS (2011)

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Article Biotechnology & Applied Microbiology

Characterization of the Protocatechuate 4,5-Cleavage Pathway Operon in Comamonas sp Strain E6 and Discovery of a Novel Pathway Gene

Naofumi Kamimura et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2010)

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Article Microbiology

PcaO Positively Regulates pcaHG of the β-Ketoadipate Pathway in Corynebacterium glutamicum

Ke-Xin Zhao et al.

JOURNAL OF BACTERIOLOGY (2010)

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Article Biotechnology & Applied Microbiology

Single cell oil production by Gordonia sp DG using agro-industrial wastes

Mona K. Gouda et al.

WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY (2008)

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Article Microbiology

Roles of ring-hydroxylating dioxygenases in styrene and benzene catabolism in Rhodococcus jostii RHA1

Marianna A. Patrauchan et al.

JOURNAL OF BACTERIOLOGY (2008)

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Article Biochemistry & Molecular Biology

Polychlorinated biphenyl/biphenyl degrading gene clusters in Rhodococcus sp K37, HA99, and TA431 are different from well-known bph gene clusters of rhodococci

Katsuhiko Taguchi et al.

BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY (2007)

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Article Biochemical Research Methods

Analysis of aromatic catabolic pathways in Pseudomonas putida KT 2440 using a combined proteomic approach:: 2-DE/MS and cleavable isotope-coded affinity tag analysis

YH Kim et al.

PROTEOMICS (2006)

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Article Biochemistry & Molecular Biology

Constitutive expression of catABC genes in the aniline-assimilating bacterium Rhodococcus species AN-22: production, purification, characterization and gene analysis of CatA, CatB and CatC

E Matsumura et al.

BIOCHEMICAL JOURNAL (2006)

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Article Microbiology

Phenylacetate catabolism in Rhodococcus sp strain RHA1:: a central pathway for degradation of aromatic compounds

JM Navarro-Llorens et al.

JOURNAL OF BACTERIOLOGY (2005)

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Article Microbiology

Catabolism of benzoate and phthalate in Rhodococcus sp strain RHA1:: Redundancies and convergence

MA Patrauchan et al.

JOURNAL OF BACTERIOLOGY (2005)

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Article Biochemistry & Molecular Biology

Functional genomics by NMR spectroscopy -: Phenylacetate catabolism in Escherichia coli

W Ismail et al.

EUROPEAN JOURNAL OF BIOCHEMISTRY (2003)

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Article Biotechnology & Applied Microbiology

2-hydroxypenta-2,4-dienoate metabolic pathway genes in a strong polychlorinated biphenyl degrader, Rhodococcus sp strain RHA1

M Sakai et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2003)

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