The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences

Helicobacter pylori γ-glutamyltransferase is linked to proteomic adaptions important for colonization

Helicobacter pylori γ-glutamyltransferase (gGT) is a virulence factor that promotes bacterial colonization and immune tolerance. Although some studies addressed potential functional mechanisms, the supportive role of gGT for in vivo colonization remains unclear. Additionally, it is unknown how different gGT expression levels may lead to compensatory mechanisms ensuring infection and persistence. Hence, it is crucial to unravel the in vivo function of gGT. We assessed acid survival under conditions mimicking the human gastric fluid and elevated the pH in the murine stomach prior to H. pylori infection to link gGT-mediated acid resistance to colonization. By comparing proteomes of gGT-proficient and -deficient isolates before and after infecting mice, we investigated proteomic adaptations of gGT-deficient bacteria during infection. Our data indicate that gGT is crucial to sustain urease activity in acidic environments, thereby supporting survival and successful colonization. Absence of gGT triggers expression of proteins involved in the nitrogen and iron metabolism and boosts the expression of adhesins and flagellar proteins during infection, resulting in increased motility and adhesion capacity. In summary, gGT-dependent mechanisms confer a growth advantage to the bacterium in the gastric environment, which renders gGT a valuable target for the development of new treatments against H. pylori infection.

Peptidomic and proteomic analysis of precision-cut lung slice supernatants

The precision-cut lung slice (PCLS) model is an ex vivo tissue system that has been used to model disease and examine the effects of exogenous compounds. Few studies have been carried out on the complement of proteins (proteome) and peptides (peptidome) secreted by PCLS and other tissue sections, during tissue culture, although such data are likely to provide critical information on the biology of tissue slices and the changes these undergo. In this study, a workflow was developed to examine the peptidome and proteome of PCLS supernatants using a modified single-pot, solid-phase-enhanced sample preparation (SP3) workflow. The performance of the SP3 workflow was evaluated in a head-to-head comparison against ultrafiltration by quantifying the recovery of synthetic peptide constructs. The SP3 workflow outperformed ultrafiltration in terms of recovery of small synthetic peptides regardless of the organic solvent used in SP3 (acetone or acetonitrile) and ultrafiltration molecular mass cut-off (2 or 10 kDa). The developed SP3 workflow provided robust data when analyzing PCLS supernatants across different conditions. The method allows, within a single workflow from individual samples, the identification of both large numbers of different native peptides (489) and also proteins (370) released from the tissue to the supernatants. This approach therefore has the capacity to provide both broad and in-depth peptidome and proteome data, with potential wide applicability to analyze the secretome of cultured tissue samples.

Anoxic desulfurization of biogas rich in hydrogen sulfide through feedback control using biotrickling filters: Operational limits and multi-omics analysis

Biodesulfurization is crucial for sustainable biogas purification from hydrogen sulfide (H2S). This study investigates the operational limits of anoxic biotrickling filters (BTFs) for treating biogas with high H2S concentrations (up to 20,000 ppmv) using nitrite, along with simulated interruptions in H2S supply. The BTF achieved a maximum elimination capacity of 312 g S-H2S m-3 h-1 with an H2S removal efficiency of 98 % at an empty bed residence time of 284 s. A proportional-integral-derivative (PID) feedback control system was successfully employed to maintain an H2S outlet concentration close to the requisite setpoint (100 and 500 ppmv) by adjusting the nitrite flow rate, thereby minimizing its accumulation. Continuous nitrite feeding after interruptions in H2S supply was essential to avoid H2S release due to sulfate-reducing bacteria. Multi-omics analyses, combining metagenomics and proteomics, revealed Sulfurimonas as the dominant sulfur-oxidizing bacteria, which downregulates most enzyme genes involved in nitrogen and sulfur metabolism in response to substrate starvation. These findings underscore the resilience of BTFs under extreme conditions and the value of multi-omics approaches in understanding microbial population dynamics, positioning BTFs as a robust solution for large-scale biogas purification.

Potential targets for synergistic bipolar irreversible electroporation in tumor suppression through transcriptomics and proteomics analysis

Previous studies have demonstrated that synergistic bipolar irreversible electroporation (SBIRE) is a promising non-thermal tumor ablation technique that effectively targets tumors without causing muscle contractions. Despite its clinical potential, the mechanistic understanding of SBIRE's tumor-suppressive effects remains underexplored. This study aims to identify potential molecular targets for SBIRE-mediated tumor suppression through comprehensive transcriptomics and proteomics analyses. Mice were selected as subjects for the creation of tumor models by the subcutaneous tumor-bearing method. Following the SBIRE intervention, tumor surveillance and pathological investigations were carried out. A comprehensive investigation was conducted using RNA sequencing-based transcriptomics and label-free quantitative proteomics to examine normal and SBIRE treated tumor samples. Differentially expressed genes (DEGs) and crucial signaling pathways were found using bioinformatics analysis. Western blot (WB), immunohistochemistry (IHC), and quantitative real-time PCR (qRT-PCR) were used to validate potentially associated genes. The results demonstrate that a substantial reduction in tumor size was achieved following SBIRE treatment. A total of 86 genes exhibited differential expression in tumors, with 84 genes showing upregulation and 2 genes showing downregulation. According to bioinformatics research, these DEGs were involved in a wide variety of biological activities, such as cell adhesion, positive regulation of tumor necrosis factor production, and immune system process. Beside major enrichment pathways like Efferocytosis, Endocytosis, PPAR signaling pathway and Metabolic pathways. The upregulation of WDFY family member 4 (WDFY4), Thrombospondin 1(THBS1), Pentraxin 3 (PTX3), Superoxide dismutase 3 (SOD3) and Glutathione peroxidase 3 (GPX3) genes were confirmed. These insights into the molecular underpinnings of SBIRE offer a novel therapeutic strategy for enhancing tumor suppression and improving clinical outcomes in cancer treatment.

A collagen IV fluorophore knock-in toolkit reveals trimer diversity in C. elegans basement membranes

The type IV collagen triple helix, composed of three ⍺-chains, is a core basement membrane (BM) component that assembles into a network within BMs. Endogenous tagging of all ⍺-chains with genetically encoded fluorophores has remained elusive, limiting our understanding of this crucial BM component. Through genome editing, we show that the C termini of the C. elegans type IV collagen ⍺-chains EMB-9 and LET-2 can be fused to a variety of fluorophores to create a strain toolkit with wild-type health. Using quantitative imaging, our results suggest a preference for LET-2-LET-2-EMB-9 trimer construction, but also tissue-specific flexibility in trimers assembled driven by differences in ⍺-chain expression levels. By tagging emb-9 and let-2 mutants that model human Gould syndrome, a complex multitissue disorder, we further discover defects in extracellular accumulation and turnover that might help explain disease pathology. Together, our findings identify a permissive tagging site in C. elegans that will allow diverse studies on type IV collagen regulation and function in animals.

PML mutants from arsenic-resistant patients reveal SUMO1-TOPORS and SUMO2/3-RNF4 degradation pathways

Arsenic effectively treats acute promyelocytic leukemia by inducing SUMO and ubiquitin-dependent degradation of the promyelocytic leukemia (PML)-retinoic acid receptor alpha oncogenic fusion protein. However, some patients relapse with arsenic-resistant disease because of missense mutations in PML. To determine the mechanistic basis for arsenic resistance, PML-/- cells were reconstituted with YFP fusions of wild-type PML-V and two common patient mutants: A216T and L217F. Both mutants were resistant to degradation by arsenic but for different biochemical reasons. Arsenic did not trigger SUMOylation of A216T PML, which failed to recruit the SUMO-targeting ubiquitin ligases RNF4 and TOPORS. L217F PML did respond with increased SUMO2/3 conjugation that facilitated RNF4 engagement but failed to reach the threshold of SUMO1 conjugation required to recruit TOPORS. Thus, neither mutant accumulated the appropriate polyubiquitin signal required for p97 binding. These PML mutants have revealed a convergence of SUMO1, SUMO2/3, TOPORS, and RNF4 that facilitates the arsenic-induced degradation of PML.

Structural characterization and inhibition of the interaction between ch-TOG and TACC3

The mitotic spindle is a bipolar array of microtubules, radiating from the poles which each contain a centrosome, embedded in pericentriolar material. Two proteins, ch-TOG and TACC3, have multiple functions at the mitotic spindle due to operating either alone, together, or in complex with other proteins. To distinguish these activities, we need new molecular tools to dissect their function. Here, we present the structure of the α-helical bundle domain of ch-TOG that mediates its interaction with TACC3 and a structural model describing the interaction, supported by biophysical and biochemical data. We have isolated Affimer tools to precisely target the ch-TOG-binding site on TACC3 in live cells, which displace ch-TOG without affecting the spindle localization of other protein complex components. Inhibition of the TACC3-ch-TOG interaction led unexpectedly to fragmentation of the pericentriolar material in metaphase cells and delayed mitotic progression, uncovering a novel role of TACC3-ch-TOG in maintaining pericentriolar material integrity during mitosis to ensure timely cell division.

An advanced toolset to manipulate and monitor subcellular phosphatidylinositol 3,5-bisphosphate

Phosphatidylinositol (PI) 3,5-bisphosphate (PI(3,5)P2) is a minor inositol-containing phospholipid that serves as an important regulator of endolysosomal functions. However, the precise sites of subcellular enrichment and molecular targets of this regulatory lipid are poorly understood. Here, we describe the generation and detailed characterization of a short engineered catalytic fragment of the human PIKfyve enzyme, which potently converts PI 3-phosphate to PI(3,5)P2. This novel tool allowed for the evaluation of reported PI(3,5)P2-sensitive biosensors and showed that the recently identified phox homology (PX) domain of the Dictyostelium discoideum (Dd) protein, SNXA, can be used to monitor the production of PI(3,5)P2 in live cells. Modification and adaptation of the DdSNXAPX-based probes into compartment-specific bioluminescence resonance energy transfer-based biosensors allows for the real-time monitoring of PI(3,5)P2 generation within the endocytic compartments of entire cell populations. Collectively, these molecular tools should allow for exciting new studies to better understand the cellular processes controlled by localized PI(3,5)P2 metabolism.

Incremental Modification in the Existing Approaches for Affinity Chromatographic Enrichment of Phosphoproteins Improves Their Profile in Liquid Chromatography-Tandem Mass Spectrometry Analysis

Cell signalling is a vital process in cell physiology, which is driven by protein phosphorylation. Global phosphoproteome analysis by liquid chromatography-tandem mass spectrometry (LC-MS/MS) has thus gained importance in cell signalling research. However, phosphoprotein identification by LC-MS/MS in whole cell lysates, which are complex protein mixtures, is hindered by their poor ionization coupled with suppression of peaks due to low abundance. Enrichment by immobilized metal ion- and metal oxide-affinity chromatography (IMAC and MOAC), which preferentially enrich multi- and mono-phosphorylated proteins, respectively, have improved their detection by MS. However, preferential enrichment limits phosphoproteome coverage in global analyses of cell lysates which contain mono- and multi-phosphorylated proteins. Improvement in their coverage by sequential elution approach that exploits the complementary chemistries of these matrices has been reported. In this study, we observed that the number of phosphoproteins detected using the sequential elution approach was lower (∼250-400) as compared to the theoretically predicted number (>500) based on their reported 30% abundance in the cell proteome (1700-2200 proteins detected by MS in our cell lines). Acknowledging the merit of using multiple matrices, we used IMAC and MOAC individually and pooled the data. We observed a remarkable increase (>30%) in phosphoproteome coverage. Further, though 98% of phosphoproteins were enriched by IMAC, among the remaining 2%, those detected exclusively by MOAC were biologically important. This justified the use of multiple matrices. Thus, an incremental modification of using multiple matrices individually rather than sequentially and pooling the data markedly improved the phosphoproteome coverage, which can positively impact cell signalling research.

A new perspective on the antimicrobial mechanism of linezolid against Staphylococcus aureus revealed by proteomics and metabolomics analysis

Understanding bacterial responses to antimicrobials is crucial for identifying tolerance mechanisms and for developing new therapies. Using mass spectrometry-based metabolomics and proteomics, this study examines the response of Staphylococcus aureus to linezolid (LZD) treatment. Under LZD stress, significant fluctuations were observed in key metabolic pathways such as amino acid biosynthesis and the TCA cycle, alongside a general increase in ribosomal protein complexes. Additionally, LZD disrupted nucleotide metabolism, particularly affecting pyrimidine pathways. Combining LZD with the pyrimidine synthesis inhibitor leflunomide enhanced bactericidal effects both in vitro and in vivo, highlighting the importance of targeting pyrimidine biosynthesis to amplify the antimicrobial efficacy of protein inhibitors. These results underscore downstream metabolic processes as viable targets for synergistic drug combinations, suggesting a strategy to potentially improve the clinical effectiveness of LZD.

Morpholino nicotinamide analogs of ponatinib, dual MNK, p70S6K inhibitors, display efficacy against lung and breast cancers

Therapeutic options for aggressive cancer types such as breast and lung remain limited; disease relapse and death occur in 30-60% of non-small cell lung cancer (NSCLC) patients, whereas in triple-negative breast cancer or TNBC, recurrence-free survival occurs in less than 30% patients. The kinases, MNK and p70S6K have been proposed as targets for the potential treatment of breast cancer (BC) and lung cancer but currently, no drug that was purposely designed to inhibit these kinases have been approved by the FDA for the treatment of BC or NSCLC. In this study, we have identified HSND80 (a morpholino nicotinamide analog of ponatinib) as a potent MNK/p70S6K inhibitor that has excellent activity against TNBC and NSCLC cell lines. HSND80 has a longer target residence time (τ) of 45 mins and 58 mins against MNK1 and MNK2 respectively, compared to τ of eFT508 (tomivosertib) against MNK1 and MNK2 (τ = 1 min and 5 min, respectively). Molecular dynamics simulation was used to provide some insights into the binding of HSND80 to MNK and p70S6K kinases. Western blotting analysis and phosphoproteomics analysis of the TNBC cell line, MDA-MB-231, revealed that phosphorylations of elF4E (MNK target) and elF4B and S6 (p70S6K targets) were reduced upon compound treatment, which is in line with the proposed mechanism of action; dual MNK/p70S6K targeting. HSND80 could be dosed orally at 15 and 30 mg/kg and at such doses, could reduce tumor volume in a syngeneic NSCLC mouse model.

Subcellular targets and recognition mechanism of Ralstonia solanacearum effector RipE1

Some plant NLRs carry unusual integrated protein domains (IDs) that mimic host targets of pathogen effectors. RipE1 is a core Ralstonia solanacearum Type III effector with a predicted cysteine protease activity that activates defense responses in resistant plants. In this study, we used a library of NLR-IDs as an investigative tool to screen for potential host-cell targets of RipE1. Based on these findings and the effector's localization, we identified two plant membrane trafficking components as RipE1's subcellular targets. Depending on its protease activity, RipE1 promotes the degradation of both exocyst complex subunit Exo70B1 and its known interactor RPM1-interacting protein-4 (RIN4), a known plant immunity regulator. RipE1 protease activity is recognized by the RIN4-guarding NLR Pseudomonas tomato race 1 (Ptr1) in Nicotiana benthamiana. Overall, the data presented here, along with the existing literature, suggest a possible link between RipE1 activity upon the host secretion machinery and its NLR-mediated recognition.

Aberrant oxidative modifications of neutrophil myeloperoxidase in anti-neutrophil cytoplasmic antibody-associated vasculitis

Anti-neutrophil cytoplasmic antibodies directed to myeloperoxidase (MPO-ANCA) are key molecules in the pathogenesis of ANCA-associated vasculitis (AAV), however, the mechanisms of autoantibody production have not been elucidated. We hypothesized that an aberrant PTM occurs in the MPO of MPO-ANCA-positive AAV (MPO-AAV), which induces immune responses to self MPO. To test this, we purified MPO proteins from neutrophils of 8 patients with MPO-AAV and 8 healthy subjects, digested them with trypsin, and comprehensively quantified PTMs of the MPO peptides using the sequential window acquisition of all theoretical fragment ion spectra (SWATH) method of LC-MS. Among the 1034 detected MPO peptides, 38 peptides were increased in the patients with MPO-AAV relative to the healthy subjects, whereas 10 peptides were decreased in the patients (p < 0.05). Interestingly, oxidative modifications were found in 11 of the 38 increased peptides (1.14- to 3.29-fold), but not in the decreased peptides. These included oxidation of Met577, Phe686, Met688 and Met719, dioxidation of Met409, Phe605, Trp679 and Met719, and kynurenylation of Trp255. Conversely, glycosylation was detected in 4 of the 10 decreased peptides (-1.32- to -2.32-fold), but not in the increased peptides. They were O-type glycans at Ser357 and Ser731, and N-type glycans at Asn355 and Asn729. In animal experiments, immunization of mice with in vitro oxidized or unoxidized mouse MPO (mMPO) showed that not only anti-oxidized mMPO antibodies but also anti-unoxidized mMPO antibodies were preferentially produced in the oxidized mMPO-immunized mice relative to the unoxidized mMPO-immunized mice (anti-oxidized mMPO antibodies, 6/8 vs 1/9, p < 0.05; anti-unoxidized mMPO antibodies, 4/8 vs 0/9, p < 0.05). Our results suggest that the increased oxidative modifications of MPO in MPO-AAV may break immune tolerance and trigger the MPO-ANCA production. SIGNIFICANCE: AAV is a systemic and refractory disease that causes life-threatening multi-organ involvement such as necrotizing glomerulonephritis and lung hemorrhage. MPO-ANCA is an autoantibody that plays a key role in the pathogenesis of AAV. Therefore, elucidation of the mechanism of MPO-ANCA production is crucial to overcoming this disease. In this study, we applied a SWATH-MS analysis to the detection of aberrant PTMs, and found increased oxidative modifications of neutrophil MPO in patients with MPO-AAV for the first time. Immunization of in vitro oxidized MPO induced autoantibodies to the intact unoxidized MPO, suggesting that the increased oxidative modifications of MPO may break the immune tolerance in MPO-AAV. This study suggests a novel trigger mechanism for MPO-ANCA production.

Expanded characterization and localization of male seminal fluid proteins within the female reproductive tract of the dengue vector mosquito Aedes aegypti

Aedes aegypti mosquitoes transmit numerous viruses that impact human health. Contemporary biological control programs aim to reduce Aedes fertility despite our limited understanding of interactions between the sexes required for reproduction. During mating, males transfer seminal fluid proteins (SFPs) to females which alter their post-mating behavior, physiology and gene regulation, but the contribution of individual SFPs to fertility remains uncharacterized. In Drosophila, a small subset of SFPs localize to the sperm storage organs and oviducts or enter the hemolymph which suggests their participation in specific post-mating processes. We used mass spectrometry-based proteomics in conjunction with whole animal heavy labelling to expand the characterization of the Ae. aegypti ejaculate and identify SFPs that leave the site of insemination and localize to other female tissues. We identified 1031 ejaculate proteins, including a suite of novel SFPs. The expanded ejaculate proteome shows low conservation amongst SFPs when compared to insect model Drosophila, consistent with rapid evolutionary turnover at the genetic and proteomic levels. Further, we identify 25 SFPs that localize to the spermathecae, oviducts, and/or enter the hemolymph. This study expands our knowledge of the Ae. aegypti seminal fluid proteome and identifies candidate SFPs that may have tissue-specific, postcopulatory roles which support fertility. SIGNIFICANCE: Male-derived seminal fluid proteins (SFPs), transferred to females along with sperm during mating, are essential for the fertility of a mating pair. SFPs in aggregate induce several physiological and behavioral changes in mated females. Studies in the insect model Drosophila have shown that individual SFPs often participate in specific post-mating processes. In the dengue vector mosquito Aedes aegypti, 177 high confidence SFPs have been identified, but the contribution of individual SFPs in female fertility has yet not been characterized. In Drosophila, a small subset of SFPs leave the site of insemination and localize to the oviduct and sperm storage organs of the female reproductive tract or are transported to the female hemolymph, with patterns of SFP localization suggesting participation in a specific post-mating process. We used MS/MS proteomic characterization coupled with whole animal heavy labeling to expand characterization of the Ae. aegypti ejaculate proteome, increasing the number of known ejaculate proteins to 1378, including identification of 40 novel SFPs. Further, we identified 25 SFPs that leave the site of insemination and localize to the oviducts and/or spermathecae or enter the hemolymph, which can now be assessed for potential tissue-specific functions in female fertility.

Sex-specific molecular hallmarks point to increased atherogenesis susceptibility in male senescence-accelerated mice

AIMS

The senescence-accelerated mouse (SAM) model has been extensively used to study neurological alterations associated with aging. The SAM model has also proved to be useful in the study of vascular aging, but there is still work to be done to better define its utility as a model of atherosclerosis, since contradictory data have been published and sex seems to play a crucial role in potential divergences.

MATERIALS AND METHODS

With this in mind, we aimed to decipher the molecular mechanisms underlying early vascular aging on SAMP8 mice, analyzing the aorta of 10 months-old animals by means of in-depth proteomic analysis, considering sex-specific differences. Validation of the results obtained were performed by western blot in an independent cohort of mice, as well as in human aortic smooth muscle cells (HASMC). Besides, an exhaustive lipoprotein and glycoprotein analysis was performed in blood plasma.

KEY FINDINGS

Distinct proteomic, lipoprotein and glycoprotein profiles have been found in SAMP8 mice, according to sex. Male SAMP8 mice showed signs of increased atherogenesis susceptibility due to several sex-specific alterations: 1) increased number of VLDLs, as well as in their cholesterol and TG content; 2) upregulation of inflammatory glycoproteins in plasma; and 3) increased features of SASP and vascular calcification: upregulation of exocytic vesicular transport and downregulation of the protein Gas6. On the contrary, female mice showed a much better proteomic and lipoprotein profile.

SIGNIFICANCE

The results obtained suggest that male SAMP8 mice will be more susceptible to develop atherosclerosis under a HFD than female mice.

TamL is a Key Player of the Outer Membrane Homeostasis in Bacteroidota

In Proteobacteria, the outer membrane protein TamA and the inner membrane-anchored protein TamB form the Translocation and Assembly Module (TAM) complex, which facilitates the transport of autotransporters, virulence factors, and likely lipids across the two membranes. In Bacteroidota, TamA is replaced by TamL, a TamA-like lipoprotein with a lipid modification at its N-terminus that likely anchors it to the outer membrane. This structural difference suggests that TamL may have a distinct function compared to TamA. However, the role of TAM in bacterial phyla other than Proteobacteria remains unexplored. Our study aimed to elucidate the function of TamL in Flavobacterium johnsoniae, an environmental Bacteroidota. Unlike its homologs in Proteobacteria, we found that TamL and TamB are essential in F. johnsoniae. Through genetic, phenotypic, proteomic, and lipidomic analyses, we show that TamL depletion severely compromises outer membrane integrity, as evidenced by reduced cell viability, altered cell shape, increased susceptibility to membrane-disrupting agents, and elevated levels of outer membrane lipoproteins. Notably, we did not observe an overall decrease in the levels of β-barrel outer membrane proteins, nor substantial alterations in outer membrane lipid composition. By pull-down assays, we found TamL co-purifying with TamB in F. johnsoniae, suggesting an interaction. Furthermore, we found that while TamL and TamB monocistronic genes are conserved among Bacteroidota, only some species encode multiple TamL, TamB and TamA proteins. To our knowledge, this study is the first to provide functional insights into a TAM subunit beyond Proteobacteria.

SNX10 functions as a modulator of piecemeal mitophagy and mitochondrial bioenergetics

We here identify the endosomal protein SNX10 as a negative regulator of piecemeal mitophagy of OXPHOS machinery components. In control conditions, SNX10 localizes to early endocytic compartments in a PtdIns3P-dependent manner and modulates endosomal trafficking but also shows dynamic connections with mitochondria. Upon hypoxia-mimicking conditions, SNX10 localizes to late endosomal structures containing selected mitochondrial proteins, including COX-IV and SAMM50, and the autophagy proteins SQSTM1/p62 and LC3B. The turnover of COX-IV was enhanced in SNX10-depleted cells, with a corresponding reduced mitochondrial respiration and citrate synthase activity. Importantly, zebrafish larvae lacking Snx10 show reduced levels of Cox-IV, as well as elevated ROS levels and ROS-mediated cell death in the brain, demonstrating the in vivo relevance of SNX10-mediated modulation of mitochondrial bioenergetics.

Physiological, microscopic and proteomic performance of Escherichia coli O157:H7 biofilms challenged with antagonistic lactic acid bacteria as a bio-decontamination tool for the food industry

Enterohemorrhagic Escherichia coli O157:H7 (EHEC) biofilms are a critical concern in food industry due to their resilience, persistence, and ability to enhance pathogen survival on processing surfaces. Controlling these biofilms is paramount to mitigating the risks associated with EHEC. This work evaluates the potential of three lactic acid bacteria (LAB) strains-Lactiplantibacillus plantarum CRL1075, L. plantarum CRL1482, and Pediococcus pentosaceus CRL2145-as biocontrol agents to inhibit EHEC biofilms through exclusion, competition, and displacement strategies under conditions mimicking meat industry environment (12 °C, stainless steel, and meat-based culture medium). EHEC biofilms showed by scanning electron microscopy and confocal laser scanning microscopy high adherence and robustness. Introducing LAB strains led to substantial reductions in EHEC biofilm formation, with the competition strategy emerging most effective, reducing biofilms by up to 6.5 log units. Exclusion and displacement strategies also decreased pathogen viability, with P. pentosaceus CRL2145 showing consistent inhibitory effects across all conditions. EHEC-CRL2145 mixed biofilms exhibited reduced biomass and covered surface area, with LAB clustered around E. coli cells, limiting their growth and adhesion. Proteomic analysis revealed repression of 85 EHEC proteins associated with essential metabolic pathways, stress responses, and biofilm maintenance, which compromised the pathogen's ability to sustain biofilm integrity and viability. Additionally, some EHEC proteins involved in adhesion and virulence were upregulated, possibly as stress response to LAB antagonism. Importantly, while the antimicrobial potential of LAB against foodborne pathogens was recently reported, this is the first study to describe the metabolic response of EHEC biofilms when challenged by LAB.

Age-related loss of large dendritic spines in the precuneus is statistically mediated by proteins which are predicted targets of existing drugs

Preservation of dendritic spines is a putative mechanism of protection against cognitive impairment despite development of Alzheimer Disease (AD)-related pathologies. Aging, the chief late-onset AD risk factor, is associated with dendritic spine loss in select brain areas. However, no study to our knowledge has observed this effect in precuneus, an area selectively vulnerable to early accumulation of AD-related pathology. We therefore quantified dendritic spine density in precuneus from 98 subjects without evidence of neurocognitive decline, spanning ages 20-96, and found a significant negative correlation between age and large dendritic spine density. In these same subjects, we conducted liquid chromatography-tandem mass spectrometry of >5000 proteins and identified 203 proteins which statistically mediate the effect of age on large dendritic spine density. Using computational pharmacology, we identified ten drugs which are predicted to target these mediators, informing future studies designed to test their effects on age-related dendritic spine loss and cognitive decline.

Multi-omic analysis of meningeal cerebral amyloid angiopathy reveals enrichment of unsubstituted glucosamine and extracellular proteins

Cerebral amyloid angiopathy (CAA) is a common feature of Alzheimer's disease in which amyloid-β (Aβ) deposits in cerebral and leptomeningeal vessel walls, predisposing vessels to micro- and macro-hemorrhages. The vessel walls contain distinct proteins and heparan sulfate (HS), yet how vascular proteins and HS jointly associate with Aβ is unknown. We conducted the first multi-omics study to systematically characterize the proteins as well as the HS abundance, sulfation level, and disaccharide composition of leptomeninges from 23 moderate to severe CAA cases and controls. We then analyzed the associations between Aβ and other proteins, HS, and apolipoprotein E genotype. We found an increase in a minor HS disaccharide containing unsubstituted glucosamine, as well as 6-O sulfated disaccharides; Aβ40 levels positively correlated with unsubstituted glucosamine. There was also an increase in extracellular proteins derived from brain parenchyma or plasma, including olfactomedin-like protein 3, fibrinogen, serum amyloid protein, apolipoprotein E, and secreted frizzled related protein-3. Our findings of vascular HS and protein alterations specific to CAA-affected leptomeningeal vessels provide molecular insight into the extracellular remodeling that co-occurs with Aβ deposits and may indicate a basis for antemortem diagnostic assay development and therapeutic strategies to impede Aβ-HS interactions.

The late-onset Alzheimer's disease risk factor RHBDF2 is a modifier of microglial TREM2 proteolysis

The cell surface receptor TREM2 is a key genetic risk factor and drug target in Alzheimer's disease (AD). In the brain, TREM2 is expressed in microglia, where it undergoes proteolytic cleavage, linked to AD risk, but the responsible protease in microglia is still unknown. Another microglial-expressed AD risk factor is catalytically inactive rhomboid 2 (iRhom2, RHBDF2), which binds to and acts as a non-catalytic subunit of the metalloprotease ADAM17. A potential role in TREM2 proteolysis is not yet known. Using microglial-like BV2 cells, bone marrow-derived macrophages, and primary murine microglia, we identify iRhom2 as a modifier of ADAM17-mediated TREM2 shedding. Loss of iRhom2 increased TREM2 in cell lysates and at the cell surface and enhanced TREM2 signaling and microglial phagocytosis of the amyloid β-peptide (Aβ). This study establishes ADAM17 as a physiological TREM2 protease in microglia and suggests iRhom2 as a potential drug target for modulating TREM2 proteolysis in AD.

Endogenous interactomes of MFN1 and MFN2 provide novel insights into interorganelle communication and autophagy

MFN1 (mitofusin 1) and MFN2 are key players in mitochondrial fusion, endoplasmic reticulum (ER)-mitochondria juxtaposition, and macroautophagy/autophagy. However, the mechanisms by which these proteins participate in these processes are poorly understood. Here, we studied the interactomes of these two proteins by using CRISPR-Cas9 technology to insert an HA-tag at the C terminus of MFN1 and MFN2, and thus generating HeLa cell lines that endogenously expressed MFN1-HA or MFN2-HA. HA-affinity isolation followed by mass spectrometry identified potential interactors of MFN1 and MFN2. A substantial proportion of interactors were common for MFN1 and MFN2 and were regulated by nutrient deprivation. We validated novel ER and endosomal partners of MFN1 and/or MFN2 with a potential role in interorganelle communication. We characterized RAB5C (RAB5C, member RAS oncogene family) as an endosomal modulator of mitochondrial homeostasis, and SLC27A2 (solute carrier family 27 (fatty acid transporter), member 2) as a novel partner of MFN2 relevant in autophagy. We conclude that MFN proteins participate in nutrient-modulated pathways involved in organelle communication and autophagy.Abbreviations: ACTB: actin, beta; ATG2: autophagy related 2; ATG5: autophagy related 5; ATG12: autophagy related 12; ATG14: autophagy related 14; ATG16L1: autophagy related 16 like 1; Baf A1: bafilomycin A1; BECN1: beclin 1, autophagy related; BFDR: Bayesian false discovery rate; Cas9: CRISPR-associated endonuclease Cas9; CRISPR: clustered regularly interspaced short palindromic repeats; DNM1L/DRP1: dynamin 1-like; ER: endoplasmic reticulum; Faa1: fatty acid activation 1; FC: fold change; FDR: false discovery rate; FIS1: fission, mitochondrial 1; GABARAP: gamma-aminobutyric acid receptor associated protein; GABARAPL2: GABA type A receptor associated protein like 2; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; HA: hemagglutinin; KO: knockout; LIR: LC3-interacting region; MAP1LC3B/LC3B: microtubule-associated protein 1 light chain 3 beta; MARCHF5: membrane associated ring-CH-type finger 5; MDVs: mitochondria-derived vesicles; MFN1: mitofusin 1; MFN2: mitofusin 2; NDFIP2: Nedd4 family interacting protein 2; OMM: outer mitochondrial membrane; OPA1: OPA1, mitochondrial dynamin like GTPase; OXPHOS: oxidative phosphorylation; PE: phosphatidylethanolamine; PINK1: PTEN induced putative kinase 1; PS: phosphatidylserine; RAB5C: RAB5C, member RAS oncogene family; S100A8: S100 calcium binding protein A8 (calgranulin A); S100A9: S100 calcium binding protein A9 (calgranulin B); SLC27A2: solute carrier family 27 (fatty acid transporter), member 2; TIMM44: translocase of inner mitochondrial membrane 44; TOMM20: translocase of outer mitochondrial membrane 20; ULK1: unc-51 like kinase 1; VCL: vinculin; VDAC1: voltage-dependent anion channel 1; WT: wild type.

Ergosterol-induced immune response in barley involves phosphorylation of phosphatidylinositol phosphate metabolic enzymes and activation of diterpene biosynthesis

Lipids play crucial roles in plant-microbe interactions, functioning as structural components, signaling molecules, and microbe-associated molecular patterns (MAMPs). However, the mechanisms underlying lipid perception and signaling in plants remain largely unknown. Here, we investigate the immune responses activated in barley (Hordeum vulgare) by lipid extracts from the beneficial root endophytic fungus Serendipita indica and compare them to responses elicited by chitohexaose and the fungal sterol ergosterol. We demonstrate that S. indica lipid extract induces hallmarks of pattern-triggered immunity (PTI) in barley. Ergosterol emerged as the primary immunogenic component and was detected in the apoplastic fluid of S. indica-colonized barley roots. Notably, S. indica colonization suppresses the ergosterol-induced burst of reactive oxygen species (ROS) in barley. By employing a multi-omics approach, which integrates transcriptomics, phosphoproteomics, and metabolomics, we provide evidence for the phosphorylation of phosphatidylinositol phosphate (PIP) metabolic enzymes and activation of diterpene biosynthesis upon exposure to fungal lipids. Furthermore, we show that phosphatidic acid (PA) enhances lipid-mediated apoplastic ROS production in barley. These findings indicate that plant lipids facilitate immune responses to fungal lipids in barley, providing new insights into lipid-based signaling mechanisms in plant-microbe interactions.

Proteome Reprogramming and Acquired Stress Tolerance in Potato Cells Exposed to Acute or Stepwise Water Deficit

Water deficit negatively impacts crop productivity and quality. Plants face these challenges by adjusting biological processes and molecular functions according to the intensity and duration of the stress. The cultivated potato (Solanum tuberosum) is considered sensitive to water deficit, thus breeding efforts are needed to enhance its resilience. To capture novel functional information and gene regulatory networks, we carried out mass spectrometry-based proteomics in potato cell suspensions exposed to abrupt or stepwise osmotic stresses. Both forms of stress triggered significant alterations in protein expression, though with divergent response mechanisms. Stress response pathways orchestrated by key proteins enrolled in primary and secondary metabolism, antioxidant processes, transcriptional and translational machinery and chromatin organization were found in adapted cells. Target metabolites and reactive oxygen species levels were quantified to associate functional outcomes with the proteome study. Remarkably, we also showed that adapted cells tolerate an array of diverse conditions, including anoxia, salt and heat stress. Finally, the expression patterns of genes encoding selected differentially expressed proteins were investigated in potato plants subjected to either drought or salt stress. Collectively, our findings reveal the complex cellular strategies of osmotic stress adaptation, identifying new fundamental genes that could enhance potato resilience.

Longitudinal Proteomic Profiling of Cognition across an Aerobic Exercise Intervention

The physiological basis of cognitive decline remains largely uncharacterized. We identified a protein panel signature, in living humans, that correlates to improvement in neurocognition over a period of 5 years. Our signature is composed of complement proteins, coagulation cascade, and extracellular matrix regulators. In our cohort, SERPINF1 is associated with greater maximal oxygen uptake after an aerobic exercise intervention. Sleep quality is also a key factor in relation to inter-alpha-trypsin inhibitor heavy chain H2, which was associated with greater sleep efficiency. Additionally, we validate that the coagulation profile of decliners' plasma contains procoagulant agonists, leading to greater platelet activation. ANN NEUROL 2025;97:1007-1018.

A comprehensive investigation of the impact of cross-linker backbone structure on protein dynamics analysis: A case study with Pin1

Understanding protein structure is essential for elucidating its function. Cross-linking mass spectrometry (XL-MS) has been widely recognized as a powerful tool for analyzing protein complex structures. However, the effect of cross-linker backbone structure on protein dynamic conformation analysis remains less understood. In this study, we investigated the impact of cross-linker backbone structure on resolving the dynamic conformations of Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (Pin1), which features a blend of relatively steady intradomain structures and dynamic interdomain regions. Three cross-linkers with varying arm lengths and different oxygen-containing backbones, Disuccinimidyl tartrate (DST), Bis(succinimidyl) di(ethylene glycol) (BS(PEG)2), and Disuccinimidyl dihydroxydodecanedioate (DSDHD), were selected based on the theoretical inter-lysine distances within Pin1. By employing all-atom molecular dynamics (MD) simulations and solution nuclear magnetic resonance (NMR), we characterized the kinetic properties of cross-linkers and their perturbations to the protein structure. Additionally, we systematically evaluated the capability of cross-linkers with different backbones to analyze the structure and interdomain dynamics of Pin1. The results suggest that BS(PEG)2, with its optimal arm length and ability to rapidly transition between compact and extended states, provides more interdomain dynamic conformational information of Pin1, while achieving a comparable level of intradomain structural detail to that obtained with the shorter cross-linker DST. Overall, this study highlights the critical role of cross-linker backbone structure in structural analysis of protein dynamics using mass spectrometry.

Comparative analysis of the structural dynamics of diphtheria toxin and CRM197 carrier proteins used in the development of conjugate vaccines

Carrier proteins are chemically linked to poorly immunogenic antigens to generate conjugate vaccines, significantly improving immunogenicity. CRM197, a genetically detoxified diphtheria toxin (DT) mutant carrying the G52E mutation, is a widely used carrier protein as it retains lysine residues for antigen conjugation. In the past, CRM197 has been expressed in Corynebacterium diphtheriae, but low yields and high costs have prompted the exploration of alternative expression systems. Although high-yield expression and native refolding of CRM197 in E. coli are challenging due to its reducing cytoplasm, recent advances have enabled the production of soluble and well-folded recombinant CRM197 proteins, namely EcoCRM® and EcoCRM®(-Met). In this study, we use Hydrogen/Deuterium eXchange Mass Spectrometry (HDX-MS) to compare the structural dynamics of EcoCRM and EcoCRM(-Met) with DT wild-type. Our HDX-MS data show that the presence or the absence of the N-terminal methionine does not affect the structural dynamics of the two recombinant EcoCRM proteins. Furthermore, our results elucidate the molecular mechanism underlying the lack of toxicity of CRM197 compared to DT wild-type: the G52E mutation in the CRM197 proteins exclusively alters the stability of the NAD-binding pocket and induces allosteric effects within the receptor-binding domain. Altogether, these insights support the substitution of CRM197 produced by C. diphtheriae with the recombinant EcoCRM and EcoCRM(-Met) proteins produced in E. coli, offering a cost-effective solution for use in conjugate vaccines. Data are available via ProteomeXchange with identifier PXD057388.

Comparative evaluation of peptide vs. protein-based calibration for quantification of cardiac troponin I using ID-LC-MS/MS

OBJECTIVES

An analytical protocol based on isotope dilution liquid chromatography-tandem mass spectrometry (ID-LC-MS/MS), which includes a peptide-based calibration strategy, was developed and validated for the determination of cardiac troponin I (cTnI) levels in clinical samples. Additionally, the developed method was compared with a protein-based calibration strategy, using cTnI serving as a model for low-abundant proteins. The aim is to evaluate new approaches for protein quantification in complex matrices, supporting the metrology community in implementing new methods and developing fit-for-purpose SI- traceable peptide or protein primary calibrators.

METHODS

To establish traceability to SI units, peptide impurity correction amino acid analysis (PICAA) was conducted to determine the absolute content of signature peptides in the primary standards. Immunoaffinity enrichment was used to capture cTnI from human serum, with a comparison between microbeads and nanobeads to improve enrichment efficiency. Parallel reaction monitoring was used to monitor two signature peptides specific to cTnI. Various digestion parameters were optimized to achieve complete digestion.

RESULTS

The analytical method demonstrated selectivity and specificity, allowing the quantification of cTnI within 0.9-22.0 μg/L. The intermediate precision RSD was below 28.9 %, and the repeatability RSD was below 5.8 % at all concentration levels, with recovery rates ranging from 87 % to 121 %. The comparison of calibration strategies showed similar LOQ values, but the peptide-based calibration exhibited significant quantitative bias in recovery rates. The data are available via ProteomeXchange (PXD055104).

CONCLUSIONS

This isotope dilution liquid chromatography-tandem mass spectrometry (ID-LC-MS/MS) method, based on peptide calibration, successfully quantified cTnI in human serum. Comparing this with protein-based calibration highlighted both the strengths and potential limitations of peptide-based strategies.

Coxiella burnetii manipulates the lysosomal protease cathepsin B to facilitate intracellular success

The obligate intracellular bacterium Coxiella burnetii establishes an intracellular replicative niche termed the Coxiella-containing vacuole (CCV), which has been characterised as a bacterially modified phagolysosome. How C. burnetii withstands the acidic and degradative properties of this compartment is not well understood. We demonstrate that the key lysosomal protease cathepsin B is actively and selectively removed from C. burnetii-infected cells through a mechanism involving the Dot/Icm type IV-B secretion system effector CvpB. Overexpression of cathepsin B leads to defects in CCV biogenesis and bacterial replication, indicating that removal of this protein represents a strategy to reduce the hostility of the intracellular niche. In addition, we show that C. burnetii infection of mammalian cells induces the secretion of a wider cohort of lysosomal proteins, including cathepsin B, to the extracellular milieu via a mechanism dependent on retrograde traffic. This study reveals that C. burnetii is actively modulating the hydrolase cohort of its replicative niche to promote intracellular success and demonstrates that infection incites the secretory pathway to maintain lysosomal homoeostasis.

RAS-p110α signalling in macrophages is required for effective inflammatory response and resolution of inflammation

Macrophages are crucial in the body's inflammatory response, with tightly regulated functions for optimal immune system performance. Our study reveals that the RAS-p110α signalling pathway, known for its involvement in various biological processes and tumourigenesis, regulates two vital aspects of the inflammatory response in macrophages: the initial monocyte movement and later-stage lysosomal function. Disrupting this pathway, either in a mouse model or through drug intervention, hampers the inflammatory response, leading to delayed resolution and the development of more severe acute inflammatory reactions in live models. This discovery uncovers a previously unknown role of the p110α isoform in immune regulation within macrophages, offering insight into the complex mechanisms governing their function during inflammation and opening new avenues for modulating inflammatory responses.

Comprehensive analysis of blood proteome response to necrotic enteritis in broiler chicken

Necrotic enteritis (NE) in broiler chickens is caused by the overgrowth of toxin-producing strains of Clostridium (C.) perfringens. This study aims to analyze the blood proteome of broiler chickens affected by NE, providing insights into the host's response to the infection. Using MS/MS-based proteomics, blood plasma samples from broilers with necrotic lesions of different severity were analyzed and compared to healthy controls. A total of 412 proteins were identified, with 63 showing significant differences; for 25 of those correlation with disease severity was observed. Functional analysis revealed that proteins affected by NE were predominantly associated with the immune and signaling processes and extracellular matrix (ECM) structures. Notably, regulated proteins were significantly involved in bioprocesses related to complement activation, acute phase reaction, proteolysis and humoral immune response. The proteomics findings suggest that the changes in plasma proteins in response to NE are driven by the host's intensified efforts to counteract the infection, demonstrating a.o. activation of ECM-degrading proteases (MMP2, TIMP2), acute phase response (HPS5, CP, EXFABP, TF, VNN) and notable reduction in basement membrane (BM) and ECM-related peptides (PLOD2, POSTN, COL1A1/2, HSPG2, NID2) detected in the blood of NE-affected birds. Moreover, the findings underscore a coordinated effort of the host to mitigate the C. perfringens infection via activating immune (a.o., C3, CFH, MASP2, MBL2) and acute phase (CP, ORM, TF, ExFAB) related proteins. This study provides a deeper understanding of the host-pathogen interactions and identifies potential biomarkers and targets for therapeutic intervention. Data are available via ProteomeXchange with identifier PXD054172.

Differential unfolded protein response regulation in KRAS silencing sensitive and innately resistant colorectal cancer cells

Despite the development of mutant-selective KRAS inhibitors, colorectal cancer (CRC) responses remain limited, with stable disease and rapid recurrence being common outcomes. The molecular mechanisms enabling CRC cells to tolerate KRAS inhibition and ultimately develop resistance remain poorly understood. Here, we investigated early transcriptional and proteomic responses to KRAS silencing in 3D CRC cell line spheroid models, aiming to identify pathways associated with sensitivity or resistance to KRAS blockade. Cell lines were stratified into KRAS silencing-sensitive (HCT116 and SW480) and -resistant (LS174T and SW837) groups based on spheroid growth, cell cycle progression, and apoptosis induction. Transcriptional profiling revealed the unfolded protein response (UPR) and WNT/β-catenin signaling as pathways specifically upregulated in KRAS silencing-sensitive cells and downregulated in resistant cells. Proteomic analysis of membrane-enriched fractions further supported UPR deregulation, showing a pronounced downregulation of translation-related proteins in sensitive cells. Functional assays validated that the sensitive cell line HCT116 exhibits reduced protein aggregation and lower translational capacity upon KRAS knockdown, consistent with UPR activation. Pharmacological inhibition of IRE1α-mediated UPR signaling did not revert KRAS silencing-induced cell cycle arrest or apoptosis in this cell line. Collectively, our results highlight the UPR activation as an early adaptive response of KRAS-dependent CRC cells to KRAS silencing.

Structural and functional significance of Aedes aegypti AgBR1 flavivirus immunomodulator

Zika virus (ZIKV), an arbovirus, relies on mosquitoes as vectors for its transmission. During blood feeding, mosquitoes inoculate saliva containing various proteins. Recently, AgBR1, an Aedes aegypti salivary gland protein, has gained attention for its immunomodulatory potential, along with another protein, called NeSt1. We have determined the crystal structure of AgBR1 at 1.2 Å resolution. Despite its chitinase-like fold, we demonstrated that AgBR1 does not bind to chitobiose or chitinhexaose, while a key mutation in the catalytic site abrogates enzymatic activity, suggesting that the protein's function has been repurposed. Our study also shows that AgBR1 and NeSt1, when presented to murine primary macrophages, alter cellular pathways related to virus entry by endocytosis, immune response, and cell proliferation. AgBR1 (and NeSt1) do not directly bind to the Zika virus or modulate its replication. We propose that their immunomodulatory effects on Zika virus transmission are through regulation of host-cell response, a consequence of evolutionary cross talk and virus opportunism. These structural and functional insights are prerequisites for developing strategies to halt the spread of mosquito-borne disease.IMPORTANCEOur study informs on the structural and functional significance of a mosquito salivary gland protein, AgBR1 (along with another protein called NeSt1), in the transmission of the Zika virus (ZIKV), a mosquito-borne virus that has caused global health concerns. By analyzing AgBR1's three-dimensional structure in combination with cellular and interaction studies, we discovered that AgBR1 does not function like typical proteins in its family-it does not degrade sugars. However, we show that it primes immune cells in a way that could help the virus enter cells more easily but not by interacting with the virus or altering viral replication. This finding is significant because it reveals how mosquito proteins, repurposed by evolution, can influence virus transmission without the virus's direct presence. Understanding how proteins like AgBR1 work could guide the development of new strategies to prevent Zika virus spread, with potential relevance for other mosquito-borne viruses.

VCL/ICAM-1 pathway is associated with lung inflammatory damage in SARS-CoV-2 Omicron infection

SARS-CoV-2 variants present diverse clinical manifestations, necessitating deeper insights into their pathogenic effects. This study employs multi-omics approaches to investigate the molecular mechanisms underlying SARS-CoV-2 infection, focusing on vascular damage. Plasma proteomic analysis of unvaccinated participants infected with Omicron BA.2.76 or ancestral variants identifies key signaling pathways associated with endothelial dysfunction, with the vinculin (VCL) pathway emerging as a hallmark of Omicron infections, contributing to lung exudation. Metabolomic analysis of plasma samples from the same cohort reveals disruptions in immune function, cell membrane integrity, and metabolic processes, including altered tricarboxylic acid cycle and glycolysis pathways. An integrated analysis of proteomic and metabolomic data underscores the role of VCL in inflammation and extravasation, highlighting its interactions with adhesion molecules and inflammatory metabolites. A validation cohort of plasma samples from Omicron-infected participants confirms this association by replicating proteomic analysis, showing elevated VCL levels correlated with inflammatory markers. Functional studies in a male rat model of lung injury demonstrate that anti-VCL intervention reduces plasma VCL levels, mitigates alveolar edema, and restores alveolar-capillary barrier integrity, as assessed by histological staining and electron microscopy, thereby illustrating VCL modulation's impact on vascular leakage and extravasation. These findings establish VCL as a potential therapeutic target for mitigating vascular complications in SARS-CoV-2 infections.

Alternate routes to acetate tolerance lead to varied isoprenol production from mixed carbon sources in Pseudomonas putida

Lignocellulose is a renewable resource for the production of a diverse array of platform chemicals, including the biofuel isoprenol. Although this carbon stream provides a rich source of sugars, other organic compounds, such as acetate, can be used by microbial hosts. Here, we examined the growth and isoprenol production in a Pseudomonas putida strain pre-tolerized ("PT") background where its native isoprenol catabolism pathway is deleted, using glucose and acetate as carbon sources. We found that PT displays impaired growth in minimal medium containing acetate and often fails to grow in glucose-acetate medium. Using a mutant recovery-based approach, we generated tolerized strains that overcame these limitations, achieving fast growth and isoprenol production in the mixed carbon feed. Changes in the glucose and acetate assimilation routes, including an upregulation in PP_0154 (SpcC, succinyl-CoA:acetate CoA-transferase) and differential expression of the gluconate assimilation pathways, were key for higher isoprenol titers in the tolerized strains, whereas a different set of mechanisms were likely enabling tolerance phenotypes in media containing acetate. Among these, a coproporphyrinogen-III oxidase (HemN) was upregulated across all tolerized strains and in one isolate required for acetate tolerance. Utilizing a defined glucose and acetate mixture ratio reflective of lignocellulosic feedstocks for isoprenol production in P. putida allowed us to obtain insights into the dynamics and challenges unique to dual carbon source utilization that are obscured when studied separately. Together, this enabled the development of a P. putida bioconversion chassis able to use a more complex carbon stream to produce isoprenol.IMPORTANCEAcetate is a relatively abundant component of many lignocellulosic carbon streams and has the potential to be used together with sugars, especially in microbes with versatile catabolism such as P. putida. However, the use of mixed carbon streams necessitates additional optimization. Furthermore, the use of P. putida for the production of the biofuel target, isoprenol, requires the use of engineered strains that have additional growth and production constraints when cultivated in acetate and glucose mixtures. In this study, we generate acetate-tolerant P. putida strains that overcome these challenges and examine their ability to produce isoprenol. We show that acetate tolerance and isoprenol production, although independent phenotypes, can both be optimized in a given P. putida strain. Using proteomics and whole genome sequencing, we examine the molecular basis of both phenotypes and show that tolerance to acetate can occur via alternate routes and result in different impacts on isoprenol production.

Unifying the analysis of bottom-up proteomics data with CHIMERYS

Proteomic workflows generate vastly complex peptide mixtures that are analyzed by liquid chromatography-tandem mass spectrometry, creating thousands of spectra, most of which are chimeric and contain fragment ions from more than one peptide. Because of differences in data acquisition strategies such as data-dependent, data-independent or parallel reaction monitoring, separate software packages employing different analysis concepts are used for peptide identification and quantification, even though the underlying information is principally the same. Here, we introduce CHIMERYS, a spectrum-centric search algorithm designed for the deconvolution of chimeric spectra that unifies proteomic data analysis. Using accurate predictions of peptide retention time, fragment ion intensities and applying regularized linear regression, it explains as much fragment ion intensity as possible with as few peptides as possible. Together with rigorous false discovery rate control, CHIMERYS accurately identifies and quantifies multiple peptides per tandem mass spectrum in data-dependent, data-independent or parallel reaction monitoring experiments.

Extensive modulation of the circulating blood proteome by hormonal contraceptive use across two population studies

BACKGROUND

The study of circulating blood proteins in population cohorts offers new avenues to explore lifestyle-related and genetic influences describing and shaping human health.

METHODS

Utilizing high-throughput mass spectrometry, we quantified 148 highly abundant proteins, functioning in the innate and adaptive immune system, coagulation and nutrient transport in 3632 blood plasma, and 500 serum samples from the CHRIS and BASE-II cross-sectional population studies, respectively. Through multiple regression analyses, we aimed to identify the main factors influencing the circulating proteome at population level.

RESULTS

Many demographic covariates and common medications affect the concentration of high-abundant plasma proteins, but the most significant changes are linked to the use of hormonal contraceptives (HCU). HCU particularly alters amongst others the levels of Angiotensinogen and Transcortin. We robustly replicated these findings in the BASE-II cohort. Furthermore, our results indicate that combined hormonal contraceptives with ethinylestradiol have a stronger effect compared to bioidentical estrogens. Our analysis detects no lasting impact of hormonal contraceptives on the plasma proteome.

CONCLUSIONS

HCU is the dominant factor reshaping the high-abundant circulating blood proteome in two population studies. Given the high prevalence of HCU among young women, it is essential to account for this treatment in human proteome studies to avoid misinterpreting its impact as sex- or age-related effects. Although we did not investigate the influence of HCU-induced proteomic changes on human health, our data suggest that future studies on this topic are warranted.

Integrative multiomic approaches reveal ZMAT3 and p21 as conserved hubs in the p53 tumor suppression network

TP53, the most frequently mutated gene in human cancer, encodes a transcriptional activator that induces myriad downstream target genes. Despite the importance of p53 in tumor suppression, the specific p53 target genes important for tumor suppression remain unclear. Recent studies have identified the p53-inducible gene Zmat3 as a critical effector of tumor suppression, but many questions remain regarding its p53-dependence, activity across contexts, and mechanism of tumor suppression alone and in cooperation with other p53-inducible genes. To address these questions, we used Tuba-seqUltra somatic genome editing and tumor barcoding in a mouse lung adenocarcinoma model, combinatorial in vivo CRISPR/Cas9 screens, meta-analyses of gene expression and Cancer Dependency Map data, and integrative RNA-sequencing and shotgun proteomic analyses. We established Zmat3 as a core component of p53-mediated tumor suppression and identified Cdkn1a as the most potent cooperating p53-induced gene in tumor suppression. We discovered that ZMAT3/CDKN1A serve as near-universal effectors of p53-mediated tumor suppression that regulate cell division, migration, and extracellular matrix organization. Accordingly, combined Zmat3-Cdkn1a inactivation dramatically enhanced cell proliferation and migration compared to controls, akin to p53 inactivation. Together, our findings place ZMAT3 and CDKN1A as hubs of a p53-induced gene program that opposes tumorigenesis across various cellular and genetic contexts.

ARC/ARG3.1 binds the nuclear polyadenylate-binding protein RRM and regulates neuronal activity-dependent formation of nuclear speckles

ARC is a neuronal activity-induced protein interaction hub with critical roles in synaptic plasticity and memory. ARC localizes to synapses and the nucleus, but its nuclear functions are little known. Following in vivo long-term potentiation (LTP) induction in the dentate gyrus, we show that ARC accumulates in the nucleosol fraction and interchromatin space of granule cells. Proteomic analysis of immunoprecipitated ARC complexes identifies proteins involved in pre-mRNA processing. We demonstrate endogenous ARC protein-protein interaction with polyadenylate-binding nuclear protein 1 (PABPN1) and the paraspeckles protein polypyrimidine tract-binding protein (PTB)-associated splicing factor (PSF). In vitro peptide binding arrays show direct binding of purified ARC to the PABPN1 poly(A)-RNA recognition motif. 3D morphometric imaging reveals structural changes in PABPN1 foci corresponding to classical nuclear speckles following in vivo and in vitro LTP. Depletion of ARC disrupts the maintenance and activity-dependent formation of PABPN1 speckles, thus implicating ARC in regulation of nuclear speckle dynamics and pre-mRNA processing.

SMYD5 is a ribosomal methyltransferase that trimethylates RPL40 lysine 22 through recognition of a KXY motif

The eukaryotic ribosome is highly modified by protein methylation, yet many of the responsible methyltransferases remain unknown. Here, we identify SET and MYND domain-containing protein 5 (SMYD5) as a ribosomal protein methyltransferase that catalyzes trimethylation of RPL40/eL40 at lysine 22. Through a systematic mass spectrometry-based approach, we identify 12 primary sites of protein methylation in ribosomes from K562 cells, including at RPL40 K22. Through in vitro methylation of synthetic RPL40 using fractionated lysate, we then identify SMYD5 as a candidate RPL40 K22 methyltransferase. We show that recombinant SMYD5 has robust activity toward RPL40 K22 in vitro and that active site mutations ablate this activity. Knockouts of SMYD5 in K562 cells show a complete loss of RPL40 K22 methylation and decreased polysome levels. We show that SMYD5 does not methylate histones in vitro, and by systematic analysis of its recognition motif, we find that SMYD5 requires a KXY motif for methylation, explaining its lack of activity toward histones.

Host genetic variation governs PCV2 susceptibility through CXCL13 and ELK1-mediated immune regulation

Pathogenic viruses can drive evolutionary adaptations in host biology, leading to diversified immune responses and variable susceptibility among individuals. This study examined how genetic variation in host regulatory regions impacts susceptibility to viral infections. Utilizing a porcine model, we identified the single nucleotide polymorphism (SNP) g.-1014G>A as a critical determinant of CXCL13 expression levels following PCV2 viral exposure. Structural analyses showed that the transcription factor ELK1 specifically recognized and bound to the g.-1014G allele, but not to the g.-1014A allele, through essential residues such as Arg65. This allele-specific binding led to differential CXCL13 expression, with the G allele associated with increased resistance to viral infection. Functional studies demonstrated that CXCL13 played a multifaceted role in antiviral immunity, including the inhibition of viral replication, modulation of immune-related pathways, and attenuation of virus-induced apoptosis. The CXCL13-mediated response involved the activation of the PI3K/Akt pathway, enhancing cell survival during viral challenges. This SNP-dependent regulation of a host factor represented a novel mechanism underlying genetic differences in viral susceptibility, with potential implications for developing broadly applicable antiviral strategies.

Proximity-based activation of AURORA A by MPS1 potentiates error correction

Faithful cell division relies on mitotic chromosomes becoming bioriented with each pair of sister kinetochores bound to microtubules oriented toward opposing spindle poles. Erroneous kinetochore-microtubule attachments often form during early mitosis but are destabilized through the phosphorylation of outer kinetochore proteins by centromeric AURORA B kinase (ABK) and centrosomal AURORA A kinase (AAK), thus allowing for re-establishment of attachments until biorientation is achieved.1,2,3,4,5,6,7,8,9 MPS1-mediated phosphorylation of NDC80 has also been shown to directly weaken the kinetochore-microtubule interface in yeast.10 In human cells, MPS1 has been proposed to transiently accumulate at end-on attached kinetochores11 and phosphorylate SKA3 to promote microtubule release.12 Whether MPS1 directly targets NDC80 and/or promotes the activity of AURORA kinases in metazoans remains unclear. Here, we report a novel mechanism involving communication between kinetochores and centrosomes, wherein MPS1 acts upstream of AAK to promote error correction. MPS1 on pole-proximal kinetochores phosphorylates the C-lobe of AAK, thereby increasing its activation at centrosomes. This proximity-based activation ensures the establishment of a robust AAK activity gradient that locally destabilizes mal-oriented kinetochores near spindle poles. Accordingly, MPS1 depletion from Drosophila cells causes severe chromosome misalignment and erroneous kinetochore-microtubule attachments, which can be rescued by tethering either MPS1 or constitutively active AAK mutants to centrosomes. Proximity-based activation of AAK by MPS1 also occurs in human cells to promote AAK-mediated phosphorylation of the NDC80 N-terminal tail. These findings uncover an MPS1-AAK crosstalk that is required for efficient error correction, showcasing the ability of kinetochores to modulate centrosome outputs to ensure proper chromosome segregation.

Transformation of the drug ibuprofen by Priestia megaterium: reversible glycosylation and generation of hydroxylated metabolites

As one of the most-consumed drugs worldwide, ibuprofen (IBU) reaches the environment in considerable amounts as environmental pollutant, necessitating studies of its biotransformation as potential removal mechanism. Here, we screened bacteria with known capabilities to degrade aromatic environmental pollutants, belonging to the genera Bacillus, Priestia (formerly also Bacillus), Paenibacillus, Mycobacterium, and Cupriavidus, for their ability to transform ibuprofen. We identified seven transformation products, namely 2-hydroxyibuprofen, carboxyibuprofen, ibuprofen pyranoside, 2-hydroxyibuprofen pyranoside, 4-carboxy-α-methylbenzene-acetic acid, 1-[4-(2-hydroxy-2-methylpropyl)phenyl]ethanone, and 2-hydroxyibuprofenmethyl ester. Based on our screening results, we focused on ibuprofen biotransformation by Priestia megaterium SBUG 518, to identify structures of transformation products, and to shed light on the drug's impact on bacterial physiology. Biotransformation reactions by P. megaterium SBUG 518 involved (A) the hydroxylation of the isobutyl side chain at two positions, and (B) conjugate formation via esterification with a sugar molecule of the carboxylic group of ibuprofen and an ibuprofen hydroxylation product. Glycosylation seems to be a detoxification process, since the ibuprofen conjugate (ibuprofen pyranoside) was considerably less toxic than the parent compound to P. megaterium SBUG 518. Based on proteome profile changes and inhibition assays, cytochrome P450 systems appear to be central for ibuprofen transformation in P. megaterium SBUG 518. The toxic effect of ibuprofen appears to be caused by interference of the drug with different physiological pathways, especially sporulation.

Phosphoproteomics Uncovers Exercise Intensity-Specific Skeletal Muscle Signaling Networks Underlying High-Intensity Interval Training in Healthy Male Participants

BACKGROUND

In response to exercise, protein kinases and signaling networks are engaged to blunt homeostatic threats generated by acute contraction-induced increases in skeletal muscle energy and oxygen demand, as well as serving roles in the adaptive response to chronic exercise training to blunt future disruptions to homeostasis. High-intensity interval training (HIIT) is a time-efficient exercise modality that induces superior or similar health-promoting skeletal muscle and whole-body adaptations compared with prolonged, moderate-intensity continuous training (MICT). However, the skeletal muscle signaling pathways underlying HIIT's exercise intensity-specific adaptive responses are unknown.

OBJECTIVE

We mapped human muscle kinases, substrates, and signaling pathways activated/deactivated by an acute bout of HIIT versus work-matched MICT.

METHODS

In a randomized crossover trial design (Australian New Zealand Clinical Trials Registry number ACTRN12619000819123; prospectively registered 6 June 2019), ten healthy male participants (age 25.4 ± 3.2 years; BMI 23.5 ± 1.6 kg/m2;V ˙ O 2 max 37.9 ± 5.2 ml/kg/min, mean values ± SD) completed a single bout of HIIT and MICT cycling separated by ≥ 10 days and matched for total work (67.9 ± 10.2 kJ) and duration (10 min). Mass spectrometry-based phosphoproteomic analysis of muscle biopsy samples collected before, during (5 min), and immediately following (10 min) each exercise bout, to map acute temporal signaling responses to HIIT and MICT, identified and quantified 14,931 total phosphopeptides, corresponding to 8509 phosphorylation sites.

RESULTS

Bioinformatic analyses uncovered exercise intensity-specific signaling networks, including > 1000 differentially phosphorylated sites (± 1.5-fold change; adjusted P < 0.05; ≥ 3 participants) after 5 min and 10 min HIIT and/or MICT relative to rest. After 5 and 10 min, 92 and 348 sites were differentially phosphorylated by HIIT, respectively, versus MICT. Plasma lactate concentrations throughout HIIT were higher than MICT (P < 0.05), and correlation analyses identified > 3000 phosphosites significantly correlated with lactate (q < 0.05) including top functional phosphosites underlying metabolic regulation.

CONCLUSIONS

Collectively, this first global map of the work-matched HIIT versus MICT signaling networks has revealed rapid exercise intensity-specific regulation of kinases, substrates, and pathways in human skeletal muscle that may contribute to HIIT's skeletal muscle adaptations and health-promoting effects.  Preprint: The preprint version of this work is available on medRxiv, https://doi.org/10:1101/2024.07.11.24310302 .

Temozolomide promotes glioblastoma stemness expression through senescence-associated reprogramming via HIF1α/HIF2α regulation

A critical challenge in glioblastoma multiforme (GBM) treatment is that tumors recurring after temozolomide (TMZ) therapy become more malignant, exhibiting increased invasiveness and stemness compared to the primary tumor. However, the underlying mechanisms remain unclear. While the majority of GBM cells are eradicated by TMZ, a subset enters cell cycle arrest, adopts a senescence-associated secretory phenotype (SASP), and activates senescence-related signaling pathways. These cells eventually escape senescence, re-enter the cell cycle, and form aggregates exhibiting stem-like characteristics such as elevated stemness marker expression, enhanced colony formation, increased invasiveness, and resistance to chemotherapy. Furthermore, these aggregates promote the invasion and chemotherapy resistance of surrounding cells. Gene Set Enrichment Analysis (GSEA) and KEGG pathway analysis of miRNA and mRNA sequences revealed activation of hallmark hypoxia and HIF1 signaling pathways. The study demonstrated that HIF1α and HIF2α expression fluctuates during and after TMZ treatment. Knockout of HIF1α and HIF2α in GBM cells exposed to TMZ reduced the formation of senescent cells and stem-like aggregates. These findings challenge the efficacy of TMZ therapy by highlighting its role in inducing the process of cellular senescence, thereby contributing to the enhanced stemness and malignancy of recurrent GBM. The regulatory roles of HIF1α and HIF2α are emphasized, underscoring the necessity of preventing senescent cell formation and inhibiting HIF1α/HIF2α expression to improve therapeutic outcomes.

Deep Learning-Based Prediction of Decoy Spectra for False Discovery Rate Estimation in Spectral Library Searching

With the advantage of extensive coverage, predicted spectral libraries are becoming an attractive alternative in proteomic data analysis. As a popular false discovery rate estimation method, target decoy search has been adopted in library search workflows. While existing decoy methods for curated experimental libraries have been tested, their performance in predicted library scenarios remains unknown. Current methods rely on perturbing real spectra templates, limiting the diversity and number of decoy spectra that can be generated for a given library. In this study, we explore the shuffle-and-predict decoy library generation approach, which can generate decoy spectra without the need for template spectra. Our experiments shed light on decoy method performance for predicted library scenarios and demonstrate the quality of predicted decoys in FDR estimation.

Unveiling the substrate specificity of the ABC transporter Tba and its role in glycopeptide biosynthesis

Glycopeptide antibiotics (GPA) such as vancomycin are essential last-resort antibiotics produced by actinomycetes. Their biosynthesis is encoded within biosynthetic gene clusters, also harboring genes for regulation, and transport. Diverse types of GPAs have been characterized that differ in peptide backbone composition and modification patterns. However, little is known about the ATP-binding cassette (ABC) transporters facilitating GPA export. Employing a multifaceted approach, we investigated the substrate specificity of GPA ABC-transporters toward the type-I GPA balhimycin. Phylogenetic analysis suggested and trans-complementation experiments confirmed that balhimycin is exported only by the related type I GPA transporters Tba and Tva (transporter of vancomycin). Molecular dynamics simulations and mutagenesis experiments showed that Tba exhibits specificity toward the peptide backbone rather than the modifications. Unexpectedly, deletion or functional inactivation of Tba halted balhimycin biosynthesis. Combined with proximity biotinylation experiments, this suggested that the interaction of the active transporter with the biosynthetic machinery is required for biosynthesis.

Hypoxic Preconditioning Enhances the Potential of Mesenchymal Stem Cells to Treat Neonatal Hypoxic-Ischemic Brain Injury

BACKGROUND

Neonatal hypoxic-ischemic (HI) brain injury is one of the leading causes of long-term neurological morbidity in newborns. Current treatment options for HI brain injury are limited, but mesenchymal stem cell (MSC) therapy is a promising strategy to boost neuroregeneration after injury. Optimization strategies to further enhance the potential of MSCs are under development. The current study aimed to test the potency of hypoxic preconditioning of MSCs to enhance the therapeutic efficacy in a mouse model of neonatal HI injury.

METHODS

HI was induced on postnatal day 9 in C57Bl/6 mouse pups. MSCs were cultured under hypoxic (hypoxic-preconditioned MSCs [HP-MSCs], 1% O2) or normoxic-control (normoxic-preconditioned MSCs, 21% O2) conditions for 24 hours before use. At 10 days after HI, HP-MSCs, normoxic-preconditioned MSCs, or vehicle were intranasally administered. Gold nanoparticle-labeled MSCs were used to assess MSC migration 24 hours after intranasal administration. At 28 days post-HI, lesion size, sensorimotor outcome, and neuroinflammation were assessed by hematoxylin and eosin staining, cylinder rearing task, and IBA1 staining, respectively. In vitro, the effect of HP-MSCs was studied on transwell migration, neural stem cell differentiation and microglia activation, and the MSC intracellular proteomic content was profiled using quantitative LC-MS/ms.

RESULTS

Intranasally administered HP-MSCs were superior to normoxic-preconditioned MSCs in reducing lesion size and sensorimotor impairments post-HI. Moreover, hypoxic preconditioning enhanced MSC migration in an in vitro set-up, and in vivo to the lesioned hemisphere after intranasal application. In addition, HP-MSCs enhanced neural stem cell differentiation into more complex neurons in vitro but had similar anti-inflammatory effects compared with normoxic-preconditioned MSCs. Lastly, hypoxic preconditioning led to elevated abundances of proteins in MSCs related to extracellular matrix remodeling.

CONCLUSIONS

This study shows for the first time that hypoxic preconditioning enhanced the therapeutic efficacy of MSC therapy in a mouse model of neonatal HI brain injury by increasing the migratory and neuroregenerative capacity of MSCs.

Structure of human PINK1 at a mitochondrial TOM-VDAC array

Mutations in the ubiquitin kinase PINK1 cause early-onset Parkinson's disease, but how PINK1 is stabilized at depolarized mitochondrial translocase complexes has remained poorly understood. We determined a 3.1-angstrom resolution cryo-electron microscopy structure of dimeric human PINK1 stabilized at an endogenous array of mitochondrial translocase of the outer membrane (TOM) and voltage-dependent anion channel (VDAC) complexes. Symmetric arrangement of two TOM core complexes around a central VDAC2 dimer is facilitated by TOM5 and TOM20, both of which also bind PINK1 kinase C-lobes. PINK1 enters mitochondria through the proximal TOM40 barrel of the TOM core complex, guided by TOM7 and TOM22. Our structure explains how human PINK1 is stabilized at the TOM complex and regulated by oxidation, uncovers a previously unknown TOM-VDAC assembly, and reveals how a physiological substrate traverses TOM40 during translocation.

Unveiling transcriptional mechanisms of B7-H3 in breast cancer stem cells through proteomic approaches

B7-H3, an immune checkpoint molecule, is prominently overexpressed in various solid tumors, correlating with poor clinical outcomes. Despite its critical role in promoting tumorigenesis, metastasis, and immune evasion, the regulatory mechanisms governing B7-H3 expression, particularly in cancer stem cells (CSCs), remain elusive. In this comprehensive study, we focused on breast CSCs to uncover the transcriptional regulators driving B7-H3 overexpression. Utilizing DNA affinity purification-mass spectrometry (DAP-MS) to analyze B7-H3 promoter regions, we identified a novel set of transcription factors, including DDB1, XRCC5, PARP1, RPA1, and RPA3, as key modulators of B7-H3 expression. Functional assays revealed that targeting DDB1 with nitazoxanide significantly downregulated B7-H3 expression, subsequently impairing tumor sphere formation and cell migration in breast CSCs. These findings not only elucidate the complex transcriptional network controlling B7-H3 expression but also open new avenues for developing targeted immunotherapies aimed at disrupting CSC-driven cancer progression.