Salmonella species can gain access into nonphagocytic cells, where the bacterium proliferates in a unique membrane-bounded compartment. In order to reveal bacterial adaptations to their intracellular niche, here we conducted the first comprehensive proteomic survey of Salmonella isolated from infected epithelial cells. Among ϳ3,300 identified bacterial proteins, we found that about 100 proteins were significantly altered at the onset of Salmonella intracellular replication. In addition to substantially increased iron-uptake capacities, bacterial high-affinity manganese and zinc transporters were also upregulated, suggesting an overall limitation of metal ions in host epithelial cells. We also found that Salmonella induced multiple phosphate utilization pathways. Furthermore, our data suggested upregulation of the two-component PhoPQ system as well as of many downstream virulence factors under its regulation. Our survey also revealed that intracellular Salmonella has increased needs for certain amino acids and biotin. In contrast, Salmonella downregulated glycerol and maltose utilization as well as chemotaxis pathways. While infectious diseases continue to be a major threat to human health, there is an urgent need in rational design and development of new treatment strategies. As a model for studying bacterial pathogenesis, Salmonella spp. cause millions of infections per year ranging from food poisoning to life-threatening systemic typhoid fever (1). Central to its pathogenesis is a syringelike structure known as the type III secretion system (T3SS), which delivers bacterial proteins called effectors directly into eukaryotic host cells (2, 3). The injected proteins are able to modulate various host cellular functions, and over the years extensive studies have been carried out on these effector proteins and/or their interacting host targets. While these studies have contributed substantially to our initial understanding of infection biology, daunting challenges are encountered because conventional reductionism-based studies certainly cannot explain the complex multifactorial nature of host-pathogen interactions (4). Systems-level analyses can provide a panoramic view of the functional host-pathogen interplay and thus are promising in this regard.During infection, the intracellular environment is likely to be very different from what bacteria encounter in rich culture media. It has long been known that various nutritional and environmental differences within host cells force bacterial pathogens to reprogram their gene expression. In fact, transcriptomic studies of intracellular Salmonella within infected macrophages and epithelial cells contributed to our initial understanding of bacterial adaptations in the host environment (5, 6). Because proteins are the final gene products and their changes may not correlate with those of mRNA, direct readout of the bacterial proteome is highly desired. Such measurements, however, have been technically challenging due to the presence of vast amounts of host proteins (7). As a ...
The photo-induced reactions of diaryltetrazoles with carboxylic acids in aqueous solution were investigated. Besides measuring the apparent second-order rate constant and evaluating the functional group compatibility of these reactions, we further incorporated the tetrazoles into SAHA, leading to a new active-site-directed probe for labelling HDACs in both cell lysates and living cells.
To address the increasing need for detecting and validating protein biomarkers in clinical specimens, mass spectrometry (MS)-based targeted proteomic techniques, including the selected reaction monitoring (SRM), parallel reaction monitoring (PRM), and massively parallel data-independent acquisition (DIA), have been developed. For optimal performance, they require the fragment ion spectra of targeted peptides as prior knowledge. In this report, we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue samples. To build the spectral resource, we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on Docker. We then applied the workflow to generate DPHL, a comprehensive DIA pan-human library, from 1096 data-dependent acquisition (DDA) MS raw files for 16 types of cancer samples. This extensive spectral resource was then applied to a proteomic study of 17 prostate cancer (PCa) patients. Thereafter, PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was validated. As a second application, the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma (DLBCL) patients and 18 healthy control subjects. Differentially expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by PRM. These data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker discovery. DPHL is freely accessible at https://www.iprox.org/page/project.html?id=IPX0001400000.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.