Whole-genome sequencing, genome mining, metabolic reconstruction and evolution of pentachlorophenol and other xenobiotic degradation pathways in Bacillus tropicus strain AOA-CPS1

Pentachlorophenol degradation by activated sludge with phenol and glucose as growth substrates

(2023) Magdalena Niesler et al.   Archives of Environmental Protection

Lateral transfers of large DNA fragments spread functional genes among grasses

(2019) Luke T. Dunning et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Helicase Mechanisms During Homologous Recombination in Saccharomyces cerevisiae

(2019) J. Brooks Crickard et al.   Annual Review of Biophysics

Structure of full-length human phenylalanine hydroxylase in complex with tetrahydrobiopterin

(2019) Marte Innselset Flydal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pentachlorophenol alters the acetate-assimilating microbial community and redox cycling in anoxic soils

(2019) Yan Xu et al.   SOIL BIOLOGY & BIOCHEMISTRY

On the evolutionary significance of horizontal gene transfers in plants

(2019) David A. Wickell et al.   NEW PHYTOLOGIST

The EMBL-EBI search and sequence analysis tools APIs in 2019

(2019) Fábio Madeira et al.   NUCLEIC ACIDS RESEARCH

Phenylalanine 4-monooxygenase: the “sulfoxidation polymorphism”

(2019) Stephen C. Mitchell et al.   XENOBIOTICA

The genomes of polyextremophilic cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions

(2019) Alessandro W Rossoni et al.   eLife

Phenol hydroxylase from Pseudomonas sp. KZNSA: Purification, characterization and prediction of three-dimensional structure

(2019) Boitumelo Setlhare et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Microbial Metabolic Capacity for Intestinal Folate Production and Modulation of Host Folate Receptors

(2019) Melinda A. Engevik et al.   Frontiers in Microbiology

Pentachlorophenol, polychlorinated dibenzo-p-dioxins and polychlorinated dibenzo furans in surface soil surrounding pentachlorophenol-treated utility poles on the Kenai National Wildlife Refuge, Alaska USA

(2018) Lori A. Verbrugge et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Bacterial-mediated biodegradation of pentachlorophenol via electron shuttling

(2018) Heba A. El-Bialy et al.   ENVIRONMENTAL TECHNOLOGY

Chloroacetaldehyde dehydrogenase from Ancylobacter aquaticus UV5: Cloning, expression, characterization and molecular modeling

(2018) Ajit Kumar et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI

(2018) Stacy Ciufo et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Unrivalled diversity: the many roles and reactions of bacterial cytochromes P450 in secondary metabolism

(2018) Anja Greule et al.   NATURAL PRODUCT REPORTS

Bacterial folate biosynthesis and colorectal cancer risk: more than just a gut feeling

(2018) Dieuwertje E. Kok et al.   CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION

The Many Nuanced Evolutionary Consequences of Duplicated Genes

(2018) Ashley I Teufel et al.   MOLECULAR BIOLOGY AND EVOLUTION

PubChem 2019 update: improved access to chemical data

(2018) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

RefSeq: an update on prokaryotic genome annotation and curation

(2017) Daniel H Haft et al.   NUCLEIC ACIDS RESEARCH

Pentachlorophenol degradation by Pseudomonas fluorescens

(2017) Rim Werheni Ammeri et al.   WATER QUALITY RESEARCH JOURNAL OF CANADA

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

NCBI prokaryotic genome annotation pipeline

(2016) Tatiana Tatusova et al.   NUCLEIC ACIDS RESEARCH

Meeting report: GenBank microbial genomic taxonomy workshop (12–13 May, 2015)

(2016) Scott Federhen et al.   Standards in Genomic Sciences

Bacterial Biotransformation of Pentachlorophenol and Micropollutants Formed during Its Production Process

(2016) Eglantina Lopez-Echartea et al.   International Journal of Environmental Research and Public Health

Multi-substrate biodegradation of chlorophenols by defined microbial consortium

(2016) Bhishma P. Patel et al.   3 Biotech

Multi-substrate biodegradation of chlorophenols by defined microbial consortium

(2016) Bhishma P. Patel et al.   3 Biotech

Optimization study for maximizing 2,4-dichlorophenol degradation byKocuria rhizophilastrain using response surface methodology and kinetic study

(2015) Bhishma P. Patel et al.   Desalination and Water Treatment

From the affinity constant to the half-saturation index: Understanding conventional modeling concepts in novel wastewater treatment processes

(2015) Marina Arnaldos et al.   WATER RESEARCH

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

(2015) Thomas Brettin et al.   Scientific Reports

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Interactions with the Bifunctional Interface of the Transcriptional Coactivator DCoH1 Are Kinetically Regulated

(2014) Dongli Wang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Enhanced selection of micro-aerobic pentachlorophenol degrading granular sludge

(2014) Yuancai Lv et al.   JOURNAL OF HAZARDOUS MATERIALS

Pentachlorophenol Degradation byJanibactersp., a New Actinobacterium Isolated from Saline Sediment of Arid Land

(2014) Amel Khessairi et al.   Biomed Research International

Role of the Phenylalanine-Hydroxylating System in Aromatic Substance Degradation and Lipid Metabolism in the Oleaginous Fungus Mortierella alpina

(2013) Hongchao Wang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial Persistence and the Road to Drug Resistance

(2013) Nadia R. Cohen et al.   Cell Host & Microbe

Phenylalanine hydroxylase: Function, structure, and regulation

(2013) Marte I. Flydal et al.   IUBMB LIFE

Structural characterization of 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA) fromSphingobium chlorophenolicum, a new type of aromatic ring-cleavage enzyme

(2013) Robert P. Hayes et al.   MOLECULAR MICROBIOLOGY

The pentachlorophenol-dehalogenating Desulfitobacterium hafniense strain PCP-1

(2013) R. Villemur   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Sequestration of a highly reactive intermediate in an evolving pathway for degradation of pentachlorophenol

(2013) I. Yadid et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Toxicological Profile of Chlorophenols and Their Derivatives in the Environment: The Public Health Perspective

(2013) Etinosa O. Igbinosa et al.   TheScientificWorldJOURNAL

Pentachlorophenol Hydroxylase, a Poorly Functioning Enzyme Required for Degradation of Pentachlorophenol by Sphingobium chlorophenolicum

(2012) Klara Hlouchova et al.   BIOCHEMISTRY

The automatic annotation of bacterial genomes

(2012) E. J. Richardson et al.   BRIEFINGS IN BIOINFORMATICS

Changing the Regioselectivity of a P450 from C15 to C11 Hydroxylation of Progesterone

(2012) Kim Thoa Nguyen et al.   CHEMBIOCHEM

Linear Chromosome-generating System ofAgrobacterium tumefaciensC58

(2012) Wai Mun Huang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Phenylalanine Hydroxylase from Legionella pneumophila Is a Thermostable Enzyme with a Major Functional Role in Pyomelanin Synthesis

(2012) Marte I. Flydal et al.   PLoS One

Identification of Phenylalanine 3-Hydroxylase formeta-Tyrosine Biosynthesis

(2011) Wenjun Zhang et al.   BIOCHEMISTRY

S-glutathionyl-(chloro)hydroquinone reductases: a new class of glutathione transferases functioning as oxidoreductases

(2011) Sara M. Belchik et al.   DRUG METABOLISM REVIEWS

The Whole Genome Sequence of Sphingobium chlorophenolicum L-1: Insights into the Evolution of the Pentachlorophenol Degradation Pathway

(2011) Shelley D. Copley et al.   Genome Biology and Evolution

Microbial degradation of aromatic compounds — from one strategy to four

(2011) Georg Fuchs et al.   NATURE REVIEWS MICROBIOLOGY

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Bacterial phenylalanine and phenylacetate catabolic pathway revealed

(2010) R. Teufel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enrichment, isolation and characterization of pentachlorophenol degrading bacterium Acinetobacter sp. ISTPCP-3 from effluent discharge site

(2009) Ashwani Sharma et al.   BIODEGRADATION

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Phenylalanine 4-monooxygenase and the role of endobiotic metabolism enzymes in xenobiotic biotransformation

(2009) Glyn B Steventon et al.   Expert Opinion on Drug Metabolism & Toxicology

Redundancy of Enzymes for Formaldehyde Detoxification in Pseudomonas putida

(2009) A. Roca et al.   JOURNAL OF BACTERIOLOGY

Genome Sequences of Three Agrobacterium Biovars Help Elucidate the Evolution of Multichromosome Genomes in Bacteria

(2009) S. C. Slater et al.   JOURNAL OF BACTERIOLOGY

Evolution of efficient pathways for degradation of anthropogenic chemicals

(2009) Shelley D Copley   Nature Chemical Biology

Type II Hydride Transferases from Different Microorganisms Yield Nitrite and Diarylamines from Polynitroaromatic Compounds

(2008) P. van Dillewijn et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Random local neighbor joining: A new method for reconstructing phylogenetic trees

(2008) Wei Zhang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The CGView Server: a comparative genomics tool for circular genomes

(2008) J. R. Grant et al.   NUCLEIC ACIDS RESEARCH

Phylogenomic and Functional Analysis of Pterin-4a-Carbinolamine Dehydratase Family (COG2154) Proteins in Plants and Microorganisms

(2008) V. Naponelli et al.   PLANT PHYSIOLOGY