The Structure and Evolution of the Major Capsid Protein of a Large, Lipid-Containing DNA Virus

Paramecium bursaria Chlorella virus type 1 (PBCV-1) is a very large, icosahedral virus containing an internal membrane enclosed within a glycoprotein coat consisting of pseudohexagonal arrays of trimeric capsomers. Each capsomer is composed of three molecules of the major capsid protein, Vp54, the 2.0-Å resolution structure of which is reported here. Four N-linked and two O-linked glycosylation sites were identified. The N-linked sites are associated with nonstandard amino acid motifs as a result of glycosylation by virus-encoded enzymes. Each monomer of the trimeric structure consists of two eight-stranded, antiparallel β-barrel, “jelly-roll” domains related by a pseudo-sixfold rotation. The fold of the monomer and the pseudo-sixfold symmetry of the capsomer resembles that of the major coat proteins in the double-stranded DNA bacteriophage PRD1 and the double-stranded DNA human adenoviruses, as well as the viral proteins VP2-VP3 of picornaviruses. The structural similarities among these diverse groups of viruses, whose hosts include bacteria, unicellular eukaryotes, plants, and mammals, make it probable that their capsid proteins have evolved from a common ancestor that had already acquired a pseudo-sixfold organization. The trimeric capsid protein structure was used to produce a quasi-atomic model of the 1,900-Å diameter PBCV-1 outer shell, based on fitting of the Vp54 crystal structure into a three-dimensional cryoelectron microscopy image reconstruction of the virus

Distribution, Bioaccumulation, and Risks of Pharmaceutical Metabolites and Their Parents: A Case Study in an Yunliang River, Nanjing City

The occurrence, bioaccumulation, and risks of 11 pairs of pharmaceutical metabolites and their respective parents were investigated in the water, sediment, and fish of an urban river in Nanjing city, China. The results showed that most of the target metabolites and their parents were detected in all water samples, with concentrations ranging from 0.1 ng/L to 72.9 ng/L. In some cases, the concentrations of metabolites in water were significantly higher than their parents, with fold changes reaching up 4.1 in the wet season and 6.6 in the dry season, while in sediment and fish, a lower concentration was observed in most cases. A lowered concentration of detected pharmaceuticals was observed in the dry season when compared to the wet season due to the seasonal variation in pharmaceutical consumption and overflow effluent. The bioaccumulation of pharmaceuticals in different fish tissues were detected with a descending order of overall concentration as gill > brain > muscle > gonad > intestine > liver > blood. In addition, the concentrations of both metabolites and their parents also decreased along the river in two seasons. However, the concentration rates of metabolites and their parents were significantly altered along the river in both water and sediment. The relatively high concentration proportions of the detected pharmaceuticals in water suggested that pharmaceuticals were more likely to apportion in water than in sediment, especially for the metabolites. Meanwhile, the rates of the metabolite/parent pairs between fish and water/sediment were generally lower, indicating the higher excretion capacity of metabolites from fish than their parents. Most of the detected pharmaceuticals had no impact on aquatic organisms. However, the presence of ibuprofen posed a medium risk to fish. Compared to the parents, metabolites showed a relatively low risk value but a high contribution to the total risk. It highlights that metabolites in the aquatic environments cannot be ignored