The PRIDE database and related tools and resources in 2019: improving support for quantification data

Cellular internalization pathways of environmentally exposed microplastic particles: Phagocytosis or macropinocytosis?

Microplastic particles (MP) ubiquitously occur in all environmental compartments where they interact with biomolecules, forming an eco-corona on their surfaces. The eco-corona affects the surface properties of MP and consequently how they interact with cells. Proteins, an integral component within the eco-corona, may serve as a ligand driving the interaction of MP with membrane receptors. To date, it is not known, whether eco-coronae originating from different environmental media differ in their proteinaceous compositions and whether these particles interact differently with cells. We show that the protein composition of the eco-coronae formed in freshwater (FW) and salt water (SW) are distinct from each other. We did not observe different adhesion strengths between MP coated with different eco-coronae and cells. However, the internalization efficiency and the underlying internalization mechanisms significantly differed between FW- and SW eco-coronae. By inhibiting actin-driven and receptor-mediated internalization processes using Cytochalasin-D, Amiloride, and Amantadine, we show that FW microplastic particles predominantly become internalized via phagocytosis, while macropinocytosis is more important for SW microplastic particles. Overall, our findings show that the origin of eco-coronae coatings are important factors for the cellular internalization of microplastic particles. This highlights the relevance of eco-coronae for adverse effects of environmentally relevant microplastic particles on cells and organisms.

Structural and functional characterization of the cardiac mitochondria-associated reticular membranes in the ob/ob mouse model

Type 2 diabetes (T2D) and obesity strongly lead to diabetic cardiomyopathy (DCM). The involvement of mitochondria-associated reticular membranes (MAMs), a signaling hub in the cardiomyocyte, starts to be demonstrated in T2D-related metabolic disorders. We recently discovered a cardiac MAM Ca2+ uncoupling in a high-fat high-sucrose diet (HFHSD)-induced mouse model of DCM. To better determine the role of MAMs in the progression of DCM, we here aimed to characterize the proteomic composition and function of the cardiac MAMs of another obesogenic T2D mouse model, the leptin-deficient ob/ob mouse. 12-week old male C57Bl6-N ob/ob mice displayed strain rate dysfunction and concentric remodeling, while no change was observed in fractional shortening or diastolic function. Increased lipid deposition but no fibrosis was measured in the ob/ob heart compared to WT. Electron microscopy analysis revealed that cardiac MAM length and width were similar between both groups. A trend towards an increased MAM protein content was measured in the ob/ob heart. MAM proteome analyses showed mainly increased processes in ob/ob hearts: cellular response to stress, lipid metabolism, ion transport and membrane organization. Functionally, MAM-driven Ca2+ fluxes were unchanged but hypoxic stress induced a cell death increase in the ob/ob cardiomyocyte. Mitochondrial respiration, cardiomyocyte shortening, ATP and ROS content were similar between groups. To conclude, at that age, while being strongly hyperglycemic and insulin-resistant, the ob/ob mouse model rather displays a modest DCM without strong changes in MAMs: preserved structural and functional MAM Ca2+ coupling but increased response to stress.

IFITM1 as a modulator of surfaceome dynamics and aggressive phenotype in cervical cancer cells

Interferon‑induced transmembrane proteins (IFITMs) are frequently overexpressed in cancer cells, including cervical carcinoma cells, and play a role in the progression of various cancer types. However, their mechanisms of action remain incompletely understood. In the present study, by employing a combination of surface membrane protein isolation and quantitative mass spectrometry, it was comprehensively described how the IFITM1 protein influences the composition of the cervical cancer cell surfaceome. Additionally, the effects of interferon‑γ on protein expression and cell surface exposure were evaluated in the presence and absence of IFITM1. The IFITM1‑regulated membrane and membrane‑associated proteins identified are involved mainly in processes such as endocytosis and lysosomal transport, cell‑cell and cell‑extracellular matrix adhesion, antigen presentation and the immune response. To complement the proteomic data, gene expression was analyzed using reverse transcription‑quantitative PCR to distinguish whether the observed changes in protein levels were attributable to transcriptional regulation or differential protein dynamics. Furthermore, the proteomic and gene expression data are supported by functional studies demonstrating the impact of the IFITM1 and IFITM3 proteins on the adhesive, migratory and invasive capabilities of cervical cancer cells, as well as their interactions with immune cells.

Skin mucus and blood plasma as non-lethal sources of malnutrition protein biomarkers in meagre (Argyrosomus regius)

Developing dietary formulations for aquaculture that meet nutritional requirements is essential to production, as nutrition is key for fish growth and health. However, novel dietary formulations may induce malnutrition, which is complex to evaluate and often requires animal sacrifice. Therefore, finding reliable non-lethal biomarkers to diagnose malnutrition in fish is important. This study aimed to obtain vital information on potential non-lethal biomarkers from blood plasma and skin mucus to assess the fish's nutritional status using meagre (Argyrosomus regius) juveniles. For that purpose, a nutritional challenge was performed with fish fed a fish meal (FM) and fish-oil (FO) based control diet (55.1 % FM; 11 % FO, CTRL), a challenging diet (15 % FM; 7 % FO, CD), and a highly challenging diet (5 % FM; 5 % FO, ED), which, despite being nutritionally complete, may pose digestive and physiological challenges to carnivorous species. Diets significantly affected blood parameters, except for leukocyte counts, peroxidase activity, and immunoglobulin levels. Overall, blood parameters showed potential as non-lethal biomarkers to accurately identify signs of malnutrition. Meagre's plasma and skin mucus proteomes provided crucial information on the species' reaction to malnutrition, and 29 proteins connected to various physiological functions such as metabolism, development and immunity showed potential as non-lethal biomarkers. SIGNIFICANCE: The significance of this study lies in the establishment of potential non-lethal biomarkers for diagnosing malnutrition in fish. The results demonstrate that immunological, haematological, and biochemical parameters measured in fish blood can reveal signs of nutritional deficiencies. The findings further highlight that the proteomes of plasma and skin mucus provide valuable information about the fish's nutritional status. Notably, 29 proteins identified in this study, associated with various physiological functions, exhibit biomarker potential and warrant consideration in future research in the field of aquaculture nutrition. Moreover, the research provides critical insights into the proteome of meagre (Argyrosomus regius), enhancing our understanding of the species and contributing to the future improvement of its aquaculture production.

P4PP: an universal shotgun proteomics data analysis pipeline for virus identification

Humans can be infected by a wide variety of virus species. We developed a data analysis approach for shotgun proteomic data to detect these viruses. A proteome for pandemic preparedness (P4PP) pipeline, a corresponding database (P4PP v01), and a web application (P4PP) were constructed. The P4PP pipeline enables the identification of 1896 virus species from the 32 virus families, based on multiple identified discriminatory peptides, in which at least one human-infectious virus is described. P4PP was evaluated using different datasets of cell-cultivated viruses, generated at different institutes, measured with different instruments, and prepared with different sample preparation methods. In total, 174 MS datasets of 160 and 14 protein trypsin digests of virus-infected and non-infected cell lines were analyzed, respectively. Of the 160 samples, 146 were correctly identified at the species level, and an additional 4 samples were identified at the family level. In the remaining 10 samples, no virus was detected. However, all these 10 samples tested positive in follow-up samples obtained later in time series were negative samples were measured, indicating that the number of peptides derived from the virus was initially too low in the samples obtained at the start of the experiment. Furthermore, results show that Influenza A or SARS-CoV-2 can be subtyped if enough discriminative peptides of the virus are identified. In the non-infected cell lines, no virus was detected except in one sample where the in that experiment studied virus was detected. Shotgun proteomics, in combination with the developed data analysis approach, can identify all types of virus species after cultivation in a cell line. Implementing this agnostic virus proteome analysis capability in viral diagnostic laboratories has the potential to improve their capabilities to cope with unexpected, mutated or re-emerging viruses.

Activation mechanism of small heat shock protein HSPB5 revealed by disease-associated mutants

Found from bacteria to humans, small heat shock proteins (sHSPs) are the least understood protein chaperones. HSPB5 (or αB-crystallin) is among the most widely expressed of the 10 human sHSPs, including in muscle, brain, and eye lens where it is constitutively present at high levels. A high content of disorder in HSPB5 has stymied efforts to uncover how its structure gives rise to function. To uncover its mechanisms of action, we compared human HSPB5 and two disease-associated mutants, R120G and D109H. Expecting to learn how the mutations lead to loss of function, we found instead that the mutants are constitutively activated chaperones while wild-type HSPB5 can transition reversibly between nonactivated (low activity) and activated (high activity) states in response to changing conditions. Techniques that provide information regarding interactions and accessibility of disordered regions revealed that the disordered N-terminal regions (NTR) that are required for chaperone activity exist in a complicated interaction network within HSPB5 oligomers and are sequestered from solvent in nonactivated states. Either mutation or an activating pH change causes rearrangements in the network that expose parts of the NTR, making them more available to bind an aggregating client. Although beneficial in the short-term, failure of the mutants to adopt a state with lower activity and lower NTR accessibility leads to increased coaggregation propensity and, presumably, early cataract. The results support a model where chaperone activity and solubility are modulated through the quasi-ordered NTR and its multiple competing interactions.

MultiStageSearch: An Iterative Workflow for Unbiased Taxonomic Analysis of Pathogens Using Proteogenomics

The global SARS-CoV-2 pandemic emphasized the need for accurate pathogen diagnostics. While genomics is the gold standard, integrating mass spectrometry-based proteomics offers additional benefits. However, current proteomic and genomic reference databases are often biased toward specific taxa, such as pathogenic strains or model organisms, and proteomic databases are less comprehensive. These biases and gaps can lead to inaccurate identifications. To address these issues, we introduce MultiStageSearch, a multistep database search method that combines proteome and genome databases for taxonomic analysis. Initially, a generalist proteome database is used to infer potential species. Then, MultiStageSearch generates a specialized proteogenomic database for precise identification. This database is preprocessed to filter duplicates and cluster identical open reading frames to reduce genomic database biases. The workflow operates independently of strain-level NCBI taxonomy, enabling the identification of strains not represented in existing taxonomies. We benchmarked the workflow on viral and bacterial samples, demonstrating its superior performance in strain-level taxonomic inference compared to existing methods. MultiStageSearch offers a flexible and accurate approach for pathogen research and diagnostics, overcoming incomplete search spaces and biases inherent in reference databases.

Light and polyphosphate kinase 2 cooperatively regulate the production of zero-valent sulfur in a deep-sea bacterium

It is well established that different wavelengths of light exist in various deep-sea environments, and many deep-sea microorganisms have evolved specialized mechanisms for sensing and utilizing light energy. Our previous research found that blue light promotes zero-valent sulfur (ZVS) production in Erythrobacter flavus 21-3, a bacterium isolated from a deep-sea cold seep. Given that long-wavelength light is more prevalent in deep-sea environments, the present study investigates the mechanism by which E. flavus 21-3 senses infrared light (wavelength 940 nm) and regulates ZVS production. We found that the bacteriophytochrome BPHP-15570 is responsible for sensing infrared light, which induces autophosphorylation of BPHP-15570, activating the diguanylate cyclase DGC-0450 for c-di-GMP biosynthesis. Subsequently, the PilZ domain-containing protein mPilZ-1753 binds to c-di-GMP, triggering a well-established ZVS production pathway involving thiosulfate dehydrogenase (TsdA) and two homologs of thiosulfohydrolases (SoxB). Notably, polyphosphate kinase 2 (PPK2) is recruited to compete for GTP, the direct precursor of c-di-GMP biosynthesis. This competition downregulates ZVS production as well as other important metabolic processes. This negative regulatory pathway helps the bacterium avoid excessive ZVS accumulation, which could be toxic to bacterial growth. Overall, E. flavus 21-3 has evolved a sophisticated regulatory pathway to sense both blue and infrared light, triggering ZVS production. Our study provides a valuable model for understanding light utilization and its coupling with sulfur cycling in deep-sea environments.IMPORTANCEIt is widely believed that deep-sea ecosystems operate independently of light, relying primarily on chemical energy. However, the discovery of non-photosynthetic bacteria in various deep-sea environments that can sense and utilize light has challenged this assumption. In a recent study, we found that blue light significantly promotes the production of zero-valent sulfur (ZVS) in the deep-sea bacterium Erythrobacter flavus 21-3. Given that long-wavelength light is more prevalent in deep-sea environments, we investigated whether infrared light also plays a role in regulating ZVS production in E. flavus 21-3. Our results indicate that infrared light does promote ZVS formation in this bacterium. We identified PPK2 as a negative regulator, maintaining intracellular ZVS at safe levels to prevent toxicity due to excessive accumulation. Overall, our study offers a valuable model for exploring how light is utilized and its interaction with microbial sulfur cycling in the extreme conditions of the deep sea.

P.1 and P.2 SARS-CoV-2 Brazilian variants activate the unfolded protein response with a time and pathway specificity

COVID-19 is a human respiratory syndrome caused by the infection of the SARS-CoV-2 virus that has a high rate of infection and mortality. Viruses modulate the host machinery by altering cellular mechanisms that favor their replication. One of the mechanisms that viruses exploit is the protein folding and processing of post-translational modifications that occur in the endoplasmic reticulum (ER). When ER function is impaired, there is an accumulation of misfolded proteins leading to endoplasmic reticulum stress (ER stress). To maintain homeostasis, cells trigger an adaptive signaling mechanism called the Unfolded Protein Response (UPR) which helps cells deal with stress, but under severe conditions, can activate the apoptotic cell death mechanism. This study elucidated an activation of a diversity of molecular mechanisms by Brazilian variants of SARS-CoV-2 by a time-resolved and large-scale characterization of SARS-CoV-2-infected cells proteomics and immunoblotting. Furthermore, it was shown that pharmacological UPR modulation could reduce viral release by counteracting the different viral activations of its cellular response. Analysis of human clinical specimens and disease outcomes focusing on ER stress reinforces the importance of UPR modulation as a host regulatory mechanism during viral infection and could point to novel therapeutic targets. SIGNIFICANCE: Since the emergence of SARS-CoV-2 and the consequent COVID-19 pandemic, the rapid emergence of variants of this new coronavirus has been a cause for concern since many of them have significantly higher rates of transmissibility and virulence, being called Variants of Concern (VOC). In this work, we studied the VOCs Gamma (P.1) and Zeta (P.2), also known as Brazilian variants. Constant evidence has reported that there are particularities related to each variant of SARS-CoV-2, with different rates of transmissibility, replication and modulation of host biological processes being observed, in addition to the mutations present in the variants. For this reason, this work focused on infections caused by the Brazilian variants of SARS-CoV-2 in different cell lines, in which we were able to observe that the infections caused by the variants induced endoplasmic reticulum stress in the infected cells and activated the UPR pathways, presenting specific modulations of each variant in this pathway. Furthermore, transcriptome analysis of patients revealed a correlation between ER-related genes and COVID-19 progression. Finally, we observed that the use of UPR modulators in host cells decreased viral release of all variants without affecting cell viability. The data presented in this work complement the observations of other studies that aim to understand the pathogenicity of SARS-CoV-2 VOCs and possible new therapeutic strategies, mainly targeting biological processes related to the endoplasmic reticulum.

HDXRank: A Deep Learning Framework for Ranking Protein Complex Predictions with Hydrogen-Deuterium Exchange Data

Accurate modeling of protein-protein complex structures is essential for understanding biological mechanisms. Hydrogen-deuterium exchange (HDX) experiments provide valuable insights into binding interfaces. Incorporating HDX data into protein complex modeling workflows offers a promising approach to improve prediction accuracy. Here, we developed HDXRank, a graph neural network (GNN)-based framework for candidate structure ranking utilizing alignment with HDX experimental data. Trained on a newly curated HDX data set, HDXRank captures nuanced local structural features critical for accurate HDX profile prediction. This versatile framework can be integrated with a variety of protein complex modeling tools, transforming the HDX profile alignment into a model quality metric. HDXRank demonstrates effectiveness at ranking models generated by rigid docking or AlphaFold, successfully prioritizing functionally relevant models and improving prediction quality across all tested protein targets. These findings underscore HDXRank's potential to become a pivotal tool for understanding molecular recognition in complex biological systems.

ATP functions as a pathogen-associated molecular pattern to activate the E3 ubiquitin ligase RNF213

The giant E3 ubiquitin ligase RNF213 is a conserved component of mammalian cell-autonomous immunity, limiting the replication of bacteria, viruses and parasites. To understand how RNF213 reacts to these unrelated pathogens, we employ chemical and structural biology to find that ATP binding to its ATPases Associated with diverse cellular Activities (AAA) core activates its E3 function. We develop methodology for proteome-wide E3 activity profiling inside living cells, revealing that RNF213 undergoes a reversible switch in E3 activity in response to cellular ATP abundance. Interferon stimulation of macrophages raises intracellular ATP levels and primes RNF213 E3 activity, while glycolysis inhibition depletes ATP and downregulates E3 activity. These data imply that ATP bears hallmarks of a danger/pathogen associated molecular pattern, coordinating cell-autonomous defence. Furthermore, quantitative labelling of RNF213 with E3-activity probes enabled us to identify the catalytic cysteine required for substrate ubiquitination and obtain a cryo-EM structure of the RNF213-E2-ubiquitin conjugation enzyme transfer intermediate, illuminating an unannotated E2 docking site. Together, our data demonstrate that RNF213 represents a new class of ATP-dependent E3 enzyme, employing distinct catalytic and regulatory mechanisms adapted to its specialised role in the broad defence against intracellular pathogens.

ProteoPlotter: An Executable Proteomics Visualization Tool Compatible with Perseus

Mass spectrometry-based proteomics experiments produce complex data sets requiring robust statistical testing and effective visualization tools to ensure meaningful conclusions are drawn. The publicly available proteomics data analysis platform, Perseus, is extensively used to perform such tasks, but opportunities to enhance visualization tools and promote accessibility of the data exist. In this study, we developed ProteoPlotter, a user-friendly, executable tool to complement Perseus for visualization of proteomics data sets. ProteoPlotter is built on the Shiny framework for R programming and enables illustration of multidimensional proteomics data. ProteoPlotter supports mapping of one-dimensional enrichment analyses, enhanced adaptability of volcano plots through incorporation of Gene Ontology terminology, visualization of 95% confidence intervals in principal component analysis plots using data ellipses, and customizable features. ProteoPlotter is designed for intuitive use by biological and computational researchers alike, providing descriptive instructions (i.e., Help Guide) for preparing and uploading Perseus output files. Herein, we demonstrate the application of ProteoPlotter toward microbial proteome remodeling under altered nutrient conditions and highlight the diversity of visualizations enabled with the platform for enhanced biological insights. Through its comprehensive data visualization capabilities, linked to the power of Perseus data handling and statistical analyses, ProteoPlotter facilitates enhanced visualization of proteomics data to drive new biological discoveries.

Human Voltage-Activated H+ Channel is Highly Expressed in Acute Myeloid Leukemia and is Associated With the Blast Differentiated Stage

BACKGROUND

In acute myeloid leukemia (AML), hematopoietic precursors of myeloid cells proliferate rapidly but are arrested at an early stage, impeding their maturation and normal function. The human voltage-activated proton channel (hHv1) is a membrane protein with important roles in myeloid phagocytic cells. This work aimed to evaluate the expression of hHv1 channel as a novel biological marker associated with the process of cell differentiation in AML.

METHODS

In this study, we evaluated the expression of the hHv1, at both mRNA and protein levels in AML.

RESULTS

We demonstrated that the expression of hHv1 is upregulated at both mRNA and protein levels in AML. Moreover, our results indicate that hHv1 expression correlates with the degree of monocytic differentiation in AML cells in a pattern similar to that previously reported for NADPH oxidase (NOX2), a relevant cellular structure functionally coupled to the hHv1 channel. However, while increases in NOX2 components have not been associated with improved prognosis or survival, we found that the hHv1 upregulation was associated with better prognosis and survival outcomes.

CONCLUSIONS

These results suggest that hHv1 may serve as a novel biomarker for favorable prognosis in AML and may represent a promising therapeutic target.

Structural proteomics defines a sequential priming mechanism for the progesterone receptor

The progesterone receptor (PR) is a steroid-responsive nuclear receptor with two isoforms: PR-A and PR-B. Disruption of PR-A:PR-B signaling is associated with breast cancer through interactions with oncogenic co-regulatory proteins (CoRs). However, molecular details of isoform-specific PR-CoR interactions remain poorly understood. Using structural mass spectrometry, we investigate the sequential binding mechanism of purified full-length PR and intact CoRs, steroid receptor coactivator 3 (SRC3) and p300, as complexes on target DNA. Our findings reveal selective CoR NR-box binding by PR and unique interaction surfaces between PR and CoRs during complex assembly, providing a structural basis for CoR sequential binding on PR. Antagonist-bound PR showed persistent CoR interactions, challenging the classical model of nuclear receptor activation and repression. In this work, we offer a peptide-level perspective on the organization of the PR transcriptional complex and infer the mechanisms behind the interactions of these proteins, both in active and inactive conformations.

TORC1 autonomously controls its spatial partitioning via the Rag GTPase tether Tco89

The eukaryotic target of rapamycin complex 1 (TORC1) kinase is a homeostatic regulator of growth, integrating nutritional cues at the endolysosomal compartment. Amino acids activate mammalian TORC1 (mTORC1) through the Rag GTPases that recruit it to lysosomes via a short domain within the mTORC1 subunit Raptor. Intriguingly, this "Raptor claw" domain is absent in Kog1, the Raptor ortholog in yeast. Instead, as we show here, yeast utilizes the fungal-specific Tco89 to tether TORC1 to active Rag GTPases. This interaction enables TORC1 to precisely calibrate the activity of the S6K1-related effector kinase Sch9 in response to amino acid availability. TORC1 stabilizes Tco89 by phosphorylation, and its inactivation causes swift Tco89 proteolysis, provoking a redistribution of TORC1 from the vacuole to signaling endosomes and its spatial separation from Sch9. Thus, TORC1 not only operates in spatially distinct subcellular pools but also controls its own quantitative distribution between these pools to economize energy resources under fluctuating nutrient conditions.

A specialized TFIIB is required for transcription of transposon-targeting noncoding RNAs

Transposable elements (TEs) pose threats to genome stability. Therefore, small RNA-mediated heterochromatinization suppresses the transcription and hence the mobility of TEs. Paradoxically, transcription of noncoding RNA (ncRNA) from TEs is needed for the production of TE-targeting small RNAs and/or recruiting the silencing machinery to TEs. Hence, specialized RNA polymerase II (Pol II) regulators are required for such unconventional transcription in different organisms, including the developmental stage-specific Mediator complex (Med)-associated proteins in the ncRNA transcription from TE-related sequences in Tetrahymena. Yet it remains unclear how the Pol II transcriptional machinery is assembled at TE-related sequences for the ncRNA transcription. Here, we report that Pol II is regulated by Emit3, a stage-specific TFIIB-like protein specialized in TE transcription. Emit3 interacts with the TFIIH complex and localizes to TE-dense regions, especially at sites enriched with a G-rich sequence motif. Deletion of Emit3 globally abolishes Pol II-chromatin association in the meiotic nucleus, disrupts the chromatin binding of Med, and impairs the TE-biased localization of TFIIH. Conversely, Emit3's preferential localization to TE-rich loci relies in part on Med-associated proteins. These findings suggest that Emit3, TFIIH, and Med-associated proteins work together to initiate Pol II ncRNA transcription from TE-dense regions, possibly in a sequence-dependent manner.

LIPID DROPLET PROTEIN OF SEEDS is involved in the control of lipid droplet size in Arabidopsis seeds and seedlings

In oilseeds, energy-rich carbon is stored as triacylglycerols in organelles called lipid droplets (LDs). While several of the major biogenetic proteins involved in LD formation have been identified, the full repertoire of LD proteins and their functional roles remains incomplete. Here, we show that the low-abundance, seed-specific LD protein LIPID DROPLET PROTEIN OF SEEDS (LDPS) contains an amphipathic α-helix and proline hairpin motif that serves as an LD-targeting signal and a separate region that binds to the LD protein OLEOSIN 1 (OLEO1). Loss of LDPS function results in smaller LDs and less seed oil in comparison with wild type, while overexpression of LDPS results in an increase in LD size and seed oil content. Loss of LDPS function also results in an inability of LDs to undergo fusion during postgerminative seedling growth. Analysis of oleo1 and ldps single- and double-mutant seeds and freeze-thaw treatment of seeds revealed that OLEO1 suppresses the ability of LDPS to promote larger LDs. Collectively, our results identify LDPS as an important player in LD biology that functions together with OLEO1 to determine LD size in Arabidopsis (Arabidopsis thaliana) seeds and seedlings through a process that involves LD-LD fusion.

Complement 3 (C3) within the hypothalamic arcuate nucleus is a potential key mediator of the effect of enhanced nutrition on reproductive development in young bull calves

BACKGROUND

Reproductive development may be advanced in bull calves through enhanced dietary intake during the early life period. This effect between enhanced nutrition with subsequent earlier reproductive development is orchestrated through signalling within the hypothalamic-pituitary-testicular axis. Within the hypothalamus, the arcuate nucleus (ARC) is crucial for the integration of peripheral metabolic status with subsequent gonadotropin releasing hormone (GnRH) signalling; however, the precise molecular control regulating this effect is not fully known. The aim of this study was to evaluate the global transcriptomic and proteomic responses to varied plane of nutrition during early calf-hood in young dairy bull calves. Additionally, we sought to integrate these 'omics' datasets to determine key genes and proteins contributing to earlier reproductive development. Between 2-12 weeks of age, 30 Holstein-Friesian bull calves (mean age: 17.5 days; mean bodyweight 48.8 kg), were offered either a high or moderate plane of nutrition with 15 calves in each group. At 12 weeks of age, all calves were euthanised and the ARC tissue isolated from each calf. The ARC tissue was then used for global transcriptomic (miRNAseq and mRNAseq) and proteomic analyses.

RESULTS

Bioinformatic analyses were undertaken to determine differentially expressed transcripts (FDR < 0.1; fold change > 1.5) between the dietary treatment groups, resulting in the identification of 1 differentially expressed miRNA (miR-2419-3p) and 83 differentially expressed mRNA in the ARC region. mRNA target gene prediction identified Complement 3 (C3) as a target of miR-2419-3p, suggesting a relationship between the two transcripts. Furthermore, through a co-regulatory network analysis conducted on the proteomics dataset, C3 was revealed as a hub protein. Additionally, through the proteomic network analysis, C3 was interacting with proteins involved in both insulin and GnRH signalling, highlighting a potential role for C3 in mediated the effect of enhanced nutritional status with earlier reproductive development within the ARC.

CONCLUSION

This study highlights an effect of altered plane of nutrition in early life on the molecular control of the hypothalamic ARC. Additionally, results generated suggest a potential role for the C3 gene in mediating the interaction between enhanced metabolic status with reproductive development within the ARC, regulated by miR-2419-3p.

Evidence of focusing the MHC class I immunopeptidome by tapasin

Major Histocompatibility Complex class I (MHC-I) molecules bind and present peptides to cytotoxic T cells, protecting against pathogens and cancer. MHC-I is highly polymorphic and each allotype is promiscuous, and capable of binding a unique and diverse repertoire of peptide ligands. The peptide editing chaperone tapasin optimizes this allotype specific repertoire of peptides, resulting in the selection of high affinity peptides. MHC-I allotypes differ in the extent they engage tapasin. This suggests that tapasin-dependent MHC-I allotypes should present a less diverse repertoire that is enriched in higher-affinity peptides, and which are present in higher abundance, than tapasin independent MHC-I allotypes, which should present a broader repertoire containing peptides with a lower average affinity. Experimental verification of this hypothesis has been confounded by the different peptide binding specificities of MHC-I allotypes. Here, we independently investigated the peptide focusing function of tapasin by introducing a point mutation into a tapasin independent MHC-I allotype that dramatically increased its tapasin dependence without substantially altering its peptide binding specificity. This allowed us to demonstrate ligand focusing by tapasin at both the repertoire level in cellulo, and by using an in vitro system in which tapasin was artificially tethered to MHC-I, at the individual peptide level. We found that tapasin had a greater influence on tapasin dependent MHC-I molecules, and that tapasin modulated peptide selection according to peptide-MHC-I complex stability, disfavoring short-lived peptide-MHC-I complexes. Thus, tapasin dependent MHC-I molecules experience greater tapasin filtering, resulting in less diverse MHC-I immunopeptidomes that are enriched in high affinity peptide-MHC-I complexes.

Systemic Acetylome Analysis of Evolution in Fluconazole Resistance Candida auris

Candida auris is an opportunistic pathogen and has become a globally clinical concern due to multidrug resistance. In this study, we generated a series of C. auris strains (CF2, -3, -4, -5, and -6) with elevated MIC50 of fluconazole from CF1 by gradually increasing fluconazole concentration. Employing 4D label-free proteomics, we explored the contributions of acetylome alterations to the evolution of fluconazole resistance in C. auris. From 18 samples of six C. auris strains, we identified 2419 acetylated proteins with 7833 sites, quantified 3032 proteins, and 6310 sites. Compared to CF1, differentially acetylated proteins were significantly linked to cytosolic ribosomes, structural molecule activity, hexose and monosaccharide catabolism, glycolysis/gluconeogenesis, and alcohol dehydrogenase GroES-like domain. CF3 (16-32 μg/mL) and CF4 (64 μg/mL) were suggested as the key resistance inflection. CF3 was associated with a significant decrease in ribosomal protein acetylation, while CF4 witnesses a marked upsurge in acetylated proteins and sites. Upregulated proteins in CF3 were notably involved in oxidative stress, detoxification, osmotic stress, and alcohol. We drew a diagram to show acetylated sites on histones in C. auris. To the best of our knowledge, this is the first acetylome study in C. auris, providing insights into the biological and pathogenic roles of post-translational modifications (PTMs) in this organism.

Cobalt-induced stress reveals a prominent role of CzcC on the proteomic profile of Gluconacetobacter diazotrophicus PAL5

AIMS

Heavy metal accumulation in agricultural areas is a global environmental problem that affects microorganisms and plants, with serious implications for human health. This study aimed to investigate the molecular responses of the plant growth-promoting bacterium Gluconacetobacter diazotrophicus PAL5 to cobalt stress.

METHODS AND RESULTS

We evaluated bacterial growth and cell viability under cobalt stress and performed comparative proteomic and reverse genetics analyses. Cobalt significantly inhibited bacterial growth but did not cause cell death. Proteomic analysis in the presence of 2.5 mmol l-1 CoCl2, which caused ∼50% growth inhibition, revealed the induction of pathways related to iron uptake, carbohydrate metabolism, amino acid metabolism, quality control, and efflux. Knockout mutants for genes involved in these pathways (∆tbdR, ∆zwf, ∆pdhB, ∆argH, and ∆czcC) confirmed the essential role of the CzcC efflux system in cobalt tolerance.

CONCLUSIONS

Cobalt stress triggers molecular responses in G. diazotrophicus PAL5, with efflux systems playing a crucial role in stress tolerance.

Temporal Proteomic Profiling of Pheromone-Induced Cell Cycle Re-Entry in Saccharomyces cerevisiae

The regulation of cell cycle progression in response to environmental cues is essential for cellular adaptation. In Saccharomyces cerevisiae, the BAR1 gene modulates sensitivity to the mating pheromone α-factor, which induces cell cycle arrest in G1. Here, we investigated the dynamic proteomic response in the bar1 deletion strain using a 27-plex experimental design with TMTproD isobaric labeling. Asynchronous bar1Δ cells were treated with α-factor and then released from the pheromone-induced cell cycle arrest in G1. Using higher-order TMTpro sample multiplexing, we generated global temporal profiles of protein abundance associated with recovery from this arrest, with triplicate samples collected at eight time points from 0 to 165 min after washing out the pheromone. We identify specific proteins involved in cell cycle re-entry and in the attenuation of the pheromone signal, providing insights into the regulatory mechanisms of mating response in yeast. This study also contributes significantly to dynamic proteomic analysis of cell cycle progression. We present a versatile approach for investigating complex cellular processes and showcase cell cycle progression following release from pheromone-induced arrest in yeast.

irCLIP-RNP and Re-CLIP reveal patterns of dynamic protein assemblies on RNA

RNA-binding proteins (RBPs) control varied processes, including RNA splicing, stability, transport and translation1-3. Dysfunctional RNA-RBP interactions contribute to the pathogenesis of human disease1,4,5; however, characterizing the nature and dynamics of multiprotein assemblies on RNA has been challenging. Here, to address this, non-isotopic ligation-based ultraviolet-light-induced cross-linking and immunoprecipitation6 was combined with mass spectrometry (irCLIP-RNP) to identify RNA-dependent associated proteins (RDAPs) co-bound to RNA with any RBP of interest. irCLIP-RNP defined landscapes of multimeric protein assemblies on RNA, revealing patterns of RBP-RNA associations, including cell-type-selective combinatorial relationships between RDAPs and primary RBPs. irCLIP-RNP also defined dynamic RDAP remodelling in response to epidermal growth factor (EGF), revealing that EGF-induced recruitment of UPF1 adjacent to HNRNPC promotes splicing surveillance of cell proliferation mRNAs. To identify the RNAs simultaneously co-bound by multiple studied RBPs, a sequential immunoprecipitation irCLIP (Re-CLIP) method was also developed. Re-CLIP confirmed binding relationships observed in irCLIP-RNP and identified HNRNPC and UPF1 RBP co-binding on RND3 and DDX3X mRNAs. irCLIP-RNP and Re-CLIP provide a framework to identify and characterize dynamic RNA-protein assemblies in living cells.

Three ARID proteins involved in chromatin remodeling PEAT complexes are targeted by the Ralstonia solanacearum effector PopP2 and contribute to bacterial wilt disease

Like many gram-negative phytopathogenic bacteria, Ralstonia solanacearum uses a type III secretion system to deliver into host cells a cocktail of effector proteins that can interfere with plant defenses and promote infection. One of these effectors, the nuclear-targeted PopP2 acetyltransferase, was reported to inhibit many defensive WRKY transcription factors through acetylation. To gain a better understanding of the mechanisms by which PopP2 might exert its virulence functions, we searched for other PopP2-interacting partners. Here we report the identification of the Arabidopsis thaliana AT-Rich Interaction Domain protein 3 (ARID3) and its close homologs, ARID2 and ARID4, as additional targets of PopP2. These ARID proteins are core components of the chromatin remodeling PEAT complexes that regulate gene expression through histone (de)acetylation and deubiquitination. In yeast, PopP2 binds the conserved C-terminal part of ARID2/3/4, which contains an α-crystallin domain putatively involved in their homo-oligomerization. ARID2/3/4 behave as substrates of PopP2 acetyltransferase activity, which causes the acetylation of several lysine residues conserved between these three proteins and located near their α-crystallin domain. Interestingly, while PopP2 negatively affects ARID3 and ARID4 self-interactions in planta, it promotes the interaction of ARID3 and ARID4 with PWWP1, another component of PEAT complexes, with which PopP2 can also interact. This study also reveals that disruption of ARID2/3/4 results in reduced growth of R. solanacearum. Overall, our data are consistent with a model in which PopP2 targets several components of PEAT complexes to interfere with their epigenetic regulatory functions and promote Ralstonia infection in Arabidopsis.

The European Bioinformatics Community for Mass Spectrometry (EuBIC-MS): an open community for bioinformatics training and research

The European Bioinformatics Community for Mass Spectrometry (EuBIC-MS; eubic-ms.org) was founded in 2014 to unite European computational mass spectrometry researchers and proteomics bioinformaticians working in academia and industry. EuBIC-MS maintains educational resources (proteomics-academy.org) and organises workshops at national and international conferences on proteomics and mass spectrometry. Furthermore, EuBIC-MS is actively involved in several community initiatives such as the Human Proteome Organization's Proteomics Standards Initiative (HUPO-PSI). Apart from these collaborations, EuBIC-MS has organised two Winter Schools and two Developers' Meetings that have contributed to the strengthening of the European mass spectrometry network and fostered international collaboration in this field, even beyond Europe. Moreover, EuBIC-MS is currently actively developing a community-driven standard dedicated to mass spectrometry data annotation (SDRF-Proteomics) that will facilitate data reuse and collaboration. This manuscript highlights what EuBIC-MS is, what it does, and what it already has achieved. A warm invitation is extended to new researchers at all career stages to join the EuBIC-MS community on its Slack channel (eubic.slack.com).

INFERYS rescoring: Boosting peptide identifications and scoring confidence of database search results

Database search engines for bottom-up proteomics largely ignore peptide fragment ion intensities during the automated scoring of tandem mass spectra against protein databases. Recent advances in deep learning allow the accurate prediction of peptide fragment ion intensities. Using these predictions to calculate additional intensity-based scores helps to overcome this drawback. Here, we describe a processing workflow termed INFERYS™ rescoring for the intensity-based rescoring of Sequest HT search engine results in Thermo Scientific™ Proteome Discoverer™ 2.5 software. The workflow is based on the deep learning platform INFERYS capable of predicting fragment ion intensities, which runs on personal computers without the need for graphics processing units. This workflow calculates intensity-based scores comparing peptide spectrum matches from Sequest HT and predicted spectra. Resulting scores are combined with classical search engine scores for input to the false discovery rate estimation tool Percolator. We demonstrate the merits of this approach by analyzing a classical HeLa standard sample and exemplify how this workflow leads to a better separation of target and decoy identifications, in turn resulting in increased peptide spectrum match, peptide and protein identification numbers. On an immunopeptidome dataset, this workflow leads to a 50% increase in identified peptides, emphasizing the advantage of intensity-based scores when analyzing low-intensity spectra or analytes with very similar physicochemical properties that require vast search spaces. Overall, the end-to-end integration of INFERYS rescoring enables simple and easy access to a powerful enhancement to classical database search engines, promising a deeper, more confident and more comprehensive analysis of proteomic data from any organism by unlocking the intensity dimension of tandem mass spectra for identification and more confident scoring.

E-Cadherin Is a Structuring Component of Invadopodia in Pancreatic Cancer

The appearance of hybrid epithelial-mesenchymal (E/M) cells expressing E-cadherin is favourable for the establishment of pro-invasive function. Although the potential role of E-cadherin in cancer invasion is now accepted, the molecular mechanisms involved in this process are not completely elucidated. To gain further insight, we focused our analysis on invadopodia formation, an early event in the invasion process. We used models of E/M hybrid cell lines, tissue sections and patient-derived xenografts from a multi-centre clinical trial. E-cadherin involvement in invadopodia formation was assessed using a gelatin-FITC degradation assay. Mechanistic studies were performed by using proteomic analysis, siRNA strategy and proximity ligation assay. We showed that E-cadherin is a critical component of invadopodia. This unexpected localization results from a synergistic trafficking of E-cadherin and MT1-MMP through a Rab vesicle-dependent pathway. Modulation of E-cadherin expression or activation impacted invadopodia formation. Moreover, colocalization of E-cadherin and Actin in "ring structures" as precursors of invadopodia reveals that E-cadherin is required for invadopodia structuration. E-cadherin, initially localised in the adherens junctions, could be recycled to nascent invadopodia where it will interact with several components enriched in invadopodia, such as Arp2/3, Cortactin or MT1-MMP. The trans-adhesive properties of E-cadherin are therefore essential for structuring invadopodia. This new localisation of E-cadherin and its unexpected role in cell invasion shine a new light on hybrid E/M transition features in tumoral invasion.

Large-scale tandem mass spectrum clustering using fast nearest neighbor searching

RATIONALE

Advanced algorithmic solutions are necessary to process the ever-increasing amounts of mass spectrometry data that are being generated. In this study, we describe the falcon spectrum clustering tool for efficient clustering of millions of MS/MS spectra.

METHODS

falcon succeeds in efficiently clustering large amounts of mass spectral data using advanced techniques for fast spectrum similarity searching. First, high-resolution spectra are binned and converted to low-dimensional vectors using feature hashing. Next, the spectrum vectors are used to construct nearest neighbor indexes for fast similarity searching. The nearest neighbor indexes are used to efficiently compute a sparse pairwise distance matrix without having to exhaustively perform all pairwise spectrum comparisons within the relevant precursor mass tolerance. Finally, density-based clustering is performed to group similar spectra into clusters.

RESULTS

Several state-of-the-art spectrum clustering tools were evaluated using a large draft human proteome data set consisting of 25 million spectra, indicating that alternative tools produce clustering results with different characteristics. Notably, falcon generates larger highly pure clusters than alternative tools, leading to a larger reduction in data volume without the loss of relevant information for more efficient downstream processing.

CONCLUSIONS

falcon is a highly efficient spectrum clustering tool, which is publicly available as an open source under the permissive BSD license at https://github.com/bittremieux/falcon.

Cryo-EM analysis of complement C3 reveals a reversible major opening of the macroglobulin ring

The C3 protein is the central molecule within the complement system and undergoes proteolytic activation to C3b in the presence of pathogens. Pattern-independent activation of C3 also occurs via hydrolysis, resulting in C3(H2O), but the structural details of C3 hydrolysis remain elusive. Here we show that the conformation of the C3(H2O) analog, C3MA, is indistinguishable from C3b. In contrast, the reaction intermediate C3* adopts a conformation dramatically different from both C3 and C3MA. In C3*, unlocking of the macroglobulin (MG) 3 domain creates a large opening in the MG ring through which the anaphylatoxin (ANA) domain translocates through a transient opening. C3MA formation is inhibited by an MG3-specific nanobody and prevented by linking the ANA domain to the C3 β-chain. Our study reveals an unexpected dynamic behavior of C3 and forms the basis for elucidation of the in vivo contribution of C3 hydrolysis and for controlling complement upon intravascular hemolysis and surface-contact-induced activation.

Time Course of Plasma Proteomic and Oxylipin Changes Induced by LPS Challenge and Modulated by Antioxidant Supplementation in a Randomized Controlled Trial

Systemic molecular responses to pathogen-associated molecular patterns and their modulation by antioxidants are poorly understood in humans. Here, we present a two-stage clinical interventional study in healthy humans challenged with lipopolysaccharide. In the first step, the kinetics of inflammatory modulators within 8 h were investigated by plasma proteomics and lipidomics. In a second step, the effects of a placebo-controlled antioxidant intervention on the individual responses prior to another lipopolysaccharide challenge were determined. Plasma proteomics revealed an early involvement of the endothelium and platelets, followed by the induction of liver-derived acute phase proteins and an innate immune cell response. Untargeted lipidomics revealed an early release of fatty acids and taurocholic acid, followed by complex regulatory events exerted by oxylipins. The consistent lipopolysaccharide-induced downregulation of lysophospholipids suggested the involvement of the Lands cycle, and the downregulation of deoxycholic acid reinforced emerging links between the inflammasome and bile acids. Groups of molecules with similar kinetics to lipopolysaccharide challenge were observed to share precursors, synthesizing enzymes or cellular origin. Dietary antioxidant supplementation prior to lipopolysaccharide challenge had no detectable effect on protein kinetics but significantly downregulated pro-inflammatory sphingosine-1-phosphate and increased levels of oxylipins, 20-HEPE, and 22-HDoHE, which have been described to facilitate the resolution of inflammation. The present study identified a complex network of lipid mediators deregulated in plasma upon lipopolysaccharide challenge and highlighted the role of platelets, endothelial cells, and erythrocytes as potential inflammatory modulators. While dietary antioxidant supplementation hardly affected the initiation of inflammation, it may exert its effects supporting the resolution of inflammation.

Determination of ADP/ATP translocase isoform ratios in malignancy and cellular senescence

Cellular senescence has recently been recognized as a significant contributor to the poor prognosis of glioblastoma, one of the most aggressive brain tumors. Consequently, effectively eliminating senescent glioblastoma cells could benefit patients. Human ADP/ATP translocases (ANTs) play a role in oxidative phosphorylation in both normal and tumor cells. Previous research has shown that the sensitivity of senescent cells to mitochondria-targeted senolytics depends on the level of ANT2. Here, we systematically mapped the transcript and protein levels of ANT isoforms in various types of senescence and glioblastoma tumorigenesis. We employed bioinformatics analysis, targeted mass spectrometry, RT-PCR, immunoblotting, and assessment of cellular energy state to elucidate how individual ANT isoforms are expressed during the development of senescence in noncancerous and glioblastoma cells. We observed a consistent elevation of ANT1 protein levels across all tested senescence types, while ANT2 and ANT3 exhibited variable changes. Alterations in ANT protein isoform levels correlated with shifts in the cellular oxygen consumption rate. Our findings suggest that ANT isoforms are mutually interchangeable for oxidative phosphorylation and manipulating individual ANT isoforms could have potential for senolytic therapy.

Tolerogenic antigen-specific vaccine induces VISTA-enriched regulatory T cells and protects against arthritis in DRB1∗04:01 mice

Rheumatoid arthritis (RA) is a chronic autoimmune disease characterized by joint inflammation, cartilage damage, and bone erosion. Despite improvements with the introduction of biological disease-modifying anti-rheumatic drugs (DMARDs), RA remains an incurable life-long disease. Advancements in peptide-based vaccination may open new avenues for treating autoimmune diseases, including RA, by inducing immune tolerance while maintaining normal immune function. We have already demonstrated the efficacy of a potent vaccine against RA, consisting of the mouse major histocompatibility complex class II (Aq) protein bound to the immunodominant type II collagen peptide COL2259-273, which needed to be galactosylated at position 264. To translate the vaccine to humans and to further enhance vaccine efficacy, we modified the glycine residue at position 265 and conjugated it with the human DRB1∗04:01 molecule. Remarkably, this modified vaccine (named DR4-AL179) provided robust effectiveness in suppressing arthritis in DRB1∗04:01-expressing mice without the need for galactosylation at position 264. DR4-AL179 vaccination induces tolerance involving multiple immunoregulatory pathways, including the activation of V-type immunoglobulin domain-containing suppressor of T cell activation (VISTA)-positive nonconventional regulatory T cells, which contribute to a potent suppressive response preventing arthritis development in mice. This modified RA vaccine offers a novel therapeutic potential for human autoimmune diseases.

Proteomics-based characterization of ribosome heterogeneity in adult mouse organs

The translation process, leading to protein synthesis from mRNA, has been long thought to be invariable in all cellular organisms. Increasing evidence shows that it is finely regulated by variable features of the translation machinery. Notably, ribosomes, the functional units of protein synthesis, are suggested to display variations in their composition, depending on the developmental stage, cell type or physio-pathological context, thus hinting a new level of actionable regulation of gene expression. Yet, a comprehensive map of the heterogeneity of ribosome composition in ribosomal proteins (RPs) in different organs and tissues is not available. In this work, we explored tissue-specific ribosome heterogeneity using mass spectrometry-based quantitative proteomic characterization of ribosomal fractions purified from 14 adult mouse organs and tissues. We performed crossed clustering and statistical analyses of RP composition to highlight stable, variable and tissue-specific RPs across organs and tissues. Focusing on specific RPs, we validated their varying abundances using a targeted proteomic approach and western blot analyses, providing further insights into the tissue-specific ribosome RP signature. Finally, we investigated the origin of RP variations in ribosome fraction of the different tissues, by comparing RP relative amounts in our ribosomal proteomic dataset with their corresponding transcript abundances in three independent transcriptomic datasets. Interestingly, we found that, in some tissues, the RP abundance in purified ribosomes does not always correlate with the corresponding RP transcript level, arguing for a translational regulation of RP expression, and/or a regulated incorporation of RPs into ribosomes. Altogether, our data support the notion of a tissue-specific RP signature of ribosomes, which opens avenues to study how specific ribosomal composition provides an additional level of regulation to control gene expression in different tissues and organs.

The late-stage steps of Burkholderia cenocepacia protein O-linked glycan biosynthesis are conditionally essential

Periplasmic O-linked protein glycosylation is a highly conserved process observed across the Burkholderia genus. Within Burkholderia, protein glycosylation requires the five-gene cluster known as the O-glycosylation cluster (OGC, ogcXABEI), which facilitates the construction of the O-linked trisaccharide attached to periplasmic proteins. Previous studies have reported conflicting results regarding the essentiality of ogcA, predicted to be responsible for the addition of the final carbohydrate of the O-linked trisaccharide, and ogcX, the putative O-linked glycan flippase. Within this work, we aimed to dissect the impact of the loss of ogcA and ogcX on Burkholderia cenocepacia viability. We demonstrate that the loss of either ogcA or ogcX is detrimental if glycosylation is initiated, leading to marked phenotypic effects. Proteomic analysis supports that the loss of ogcA/ogcX both blocks glycosylation and drives pleotropic effects in the membrane proteome, resulting in the loss of membrane integrity. Consistent with this, strains lacking ogcA and ogcX exhibit increased sensitivity to membrane stressors, including antibiotics, and demonstrate marked changes in membrane permeability. These effects are consistent with the fouling of the undecaprenyl pool due to dead-end O-linked glycan intermediates, and consistent with this, we show that modulation of the undecaprenyl pool through the overexpression of undecaprenyl pyrophosphate synthase (UppS) or the OGC flippase (OgcX) restores viability, while expression of early-stage OGC biosynthesis genes (ogcI and ogcB) reduces B. cenocepacia viability. These findings demonstrate that disrupting O-linked glycan biosynthesis or transport appears to dramatically impact B. cenocepacia viability, supporting the assignment of ogcA and ogcX as conditionally essential.

A cobalamin-dependent pathway of choline demethylation from the human gut acetogen Eubacterium limosum

Elevated serum levels of trimethylamine N-oxide (TMAO) are reported to promote the development of atherosclerosis. TMAO is produced by hepatic oxidation of trimethylamine (TMA) produced by the gut microbiome from dietary quaternary amines such as choline. Net TMA production in the gut depends on microbial enzymes that either produce or consume TMA and its precursors. Here we report the elucidation of a novel microbial pathway consuming choline without TMA production. The human gut acetogen Eubacterium limosum grows by demethylating choline to N-N-dimethylaminoethanol. Quantitative mass spectral analysis of the proteome revealed a multi-protein choline to tetrahydrofolate (THF) methyltransferase system present only in choline-grown cells. The components are encoded in a gene cluster on the genome and include MthB, an MttB superfamily member; MthC, homologous to methylotrophic cobalamin-binding proteins; MthA, homologous to cobalamin:THF methyltransferases; and MthK, a protein related to serine kinases. Together, MthB, MthC, and MthA methylate THF with phosphocholine, but not choline or other quaternary amines. MthB specifically methylates Co(I)-MthC with phosphocholine. MthK acts as a bifunctional choline kinase which can utilize ATP or the MthB demethylation product, N,N-dimethylaminoethanol phosphate, to phosphorylate choline. Together, MthK, MthB, MthC, and MthA are proposed to carry out the methylation of THF with choline. These results outline a THF methylation pathway in which choline is first activated with ATP to phosphocholine prior to demethylation to form N,N-dimethylaminoethanol phosphate. The latter can be recycled by MthK to form more phosphocholine without expending additional ATP, thus minimizing energy utilization during choline-dependent acetogenesis.

The Chlamydia effector Dre1 binds dynactin to reposition host organelles during infection

The obligate intracellular pathogen Chlamydia trachomatis replicates in a specialized membrane-bound compartment where it repositions host organelles during infection to acquire nutrients and evade host surveillance. We describe a bacterial effector, Dre1, that binds specifically to dynactin associated with host microtubule organizing centers without globally impeding dynactin function. Dre1 is required to reposition the centrosome, mitotic spindle, Golgi apparatus, and primary cilia around the inclusion and contributes to pathogen fitness in cell-based and mouse models of infection. We utilized Dre1 to affinity purify the megadalton dynactin protein complex and determined the first cryoelectron microscopy (cryo-EM) structure of human dynactin. Our results suggest that Dre1 binds to the pointed end of dynactin and uncovers the first bacterial effector that modulates dynactin function. Our work highlights how a pathogen employs a single effector to evoke targeted, large-scale changes in host cell organization that facilitate pathogen growth without inhibiting host viability.

Histology-resolved proteomics reveals distinct tumor and stromal profiles in low- and high-grade prostate cancer

BACKGROUND

Prostate cancer is one of the most frequently diagnosed cancers in men. Prostate tumor staging and disease aggressiveness are evaluated based on the Gleason scoring system, which is further used to direct clinical intervention. The Gleason scoring system provides an estimate of tumor aggressiveness through quantitation of the serum level of prostate specific antigen (PSA) and histologic assessment of Grade Group, determined by the Gleason Grade of the tumor specimen.

METHODS

To improve our understanding of the proteomic characteristics differentiating low- versus high-grade prostate cancer tumors, we performed a deep proteomic characterization of laser microdissected epithelial and stromal subpopulations from surgically resected tissue specimens from patients with Gleason 6 (n = 23 specimens from n = 15 patients) and Gleason 9 (n = 15 specimens from n = 15 patients) prostate cancer via quantitative high-resolution liquid chromatography-tandem mass spectrometry analysis.

RESULTS

In total, 789 and 295 grade-specific significantly altered proteins were quantified in the tumor epithelium and tumor-involved stroma, respectively. Benign epithelial and stromal populations were not inherently different between Gleason 6 versus Gleason 9 specimens. Notably, 598 proteins were exclusively significantly altered between Gleason 9 (but not Gleason 6) tumor-involved stroma and benign stroma, including several proteins involved in cholesterol biosynthesis and nucleotide metabolism.

CONCLUSIONS

Proteomic alterations between Gleason 6 versus Gleason 9 were exclusive to the disease microenvironment, observed in both the tumor epithelium and tumor-involved stroma. Further, the molecular alterations measured in the tumor-involved stroma from Gleason 9 cases relative to the benign stroma have unique significance in disease aggressiveness, development, and/or progression. Our data provide supportive evidence of a need for further investigations into targeting stromal reservoirs of cholesterol and/or deoxynucleoside triphosphates in PCa tumors and further highlight the necessity for independent examination of the TME epithelial and stromal compartments.

Crystal structure of Isthmin-1 and reassessment of its functional role in pre-adipocyte signaling

Isthmin-1 (ISM1) is a recently described adipokine with insulin-like properties that can control hyperglycemia and liver steatosis. Additionally, ISM1 is proposed to play critical roles in patterning, angiogenesis, vascular permeability, and apoptosis. A key feature of ISM1 is its AMOP (adhesion-associated domain in MUC4 (Mucin-4) and other proteins) domain which is essential for many of its functions. However, the molecular details of AMOP domains remain elusive as there are no descriptions of their structure. Here we determined the crystal structure of ISM1 including its thrombospondin type I repeat (TSR) and AMOP domain. Interestingly, ISM1's AMOP domain exhibits a distinct fold with similarities to bacterial streptavidin. When comparing our structure to predicted structures of other AMOP domains, we observed that while the core streptavidin-like barrel is conserved, the surface helices and loops vary greatly. Thus, the AMOP domain fold allows for structural plasticity that may underpin its diverse functions. Furthermore, and contrary to prior studies, we show that highly purified ISM1 does not stimulate AKT phosphorylation on 3T3-F442A pre-adipocytes. Rather, we find that co-purifying growth factors are responsible for this activity. Together, our data reveal the structure and clarify functional studies of this enigmatic protein.

The membrane-associated β2e-subunit of voltage-gated calcium channels translocates to the nucleus and regulates gene expression

The β-subunit (Cavβ) is a central component of the voltage-gated calcium channel complex. It lacks transmembrane domains and exhibits both channel-related and non-related functions. Previous studies have shown that, in the absence of the Cavα1 pore-forming subunit, electrostatic interactions between the N-terminus of Cavβ2e and the plasma membrane mediate its anchoring to the cell surface. Here, we demonstrate that, upon phospholipase C activation, Cavβ2e dissociates from the plasma membrane and homogeneously distributes between the cytosol and the nucleus. Mutagenesis analysis identified critical residues in the N-terminus of the protein, including a stretch of positively charged amino acids and a dileucine motif, which serve as nuclear import and export signals, respectively. Fusion of the Cavβ2e N-terminus to a trimeric YFP chimeric construct shows that this segment suffices for nuclear shuttling. Thus, the N-terminus of Cavβ2e emerges as a regulatory hotspot region controlling the subcellular localization of the protein. Quantitative mass spectrometry analysis revealed that the heterologous expression of a nuclear-enriched Cavβ2e mutant regulates gene expression. Our findings demonstrate the presence of active nuclear localization signals in Cavβ2e that enables its nuclear targeting and regulation of protein expression. Furthermore, they establish the membrane-associated Cavβ2e as a novel signaling mediator within the phospholipase C cascade.

Proteome alterations in peripheral immune cells of DLBCL patients and evidence of cancer extracellular vesicles involvement

Diffuse large B-cell lymphoma (DLBCL) is an aggressive disease and a frequent form of non-Hodgkin lymphoma. Given the primary localization of DLBCL and the effect of tumors on the systemic immune response, we investigated the proteome of DLBCL patients' and healthy donors (HDs') peripheral immune cells (PICs). Since the ubiquitin-proteasome system has a vital role in proteome regulation and immune cells' functions, this study also explores the potential impact of DLBCL secretome on the polyubiquitination level in PICs. PICs from DLBCL patients and HDs were isolated and analyzed by mass spectrometry-based proteomics. The analysis resulted in 135 down and 51 upregulated proteins (adjusted p-value <0.05). Unsupervised principal component analysis revealed distinct proteomic profiles between DLBCL and HDs. Functional enrichment analysis for comparison between DLBCL and HDs-PICs proteome identified immune-related pathways such as innate immune system, specifically neutrophil degranulation, Fcγ receptor-dependent phagocytosis, and JAK-STAT signaling after IL-12 stimulation as downregulated. Proteomics analysis of DLBCL-PICs also showed dysregulation of proteostasis factors. This prompted the investigation of the effect of tumor secretome on viability and polyubiquitination level in mononuclear immune cells. Therefore, human HD peripheral blood mononuclear cells (PBMCs) were cultured in the presence of DLBCL cell line-derived soluble factors, small-EVs, and large-EVs in vitro. Our results revealed that exposure of mainly small-EVs, and large-EVs to HD PBMCs increased the polyubiquitination in PBMCs and decreased PIC viability. These findings suggest impaired immune responses in DLBCL-PICs, with tumor secretome-inducing polyubiquitination and reduced PIC viability.

MSFragger-DDA+ enhances peptide identification sensitivity with full isolation window search

Liquid chromatography-mass spectrometry based proteomics, particularly in the bottom-up approach, relies on the digestion of proteins into peptides for subsequent separation and analysis. The most prevalent method for identifying peptides from data-dependent acquisition mass spectrometry data is database search. Traditional tools typically focus on identifying a single peptide per tandem mass spectrum, often neglecting the frequent occurrence of peptide co-fragmentations leading to chimeric spectra. Here, we introduce MSFragger-DDA+, a database search algorithm that enhances peptide identification by detecting co-fragmented peptides with high sensitivity and speed. Utilizing MSFragger's fragment ion indexing algorithm, MSFragger-DDA+ performs a comprehensive search within the full isolation window for each tandem mass spectrum, followed by robust feature detection, filtering, and rescoring procedures to refine search results. Evaluation against established tools across diverse datasets demonstrated that, integrated within the FragPipe computational platform, MSFragger-DDA+ significantly increases identification sensitivity while maintaining stringent false discovery rate control. It is also uniquely suited for wide-window acquisition data. MSFragger-DDA+ provides an efficient and accurate solution for peptide identification, enhancing the detection of low-abundance co-fragmented peptides. Coupled with the FragPipe platform, MSFragger-DDA+ enables more comprehensive and accurate analysis of proteomics data.

Quantitative Proteomics and Phosphoproteomics Analysis of Patient-Derived Ovarian Cancer Stem Cells

High-grade serous ovarian carcinoma (HGSOC) is the deadliest gynecologic cancer. Key to the progression and ultimate lethality of this subtype is the intra-tumoral heterogeneity, which is defined as the coexistence of different cell types and populations within a single tumor. Among those, ovarian cancer stem cells (OCSCs) are a distinct subpopulation of tumor cells endowed with stem-like properties, which can survive current standard therapies, resulting in tumor recurrence. Here, we generated ex vivo primary OCSC-enriched three-dimensional (3D) spheres from 10 distinct treatment naive patient-derived adherent (2D) cultures. We used state-of-the-art quantitative mass spectrometry to characterize the molecular events associated with OCSCs by analyzing their proteome and phosphoproteome. Our data revealed a stemness-related protein signature, shared within a heterogeneous patient cohort, which correlates with chemo-refractoriness in a clinical proteomics dataset. Moreover, we identified targetable deregulated kinases and aberrant PDGF receptor activation in OCSCs. Pharmacological inhibition of PDGFR in adherent OC cells reduced the stemness potential, measured by sphere formation assay. Overall, we provide a valuable resource to identify new OCSC markers and putative targets for OCSC-directed therapies.

ERAP1 Activity Modulates the Immunopeptidome but Also Affects the Proteome, Metabolism, and Stress Responses in Cancer Cells

Endoplasmic reticulum (ER) aminopeptidase 1 (ERAP1) metabolizes peptides inside the ER and shapes the peptide repertoire available for binding to major histocompatibility complex class I molecules (MHC-I). However, it may have additional effects on cellular homeostasis, which have not been explored. To address these questions, we used both genetic silencing of ERAP1 expression as well as treatment with a selective allosteric ERAP1 inhibitor to probe changes in the immunopeptidome and proteome of the A375 melanoma cancer cell line. We observed significant immunopeptidome shifts with both methods of functional ERAP1 disruption, which were distinct for each method. Both methods of inhibition led to an enhancement, albeit slight, in tumor cell killing by stimulated human peripheral blood mononuclear cells and in significant proteomic alterations in pathways related to metabolism and cellular stress. Similar proteomic changes were also observed in the leukemia cell line THP-1. Biochemical analyses suggested that ERAP1 inhibition affected sensitivity to ER stress, reactive oxygen species production, and mitochondrial metabolism. Although the proteomics shifts were significant, their potential in shaping immunopeptidome shifts was limited since only 9.6% of differentially presented peptides belonged to proteins with altered expression and only 4.0% of proteins with altered expression were represented in the immunopeptidome shifts. Taken together, our findings suggest that modulation of ERAP1 activity can generate unique immunopeptidomes, mainly due to altered peptide processing in the ER, but also induce changes in the cellular proteome and metabolic state which may have further effects on tumor cells.

Retromer promotes the lysosomal turnover of mtDNA

Mitochondrial DNA (mtDNA) is exposed to multiple insults produced by normal cellular function. Upon mtDNA replication stress, the mitochondrial genome transfers to endosomes for degradation. Using proximity biotinylation, we found that mtDNA stress leads to the rewiring of the mitochondrial proximity proteome, increasing mitochondria's association with lysosomal and vesicle-related proteins. Among these, the retromer complex, particularly VPS35, plays a pivotal role by extracting mitochondrial components. The retromer promotes the formation of mitochondrial-derived vesicles shuttled to lysosomes. The mtDNA, however, directly shuttles to a recycling organelle in a BAX-dependent manner. Moreover, using a Drosophila model carrying a long deletion on the mtDNA (ΔmtDNA), we found that ΔmtDNA activates a specific transcriptome profile to counteract mitochondrial damage. Here, Vps35 expression restores mtDNA homoplasmy and alleviates associated defects. Hence, we demonstrate the existence of a previously unknown quality control mechanism for the mitochondrial matrix and the essential role of lysosomes in mtDNA turnover to relieve mtDNA damage.

Large-Scale Quantitative Cross-Linking and Mass Spectrometry Provide New Insight into Protein Conformational Plasticity within Organelles, Cells, and Tissues

Many proteins can exist in multiple conformational states in vivo to achieve distinct functional roles. These states include alternative conformations, variable post-translational modifications (PTMs), and associations with interacting protein, nucleotide, and ligand partners. Quantitative chemical cross-linking of live cells, organelles, or tissues together with mass spectrometry provides the relative abundance of cross-link levels formed in two or more compared samples, which depends both on the relative levels of existent protein conformational states in the compared samples and on the relative likelihood of the cross-link originating from each. Because cross-link conformational state preferences can vary widely, one expects intraprotein cross-link levels from proteins with high conformational plasticity to display divergent quantitation among samples with differing conformational ensembles. Here we use the large volume of quantitative cross-linking data available on the public XLinkDB database to cluster intraprotein cross-links according to their quantitation in many diverse compared samples to provide the first widescale glimpse of cross-links grouped according to the protein conformational state(s) from which they predominantly originate. We further demonstrate how cluster cross-links can be aligned with any protein structure to assess the likelihood that they were derived from it.

Top-Down Proteomic Profiling of Protein Corona by High-Throughput Capillary Isoelectric Focusing-Mass Spectrometry

In the rapidly evolving field of nanomedicine, understanding the interactions between nanoparticles (NPs) and biological systems is crucial. A pivotal aspect of these interactions is the formation of a protein corona when NPs are exposed to biological fluids (e.g., human plasma), which significantly influences their behavior and functionality. This study introduces an advanced capillary isoelectric focusing tandem mass spectrometry (cIEF-MS/MS) platform designed to enable high-throughput and reproducible top-down proteomic analysis of protein corona. Our cIEF-MS/MS technique completed each analysis within 30 min. It produced reproducible proteoform measurements of protein corona for at least 50 runs regarding the proteoforms' migration time [relative standard deviations (RSDs) <4%], the proteoforms' intensity (Pearson's correlation coefficients between any two runs >0.90), the number of proteoform identifications (71 ± 10), and the number of proteoform-spectrum matches (PrSMs) (196 ± 30). Of the 53 identified genes, 33 are potential biomarkers of various diseases (e.g., cancer, cardiovascular disease, and Alzheimer's disease). We identified 1-102 proteoforms per potential protein biomarker, containing various sequence variations or post-translational modifications. Delineating proteoforms in protein corona by our cIEF-MS/MS in a reproducible and high-throughput fashion will benefit our understanding of nanobiointeractions and advance both diagnostic and therapeutic nanomedicine technologies.

Unwrapping the Ciliary Coat: High-Resolution Structure and Function of the Ciliary Glycocalyx

The glycocalyx, a highly heterogeneous glycoprotein layer of cilia regulates adhesion and force transduction and is involved in signaling. The high-resolution molecular architecture of this layer is currently not understood. The structure of the ciliary coat is described in the green alga Chlamydomonas reinhardtii by cryo-electron tomography and proteomic approaches and the high-resolution cryoEM structure of the main component, FMG1B is solved. FMG1B is described as a mucin orthologue which lacks the major O-glycosylation of mammalian mucins but is N-glycosylated. FMG1A, a previously undescribed isoform of FMG1B is expressed in C. reinhardtii. By microflow-based adhesion assays, increased surface adhesion in the glycocalyx deficient double-mutant fmg1b-fmg1a is observed. It is found this mutant is capable of surface-gliding, with neither isoform required for extracellular force transduction by intraflagellar transport. The results find FMG1 to form a protective layer with adhesion-regulative instead of adhesion-conferring properties and an example of an undescribed class of mucins.

Morphophysiological and proteomic profiling unveiling mechanisms underlying nitrogen use efficiency in popcorn (Zea mays var. everta)

In this study we hypothesize that the contrasting nitrogen use efficiency (NUE) between popcorn (Zea mays var. everta) inbred lines P2 (high NUE) and L80 (low NUE) is driven by distinct morphophysiological responses and proteomic profiles found in leaves and roots. To elucidate the mechanisms involved, plants were cultivated in a greenhouse under high (100% N) and low (10% N) nitrogen conditions, in a randomized complete block design with two factorial treatment arrangements and seven blocks. Morphological and physiological traits such as photochemical and non-photochemical quenching, quantum yield of photosystem II, and potential photosynthesis were evaluated. Compared to L80, under low N, P2 exhibited 25.9% greater leaf area, 22.4% taller plants, 21.7% thicker stems and 113% higher shoot dry mass, as well as higher values of photochemical and non-photochemical quenching and quantum yield of photosystem II that drove to a maximum photosynthesis 16.5% higher than L80. Comparative proteomic analysis of the leaves identified 215 differentially accumulated proteins (DAPs) in P2 and 168 DAPs in L80, while in roots, 127 DAPs were observed in P2 and 172 in L80. Notably, in leaves, the response to oxidative stress, energy metabolism, and photosynthesis represented the main differences between P2 and L80. In roots, the nitrate transport, ammonium assimilation, and amino acid metabolism appear to have contributed to the improved NUE in P2. Consequently, this study provides valuable insights into the molecular mechanisms underlying NUE and opens avenues for molecular breeding aimed at selecting superior genotypes for the development of a more sustainable agriculture.

An atlas of protein phosphorylation dynamics during interferon signaling

Interferons (IFNs, types I-III) have pleiotropic functions in promoting antiviral and antitumor responses, as well as in modulating inflammation. Dissecting the signaling mechanisms elicited by different IFNs is therefore critical to understand their phenotypes. Here, we use mass spectrometry to investigate the early temporal dynamics of cellular protein phosphorylation in a human lung epithelial cell-line as it responds to stimulation with IFNα2, IFNβ, IFNω, IFNγ, or IFNλ1, representing all IFN types. We report an atlas of over 700 common or unique phosphorylation events reprogrammed by these different IFNs, revealing both previously known and uncharacterized modifications. While the proteins differentially phosphorylated following IFN stimulation have diverse roles, there is an enrichment of factors involved in chromatin remodeling, transcription, and RNA splicing. Functional screening and mechanistic studies identify that several proteins modified in response to IFNs contribute to host antiviral responses, either directly or by supporting IFN-stimulated gene or protein production. Among these, phosphorylation of PLEKHG3 at serine-1081 creates a phospho-regulated binding motif for the docking of 14-3-3 proteins, and together these factors contribute to coordinating efficient IFN-stimulated gene expression independent of early Janus kinase/signal transducer and activator of transcription signaling. Our findings map the global phosphorylation landscapes regulated by IFN types I, II, and III, and provide a key resource to explore their functional consequences.

Methodological Aspects of μLC-MS/MS for Wide-Scale Proteomic Analysis of Anthracycline-Induced Cardiomyopathy

The efforts to utilize microflow liquid chromatography hyphenated to tandem mass spectrometry (μLC-MS/MS) for deep-scale proteomic analysis are still growing. In this work, two-dimensional LC separation and peptide derivatization by a tandem mass tag (TMT) were used to assess the capability of μLC-MS/MS to reveal protein changes associated with the severe chronic anthracycline cardiotoxicity phenotype in comparison with nanoflow liquid chromatography (nLC-MS/MS). The analysis of the control and anthracycline-treated rabbit myocardium by μLC-MS/MS and nLC-MS/MS allowed quantification of 3956 and 4549 proteins, respectively, with 84% of these proteins shared in both data sets. Both nLC-MS/MS and μLC-MS/MS revealed marked global proteome dysregulation in severe anthracycline cardiotoxicity, with a significant change in approximately 55% of all detected proteins. The μLC-MS/MS analysis allowed less compressed and more precise determination of the TMT channel ratio and correspondingly broader fold-change protein distribution than nLC-MS/MS. The total number of significantly changed proteins was higher in nLC-MS/MS (2498 vs 2183, 1900 proteins shared), whereas the opposite was true for a number of significantly changed proteins with a fold-change cutoff ≥ 2 (535 vs 820). The profound changes concerned mainly proteins of cardiomyocyte sarcomeres, costameres, intercalated discs, mitochondria, and extracellular matrix. In addition, distinct alterations in immune and defense response were found with a remarkable involvement of type I interferon signaling that has been recently hypothesized to be essential for anthracycline cardiotoxicity pathogenesis. Hence, μLC-MS/MS was found to be a sound alternative to nLC-MS/MS that can be useful for comprehensive mapping of global myocardial proteome alterations such as those associated with severe anthracycline cardiotoxicity.