A5078547518- Genomics and Phylogenetic Studies
- Microbial Metabolic Engineering and Bioproduction
- Biofuel production and bioconversion
- Bacterial Genetics and Biotechnology
- Vibrio bacteria research studies
- RNA and protein synthesis mechanisms
- CRISPR and Genetic Engineering
- Microbial Community Ecology and Physiology
- Legionella and Acanthamoeba research
- Fungal and yeast genetics research
- Microbial Fuel Cells and Bioremediation
- Bacterial biofilms and quorum sensing
- Wastewater Treatment and Nitrogen Removal
- Probiotics and Fermented Foods
- Bacteriophages and microbial interactions
- Anaerobic Digestion and Biogas Production
- Ammonia Synthesis and Nitrogen Reduction
- Gene Regulatory Network Analysis
- Wind Energy Research and Development
- Bioinformatics and Genomic Networks
- Biochemical and biochemical processes
- DNA and Nucleic Acid Chemistry
- Molecular Biology Techniques and Applications
- Escherichia coli research studies
- DNA Repair Mechanisms
Great Lakes Bioenergy Research Center
2015-2024
University of Wisconsin–Madison
2013-2024
University of Glasgow
2023
Eunice Kennedy Shriver National Institute of Child Health and Human Development
2023
National Institutes of Health
2023
Cornell University
2017-2022
Plant (United States)
2022
Energy Center of Wisconsin
2016
General Electric (United States)
2014
University of Evansville
2006
FNR is a well-studied global regulator of anaerobiosis, which widely conserved across bacteria. Despite the importance and anaerobiosis in microbial lifestyles, factors that influence its function on genome-wide scale are poorly understood. Here, we report functional genomic analysis action. We find occupancy at many target sites strongly influenced by nucleoid-associated proteins (NAPs) restrict access to binding sites. At level, only subset predicted were bound under anaerobic fermentative...
The inability of native Saccharomyces cerevisiae to convert xylose from plant biomass into biofuels remains a major challenge for the production renewable bioenergy. Despite extensive knowledge regulatory networks controlling carbon metabolism in yeast, little is known about how reprogram S. ferment at rates comparable glucose. Here we combined genome sequencing, proteomic profiling, and metabolomic analyses identify characterize responsible mutations series evolved strains capable...
Abstract Targeted, genome-scale gene perturbation screens using Clustered Regularly Interspaced Short Palindromic Repeats interference (CRISPRi) and activation (CRISPRa) have revolutionized eukaryotic genetics, advancing medical, industrial, basic research. Although CRISPRi knockdowns been broadly applied in bacteria, options for overexpression face key limitations. Here, we develop a facile approach bacteria call, “CRISPRtOE” (CRISPR transposition OverExpression). We create platform...
Iron, a major protein cofactor, is essential for most organisms. Despite the well-known effects of O2 on oxidation state and solubility iron, impact cellular iron homeostasis not well understood. Here we report that in Escherichia coli K-12, lack dramatically changes expression genes controlled by global regulators homeostasis, transcription factor Fur small RNA RyhB. Using chromatin immunoprecipitation sequencing (ChIP-seq), found anaerobic conditions promote binding to more locations...
Chain elongation by medium-chain fatty acid (MCFA)-producing microbiomes offers an opportunity to produce valuable chemicals from organic streams that would otherwise be considered waste. However, the physiology and energetics of chain are only beginning studied, many these organisms remain uncultured. We analyzed MCFA production two uncultured were identified as main producers in a microbial community enriched anaerobic digester; this characterization, which is based on meta-multi-omic...
Abstract The genome sequences of more than 100 strains the yeast Saccharomyces cerevisiae have been published. Unfortunately, most these assemblies contain dozens to hundreds gaps at repetitive sequences, including transposable elements, tRNAs, and subtelomeric regions, which is where novel genes generally reside. Relatively few chosen for sequencing based on their biofuel production potential, leaving an additional knowledge gap. Here, we describe nearly complete sequence GLBRCY22-3...
Abstract G-quadruplex (G4) structures can form in guanine-rich DNA or RNA and have been found to modulate cellular processes, including replication, transcription, translation. Many studies on the roles of G4s focused eukaryotic systems, with far fewer probing bacterial G4s. Using a chemical-genetic approach, we identified genes Escherichia coli that are important for growth G4-stabilizing conditions. Reducing levels translation elongation factor Tu slowing initiation kasugamycin,...
Microbes can be metabolically engineered to produce biofuels and biochemicals, but rerouting metabolic flux toward products is a major hurdle without systems-level understanding of how cellular controlled. To understand rerouting, we investigated panel Saccharomyces cerevisiae strains with progressive improvements in anaerobic fermentation xylose, sugar abundant sustainable plant biomass used for biofuel production. We combined comparative transcriptomics, proteomics, phosphoproteomics...
Host iron restriction is a common mechanism for limiting the growth of pathogens. We compared regulatory network controlled by Fur in uropathogenic E. coli (UPEC) to that nonpathogenic K-12 uncover strategies pathogenic bacteria use overcome limitation. Although homeostasis functions were regulated uropathogen as expected, surprising finding was activation stringent and general stress responses fur mutant, which rescued amino acid addition. This coordinated global response could be important...
The bacterial cell envelope provides many important functions. It protects cells from harsh environments, serves as a selective permeability barrier, houses bioenergetic functions, defines sensitivity to antibacterial agents, and plays crucial role in biofilm formation, symbiosis, virulence. Despite the roles of this cellular compartment, we lack detailed understanding biosynthesis remodeling envelope. Here, report that R. sphaeroides two-component signaling system NtrYX is previously...
Identifying virulence-critical genes from pathogens is often limited by functional redundancy. To rapidly interrogate the contributions of combinations to a biological outcome, we have developed mu ltiplex, r andomized C RISPR i nterference s equencing (MuRCiS) approach. At its center new method for randomized self-assembly CRISPR arrays synthetic oligonucleotide pairs. When paired with PacBio long-read sequencing, MuRCiS allowed near-comprehensive interrogation all pairwise group 44...
Bacterial two-component systems (TCSs) often function through the detection of an extracytoplasmic stimulus and transduction a signal by transmembrane sensory histidine kinase. This kinase then initiates series reversible phosphorylation modifications to regulate activity cognate, cytoplasmic response regulator as transcription factor. Several TCSs have been implicated in regulation cell cycle dynamics, envelope integrity, or wall development Escherichia coli other well-studied Gram-negative...
The c ontrol o f v irulence gene r egulator (CovR), also called aspsule s ynthesis (CsrR), is critical to how the major human pathogen group A Streptococcus fine-tunes virulence factor production. CovR phosphorylation (CovR~P) levels are determined by its cognate sensor kinase CovS, and functional abrogating mutations in CovS can occur invasive GAS isolates leading hypervirulence. Presently, mechanism of CovR-DNA binding specificity unclear, impact inactivation on global has not been...
ABSTRACT Members of the “ Candidatus Accumulibacter” genus are widely studied as key polyphosphate-accumulating organisms (PAOs) in biological nutrient removal (BNR) facilities performing enhanced phosphorus (EBPR). This diverse lineage includes 18 Ca . species, which have been proposed based on phylogenetic divergence polyphosphate kinase 1 ( ppk1 ) gene and genome-scale comparisons metagenome-assembled genomes (MAGs). Phylogenetic classification 16S rRNA genetic marker has difficult to...
Aromatic compounds are an important source of commodity chemicals traditionally produced from fossil fuels. Aromatics derived plant lignin can potentially be converted into through depolymerization followed by microbial funneling monomers and low molecular weight oligomers. This study investigates the catabolism β-5 linked aromatic dimer dehydrodiconiferyl alcohol (DC-A) bacterium
Organic-rich industrial residues can serve as renewable feedstocks for the generation of useful products by microbial fermentation. We investigated fermenting communities enriched in a mixture ultra-filtered milk permeate (UFMP) and acid whey from cottage cheese (CAW), two dairy coproducts rich lactose. To evaluate how operational pH temperature affect fermentation products, we operated 12 bioreactors 140 days, each fed 1:1 UFMP CAW at either 35 °C or 50 4.8 5.5. The resulted incomplete...
Significance Bacterial promoters are often predicted by similarity to the Escherichia coli −10 and −35 consensus elements. Although these elements highly conserved in diverse bacterial phyla, only 30 43% of we analyzed from Rhodobacter sphaeroides two other α-proteobacteria contained −7T, a base element present 90 99% non–α-proteobacteria. Expression 15 16 R. tested vitro that lacked −7T was very weak, but identified an essential transcription factor, CarD, activated all promoters. We...
The liquid residue resulting from various agroindustrial processes is both rich in organic material and an attractive source to produce a variety of chemicals. Using microbial communities chemicals these residues active area research, but it unclear how deploy specific products the different residues. To address this, we fed anaerobic bioreactors one several (carbohydrate-rich lignocellulosic fermentation conversion residue, xylose, dairy manure hydrolysate, ultra-filtered milk permeate,...
Lignin is the most abundant aromatic polymer on Earth and a resource that could eventually substitute for fossil fuels as source of compounds industrial biotechnological applications. Engineering microorganisms production aromatic-based biochemicals requires detailed knowledge metabolic pathways degradation aromatics are present in lignin. Our isolation analysis Rhodopseudomonas palustris strain capable syringic acid reveal previously unknown route R. . This study highlights several key...
Significance Bacterial phenotypes require the concerted expression of multiple genes, usually coordinated by a transcriptional regulator. Although functions many genes in sequenced bacterial genomes can be inferred, regulatory networks that coordinate their are only known few model systems. Using bioinformatic and experimental approach, we solve DNA-specificity code extracytoplasmic function sigma factors (ECF σs), major class regulators. We develop use high-stringency pipeline to predict...
Fermentative microbial communities have the potential to serve as biocatalysts for conversion of low-value dairy coproducts into renewable chemicals, contributing a more sustainable global economy. To develop predictive tools design and operation industrially relevant strategies that utilize fermentative communities, there is need determine genomic features community members are characteristic accumulation different products. address this knowledge gap, we performed 282-day bioreactor...