A5007700514- RNA and protein synthesis mechanisms
- Bacterial Genetics and Biotechnology
- Bacteriophages and microbial interactions
- CRISPR and Genetic Engineering
- Protein Structure and Dynamics
- Vibrio bacteria research studies
- Genomics and Phylogenetic Studies
- Antibiotic Resistance in Bacteria
- SARS-CoV-2 and COVID-19 Research
- Microbial Metabolic Engineering and Bioproduction
- vaccines and immunoinformatics approaches
- Toxin Mechanisms and Immunotoxins
- Advanced Chemical Sensor Technologies
- Enzyme Structure and Function
- Heat shock proteins research
- Plant-Microbe Interactions and Immunity
- Metal Extraction and Bioleaching
- Sustainability and Ecological Systems Analysis
- Radioactive element chemistry and processing
- Sirtuins and Resveratrol in Medicine
- Escherichia coli research studies
- Evolution and Genetic Dynamics
- CAR-T cell therapy research
- Glycosylation and Glycoproteins Research
- Protist diversity and phylogeny
Lawrence Livermore National Laboratory
2022-2024
Princeton University
2011-2018
Kaiser Permanente South San Francisco Medical Center
2018
Stanford University
2015-2016
National Institutes of Health
2005
National Institute on Deafness and Other Communication Disorders
2005
Bitter taste perception in humans is mediated by receptors encoded 25 genes that together comprise the TAS2R (or T2R) gene family. The ability to identify ligand(s) for each of these dependent on understanding allelic variation genes, which may have a significant effect ligand recognition. To investigate extent coding among alleles, we performed comprehensive evaluation sequence and haplotype human bitter receptor repertoire. We found exhibit substantial diversity. In worldwide population...
The seven human sirtuins are a family of ubiquitously expressed and evolutionarily conserved NAD(+)-dependent deacylases/mono-ADP ribosyltransferases that regulate numerous cellular organismal functions, including metabolism, cell cycle, longevity. Here, we report the discovery all have broad-range antiviral properties. We demonstrate small interfering RNA (siRNA)-mediated knockdown individual drug-mediated inhibition sirtuin enzymatic activity increase production virus progeny in infected...
In Gram-negative bacteria, integral outer membrane β-barrel proteins (OMPs) are assembled by the beta-barrel assembly machine (Bam) complex. The essential components of this complex OMP BamA [which contains a carboxyl-terminal and an amino-terminal periplasmic module composed five polypeptide transport associated (POTRA) domains] lipoprotein BamD. Escherichia coli , Bam also three nonessential lipoproteins (BamBCE), all which require barrel-proximal POTRA domain (P5) for stable interactions...
The outer membrane (OM) of Gram-negative bacteria such as Escherichia coli contains lipoproteins and integral β-barrel proteins (outer-membrane proteins, OMPs) assembled into an asymmetrical lipid bilayer. Insertion the OM is mediated by a protein complex that OMP BamA four associated (BamBCDE). mechanism which Bam catalyzes assembly OMPs not known. We report here isolation characterization temperature-sensitive lethal mutation, bamAE373K , alters fifth polypeptide transport-associated...
Biogenesis of the outer membrane (OM) is an essential process in Gram-negative bacteria. One key steps OM biogenesis assembly integral beta-barrel proteins (OMPs) by a protein machine called Bam complex. In Escherichia coli, complex composed BamA and BamD three nonessential lipoproteins, BamB, BamC, BamE. Both BamC BamE are important for stabilizing interaction between BamD. We used comprehensive genetic analysis to clarify interplay BamCDE subcomplex. Combining ΔbamE allele with mutations...
The outer membrane (OM) of Gram-negative bacteria forms a robust permeability barrier that blocks entry toxins and antibiotics. Most OM proteins (OMPs) assume β-barrel fold, some form aqueous channels for nutrient uptake efflux intracellular toxins. Bam machine catalyzes rapid folding assembly OMPs. Fidelity OMP biogenesis is monitored by the σE stress response. When defects arise, proteases DegS RseP act sequentially to liberate into cytosol, enabling it activate transcription regulon....
The COVID-19 pandemic underscored the promise of monoclonal antibody-based prophylactic and therapeutic drugs
The development of synthetic biological circuits that maintain functionality over application-relevant time scales remains a significant challenge. Here, we employed overlapping sequences in which one gene is encoded or 'entangled' entirely within an alternative reading frame another gene. In this design, the toxin-encoding relE was entangled ilvA, encodes threonine deaminase, enzyme essential for isoleucine biosynthesis. A functional entanglement construct obtained upon modification...
The biogenesis of the outer membrane (OM) Escherichia coli is a conserved and vital process. assembly integral β-barrel proteins (OMPs), which represent major component OM, depends on periplasmic chaperones heteropentameric machine (Bam complex) in OM. However, not all OMPs are affected by null mutations same or nonessential Bam complex members, suggesting there categories substrates with divergent requirements for efficient assembly. We have previously demonstrated two classes substrates,...
Biofertilizers are critical for sustainable agriculture since they can replace ecologically disruptive chemical fertilizers while improving the trajectory of soil and plant health. Yet, to continue deployment, persistence designer biofertilizers within native consortia must be elucidated enhanced. Here, we describe a high-throughput, modular, automation-friendly in vitro approach screen biofertilizer organism soil-derived after co-cultivation with stable synthetic microbial communities...
Abstract The essential outer membrane β-barrel protein BamA forms a complex with four lipoprotein partners BamBCDE that assembles proteins into the of Escherichia coli. Detailed genetic studies have shown cycles through multiple conformations during substrate assembly, suggesting network residues may be involved in coordinating conformational changes and partner function. While analysis has been informative, it also slow absence straightforward selection for mutants. Here we take...
The periplasmic chaperone SurA is critical for the biogenesis of outer membrane proteins (OMPs) and, thus, maintenance integrity in Escherichia coli. activity this modular has been attributed to a core module, with only minor importance assigned two peptidyl-prolyl isomerase (PPIase) domains. In work, we used synthetic phenotypes and covalent tethering demonstrate that regulated by its PPIase domains furthermore, correlated conformational state chaperone. When combined mutations β-barrel...
Significance In all organisms, morphological and functional diversity is the product of cell type-specific genetic programs. Asymmetric division in Caulobacter yields daughter cells that differ functionally due to differential read-out their genomes. Here, we report discovery GapR, a conserved DNA-binding protein required for cycle progression. We show GapR only associates with DNA sequences high adenine thymine (AT) content, colocating master regulators control genes mediating swarmer...
ABSTRACT The ubiquitous aquatic bacterium Caulobacter crescentus is highly resistant to uranium (U) and facilitates U biomineralization thus holds promise as an agent of bioremediation. To gain understanding how C. tolerates U, we employed transposon (Tn) mutagenesis paired with deep sequencing (Tn-seq) in a global screen for genomic elements required resistance. Of the 3,879 annotated genes genome, 37 were found be specifically associated fitness under stress, 15 which subsequently tested...
Kill switches provide a biocontainment strategy in which unwanted growth of an engineered microorganism is prevented by expression toxin gene. A major challenge kill switch engineering balancing evolutionary stability with robust cell killing activity application relevant host strains. Understanding host-specific containment dynamics and modes failure helps to develop potent yet stable switches. To guide the design agriculturally strain Pseudomonas fluorescens SBW25, we present comparison...
ABSTRACT SurA is a component of the periplasmic chaperone network that plays central role in biogenesis integral outer membrane β-barrel proteins (OMPs) Escherichia coli . Although contains two well-conserved proline isomerase (PPIase) domains, contribution these domains to function unclear. In present work, we show defects OMP assembly caused by mutation factors BamA or BamB can be corrected gain-of-function mutations map first PPIase domain. These apparently bypass requirement for stable...
Most integral outer membrane proteins (OMPs) of Gram-negative bacteria, such as Escherichia coli, assume a β-barrel structure. The assembly machine (Bam), five-member complex composed OMP BamA and four associated lipoproteins, BamB, BamC, BamD, BamE, folds inserts OMPs into the membrane. two essential BamD interact to stabilize subcomplexes, BamAB BamCDE, genetic structural evidence suggests that interactions between occur via an electrostatic interaction conserved aspartate residue in...
Structural characterization of lipid A remains a challenge with respect to localizing modifications the phosphate groups found on reducing and non-reducing ends disaccharide backbone A.
Abstract Bacterial evolution through horizontal gene transfer (HGT) reflects their community interactions. In this way, HGT networks do well at mapping interactions, but offer little toward controlling them—an important step in the translation of synthetic strains into natural contexts. Toxin–antitoxin (TA) systems serve as ubiquitous and diverse agents selection; however, utility is limited by erratic distribution hosts. Here we examine heterogeneous TAs a consequence mobility. By...
ABSTRACT The COVID-19 pandemic underscored the promise of monoclonal antibody-based prophylactic and therapeutic drugs 1–3 , but also revealed how quickly viral escape can curtail effective options 4, 5 . With emergence SARS-CoV-2 Omicron variant in late 2021, many clinically used antibody drug products lost potency, including Evusheld TM its constituent, cilgavimab 6 Cilgavimab, like progenitor COV2-2130, is a class 3 that compatible with other antibodies combination 4 challenging to...
The design of two overlapping genes in a microbial genome is an emerging technique for adding more reliable control mechanisms engineered organisms increased stability. functional gene pairs challenging procedure, and computational tools are used to improve the efficiency deploy successful designs genetically systems. GENTANGLE (Gene Tuples ArraNGed overLapping Elements) high-performance containerized pipeline translated different reading frames genome. This new software package can be test...