Proteomic Profiling, Transcription Factor Modeling, and Genomics of Evolved Tolerant Strains Elucidate Mechanisms of Vanillin Toxicity in Escherichia coli

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(2017) Takaaki Horinouchi et al.   JOURNAL OF BIOTECHNOLOGY

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(2017) Ilya Shlar et al.   Journal of Proteomics

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

2016 update of the PRIDE database and its related tools

(2016) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Metabolic engineering of E. coli top 10 for production of vanillin through FA catabolic pathway and bioprocess optimization using RSM

(2016) Debkumar Chakraborty et al.   PROTEIN EXPRESSION AND PURIFICATION

Diagnosing oxidative stress in bacteria: not as easy as you might think

(2015) James A Imlay   CURRENT OPINION IN MICROBIOLOGY

Identification of membrane proteins associated with phenylpropanoid tolerance and transport in Escherichia coli BL21

(2015) Jingwen Zhou et al.   Journal of Proteomics

Cytochromecbiogenesis inCampylobacter jejunirequires cytochromec6(CccA; Cj1153) to maintain apocytochrome cysteine thiols in a reduced state for haem attachment

(2015) Yang-Wei Liu et al.   MOLECULAR MICROBIOLOGY

High-yield production of vanillin from ferulic acid by a coenzyme-independent decarboxylase/oxygenase two-stage process

(2015) Toshiki Furuya et al.   New Biotechnology

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond

(2015) Socorro Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

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(2015) Jana Karlíčková et al.   Oxidative Medicine and Cellular Longevity

AcrB drug-binding pocket substitution confers clinically relevant resistance and altered substrate specificity

(2015) Jessica M. A. Blair et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mimicking a natural pathway for de novo biosynthesis: natural vanillin production from accessible carbon sources

(2015) Jun Ni et al.   Scientific Reports

Dynamic interplay of multidrug transporters with TolC for isoprenol tolerance in Escherichia coli

(2015) Chonglong Wang et al.   Scientific Reports

Vanillin Production from Lignin and Its Use as a Renewable Chemical

(2015) Maxence Fache et al.   ACS Sustainable Chemistry & Engineering

Fine-tuning citrate synthase flux potentiates and refines metabolic innovation in the Lenski evolution experiment

(2015) Erik M Quandt et al.   eLife

Transcriptional analysis of different stress response genes inEscherichia colistrains subjected to sodium chloride and lactic acid stress

(2014) Silvio Peng et al.   FEMS MICROBIOLOGY LETTERS

Comprehensive proteome analysis of the response of Pseudomonas putida KT2440 to the flavor compound vanillin

(2014) Oliver Simon et al.   Journal of Proteomics

Synthesis and Accumulation of Aromatic Aldehydes in an Engineered Strain of Escherichia coli

(2014) Aditya M. Kunjapur et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Toward aldehyde and alkane production by removing aldehyde reductase activity in Escherichia coli

(2014) Gabriel M. Rodriguez et al.   METABOLIC ENGINEERING

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

Copper binding in IscA inhibits iron-sulphur cluster assembly inEscherichia coli

(2014) Guoqiang Tan et al.   MOLECULAR MICROBIOLOGY

Structural Diversity in the Dandelion (Taraxacum officinale) Polyphenol Oxidase Family Results in Different Responses to Model Substrates

(2014) Mareike E. Dirks-Hofmeister et al.   PLoS One

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

Biotechnological and Molecular Approaches for Vanillin Production: a Review

(2013) Baljinder Kaur et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

Genetic engineering of Pseudomonas putida KT2440 for rapid and high-yield production of vanillin from ferulic acid

(2013) Nadja Graf et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Effect of bioconversion conditions on vanillin production by Amycolatopsis sp. ATCC 39116 through an analysis of competing by-product formation

(2013) Xiao-kui Ma et al.   BIOPROCESS AND BIOSYSTEMS ENGINEERING

Anti-Sigma Factors in E. coli: Common Regulatory Mechanisms Controlling Sigma Factors Availability

(2013) Luis Treviño-Quintanilla et al.   CURRENT GENOMICS

Regulation of acrAB expression by cellular metabolites in Escherichia coli

(2013) C. Ruiz et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Vanillin causes the activation of Yap1 and mitochondrial fragmentation in Saccharomyces cerevisiae

(2013) Trinh Thi My Nguyen et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Adaptive laboratory evolution – principles and applications for biotechnology

(2013) Martin Dragosits et al.   Microbial Cell Factories

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(2013) X. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Production of Aromatic Compounds by Metabolically Engineered Escherichia coli with an Expanded Shikimate Pathway

(2012) Daisuke Koma et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Role of the small RNA RyhB in the Fur regulon in mediating the capsular polysaccharide biosynthesis and iron acquisition systems in Klebsiella pneumoniae

(2012) Su-Hua Huang et al.   BMC MICROBIOLOGY

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Transcriptional Cross Talk within themar-sox-robRegulon in Escherichia coli Is Limited to therobandmarRABOperons

(2012) Lon M. Chubiz et al.   JOURNAL OF BACTERIOLOGY

Copper-responsive gene regulation in bacteria

(2012) C. Rademacher et al.   MICROBIOLOGY-SGM

Dalliance: interactive genome viewing on the web

(2011) T. A. Down et al.   BIOINFORMATICS

Metabolic engineering of Pseudomonas fluorescens for the production of vanillin from ferulic acid

(2011) Diana Di Gioia et al.   JOURNAL OF BIOTECHNOLOGY

Iron homeostasis and management of oxidative stress response in bacteria

(2011) Pierre Cornelis et al.   Metallomics

Evolution combined with genomic study elucidates genetic bases of isobutanol tolerance in Escherichia coli

(2011) Jeremy J Minty et al.   Microbial Cell Factories

YqhD: a broad-substrate range aldehyde reductase with various applications in production of biorenewable fuels and chemicals

(2010) Laura R. Jarboe   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Evaluation of antioxidant activity of vanillin by using multiple antioxidant assays

(2010) Akihiro Tai et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

TFInfer: a tool for probabilistic inference of transcription factor activities

(2010) H. M. S. Asif et al.   BIOINFORMATICS

Escherichia coli mar and acrAB Mutants Display No Tolerance to Simple Alcohols

(2010) Jonas Ankarloo et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Copper Stress Affects Iron Homeostasis by Destabilizing Iron-Sulfur Cluster Formation in Bacillus subtilis

(2010) S. Chillappagari et al.   JOURNAL OF BACTERIOLOGY

YqhC regulates transcription of the adjacent Escherichia coli genes yqhD and dkgA that are involved in furfural tolerance

(2010) Peter C. Turner et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Silencing of NADPH-Dependent Oxidoreductase Genes (yqhD and dkgA) in Furfural-Resistant Ethanologenic Escherichia coli

(2009) E. N. Miller et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Furfural Inhibits Growth by Limiting Sulfur Assimilation in Ethanologenic Escherichia coli Strain LY180

(2009) E. N. Miller et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Depletion of the Signal Recognition Particle Receptor Inactivates Ribosomes in Escherichia coli

(2009) J. Burk et al.   JOURNAL OF BACTERIOLOGY

The Global Consequence of Disruption of the AcrAB-TolC Efflux Pump in Salmonella enterica Includes Reduced Expression of SPI-1 and Other Attributes Required To Infect the Host

(2009) M. A. Webber et al.   JOURNAL OF BACTERIOLOGY

Oxidative Stress and Covalent Modification of Protein with Bioactive Aldehydes

(2008) Paul A. Grimsrud et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Metabolic engineering of Escherichia coli for 1-butanol and 1-propanol production via the keto-acid pathways

(2008) C.R. Shen et al.   METABOLIC ENGINEERING

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY