Promoter Architecture Differences among Alphaproteobacteria and Other Bacterial Taxa

Redundancy in aromatic O-demethylation and ring opening reactions in Novosphingobium aromaticivorans and their impact in the metabolism of plant derived phenolics

(2021) Jose M. Perez et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The conserved transcriptional regulator CdnL is required for metabolic homeostasis and morphogenesis in Caulobacter

(2020) Selamawit Abi Woldemeskel et al.   PLoS Genetics

The NtrYX Two-Component System Regulates the Bacterial Cell Envelope

(2020) Kimberly C. Lemmer et al.   mBio

Genome-Scale Transcription-Translation Mapping Reveals Features of Zymomonas mobilis Transcription Units and Promoters

(2020) Jessica M. Vera et al.   mSystems

DEG 15, an update of the Database of Essential Genes that includes built-in analysis tools

(2020) Hao Luo et al.   NUCLEIC ACIDS RESEARCH

Structural basis of ECF-σ-factor-dependent transcription initiation

(2019) Wei Lin et al.   Nature Communications

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

(2019) Fábio Madeira et al.   NUCLEIC ACIDS RESEARCH

CarD contributes to diverse gene expression outcomes throughout the genome of Mycobacterium tuberculosis

(2019) Dennis X. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Database resources of the National Center for Biotechnology Information

(2019) Eric W Sayers et al.   NUCLEIC ACIDS RESEARCH

Recent trends in metabolic engineering of microbial chemical factories

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

Novosphingobium aromaticivoransuses a Nu-class glutathioneS-transferase as a glutathione lyase in breaking the β-aryl ether bond of lignin

(2018) Wayne S. Kontur et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Rapid, parallel identification of pathways for catabolism of lignin-derived aromatic compounds in Novosphingobium aromaticivorans

(2018) Jacob H. Cecil et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A heterodimeric glutathione S-transferase that stereospecifically breaks lignin’s β(R)-aryl ether bond reveals the diversity of bacterial β-etherases

(2018) Wayne S. Kontur et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Analysis of the nucleotide content of Escherichia coli promoter sequences related to the alternative sigma factors

(2018) Gabriel Dall'Alba et al.   JOURNAL OF MOLECULAR RECOGNITION

Crystal structure ofAquifex aeolicusσNbound to promoter DNA and the structure of σN-holoenzyme

(2017) Elizabeth A. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome Landscape of Mycobacterium smegmatis

(2017) Xinfeng Li et al.   Frontiers in Microbiology

Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides

(2017) Brian T. Burger et al.   mSystems

Caulobacter crescentus CdnL is a non-essential RNA polymerase-binding protein whose depletion impairs normal growth and rRNA transcription

(2017) Aránzazu Gallego-García et al.   Scientific Reports

The dynamic transcriptional and translational landscape of the model antibiotic producer Streptomyces coelicolor A3(2)

(2016) Yujin Jeong et al.   Nature Communications

Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315

(2015) Andrea M. Sass et al.   BMC GENOMICS

Synthetic biology for microbial production of lipid-based biofuels

(2015) Leo d’Espaux et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Extra Cytoplasmic Function sigma factors, recent structural insights into promoter recognition and regulation

(2015) Sébastien Campagne et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The Global Regulatory Architecture of Transcription during the Caulobacter Cell Cycle

(2015) Bo Zhou et al.   PLoS Genetics

CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex

(2015) Brian Bae et al.   eLife

A Group of Sequence-Related Sphingomonad Enzymes Catalyzes Cleavage of β-Aryl Ether Linkages in Lignin β-Guaiacyl and β-Syringyl Ether Dimers

(2014) Daniel L. Gall et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Global Transcriptional Start Site Mapping Using Differential RNA Sequencing Reveals Novel Antisense RNAs in Escherichia coli

(2014) Maureen K. Thomason et al.   JOURNAL OF BACTERIOLOGY

Towards an Informative Mutant Phenotype for Every Bacterial Gene

(2014) A. Deutschbauer et al.   JOURNAL OF BACTERIOLOGY

The Interrelationship between Promoter Strength, Gene Expression, and Growth Rate

(2014) Matthew S. Bienick et al.   PLoS One

Alphaproteobacteria species as a source and target of lateral sequence transfers

(2014) Phuong Thi Le et al.   TRENDS IN MICROBIOLOGY

Next Generation Sequencing-Based Parallel Analysis of Melting Kinetics of 4096 Variants of a Bacterial Promoter

(2013) Ewa Heyduk et al.   BIOCHEMISTRY

Transcriptomic and phylogenetic analysis of a bacterial cell cycle reveals strong associations between gene co-expression and evolution

(2013) Gang Fang et al.   BMC GENOMICS

Global insights into energetic and metabolic networks in Rhodobacter sphaeroides

(2013) Saheed Imam et al.   BMC Systems Biology

Structure and function of CarD, an essential mycobacterial transcription factor

(2013) D. B. Srivastava et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Activating Transcription in Bacteria

(2012) David J. Lee et al.   Annual Review of Microbiology

Interaction of CarD with RNA Polymerase Mediates Mycobacterium tuberculosis Viability, Rifampin Resistance, and Pathogenesis

(2012) L. A. Weiss et al.   JOURNAL OF BACTERIOLOGY

Tuning Promoter Strength through RNA Polymerase Binding Site Design in Escherichia coli

(2012) Robert C. Brewster et al.   PLoS Computational Biology

Convergence of the Transcriptional Responses to Heat Shock and Singlet Oxygen Stresses

(2012) Yann S. Dufour et al.   PLoS Genetics

Pathways Involved in Reductant Distribution during Photobiological H2Production by Rhodobacter sphaeroides

(2011) Wayne S. Kontur et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Structural Basis for Promoter −10 Element Recognition by the Bacterial RNA Polymerase σ Subunit

(2011) Andrey Feklistov et al.   CELL

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

The essential genome of a bacterium

(2011) B. Christen et al.   Molecular Systems Biology

Electron Partitioning During Light- and Nutrient-Powered Hydrogen Production by Rhodobacter sphaeroides

(2010) Luftu Safak Yilmaz et al.   BioEnergy Research

Networks of Gene Sharing among 329 Proteobacterial Genomes Reveal Differences in Lateral Gene Transfer Frequency at Different Phylogenetic Depths

(2010) T. Kloesges et al.   MOLECULAR BIOLOGY AND EVOLUTION

CdnL, a member of the large CarD-like family of bacterial proteins, is vital for Myxococcus xanthus and differs functionally from the global transcriptional regulator CarD

(2010) Diana García-Moreno et al.   NUCLEIC ACIDS RESEARCH

EcoCyc: a comprehensive database of Escherichia coli biology

(2010) I. M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Predicting strength and function for promoters of the Escherichia coli alternative sigma factor,  E

(2010) V. A. Rhodius et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology

(2009) P. D. Karp et al.   BRIEFINGS IN BIOINFORMATICS

CarD Is an Essential Regulator of rRNA Transcription Required for Mycobacterium tuberculosis Persistence

(2009) Christina L. Stallings et al.   CELL

Direct photosynthetic recycling of carbon dioxide to isobutyraldehyde

(2009) Shota Atsumi et al.   NATURE BIOTECHNOLOGY

Promoter and regulon analysis of nitrogen assimilation factor, σ54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis

(2009) Kai Zhao et al.   NUCLEIC ACIDS RESEARCH

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Bacterial Degradation of Aromatic Compounds

(2009) Jong-Su Seo et al.   International Journal of Environmental Research and Public Health

RpoHII Activates Oxidative-Stress Defense Systems and Is Controlled by RpoE in the Singlet Oxygen-Dependent Response in Rhodobacter sphaeroides

(2008) A. M. Nuss et al.   JOURNAL OF BACTERIOLOGY

Analysis of mechanisms of activation and repression at bacterial promoters

(2008) Stephen D. Minchin et al.   METHODS

Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution

(2008) T. Dagan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA