GLBRC Data Sets

This Data Catalog is a collection of data from GLBRC's Sustainability research carried out in Michigan and Wisconsin. The Data Catalog summarizes each data table in order to allow the GLBRC community to better understand the data that have been collected and encourage collaboration.

Multidrug efflux pumps are dynamic molecular machines that drive antibiotic resistance by harnessing ion gradients to export chemically diverse substrates. Despite their clinical importance, the molecular principles underlying multidrug promiscuity and energy efficiency remain poorly understood.

Genetically engineered microbes have the potential to increase efficiency in the bioeconomy by overcoming growth-limiting production stress. Screens of gene perturbation libraries against production stressors can identify high-value engineering targets, but follow-up experiments needed to guard against false positives are slow and resource-intensive.

Whole-genome duplication (WGD) has had profound macroevolutionary impacts on diverse lineages, preceding adaptive radiations in vertebrates, teleost fish, and angiosperms. In contrast to the many known ancient WGDs in animals, and especially plants, we are aware of evidence for only four WGDs in fungi.

Perennial grasses like switchgrass (Panicum virgatum) and miscanthus (Miscanthus × giganteus) are expected to supply a substantial amount of the United States bioeconomy's feedstock demand. However, uncertainties around their long-term yields challenge the viability of their potential and limit their wider adoption.

We present draft genomes of two Paraburkholderia strains and two Burkholderia strains. Three strains were isolated from surrounding soils and one from roots of switchgrass (Panicum virgatum) in Michigan, USA.

Mutator phenotypes are short-lived due to the rapid accumulation of deleterious mutations. Yet, recent observations reveal that certain fungi can undergo prolonged accelerated evolution after losing genes involved in DNA repair.

A novel Saccharomycotina yeast strain, yHQL494, was isolated from the rose hip of the wild rose Rosa californica from Castle Crags State Park, California, USA.

Tilletia maclaganii is a smut fungal pathogen that causes significant biomass reduction of switchgrass (Panicum virgatum) used for animal forage and biofuel production. Here we present the annotated genome of T. maclaganii, strain Tm001-NY21, estimated at 42.79 Mb in size, in 53 assembled contigs and encoding 10,235 predicted genes.

Nitrous oxide (N2O) is a serious concern due to its role in global warming and ozone destruction. Agricultural practices account for ∼80% of all anthropogenic N2O produced in the US, due in large part to the stimulation of microbial denitrification.

Zymomonas mobilis is a promising biocatalyst for the sustainable conversion of lignocellulosic sugars into biofuels and bioproducts, yet its response to lignocellulosic hydrolysates remains poorly understood. Here, we investigate the physiological response of Z.

Thermodynamically constrained reactions and pathways are hypothesized to impose greater protein demands on cells, requiring higher enzyme amounts to sustain a given flux compared to those with stronger thermodynamics.

Switchgrass (Panicum virgatum L.) is a native North American grass currently considered a high-potential bioenergy feedstock crop. However, previous reports questioned its effectiveness in generating soil organic carbon (SOC) gains, with resultant uncertainty regarding the monoculture switchgrass's impact on the environmental sustainability of bioenergy agriculture.

Reactive oxygen species (ROS) are highly reactive molecules encountered by yeasts during routine metabolism and during interactions with other organisms, including host infection.

The aromatic compounds used in a variety of industrial products are currently obtained from nonrenewable petroleum sources. Alternatively, the plant polymer lignin is an abundant renewable source of aromatics, and its depolymerization generates a variety of products that can include acetovanillone, a vanillin derivative containing an acetyl side chain.

Bioenergy sorghum is a highly productive drought tolerant C4 grass that accumulates ~ 80% of its harvested biomass in ~ 4 m long stems comprised of > 40 internodes that develop sequentially during an extended vegetative growth phase.

In coevolving species, parasites locally adapt to host populations as hosts locally adapt to resist parasites. Parasites often outpace host local adaptation since they have rapid life cycles, but host diversity, the strength of selection, and external environmental influence can result in complex outcomes.

The SARO_RS14285 gene, encoding a transcription factor, was deleted in Novosphingobium aromaticivorans DSM12444. The transcriptomes of the parent and ΔSARO_RS14285 strains were determined when grown in medium containing glucose with or without protocatechuic, vanillic, syringic, or 4-coumaric acid. We present the raw RNA sequencing data obtained from these cultures.

Genome-wide binding sites of 44 putative transcription factors (TFs) from Novosphingobium aromaticivorans DSM12444 were analyzed using DNA affinity purification sequencing. We report that 32 of these TFs have at least one area of enrichment. These data will help better understand aromatic metabolism and other features of N. aromaticivorans biology.