A5057105462- Bacterial Genetics and Biotechnology
- RNA and protein synthesis mechanisms
- CRISPR and Genetic Engineering
- Bacteriophages and microbial interactions
- Escherichia coli research studies
- Genomics and Phylogenetic Studies
- Antibiotic Resistance in Bacteria
- Bacterial biofilms and quorum sensing
- Vibrio bacteria research studies
- RNA modifications and cancer
- Evolution and Genetic Dynamics
- Salmonella and Campylobacter epidemiology
- DNA Repair Mechanisms
- Microbial Metabolic Engineering and Bioproduction
- Probiotics and Fermented Foods
- Enzyme Structure and Function
- Clostridium difficile and Clostridium perfringens research
- DNA and Nucleic Acid Chemistry
- Urinary Tract Infections Management
- Enterobacteriaceae and Cronobacter Research
- Innovation and Socioeconomic Development
- Gut microbiota and health
New York State Department of Health
2012-2024
Wadsworth Center
2013-2024
Enteric Escherichia coli survives the highly acidic environment of stomach through multiple acid resistance (AR) mechanisms. The most effective system, AR2, decarboxylates externally-derived glutamate to remove cytoplasmic protons and excrete GABA. first described AR1, does not require an external amino acid. Its mechanism has been determined. regulation AR systems their coordination with broader cellular metabolism fully explored.We utilized a combination ChIP-Seq gene expression analysis...
Recombineering is a widely-used approach to delete genes, introduce insertions and point mutations, epitope tags into bacterial chromosomes. Many recombineering methods have been described, for wide range of species. These are often limited by (i) low efficiency, and/or (ii) introduction "scar" DNA the chromosome. Here, we describe rapid, efficient, PCR-based method, FRUIT, that can be used scar-free deletions, tags, promoters genomes enteric bacteria. The efficiency FRUIT far higher than...
ABSTRACT Escherichia coli AraC is a well-described transcription activator of genes involved in arabinose metabolism. Using complementary genomic approaches, chromatin immunoprecipitation (ChIP)-chip, and profiling, we identify direct regulatory targets AraC, including five novel target genes: ytfQ , ydeN ydeM ygeA polB . Strikingly, only has an established connection to metabolism, suggesting that broader function than previously described. We demonstrate arabinose-dependent repression...
ABSTRACT Salmonella enterica pathogenicity island 1 (SPI-1) encodes proteins required for invasion of gut epithelial cells. The timing is tightly controlled by a complex regulatory network. transcription factor (TF) HilD the master regulator this process and senses environmental signals associated with invasion. activates genes within outside SPI-1, including six other TFs. Thus, transcriptional program host cell at least 7 However, very few targets are known these TFs, extent network...
Enterotoxigenic Escherichia coli (ETEC) cause severe diarrhoea in humans and neonatal farm animals. Annually, 380,000 human deaths, multi-million dollar losses the farming industry, can be attributed to ETEC infections. Illness results from action of enterotoxins, which disrupt signalling pathways that manage water electrolyte homeostasis mammalian gut. The resulting fluid loss is treated by oral rehydration. Hence, aqueous solutions glucose salt are ingested patient. Given central role...
ABSTRACT A complex of highly conserved proteins consisting NusB, NusE, NusA, and NusG is required for robust expression rRNA in Escherichia coli . This proposed to prevent Rho-dependent transcription termination by a process known as “antitermination.” The mechanism this antitermination poorly understood but requires association NusB NusE with specific RNA sequence BoxA. Here, we identify novel member the machinery: inositol monophosphatase SuhB. We show that SuhB associates elongating...
Recent studies have revealed large numbers of transcription factor binding sites within the genes bacteria. The function, if any, vast majority these has not been investigated.
Salmonella enterica serovar Typhimurium (S. Typhimurium) pathogenicity island 1 (SPI-1) encodes a type III secretion system required for invasion of host gut epithelial cells. Expression SPI-1 virulence genes is controlled by complex hierarchy transcription factors encoded within and outside SPI-1. The master regulator SPI-1, HilA, itself regulated three homologous factors, HilD, HilC, RtsA. HilD activates hilA other target in response to environmental conditions associated with the...
Small proteins of <51 amino acids are abundant across all domains life but often overlooked because their small size makes them difficult to predict computationally, and they refractory standard proteomic approaches. Ribosome profiling has been used infer the existence by detecting translation corresponding open reading frames (ORFs). Detection translated short ORFs ribosome can be improved treating cells with drugs that stall ribosomes at specific codons. Here, we combine analysis data for
Bacterial riboswitches are molecular structures that play a crucial role in controlling gene expression to maintain cellular balance. The Escherichia coli lysC riboswitch has been previously shown regulate through translation initiation and mRNA decay. Recent research suggests is also influenced by Rho-dependent transcription termination. Through series of silico, vitro, vivo experiments, we provide experimental evidence the directly indirectly modulates Rho Our study demonstrates...
ABSTRACT In clustered regularly interspaced short palindromic repeat (CRISPR)-Cas (CRISPR-associated) immunity systems, CRISPR RNAs (crRNAs) are bound by Cas proteins, and these complexes target invading nucleic acid molecules for degradation in a process known as interference. type I CRISPR-Cas the protein complex that binds DNA is Cascade. Association of Cascade with can also lead to acquisition new elements primed adaptation. Here, we assess specificity determinants Cascade-DNA...
Quorum sensing is a mechanism of bacterial cell-cell communication that relies on the production and detection small molecule autoinducers, which facilitate synchronous expression genes involved in group behaviors, such as virulence factor biofilm formation. The Pseudomonas aeruginosa quorum network consists multiple interconnected transcriptional regulators, with transcription factor, RhlR, acting one main drivers behaviors. RhlR LuxR-type regulates its target when bound to cognate...
Nus factors are broadly conserved across bacterial species, and often essential for viability. A complex of five (NusB, NusE, NusA, NusG SuhB) is considered to be a dedicated regulator ribosomal RNA folding, has been shown prevent Rho-dependent transcription termination. Here, we identify an additional cellular function the factor in Escherichia coli: repression factor-encoding gene, suhB. This occurs primarily by translation inhibition, followed Thus, can or promote Rho activity depending...
A hallmark of CRISPR-Cas immunity systems is the CRISPR array, a genomic locus consisting short, repeated sequences ('repeats') interspersed with variable ('spacers'). arrays are transcribed and processed into individual RNAs that each include single spacer, direct Cas proteins to complementary in invading nucleic acid. Most bacterial array transcripts unusually long for untranslated RNA, suggesting existence mechanisms prevent premature transcription termination by Rho, conserved factor...
The closely related transcription factors MarA, SoxS, Rob and RamA control overlapping stress responses in many enteric bacteria. Furthermore, constitutive expression of such regulators is linked to clinical antibiotic resistance. In this work we have mapped the binding across Salmonella Typhimurium genome. parallel, monitored changes start site use resulting from regulators. Together, these data allow direct indirect gene regulatory effects be disentangled. Promoter architecture regulon can...
The regulatory protein, GalR, is known for controlling transcription of genes related to D-galactose metabolism in Escherichia coli. Here, using a combination experimental and bioinformatic approaches, we identify novel GalR binding sites upstream several whose function not directly metabolism. Moreover, do observe regulation these by under standard growth conditions. Thus, our data indicate broader role suggest that modulated other factors. Surprisingly, detect 158 transcripts with few...
Proteus mirabilis is a leading cause of catheter-associated urinary tract infections (CAUTIs) and urolithiasis. The transcriptional regulator MrpJ inversely modulates two critical aspects P. UTI progression: fimbria-mediated attachment flagellum-mediated motility. Transcriptome data indicated network virulence-associated genes under MrpJ's control. Here, we identify the direct gene regulon its contribution to pathogenesis, discovery novel virulence targets. Chromatin immunoprecipitation...
DnaA is a widely conserved DNA-binding protein that essential for the initiation of DNA replication in many bacterial species, including
Abstract Cryptic prophages (CPs) are elements of bacterial genomes acquired from bacteriophage that infect the host cell and ultimately become stably integrated within genome. While some proteins encoded by CPs can modulate phenotypes, potential for Transcription Factors (TFs) to impact physiology regulating genes has not been thoroughly investigated. In this work, we report hundreds regulated DicC, a DNA-binding TF in Qin prophage Esherichia coli . We identified host-encoded regulatory...
ABSTRACT Quorum sensing is a mechanism of bacterial cell-cell communication that relies on the production and detection small molecule autoinducers, which facilitate synchronous expression genes involved in group behaviors, such as virulence factor biofilm formation. The Pseudomonas aeruginosa quorum network consists multiple interconnected transcriptional regulators, with transcription factor, RhlR, acting one main drivers behaviors. RhlR LuxR-type regulates its target when bound to cognate...
ABSTRACT CRISPR-Cas systems are bacterial immune that target invading nucleic acid. The hallmark of is the CRISPR array, a genetic locus includes short sequences known as “spacers”, derived from Upon exposure to an acid molecule, bacteria/archaea with functional can add new spacers their arrays in process “adaptation”. In type I systems, which represent majority found nature, adaptation occur by two mechanisms: naïve and primed. Here, we show that, for archetypal I-E system Escherichia coli...
FliA is a broadly conserved σ factor that directs transcription of genes involved in flagellar motility. We previously identified FliA-transcribed Escherichia coli and Salmonella enterica serovar Typhimurium, we showed E. transcribes many unstable, noncoding RNAs from intragenic promoters. Here, show S Typhimurium also the large numbers promoters, identify two unreported protein-coding genes. One these genes, sdiA, encodes responds to quorum-sensing signals produced by other bacteria....
ABSTRACT A hallmark of CRISPR-Cas immunity systems is the CRISPR array, a genomic locus consisting short, repeated sequences (“repeats”) interspersed with variable (“spacers”). arrays are transcribed and processed into individual RNAs (crRNAs) that each include single spacer, direct Cas proteins to complementary sequence in invading nucleic acid. Most bacterial array transcripts unusually long for untranslated RNA, suggesting existence mechanisms prevent premature transcription termination...