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D_Cell and Tissue Biology
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Publications
Peering into the Bacterial Cell: From Transcription to Functional Genomics.
Journal of molecular biology
Correction of a widespread bias in pooled chemical genomics screens improves their interpretability.
Molecular systems biology
Comprehensive double-mutant analysis of the Bacillus subtilis envelope using double-CRISPRi.
bioRxiv : the preprint server for biology
Three bacterial DedA subfamilies with distinct functions and phylogenetic distribution.
bioRxiv : the preprint server for biology
The context of the ribosome binding site in mRNAs defines specificity of action of kasugamycin, an inhibitor of translation initiation.
Proceedings of the National Academy of Sciences of the United States of America
Cold Shock Response in Bacteria.
Annual review of genetics
Chemical-genetic interrogation of RNA polymerase mutants reveals structure-function relationships and physiological tradeoffs.
Molecular cell
Expansion and re-classification of the extracytoplasmic function (ECF) σ factor family.
Nucleic acids research
Rewiring the specificity of extracytoplasmic function sigma factors.
Proceedings of the National Academy of Sciences of the United States of America
Genetic interaction mapping informs integrative structure determination of protein complexes.
Science (New York, N.Y.)
Bacterial CRISPR screens for gene function.
Current opinion in microbiology
Resistance to serine in Bacillus subtilis: identification of the serine transporter YbeC and of a metabolic network that links serine and threonine metabolism.
Environmental microbiology
Titrating gene expression using libraries of systematically attenuated CRISPR guide RNAs.
Nature biotechnology
Discovery of the extracytoplasmic function σ factors.
Molecular microbiology
Topoisomerase IV can functionally replace all type 1A topoisomerases in Bacillus subtilis.
Nucleic acids research
Modeling of Protein Complex Architectures using Combinatorial Genetic Perturbations.
Biophysical journal
Enabling genetic analysis of diverse bacteria with Mobile-CRISPRi.
Nature microbiology
Structure and Function of the Transmembrane Domain of NsaS, an Antibiotic Sensing Histidine Kinase in Staphylococcus aureus.
Journal of the American Chemical Society
A Stress Response that Monitors and Regulates mRNA Structure Is Central to Cold Shock Adaptation.
Molecular cell
Marine Mammal Microbiota Yields Novel Antibiotic with Potent Activity Against Clostridium difficile.
ACS infectious diseases
Ribosomal Architecture: Constraints Imposed by the Need for Self-Production.
Current biology : CB
Global analysis of translation termination in E. coli.
PLoS genetics
Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis.
Cell systems
Identification of Two Phosphate Starvation-induced Wall Teichoic Acid Hydrolases Provides First Insights into the Degradative Pathway of a Key Bacterial Cell Wall Component.
The Journal of biological chemistry
Depletion of Undecaprenyl Pyrophosphate Phosphatases Disrupts Cell Envelope Biogenesis in Bacillus subtilis.
Journal of bacteriology
A Chemical-Genomic Screen of Neglected Antibiotics Reveals Illicit Transport of Kasugamycin and Blasticidin S.
PLoS genetics
Phenomics in Bacteria.
Phenomics
DksA regulates RNA polymerase in Escherichia coli through a network of interactions in the secondary channel that includes Sequence Insertion 1.
Proceedings of the National Academy of Sciences of the United States of America
Bacterial CRISPR: accomplishments and prospects.
Current opinion in microbiology
High-throughput bacterial functional genomics in the sequencing era.
Current opinion in microbiology
MurJ and a novel lipid II flippase are required for cell wall biogenesis in Bacillus subtilis.
Proceedings of the National Academy of Sciences of the United States of America
Editorial overview: Cell regulation: when you think you know it all, there is another layer to be discovered.
Current opinion in microbiology
MicL, a new σE-dependent sRNA, combats envelope stress by repressing synthesis of Lpp, the major outer membrane lipoprotein.
Genes & development
Bacterial sigma factors: a historical, structural, and genomic perspective.
Annual review of microbiology
Stress-induced remodeling of the bacterial proteome.
Current biology : CB
A pause sequence enriched at translation start sites drives transcription dynamics in vivo.
Science (New York, N.Y.)
Promoter melting by an alternative σ, one base at a time.
Nature structural & molecular biology
Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters.
Molecular systems biology
Dual molecular signals mediate the bacterial response to outer-membrane stress.
Science (New York, N.Y.)
Covalent intermediate in the catalytic mechanism of the radical S-adenosyl-L-methionine methyl synthase RlmN trapped by mutagenesis.
Journal of the American Chemical Society
The crystal structure of the periplasmic domain of Vibrio parahaemolyticus CpxA.
Protein science : a publication of the Protein Society
From the regulation of peptidoglycan synthesis to bacterial growth and morphology.
Nature reviews. Microbiology
Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo.
Cell
Predicting the strength of UP-elements and full-length E. coli σE promoters.
Nucleic acids research
Unexpected stress-reducing effect of PhaP, a poly(3-hydroxybutyrate) granule-associated protein, in Escherichia coli.
Applied and environmental microbiology
Small RNAs endow a transcriptional activator with essential repressor functions for single-tier control of a global stress regulon.
Proceedings of the National Academy of Sciences of the United States of America
Signal integration by DegS and RseB governs the σ E-mediated envelope stress response in Escherichia coli.
Proceedings of the National Academy of Sciences of the United States of America
Using DNA microarrays to assay part function.
Methods in enzymology
The crystal structure Escherichia coli Spy.
Protein science : a publication of the Protein Society
Reduced capacity of alternative sigmas to melt promoters ensures stringent promoter recognition.
Genes & development
Promoter strength properties of the complete sigma E regulon of Escherichia coli and Salmonella enterica.
Journal of bacteriology
Dissection of recognition determinants of Escherichia coli sigma32 suggests a composite -10 region with an 'extended -10' motif and a core -10 element.
Molecular microbiology
Mutational analysis of Escherichia coli sigma28 and its target promoters reveals recognition of a composite -10 region, comprised of an 'extended -10' motif and a core -10 element.
Molecular microbiology
Analyzing the interaction of RseA and RseB, the two negative regulators of the sigmaE envelope stress response, using a combined bioinformatic and experimental strategy.
The Journal of biological chemistry
Convergence of molecular, modeling, and systems approaches for an understanding of the Escherichia coli heat shock response.
Microbiology and molecular biology reviews : MMBR
An extra-cytoplasmic function sigma factor and anti-sigma factor control carotenoid biosynthesis in Azospirillum brasilense.
Microbiology (Reading, England)
Analysis of sigma32 mutants defective in chaperone-mediated feedback control reveals unexpected complexity of the heat shock response.
Proceedings of the National Academy of Sciences of the United States of America
Design principles of the proteolytic cascade governing the sigmaE-mediated envelope stress response in Escherichia coli: keys to graded, buffered, and rapid signal transduction.
Genes & development
Hfq modulates the sigmaE-mediated envelope stress response and the sigma32-mediated cytoplasmic stress response in Escherichia coli.
Journal of bacteriology
Regulon and promoter analysis of the E. coli heat-shock factor, sigma32, reveals a multifaceted cellular response to heat stress.
Genes & development
Module-based analysis of robustness tradeoffs in the heat shock response system.
PLoS computational biology
Insights into transcriptional regulation and sigma competition from an equilibrium model of RNA polymerase binding to DNA.
Proceedings of the National Academy of Sciences of the United States of America
Characterization of six lipoproteins in the sigmaE regulon.
Journal of bacteriology
An open letter to Elias Zerhouni.
Science (New York, N.Y.)
Surviving heat shock: control strategies for robustness and performance.
Proceedings of the National Academy of Sciences of the United States of America
Altering the interaction between sigma70 and RNA polymerase generates complexes with distinct transcription-elongation properties.
Proceedings of the National Academy of Sciences of the United States of America
Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System.
PLoS computational biology
A chaperone network controls the heat shock response in E. coli.
Genes & development
A hydrophobic patch on the flap-tip helix of E.coli RNA polymerase mediates sigma(70) region 4 function.
Journal of molecular biology
Regulation of the Escherichia coli sigma-dependent envelope stress response.
Molecular microbiology
Minimal machinery of RNA polymerase holoenzyme sufficient for promoter melting.
Science (New York, N.Y.)
Cell regulation.
Current opinion in microbiology
Crystal structure of Escherichia coli sigmaE with the cytoplasmic domain of its anti-sigma RseA.
Molecular cell
Regulation of the alternative sigma factor sigma(E) during initiation, adaptation, and shutoff of the extracytoplasmic heat shock response in Escherichia coli.
Journal of bacteriology
Lack of a robust unfoldase activity confers a unique level of substrate specificity to the universal AAA protease FtsH.
Molecular cell
Assay of Escherichia coli RNA polymerase: sigma-core interactions.
Methods in enzymology
Multiple sigma subunits and the partitioning of bacterial transcription space.
Annual review of microbiology
DegS and YaeL participate sequentially in the cleavage of RseA to activate the sigma(E)-dependent extracytoplasmic stress response.
Genes & development
Identification of the binding sites of regulatory proteins in bacterial genomes.
Proceedings of the National Academy of Sciences of the United States of America
Impact of genomic technologies on studies of bacterial gene expression.
Annual review of microbiology
The anti-initial transcribed sequence, a portable sequence that impedes promoter escape, requires sigma70 for function.
The Journal of biological chemistry
Binding of the initiation factor sigma(70) to core RNA polymerase is a multistep process.
Molecular cell
degS (hhoB) is an essential Escherichia coli gene whose indispensable function is to provide sigma (E) activity.
Molecular microbiology
Substitutions in bacteriophage T4 AsiA and Escherichia coli sigma(70) that suppress T4 motA activation mutations.
Journal of bacteriology
The SurA periplasmic PPIase lacking its parvulin domains functions in vivo and has chaperone activity.
The EMBO journal
The interface of sigma with core RNA polymerase is extensive, conserved, and functionally specialized.
Genes & development
Structural features required for the interaction of the Hsp70 molecular chaperone DnaK with its cochaperone DnaJ.
The Journal of biological chemistry
The Escherichia coli sigma(E)-dependent extracytoplasmic stress response is controlled by the regulated proteolysis of an anti-sigma factor.
Genes & development
Interaction of the Hsp70 molecular chaperone, DnaK, with its cochaperone DnaJ.
Proceedings of the National Academy of Sciences of the United States of America
The functional and regulatory roles of sigma factors in transcription.
Cold Spring Harbor symposia on quantitative biology
SigmaE is an essential sigma factor in Escherichia coli.
Journal of bacteriology
The response to extracytoplasmic stress in Escherichia coli is controlled by partially overlapping pathways.
Genes & development
The sigmaE-mediated response to extracytoplasmic stress in Escherichia coli is transduced by RseA and RseB, two negative regulators of sigmaE.
Molecular microbiology
SurA, a periplasmic protein with peptidyl-prolyl isomerase activity, participates in the assembly of outer membrane porins.
Genes & development
Sigma domain structure: one down, one to go.
Structure (London, England : 1993)
Isolation, purification, and in vitro characterization of recessive-lethal-mutant RNA polymerases from Escherichia coli.
Journal of bacteriology
The sigma subunit of Escherichia coli RNA polymerase senses promoter spacing.
Proceedings of the National Academy of Sciences of the United States of America
Amino acid substitutions in the two largest subunits of Escherichia coli RNA polymerase that suppress a defective Rho termination factor affect different parts of the transcription complex.
The Journal of biological chemistry
Involvement of the DnaK-DnaJ-GrpE chaperone team in protein secretion in Escherichia coli.
Journal of bacteriology
Identifying interacting regions in the beta subunit of Escherichia coli RNA polymerase.
Journal of molecular biology
A structure/function analysis of Escherichia coli RNA polymerase.
Philosophical transactions of the Royal Society of London. Series B, Biological sciences
Analysis of three DnaK mutant proteins suggests that progression through the ATPase cycle requires conformational changes.
The Journal of biological chemistry
rpoE, the gene encoding the second heat-shock sigma factor, sigma E, in Escherichia coli.
The EMBO journal
Identification and characterization of an outer membrane protein, OmpX, in Escherichia coli that is homologous to a family of outer membrane proteins including Ail of Yersinia enterocolitica.
Journal of bacteriology
Four contiguous amino acids define the target for streptolydigin resistance in the beta subunit of Escherichia coli RNA polymerase.
The Journal of biological chemistry
Amino-terminal amino acids modulate sigma-factor DNA-binding activity.
Genes & development
The activity of sigma E, an Escherichia coli heat-inducible sigma-factor, is modulated by expression of outer membrane proteins.
Genes & development
Accumulation of secretory protein precursors in Escherichia coli induces the heat shock response.
Journal of bacteriology
The role of the sigma subunit in promoter recognition by RNA polymerase.
Cellular & molecular biology research
How a mutation in the gene encoding sigma 70 suppresses the defective heat shock response caused by a mutation in the gene encoding sigma 32.
Journal of bacteriology
DnaK, DnaJ, and GrpE are required for flagellum synthesis in Escherichia coli.
Journal of bacteriology
A mutant sigma 32 with a small deletion in conserved region 3 of sigma has reduced affinity for core RNA polymerase.
Journal of bacteriology
Partial loss of function mutations in DnaK, the Escherichia coli homologue of the 70-kDa heat shock proteins, affect highly conserved amino acids implicated in ATP binding and hydrolysis.
Proceedings of the National Academy of Sciences of the United States of America
DnaK and DnaJ heat shock proteins participate in protein export in Escherichia coli.
Genes & development
The sigma 70 family: sequence conservation and evolutionary relationships.
Journal of bacteriology
Physiological effects of the fructose-1,6-diphosphate aldolase ts8 mutation on stable RNA synthesis in Escherichia coli.
Journal of bacteriology
Development of RNA polymerase-promoter contacts during open complex formation.
Journal of molecular biology
RpoB8, a rifampicin-resistant termination-proficient RNA polymerase, has an increased Km for purine nucleotides during transcription elongation.
The Journal of biological chemistry
Translational regulation of sigma 32 synthesis: requirement for an internal control element.
Journal of bacteriology
DnaK, DnaJ, and GrpE heat shock proteins negatively regulate heat shock gene expression by controlling the synthesis and stability of sigma 32.
Genes & development
Interaction of Escherichia coli RNA polymerase holoenzyme containing sigma 32 with heat shock promoters. DNase I footprinting and methylation protection.
Journal of molecular biology
Intermediates in the formation of the open complex by RNA polymerase holoenzyme containing the sigma factor sigma 32 at the groE promoter.
Journal of molecular biology
The activity of sigma 32 is reduced under conditions of excess heat shock protein production in Escherichia coli.
Genes & development
Identification of the sigma E subunit of Escherichia coli RNA polymerase: a second alternate sigma factor involved in high-temperature gene expression.
Genes & development
Altered promoter recognition by mutant forms of the sigma 70 subunit of Escherichia coli RNA polymerase.
Journal of molecular biology
A collection of strains containing genetically linked alternating antibiotic resistance elements for genetic mapping of Escherichia coli.
Microbiological reviews
A collection of strains containing genetically linked alternating antibiotic resistance elements for genetic mapping of Escherichia coli.
Microbiology and Molecular Biology Reviews
Escherichia coli heat shock gene mutants are defective in proteolysis.
Genes & development
Mutations in rpoD that increase expression of genes in the mal regulon of Escherichia coli K-12.
Journal of molecular biology
Mutations in rpoD, the gene encoding the sigma 70 subunit of Escherichia coli RNA polymerase, that increase expression of the lac operon in the absence of CAP-cAMP.
Journal of molecular biology
Isolation and characterization of Escherichia coli mutants that lack the heat shock sigma factor sigma 32.
Journal of bacteriology
Regulation of the promoters and transcripts of rpoH, the Escherichia coli heat shock regulatory gene.
Genes & development
Sigma 32 synthesis can regulate the synthesis of heat shock proteins in Escherichia coli.
Genes & development
Regulation of the Heat-Shock Response in Escherichia coli.
New Frontiers in the Study of Gene Functions
Stringent response in Escherichia coli induces expression of heat shock proteins.
Journal of molecular biology
Consensus sequence for Escherichia coli heat shock gene promoters.
Proceedings of the National Academy of Sciences of the United States of America
Mutations in the sigma subunit of E. coli RNA polymerase which affect positive control of transcription.
Molecular & general genetics : MGG
The regulation of transcription initiation in bacteria.
Annual review of genetics
A gene regulating the heat shock response in Escherichia coli also affects proteolysis.
Proceedings of the National Academy of Sciences of the United States of America
Regulation of cyclic AMP synthesis in Escherichia coli K-12: effects of the rpoD800 sigma mutation, glucose, and chloramphenicol.
Journal of bacteriology
Effects of the mutant sigma allele rpoD800 on the synthesis of specific macromolecular components of the Escherichia coli K12 cell.
Journal of molecular biology
Mu dX, a derivative of Mu d1 (lac Apr) which makes stable lacZ fusions at high temperature.
Journal of bacteriology
Marker rescue with plasmids bearing deletions in rpoD identifies a dispensable part of E. coli sigma factor.
Molecular & general genetics : MGG
The nucleotide sequence of the cloned rpoD gene for the RNA polymerase sigma subunit from E coli K12.
Nucleic acids research
Isolation and characterization of transducing phage coding for sigma subunit of Escherichia coli RNA polymerase.
Proceedings of the National Academy of Sciences of the United States of America
Altered chemical properties in three mutants of E. coli RNA polymerase sigma subunit.
Molecular & general genetics : MGG
Measurement of binding constants for protein-DNA interactions by DNA-cellulose chromatography.
Biochemistry
Quantitation of RNA polymerase subunits in Escherichia coli during exponential growth and after bacteriophage T4 infection.
Molecular Genetics and Genomics
Non-specific DNA binding of genome regulating proteins as a biological control mechanism: I. The lac operon: equilibrium aspects.
Proceedings of the National Academy of Sciences of the United States of America