T7 RNA Polymerase Functions In Vitro without Clustering

Many nucleic acid polymerases function in clusters known as factories. We investigate whether the RNA polymerase (RNAP) of phage T7 also clusters when active. Using ‘pulldowns’ and fluorescence correlation spectroscopy we find that elongation complexes do not interact in vitro with a Kd<1 µM. Chromosome conformation capture also reveals that genes located 100 kb apart on the E. coli chromosome do not associate more frequently when transcribed by T7 RNAP. We conclude that if clustering does occur in vivo, it must be driven by weak interactions, or mediated by a phage-encoded protein

Glycosylation site prediction using ensembles of Support Vector Machine classifiers

Article discussing the performance of different computational methods for prediction of glycosylation sites from amino acid sequences

Austral birds offer insightful complementary models in ecology and evolution

Theuerkauf J, Villavicencio CP, Adreani NM, et al. Austral birds offer insightful complementary models in ecology and evolution. Trends in Ecology &amp; Evolution. 2022;37(9):759-767.The Southern Hemisphere differs in many aspects from the Northern Hemisphere. However, most ecological and evolutionary research is conducted in the Northern Hemisphere and its conclusions are extrapolated to the entire globe. Therefore, unique organismal and evolutionary characteristics of the south are overlooked. We use ornithology to show the importance of including a southern perspective. We present examples of plumage pigmentation, brood-parasitic nestling ejection, flightlessness, female song, and female aggression modulated by progesterone as complementary models for investigating fundamental biological questions. More research in the Southern Hemisphere, together with increased cooperation among researchers across the hemispheres and within the Southern Hemisphere, will provide a greater global outlook into ecology and evolution

Pandora's flying box - Borrelia burgdorferi sensu lato prevalence in Ixodes species from birds throughout Europe

Birds are important hosts for ticks and may act as reservoirs for several zoonotic pathogens. Because of their high mobility, especially of the long distance migratory species, they can act as dispersers for ticks and pathogens, ultimately affecting their distribution and phylogeography.N/

Proper Protein Glycosylation Promotes Mitogen-Activated Protein Kinase Signal Fidelity

The ability of cells to sense and respond appropriately to changing environmental conditions is often mediated by signal transduction pathways that employ mitogen-activated protein kinases (MAPKs). In the yeast Saccharomyces cerevisiae, the high osmolarity glycerol (HOG) and the filamentous growth (FG) pathways are activated following hyperosmotic stress and nutrient deprivation, respectively. Whereas the HOG pathway requires the MAPK Hog1, the FG pathway employs the MAPK Kss1. We conducted a comprehensive screen of nearly 5,000 gene deletion strains for mutants that exhibit inappropriate cross-talk between the HOG and FG pathways. We identified two novel mutants, mnn10Δ and mnn11Δ, that allow activation of Kss1 under conditions that normally stimulate Hog1. MNN10 and MNN11 encode mannosyltransferases that are part of the N-glycosylation machinery within the Golgi apparatus; deletion of either gene results in N-glycosylated proteins that have shorter mannan chains. Deletion of the cell surface mucin Msb2 suppressed the mnn11Δ phenotype, while mutation of a single glycosylation site within Msb2 was sufficient to confer inappropriate activation of Kss1 by salt stress. These findings reveal new components of the N-glycosylation machinery needed to ensure MAPK signaling fidelity

Structure of human mitochondrial RNA polymerase elongation complex

Here we report the crystal structure of the human mitochondrial RNA polymerase (mtRNAP) transcription elongation complex, determined at 2.65-Å resolution. The structure reveals a 9-bp hybrid formed between the DNA template and the RNA transcript and one turn of DNA both upstream and downstream of the hybrid. Comparisons with the distantly related RNA polymerase (RNAP) from bacteriophage T7 indicates conserved mechanisms for substrate binding and nucleotide incorporation but also strong mechanistic differences. Whereas T7 RNAP refolds during the transition from initiation to elongation, mtRNAP adopts an intermediary conformation that is capable of elongation without refolding. The intercalating hairpin that melts DNA during T7 RNAP initiation separates RNA from DNA during mtRNAP elongation. Newly synthesized RNA exits toward the pentatricopeptide repeat (PPR) domain, a unique feature of mtRNAP with conserved RNA-recognition motifs