HCMV pUS28 initiates pro-migratory signaling via activation of Pyk2 kinase

Background: Human Cytomegalovirus (HCMV) has been implicated in the acceleration of vascular disease and chronic allograft rejection. Recently, the virus has been associated with glioblastoma and other tumors. We have previously shown that the HCMV-encoded chemokine receptor pUS28 mediates smooth muscle cell (SMC) and macrophage motility and this activity has been implicated in the acceleration of vascular disease. pUS28 induced SMC migration involves the activation of the protein tyrosine kinases (PTKs) Src and Focal adhesion kinase as well as the small GTPase RhoA. The PTK Pyk2 has been shown to play a role in cellular migration and formation of cancer, especially glioblastoma. The role of Pyk2 in pUS28 signaling and migration are unknown. Methods: In the current study, we examined the involvement of the PTK Pyk2 in pUS28-induced cellular motility. We utilized in vitro migration of SMC to determine the requirements for Pyk2 in pUS28 pro-migratory signaling. We performed biochemical analysis of Pyk2 signaling in response to pUS28 activation to determine the mechanisms involved in pUS28 migration. We performed mass spectrometric analysis of Pyk2 complexes to identify novel Pyk2 binding partners. Results: Expression of a mutant form of Pyk2 lacking the autophosphorylation site (Tyr-402) blocks pUS28-mediated SMC migration in response to CCL5, while the kinase-inactive Pyk2 mutant failed to elicit the same negative effect on migration. pUS28 stimulation with CCL5 results in ligand-dependent and calcium-dependent phosphorylation of Pyk2 Tyr-402 and induced the formation of an active Pyk2 kinase complex containing several novel Pyk2 binding proteins. Expression of the autophosphorylation null mutant Pyk2 F402Y did not abrogate the formation of an active Pyk2 kinase complex, but instead prevented pUS28-mediated activation of RhoA. Additionally, pUS28 activated RhoA via Pyk2 in the U373 glioblastoma cells. Interestingly, the Pyk2 kinase complex in U373 contained several proteins known to participate in glioma tumorigenesis. Conclusions: These findings represent the first demonstration that pUS28 signals through Pyk2 and that this PTK participates in pUS28-mediated cellular motility via activation of RhoA. Furthermore, these results provide a potential mechanistic link between HCMV-pUS28 and glioblastoma cell activation

Mechanisms of manganese(II) oxidation by filamentous ascomycete fungi vary with species and time as a function of secretome composition

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Zeiner, C. A., Purvine, S. O., Zink, E., Wu, S., Pasa-Tolic, L., Chaput, D. L., Santelli, C. M., & Hansel, C. M. Mechanisms of manganese(II) oxidation by filamentous ascomycete fungi vary with species and time as a function of secretome composition. Frontiers in Microbiology, 12, (2021): 610497, https://doi.org/10.3389/fmicb.2021.610497.Manganese (Mn) oxides are among the strongest oxidants and sorbents in the environment, and Mn(II) oxidation to Mn(III/IV) (hydr)oxides includes both abiotic and microbially-mediated processes. While white-rot Basidiomycete fungi oxidize Mn(II) using laccases and manganese peroxidases in association with lignocellulose degradation, the mechanisms by which filamentous Ascomycete fungi oxidize Mn(II) and a physiological role for Mn(II) oxidation in these organisms remain poorly understood. Here we use a combination of chemical and in-gel assays and bulk mass spectrometry to demonstrate secretome-based Mn(II) oxidation in three phylogenetically diverse Ascomycetes that is mechanistically distinct from hyphal-associated Mn(II) oxidation on solid substrates. We show that Mn(II) oxidative capacity of these fungi is dictated by species-specific secreted enzymes and varies with secretome age, and we reveal the presence of both Cu-based and FAD-based Mn(II) oxidation mechanisms in all 3 species, demonstrating mechanistic redundancy. Specifically, we identify candidate Mn(II)-oxidizing enzymes as tyrosinase and glyoxal oxidase in Stagonospora sp. SRC1lsM3a, bilirubin oxidase in Stagonospora sp. and Paraconiothyrium sporulosum AP3s5-JAC2a, and GMC oxidoreductase in all 3 species, including Pyrenochaeta sp. DS3sAY3a. The diversity of the candidate Mn(II)-oxidizing enzymes identified in this study suggests that the ability of fungal secretomes to oxidize Mn(II) may be more widespread than previously thought.This work was supported by the National Science Foundation, grant numbers EAR-1249489 and CBET-1336496, both awarded to CH, by a JGI-EMSL Collaborative Science Initiative grant (proposal number 48100) awarded to CH and CS, and by the University of St. Thomas. Personal support for CZ was also provided by Harvard University and by a Ford Foundation Predoctoral Fellowship administered by the National Academies. A portion of this research was performed under the Facilities Integrating Collaborations for User Science (FICUS) program and used resources at the DOE Joint Genome Institute and the Environmental Molecular Sciences Laboratory (grid.436923.9), which are DOE Office of Science User Facilities. Both facilities are sponsored by the Biological and Environmental Research Program and operated under Contract Nos. DE-AC02-05CH11231 (JGI) and DE-AC05-76RL01830 (EMSL). Part of this research was performed at the Bauer Core Facility of the FAS Center for Systems Biology at Harvard University. A portion of the bioinformatics analysis was performed at Harvard’s FAS Research Computing facility

Genes for the Major Structural Components of Thermotogales Species’ Togas Revealed by Proteomic and Evolutionary Analyses of OmpA and OmpB Homologs

The unifying structural characteristic of members of the bacterial order Thermotogales is their toga, an unusual cell envelope that includes a loose-fitting sheath around each cell. Only two toga-associated structural proteins have been purified and characterized in Thermotoga maritima: the anchor protein OmpA1 (or Ompα) and the porin OmpB (or Ompβ). The gene encoding OmpA1 (ompA1) was cloned and sequenced and later assigned to TM0477 in the genome sequence, but because no peptide sequence was available for OmpB, its gene (ompB) was not annotated. We identified six porin candidates in the genome sequence of T. maritima. Of these candidates, only one, encoded by TM0476, has all the characteristics reported for OmpB and characteristics expected of a porin including predominant β-sheet structure, a carboxy terminus porin anchoring motif, and a porin-specific amino acid composition. We highly enriched a toga fraction of cells for OmpB by sucrose gradient centrifugation and hydroxyapatite chromatography and analyzed it by LC/MS/MS. We found that the only porin candidate that it contained was the TM0476 product. This cell fraction also had β-sheet character as determined by circular dichroism, consistent with its enrichment for OmpB. We conclude that TM0476 encodes OmpB. A phylogenetic analysis of OmpB found orthologs encoded in syntenic locations in the genomes of all but two Thermotogales species. Those without orthologs have putative isofunctional genes in their place. Phylogenetic analyses of OmpA1 revealed that each species of the Thermotogales has one or two OmpA homologs. T. maritima has two OmpA homologs, encoded by ompA1 (TM0477) and ompA2 (TM1729), both of which were found in the toga protein-enriched cell extracts. These annotations of the genes encoding toga structural proteins will guide future examinations of the structure and function of this unusual lineage-defining cell sheath

Biological Interactions and Dynamics Science Theme Advisory Panel (BID-STAP)

This report contains the charge to the panel, the panel's discussions and panel recommendations

EMSL Geochemistry, Biogeochemistry and Subsurface Science-Science Theme Advisory Panel Meeting

This report covers the topics of discussion and the recommendations of the panel members. On December 8 and 9, 2010, the Geochemistry, Biogeochemistry, and Subsurface Science (GBSS) Science Theme Advisory Panel (STAP) convened for a more in-depth exploration of the five Science Theme focus areas developed at a similar meeting held in 2009. The goal for the fiscal year (FY) 2011 meeting was to identify potential topical areas for science campaigns, necessary experimental development needs, and scientific members for potential research teams. After a review of the current science in each of the five focus areas, the 2010 STAP discussions successfully led to the identification of one well focused campaign idea in pore-scale modeling and five longer-term potential research campaign ideas that would likely require additional workshops to identify specific research thrusts. These five campaign areas can be grouped into two categories: (1) the application of advanced high-resolution, high mass accuracy experimental techniques to elucidate the interplay between geochemistry and microbial communities in terrestrial ecosystems and (2) coupled computation/experimental investigations of the electron transfer reactions either between mineral surfaces and outer membranes of microbial cells or between the outer and inner membranes of microbial cells

Dengue Virus Infection Perturbs Lipid Homeostasis in Infected Mosquito Cells

Dengue virus causes ∼50–100 million infections per year and thus is considered one of the most aggressive arthropod-borne human pathogen worldwide. During its replication, dengue virus induces dramatic alterations in the intracellular membranes of infected cells. This phenomenon is observed both in human and vector-derived cells. Using high-resolution mass spectrometry of mosquito cells, we show that this membrane remodeling is directly linked to a unique lipid repertoire induced by dengue virus infection. Specifically, 15% of the metabolites detected were significantly different between DENV infected and uninfected cells while 85% of the metabolites detected were significantly different in isolated replication complex membranes. Furthermore, we demonstrate that intracellular lipid redistribution induced by the inhibition of fatty acid synthase, the rate-limiting enzyme in lipid biosynthesis, is sufficient for cell survival but is inhibitory to dengue virus replication. Lipids that have the capacity to destabilize and change the curvature of membranes as well as lipids that change the permeability of membranes are enriched in dengue virus infected cells. Several sphingolipids and other bioactive signaling molecules that are involved in controlling membrane fusion, fission, and trafficking as well as molecules that influence cytoskeletal reorganization are also up regulated during dengue infection. These observations shed light on the emerging role of lipids in shaping the membrane and protein environments during viral infections and suggest membrane-organizing principles that may influence virus-induced intracellular membrane architecture

Fishing For Peptides

In the field of proteomics, samples come from an unlimited variety of sources depending on what the research goals are. During preparation for analysis by mass spectrometry (MS), there is a need to separate peptides from other molecules used in the digestion process. Solid Phase Extraction (SPE) is a common cleanup step used to capture peptides, allowing the researcher to remove unwanted chemicals (e.g. salts, denaturants, surfactants) which results in a sample that can be effectively analyzed by MS. For our testing procedures we performed an in solution digest of Shewanella oneidensis with trypsin, mimicking the preparation for membrane-bound peptides which included a surfactant in the digestion solution. Common steps used in SPE are: condition, equilibrate, load sample, wash, and elute. A Strong Cation Exchange (SCX) SPE column was used to retain peptides in order to get rid of the surfactant. After SPE, a bicinchoninic acid (BCA) assay was performed for quantitation of the peptides recovered. Initially, two new methods were being compared to a standard method used routinely in the lab. From the results, we observed that the percent recovery from the standard method is much higher and has better reproducibility when compared to two additional methods being tested (OMIX & Kim). Another part of the investigation involved the use of two types of SCX SPE columns. Strata (from Phenomenex) columns were compared to the standard Supelclean (Sigma-Aldrich) to see if they would have better performance. Overall, Strata columns had lower yields when compared to Supelclean columns. It is possible that Strata columns have lower peptide binding capacity than the Supelclean columns or that a new method must be developed to increase peptide binding/release from the Strata columns. Further experiments will likely be performed on new methods and SPE columns in order to find a combination that is efficient, reproducible, and obtains higher recoveries

Shining a spotlight on intact proteins

International audienc

Advances in mass spectrometry-enabled multiomics at single-cell resolution

Biological organisms are multifaceted, intricate systems where slight perturbations can result in extensive changes in gene expression, protein abundance and/or activity, and metabolic flux. These changes occur at different timescales, spatially across cells of heterogenous origins, and within single cells. Hence multimodal measurements at the smallest biological scales are necessary to capture dynamic changes in heterogenous biological systems. Of the analytical techniques used to measure biomolecules, mass spectrometry has proven to be a powerful option due to its sensitivity, robustness, and flexibility with regards to breadth of biomolecules that can be analyzed. Recently many studies have coupled mass spectrometry to other analytical techniques with the goal of measuring multiple modalities from the same single-cell. It is with these concepts in mind that we focus this Review on mass spectrometry-enabled multiomic measurements at single-cell or near-single-cell resolution