Proteomics-guided isolation of a novel serine protease with milk-clotting activity from tamarillo (Solanum betaceum Cav.)

Tamarillo is widely grown in Yunnan Province, China, and has been found that it can be used in cheese-making with a distinctive fruity flavour. However, this primary component responsible for curdling milk remains unclear. This study aimed to identify the main component in tamarillo responsible for curdling milk using proteomics and ammonium sulfate (AS) precipitation. Herein, 3199 proteins were identified in tamarillo, of which 546 exhibited hydrolase activity. In particular, a novel serine protease with milk-clotting activity (MCA) and a molecular weight of 79.1 kDa, named "MCP746", was isolated from tamarillo. The milk-clotting proteases (MCPs) from tamarillo exhibited the highest MCA at 80 °C and stability under incubation temperatures below 70 °C, pH range of 5-8, and NaCl concentrations below 1 mol/L. This study revealed that serine protease is the primary MCPs of tamarillo along with a characterization of its milk-clotting characteristics, providing valuable insights into its potential application in cheese-making.

Proteomics reveals the enhancing mechanism for eliminating toxic hydroxylamine from water by nanocompartments containing hydroxylamine oxidase

Hydroxylamine (NH₂OH) is a potentially toxic pollutant when it is present in water, as it can damage both bacteria and the human body. It is still difficult to eliminate the toxic NH₂OH in water. Here, we showed that the model bacterium (Escherichia coli) with nanocompartments encapsulated with hydroxylamine oxidase (HAO) can remove NH₂OH from water. In addition, the removal efficiency of NH₂OH by genetically modified bacteria (with HAO-nanocompartments) was 3.87 mg N L^-1 h^-1, and that of wild-type bacteria (without HAO-nanocompartments) was only 1.86 mg N L^-1 h^-1. Label-free quantitative proteomics indicated that the nanocompartments containing HAO enhanced bacterial activity by inducing the up-regulation of proteins involved in stress and stimulus responses, and decreased their intracellular NH₂OH concentration. Moreover, the synthesis of proteins involved in energy metabolism, gene expression, and other processes in bacterial was enhanced under hydroxylamine stress, and these changes increased the resistance of bacterial to NH₂OH. This work can aid our understanding of the toxic effects of NH₂OH on bacteria as well as the development of new approaches to eliminate NH₂OH in water.

Comprehensive comparison of sample preparation workflows for proteomics

Mass spectrometry-based proteomics experiments can be subject to a large variability, which forms an obstacle to obtaining deep and accurate protein identification. Here, to obtain an optimal sample preparation workflow...

Bacterially self-assembled encapsulin nanocompartment for removing silver from water

Compartmentalization can protect cells from the interference of external toxic substances by sequestering toxic products. We hypothesized that proteinaceous nanocompartments may be a feasible candidate material to be added to genetically modified bacteria for the sequestration of toxic environmental products, which would open up a new bioremediation pathway. Here, we showed that the model bacterium (Escherichia coli) with self-assembling nanocompartments can remove silver (Ag) from water. Transmission electron microscopy and energy dispersive X-ray (TEM-EDX) analysis showed that the nanocompartments combined stably with silver in vitro. In addition, when exposed to 30 μM AgNO₃, the survival rate of genetically modified bacteria (with nanocompartments) was 86%, while it was just 59% in the wild-type bacteria (without nanocompartments). Label-free quantitative proteomics indicated that the nanocompartments enhanced bacterial activity by inducing the up-regulation of protein processing and secondary metabolites, and decreased their intracellular silver concentration, both of which contributed to their increased resistance to toxic silver. This study on nanocompartments has contributed to a deeper understanding of how bacteria respond to environmental stressors like heavy metal pollutants in water. The technology promises to provide a new strategy for recycling heavy metals from sewage.

DIA proteomics reveals hypotensive and immune-enhancing constituents in buffalo whey from different altitudes

The selection of raw milk with high levels of functional components that have health-promoting activities is very important for the exploitation and production of functional milk, but the differences in the functional components of whey from buffalo raised at different altitudes have not been thoroughly investigated. Here, we detected the effects of altitudes on the functional components in whey from dairy buffalo farms situated at low altitude (LA), medium altitude (MA), and high altitude (HA) sites with data-independent acquisition proteomic approaches. In 33 samples, 9331 peptides corresponding to 1008 high-confidence proteins were detected. HA-whey had a lower level of angiotensinogen than that of the LA- and MA-whey, and conversely contained higher levels of immune-enhancing components than for the latter two groups. Differential proteins were involved in vascular smooth muscle contraction, complement and coagulation cascades, and the secretion, production and regulation pathways in immune components. LA-whey showed higher levels of lymphocyte antigen and selenoprotein F than that of the HA-whey. Owing to the biological functions of their most abundant components, HA- and LA-whey are suitable for the processing of functional milk for lowering blood pressure, and the production of immune milk, respectively.

Enhanced electrophoretic separation of proteins by tethered SiO2 nanoparticles in an SDS-polyacrylamide gel network

Nanoparticles (NPs) are able to improve the separation efficiency of proteins in SDS-polyacrylamide gel electrophoresis (SDS-PAGE) due to their capability of enhancing heat dissipation during electrophoresis. However, the intrinsic surface charges of NPs (at buffer pH or charge induced due to the SDS coating) make them acquire electrophoretic mobility and movement in the gel. Such a movement leads to viscosity and temperature gradients in the gel and deteriorates the separation. In this work, we proposed a novel method by using tethered NPs in the gel. Silica NPs, as the model NPs, were prepared and their surfaces were modified using 3-[(methacryloxy)propyl] trimethoxysilane (MPS) which locks the NPs in the gel via covalent bonds (M-SiO₂/PA (polyacrylamide)). SiO₂ NPs were embedded into the gel (SiO₂/PA) as the positive control, while pure PA gel was chosen as the negative control. The results showed that at a relatively high voltage of 250 V, although the Joule heat generated during electrophoresis disturbed the separation in the pure gel, the SiO₂/PA and M-SiO₂/PA nanocomposite gels showed better performances. In comparison with the pure PA gel, the resolution increased by 3 and 32% for SiO₂/PA and M-SiO₂/PA, respectively, in a relatively short separation time of 35 min. The gel with tethered NPs presented a more efficient separation in terms of band broadening and resolution compared with the gel with free NPs probably due to the movement of free charged particles in the gel. Evidently, the migration speed of protein bands in the gels decreased especially for larger proteins in the presence of the NPs compared to the pristine gel due to the steric hindrance of the NPs. Finally, we separated E. coli proteins, as a real sample. Among the three gels (pure PA, SiO₂/PA, and M-SiO₂/PA), the gel containing M-SiO₂ showed the best performance.

Omics Analyses of Gut Microbiota in a Circadian Rhythm Disorder Mouse Model Fed with Oolong Tea Polyphenols

Microbiome has been revealed as a key element involved in maintaining the circadian rhythms. Oolong tea polyphenols (OTP) has been shown to have potential prebiotic activity. Therefore, this study focused on the regulation mechanisms of OTP on host circadian rhythms. After 8 weeks of OTP administration, a large expansion in the relative abundance of Bacteroidetes with a decrease in Firmicutes was observed, which reflected the positive modulatory effect of OTP on gut flora. In addition, Kyoto Encyclopedia of Genes and Genomes pathways of ATP-binding cassette transporters, two-component system, and the biosynthesis of amino acids enriched the most differentially expressed genes after OTP treatment. Of the differentially expressed proteins identified, most were related to metabolism, genetic information processing, and environmental information processing. It underscores the ability of OTP to regulate circadian rhythm by enhancing beneficial intestinal microbiota and affecting metabolic pathways, contributing to the improvement of host microecology.

Aqueous raw and ripe Pu-erh tea extracts alleviate obesity and alter cecal microbiota composition and function in diet-induced obese rats

Pu-erh tea is attracting increased attention worldwide because of its unique flavor and health effects, but its impact on the composition and function of the gut microbiota remains unclear. The aim of this study was to investigate the effects of aqueous extracts of fermented (ripe) and non-fermented (raw) Pu-erh teas on the composition and function of the intestinal microbiota of rats with diet-induced obesity. We conducted a comparative metagenomic and meta-proteomic investigation of the microbial communities in cecal samples taken from obese rats treated with or without extracts of raw or ripe Pu-erh teas. By analyzing the composition and diversity of 16S rRNA amplicons and expression profiles of 814 distinct proteins, we found that despite differences in the chemical compositions of raw and ripe Pu-erh teas, administration of either tea at two doses (0.15- and 0.40-g/kg body weight) significantly (P < 0.05) increased microbial diversity and changed the composition of cecal microbiota by increasing the relative abundances of Firmicutes and decreasing those of Bacteroidetes. Community metabolic processes, including sucrose metabolism, glycolysis, and syntheses of proteins, rRNAs, and antibiotics were significantly (P < 0.05) promoted or had a tendency (0.10 < P < 0.05) to be promoted due to the enrichment of relevant enzymes. Furthermore, evidence at population, molecular, and metabolic levels indicated that polyphenols of raw Pu-erh tea and their metabolites potentially promote Akkermansia muciniphila growth by stimulating a type II and III secretion system protein, the elongation factor Tu, and a glyceraldehyde-3-phosphate dehydrogenase. This study provides new evidence for the prebiotic effects of Pu-erh tea.

Soil and leaf litter metaproteomics-a brief guideline from sampling to understanding

The increasing application of soil metaproteomics is providing unprecedented, in-depth characterization of the composition and functionality of in situ microbial communities. Despite recent advances in high-resolution mass spectrometry, soil metaproteomics still suffers from a lack of effective and reproducible protein extraction protocols and standardized data analyses. This review discusses the opportunities and limitations of selected techniques in soil-, and leaf litter metaproteomics, and presents a step-by-step guideline on their application, covering sampling, sample preparation, extraction and data evaluation strategies. In addition, we present recent applications of soil metaproteomics and discuss how such approaches, linking phylogenetics and functionality, can help gain deeper insights into terrestrial microbial ecology. Finally, we strongly recommend that to maximize the insights environmental metaproteomics may provide, such methods should be employed within a holistic experimental approach considering relevant aboveground and belowground ecosystem parameters.

Mapping and analyzing the human liver proteome: progress and potential

INTRODUCTION

The liver is an important organ in humans. Hepatocellular carcinoma (HCC) is one of the deadliest cancers in the world. Progress in the Human Liver Proteome Project (HLPP) has improved understanding of the liver and the liver cancer proteome.

AREAS COVERED

Here, we summarize the recent progress in liver proteome modification profiles, proteomic studies in liver cancer, proteomic study in the search for novel liver cancer biomarkers and drug targets, and progress of the Chromosome Centric Human Proteome Project (CHPP) in the past five years in the Institutes of Biomedical Sciences (IBS) of Fudan University. Expert commentary: Recent advances and findings discussed here provide great promise of improving the outcome of patients with liver cancer.