Phylotype resolved spatial variation and association patterns of planktonic Thaumarchaeota in eastern Chinese marginal seas.

The majority of marine ammonia oxidizers belong to Thaumarchaeota, a phylum of Archaea, which is distributed throughout the water column. Marine surface waters contain distinct thaumarchaeotal phylotypes compared to the deeper ocean, but spatial dynamics of the surface-associated lineages are largely unsolved. This study of 120 seawater samples from the eastern Chinese marginal seas identified contrasting distribution and association patterns among thaumarchaeotal phylotypes across different dimensions. Horizontally, Nitrosopumilus-like and Nitrosopelagicus-like phylotypes dominated the surface water (3 m) of the Yellow Sea (YS) and East China Sea (ECS), respectively, along with increased abundance of total free-living Thaumarchaeota in ECS. Similar compositional changes were observed in the surface microlayer. The spatial heterogeneity of particle-attached Thaumarchaeota was less clear in surface microlayers than in surface waters. Vertically, the Nitrosopelagicus-like phylotype increased in abundance from surface to 90 m in ECS, which led to an increase in the proportion of Thaumarchaeota relative to total prokaryotes. This occurred mainly in the free-living fraction. These results indicate a clear size-fractionated niche partitioning, which is more pronounced at lower depths than in the surface water/surface microlayer. In addition, associations of Thaumarchaeota with other microbial taxa varied between phylotypes and size fractions. Our results show that a phylotype-resolved and size-fractionated spatial heterogeneity of the thaumarchaeotal community is present in surface oceanic waters and a vertical variation of the Nitrosopelagicus-like phylotype is present in shallow shelf waters. Supplementary Information: The online version contains supplementary material available at 10.1007/s42995-023-00169-y.

Allosteric binding on nuclear receptors: Insights on screening of non-competitive endocrine-disrupting chemicals.

Endocrine-disrupting chemicals (EDCs) can compete with endogenous hormones and bind to the orthosteric site of nuclear receptors (NRs), affecting normal endocrine system function and causing severe symptoms. Recently, a series of pharmaceuticals and personal care products (PPCPs) have been discovered to bind to the allosteric sites of NRs and induce similar effects. However, it remains unclear how diverse EDCs work in this new way. Therefore, we have systematically summarized the allosteric sites and underlying mechanisms based on existing studies, mainly regarding drugs belonging to the PPCP class. Advanced methods, classified as structural biology, biochemistry and computational simulation, together with their advantages and hurdles for allosteric site recognition and mechanism insight have also been described. Furthermore, we have highlighted two available strategies for virtual screening of numerous EDCs, relying on the structural features of allosteric sites and lead compounds, respectively. We aim to provide reliable theoretical and technical support for a broader view of various allosteric interactions between EDCs and NRs, and to drive high-throughput and accurate screening of potential EDCs with non-competitive effects.

Microbacterium helvum sp. nov., a novel actinobacterium isolated from cow dung.

A Gram-positive, aerobic, non-motile, non-spore-forming, short rod-shaped strain, NEAU-LLCT, was isolated from cow dung in Shangzhi City, Heilongjiang Province, Northeast China and identified by a polyphasic taxonomic study. Colonies was light yellow, round, with entire margin. Strain NEAU-LLCT was grown at 15-45 â„ƒ and pH 6.0-10.0. NaCl concentration ranged from 0 to 5% (W/V). The 16S rRNA gene sequence of NEAU-LLCT showed the high similarities with Microbacterium kyungheense JCM 18735T (98.5%), Microbacterium trichothecenolyticum JCM 1358T (98.3%) and Microbacterium jejuense JCM 18734T (98.2%). The whole-cell sugars were glucose, rhamnose and ribose. The menaquinones contained MK-12 and MK-13. Ornithine, glutamic acid, lysine and a small amount of alanine and glycine were the amino acids in the hydrolyzed products of the cell wall. The major fatty acids were iso-C16:0, iso-C18:0, anteiso-C15:0 and anteiso-C17:0. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol and an unidentified glycolipid. The genome of NEAU-LLCT was 4,369,375 bp and G + C content is 70.28 mol%. A combination of DNA-DNA hybridization result and some phenotypic characteristics demonstrated that strain NEAU-LLCT could be distinguished from its closely related strains. Therefore, the strain NEAU-LLCT was considered to represent a novel species, which was named Microbacterium helvum sp. (Type strain NEAU-LLCT = CCTCC AA 2018026T = JCM 32661T).

Expression, characterization and crystal structure of thioredoxin from Schistosoma japonicum.

Schistosoma japonicum, a human blood fluke, causes a parasitic disease affecting millions of people in Asia. Thioredoxin-glutathione system of S. japonicum plays a critical role in maintaining the redox balance in parasite, which is a potential target for development of novel antischistosomal agents. Here we cloned the gene of S. japonicum thioredoxin (SjTrx), expressed and purified the recombinant SjTrx in Escherichia coli. Functional assay shows that SjTrx catalyses the dithiothreitol (DTT) reduction of insulin disulphide bonds. The coupling assay of SjTrx with its endogenous reductase, thioredoxin glutathione reductase from S. japonicum (SjTGR), supports its biological function to maintain the redox homeostasis in the cell. Furthermore, the crystal structure of SjTrx in the oxidized state was determined at 2.0 Å resolution, revealing a typical architecture of thioredoxin fold. The structural information of SjTrx provides us important clues for understanding the maintenance function of redox homeostasis in S. japonicum and pathogenesis of this chronic disease.

Expression, crystallization and preliminary X-ray diffraction analysis of thioredoxin glutathione reductase from Schistosoma japonicum in complex with FAD.

Thioredoxin glutathione reductase from Schistosoma japonicum (SjTGR), a multifunctional enzyme, plays a vital role in antioxidant pathways and is considered to be a potential drug target for the development of antischistosomal chemotherapy. In this study, two constructs of a truncated form of SjTGR without the last two residues (Sec597-Gly598) were cloned, overexpressed and purified using wild-type and codon-optimized genes. Only SjTGR from the wild-type gene was found to form a complex with flavin adenine dinucleotide (FAD), which could be crystallized in the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 84.185, b = 86.47, c = 183.164 Å, at 295 K using the hanging-drop vapour-diffusion method. One dimer was present in the crystallographic asymmetric unit and the calculated Matthews coefficient (VM) and solvent content were 2.6 Å(3) Da(-1) and 52.8%, respectively. Structural determination of SjTGR is in progress using the molecular-replacement method.