Housekeeping Proteins Research Articles

The promiscuous biotin ligase TurboID reveals the proxisome of the T3SS chaperone IpgC in Shigella flexneri.

Promiscuous biotin ligases derived from the bacterial enzyme BirA are used to identify proteins vicinal to a bait protein, thereby defining its proxisome. Despite the popularity of this approach, surprisingly little is known about its use in prokaryotes. Here, we compared the activity of four widely used promiscuous biotin ligases in the cytoplasm of Shigella flexneri, a pathogenic subgroup of Escherichia coli. Our data indicate that the kinetics of TurboID's biotinylating activity is the highest of those tested. In addition, TurboID showed reduced interaction with the natural BirA binding partners, BccP and the biotin operator, when compared to its ancestor BioID. We therefore evaluated the ability of TurboID to probe the proxisome of the type III secretion system (T3SS) chaperone IpgC and the transcriptional activator MxiE. When the T3SS is inactive (off-state), these proteins are inhibited by forming complexes with the T3SS substrates OspD1 and IpaBC, respectively. In contrast, when the T3SS is active (on-state), OspD1 and IpaBC are secreted allowing MxiE and IpgC to interact together and activate their target genes. The results obtained with the IpgC and TurboID fusions capture a good fraction of these known interactions. It also suggests that the availability of IpgC increases in the on-state, resulting in a greater number of proteins detected in its vicinity. Among these is the T3SS ATPase SpaL (also known as Spa47 or SctN), further supporting the notion that chaperones escort their substrate to the T3SS. Interestingly, a specific subset of proteins conserved in E. coli completes the IpgC proxisome in the on-state.IMPORTANCEPromiscuous biotin ligases are widely used to study protein function in eukaryotes. Strikingly, their use in prokaryotes has been rare. Indeed, the small volume and the cytoplasmic location of the biotin ligase's natural binding partners in these organisms pose unique challenges that can interfere with the study of the proxisome of proteins of interest. Here, we evaluated four of the most common promiscuous biotin ligases and found TurboID was best suited for use in the cytoplasm of Shigella flexneri. Using this method, we extended the proxisome of IpgC beyond its known direct binding partners involved in the regulation of the type III secretion system (T3SS) signaling cascade. Of particular interest for further study are transcription factors and housekeeping proteins that are enriched around IpgC when the T3SS is active. We propose a model in which the increased availability of IpgC in the on-state may allow cross-talk of the T3SS with other cellular processes.

New insights into the pathophysiology of rheumatic valve disease based on different genetic and proteomics profiles

Abstract Introduction Rheumatic heart disease (RHD) pathogenesis is not fully understood. Purpose The protein profile in rheumatic heart disease may have a different fingerprint in the aortic and mitral valves, which results in different evolution in terms of valve damage. Methods To evaluate the genetic profile in symptomatic RHD, 4 simultaneous mitral and aortic valves were obtained during valve replacement, as well as 4 "normal" valves from cadavers (Control Group). The expression of 90 genes was evaluated using a customized RT-PCR array kit. A second experiment was carried out to evaluate proteomics. Then, 7 mitral and aortic valves, from the same patient, were also collected during valve surgery. The Control Group consisted of 6 mitral and aortic valves obtained from explanted hearts during heart transplantation due to non-valvular pathologies. Additionally, histopathological and sectoral proteomic analysis of amyloid deposits, found in some mitral and aortic valves, from the second experiment, were also reported. Results Mitral rheumatic valves exhibited higher expression of genes linked to calcification and immuno-inflammation compared to aortic rheumatic valves (Figure 1). Proteomic analysis, visualized through PCA graphs, highlighted differences in proteomic patterns. Despite having the same genetic pattern, control valves exhibited different proteomic profiles (Figure 1) Rheumatic mitral and aortic valves, even from the same individual, showed distinct proteomic fingerprint (Figure 1). A total of 49 significant proteins were identified in distinguishing healthy mitral and aortic valves from the same individual (Figure 1). The aortic valve displayed a richer extracellular matrix and higher levels of housekeeping proteins that maintain valve homeostasis compared to the mitral valve (Figure 1). The dominant proteomic pattern in valvular rheumatic disease was identified as alterations in critical mitochondrial metabolic activities related to proteostasis. (Figure 2). Particularly notable was the upregulation of pathways associated with lipid metabolism (Figure 2). Finally, amyloid deposits suggested APOA1 as a potential deposit protein in RHD (Figure 2). Conclusion The study confirms distinct constitutional differences between mitral and aortic valves affecting rheumatic disease progression. It emphasizes the role of altered proteostasis and altered proteins deposit, mitochondrial metabolic changes, and inflammatory responses in the disease's pathophysiology, highlighting the complexity of valvular rheumatic disease involvement.For the first time amyloid deposition has been reported as a likely consequence of significant disruption in valvular proteostasis and the proteins potentially comprising this deposit within a rheumatic valve.Genomic and proteomic overviewproteomic fingerprint of RHD and amyloid

Abstract B073: Organ-specific diversity of tumor immune microenvironment in metastatic pancreatic cancer

Abstract Pancreatic ductal adenocarcinoma (PDAC) that is refractory to treatment frequently leads to extensive systemic and multi-organ metastases. PDAC is characterized as an immune “cold” cancer; however, the persistence of this “cold” tumor immune microenvironment (TIME) across distant metastases, and the mechanisms by which metastases influence their respective TIME, remain poorly understood. In this study, we conducted spatial protein expression profiling of the TIME using the Nanostring GeoMx Digital Spatial Profiling (DSP) platform. We employed a 43- plex panel on 54 tissue samples, including 14 primary tumors and 40 matched metastases from organs commonly affected by PDAC metastases (liver, lung, and peritoneum), obtained through a rapid (“warm”) autopsy program. We quantified protein expression in three cellular compartments: PanCK+ epithelial cells, α-SMA+ fibroblasts, and CD45+ immune cells, across 181 regions of interest (ROIs). Our analysis revealed a significant enrichment of CD45+ immune cells in lung metastases compared to other organ sites, with a notably lower presence of these cells in liver metastases. Focusing on the immune cell compartment, we analyzed the CD45 segments for further investigation. After normalization using housekeeping proteins, including Histone H3, GAPDH, and ribosomal protein S6, we found that the immune profiles were most distinct between liver and lung metastases. Specifically, liver metastases exhibited the greatest deviation in immune profile compared to primary PDAC, lung, and peritoneal metastases. We scored protein expression signatures for various immune cell subsets based on specific marker expressions. When comparing liver to lung metastases, scores for T cells, myeloid cells, checkpoint markers, macrophages, and interferon signaling were significantly lower in the liver, underscoring the immune “coldness” of the liver metastasis environment. Our cohort included six untreated patients and nine patients treated with chemotherapies. We compared protein expressions in each organ site between untreated and treated patients. Notably, treatment induced divergent expression patterns of multiple proteins between liver and lung metastases. While treatment significantly reduced the expression of several immune markers, including CD45 (total immune), CD3 (T cell), CD4 (T helper cell), CD45RO (memory T cell), CD163 (M2 macrophage), and B7-H3 (checkpoint marker), in lung metastases, these markers were significantly upregulated in liver metastases of treated patients. This finding indicates a pronounced divergence in TIME modulation in response to treatment between liver and lung metastases, potentially fostering a treatment-resistant environment in PDAC patients with multi- organ metastasis. Consequently, this urges the need to develop tailored therapeutic strategies for PDAC metastasis, taking into account the distinct immune landscapes of different metastasis sites. Citation Format: Jimin Min, Vittorio Branchi, Kimal I Rajapakshe, Nisha Narayanan, Guangsheng Pei, Linghua Wang, Jean L Grem, Thomas C Caffrey, Paul M Grandgenett, Michael A Hollingsworth, Paola A Guerrero, Anirban Maitra. Organ-specific diversity of tumor immune microenvironment in metastatic pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pancreatic Cancer Research; 2024 Sep 15-18; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl_2):Abstract nr B073.

Structure-Based Design and Development of Phosphine Oxides as a Novel Chemotype for Antibiotics that Dysregulate Bacterial ClpP Proteases.

A series of arylsulfones and heteroarylsulfones have previously been demonstrated to dysregulate the conserved bacterial ClpP protease, causing the unspecific degradation of essential cellular housekeeping proteins and ultimately resulting in cell death. A cocrystal structure of a 2-β-sulfonylamide analog, ACP1-06, with Escherichia coli ClpP showed that its 2-pyridyl sulfonyl substituent adopts two orientations in the binding site related through a sulfone bond rotation. From this, a new bis-aryl phosphine oxide scaffold, designated as ACP6, was designed based on a "conformation merging" approach of the dual orientation of the ACP1-06 sulfone. One analog, ACP6-12, exhibited over a 10-fold increase in activity over the parent ACP1-06 compound, and a cocrystal X-ray structure with ClpP confirmed its predicted binding conformation. This allowed for a comparative analysis of how different ligand classes bind to the hydrophobic binding site. The study highlights the successful application of structure-based rational design of novel phosphine oxide-based antibiotics.

Molecular docking, MD simulation, and MMGBSA-binding free energy estimation study identify antibiotic analogs as potential antimalarials targeting housekeeping proteins of Plasmodium falciparum apicoplast

ABSTRACT Plasmodium falciparum exclusively harbours a non-photosynthetic plastid-like organelle called ‘apicoplast,’ crucial for survival. The apicoplast genome resembles chloroplasts, albeit much reduced at 35 kb. The housekeeping functions of the apicoplast are similar to prokaryotes, and several antibiotics have been reported to kill the malaria parasite by targeting its housekeeping functions. However, a significant structural difference between bacterial and apicoplast housekeeping proteins promotes the discovery of antibiotic analogs specifically targeting apicoplast proteins. In this study, we used a high-throughput virtual screening approach to analyze 80% of structurally similar antibiotic analog libraries against five protein targets, including histone-like protein (PfHU), gyrase A subunit (PfGyrA), RNA polymerase β subunit (PfRpoβ), elongation factor G (PfEF-G), and elongation factor Tu (PfEF-Tu) involved in different housekeeping functions of the apicoplast. This computational screening identified molecules with better binding affinities than those antibiotics shown to have antimalarial activities, suggesting they may be more potent antimalarial compounds. The molecular dynamics simulations study revealed stable conformational changes with strong hydrogen bonds between the protein–ligand complexes. The top-hit antibiotic analogs exhibit favourable drug-like characteristics, making them promising candidates for future clinical studies. We propose further biochemical and phenotypic testing of these antibiotic analogs to develop more effective apicoplast-targeting antimalarials.

Resolving the current controversy of use and reuse of housekeeping proteins in ageing research: Focus on saving people’s tax dollars

The use of housekeeping genes and proteins to normalize mRNA and protein levels in biomedical research has faced growing scrutiny. Researchers encounter challenges in determining the optimal frequency for running housekeeping proteins such as β-actin, Tubulin, and GAPDH for nuclear-encoded proteins, and Porin, HSP60, and TOM20 for mitochondrial proteins alongside experimental proteins. The regulation of these proteins varies with age, gender, disease progression, epitope nature, gel running conditions, and their reported sizes can differ among antibody suppliers. Additionally, anonymous readers have raised concerns about peer-reviewed and published articles, creating confusion and concern within the research and academic institutions. To clarify these matters, this minireview discusses the role of reference housekeeping proteins in Western blot analysis and outlines key considerations for their use as normalization controls. Instead of Western blotting of housekeeping proteins, staining of total proteins, using Amido Black and Coomassie Blue can be visualized the total protein content on a membrane. The reducing repeated Western blotting analysis of housekeeping proteins, will save resources, time and efforts and in turn increase the number of competitive grants from NIH and funding agencies. We also discussed the use of dot blots over traditional Western blots, when protein levels are low in rare tissues/specimens and cell lines. We sincerely hope that the facts, figures, and discussions presented in this article will clarify the current controversy regarding housekeeping protein(s) use, reuse, and functional aspects of housekeeping proteins. The contents presented in our article will be useful to students, scholars and researchers of all levels in cell biology, protein chemistry and mitochondrial research.

Structure-function analysis of nucleotide housekeeping protein HAM1 from human malaria parasite Plasmodium falciparum.

Non-canonical nucleotides, generated as oxidative metabolic by-products, significantly threaten the genome integrity of Plasmodium falciparum and thereby, their survival, owing to their mutagenic effects. PfHAM1, an evolutionarily conserved inosine/xanthosine triphosphate pyrophosphohydrolase, maintains nucleotide homeostasis in the malaria parasite by removing non-canonical nucleotides, although structure-function intricacies are hitherto poorly reported. Here, we report the X-ray crystal structure of PfHAM1, which revealed a homodimeric structure, additionally validated by size-exclusion chromatography-multi-angle light scattering analysis. The two monomeric units in the dimer were aligned in a parallel fashion, and critical residues associated with substrate and metal binding were identified, wherein a notable structural difference was observed in the β-sheet main frame compared to human inosine triphosphate pyrophosphatase. PfHAM1 exhibited Mg++-dependent pyrophosphohydrolase activity and the highest binding affinity to dITP compared to other non-canonical nucleotides as measured by isothermal titration calorimetry. Modifying the pfham1 genomic locus followed by live-cell imaging of expressed mNeonGreen-tagged PfHAM1 demonstrated its ubiquitous presence in the cytoplasm across erythrocytic stages with greater expression in trophozoites and schizonts. Interestingly, CRISPR-Cas9/DiCre recombinase-guided pfham1-null P. falciparum survived in culture under standard growth conditions, indicating its assistive role in non-canonical nucleotide clearance during intra-erythrocytic stages. This is the first comprehensive structural and functional report of PfHAM1, an atypical nucleotide-cleansing enzyme in P. falciparum.

Decrypting the effect of sulfate stress on the cyanobacterium Anabaena sp. PCC 7120 using physiological, proteome and transcript analysis in conjunction with bioinformatics

Sulfate limitation affects growth and various metabolic processes in cyanobacteria. However, there is little understanding of the underlying mechanism of these processes. Hence, the study investigated the effects of sulfate limitation in the cyanobacterium, Anabaena sp. PCC 7120. Results showed that sulfate stress affected photopigment contents in the test cyanobacterium delineating reduced growth. Proteome profile showed that differential expression profiles of different proteins involved in the various metabolic pathways suggested sulfur-dependent pathways were altered due to sulfate limitation. The most damaging effect was observed on the proteins belonging to the photosynthesis pathway, affirming the relationship between sulfur and carbon metabolism. Expression of proteins involved in the pathways such as nitrogen, protein synthesis, chaperone category, amino acid biosynthesis, and redox-responsive proteins were down-regulated. Moreover, forty-seven hypothetical proteins were also influenced by sulfate limitation. Molecular chaperones act as a physical barrier to prevent the aggregation of housekeeping proteins. Down expression of these proteins might affect the sustainability of the other proteins. Besides, transcript levels of the selected proteins were in concordance with physiological as well as proteome data. Additionally, template-based modeling and ab initio full atomic relaxation were performed via bioinformatic analysis through different tools to gain deeper insight into the structural and functional attributes of hypothetical proteins. Based on study, it could be concluded that mostly the proteins were downregulated which may lead to PCD in the cyanobacterium and also suggested that sulfur is a central hub and crucial for various sulfur-dependent pathways.

Leucyl-tRNA Synthetase Contributes to Muscle Weakness through Mammalian Target of Rapamycin Complex 1 Activation and Autophagy Suppression in a Mouse Model of Duchenne Muscular Dystrophy

Duchenne muscular dystrophy (DMD), caused by loss-of-function mutations in the dystrophin gene, results in progressive muscle weakness and early fatality. Impaired autophagy is one of the cellular hallmarks of DMD, contributing to the disease progression. Molecular mechanisms underlying the inhibition of autophagy in DMD are not well understood. In the current study, the DMD mouse model mdx was used for the investigation of signaling pathways leading to suppression of autophagy. Mammalian target of rapamycin complex 1 (mTORC1) was hyperactive in the DMD muscles, accompanying muscle weakness and autophagy impairment. Surprisingly, Akt, a well-known upstream regulator of mTORC1, was not responsible for mTORC1 activation or the dystrophic muscle phenotypes. Instead, leucyl-tRNA synthetase (LeuRS) was overexpressed in mdx muscles compared with the wild type. LeuRS activates mTORC1 in a noncanonical mechanism that involves interaction with RagD, an activator of mTORC1. Disrupting LeuRS interaction with RagD by the small-molecule inhibitor BC-LI-0186 reduced mTORC1 activity, restored autophagy, and ameliorated myofiber damage in the mdx muscles. Furthermore, inhibition of LeuRS by BC-LI-0186 improved dystrophic muscle strength in an autophagy-dependent manner. Taken together, our findings uncovered a noncanonical function of the housekeeping protein LeuRS as a potential therapeutic target in the treatment of DMD.

Vascular endothelial growth factor receptor 2 contributes to shear stress-induced endothelial nitric oxide synthase expression in human lung microvascular endothelial cells

Introduction: Physiological shear stress (pSS) helps to maintain endothelial homeostasis via numerous intracellular signaling pathways. We previously showed that pSS upregulates mRNA and protein levels of endothelial nitric oxide synthase (eNOS) in primary human lung microvascular endothelial cells (hLMVECs), and that phosphorylation of Akt (p-Akt), a phosphatidylinositol 3-kinase (PI3K) target, is increased. Upstream regulatory mechanisms for these responses have not been fully studied. Since vascular endothelial growth factor receptor 2 (VEGFR2) is an integral component of the mechanosensory complex that transduces shear stress-mediated signaling pathways in endothelial cells, we hypothesized that VEGFR2 is required for shear stress-induced eNOS expression and PI3K activation in hLMVECs. Methods: We cultured early passage (p≤7) primary hLMVECs from 4 unique donor lots in standard 6-well culture plates using a fixed volume (depth) and viscosity of tissue culture media. We exposed cells to shear stress for 24 hours using an orbital shaker and calculated the magnitude of shear stress exerted on hLMVECs using the extended solution to Stokes’ second problem. We defined the magnitude of pSS as 12 dyn/cm2. In some experiments, we exposed cells to pSS in the presence of chemical inhibitors of VEGFR2 (SU5416; 5 or 10 μM) or PI3K (LY294002; 10 μM). We collected whole cell lysates and performed immunoblotting to probe for phosphorylated eNOS (p-eNOS; Serine 1177), total eNOS, p-Akt (Serine 473), total Akt and housekeeping protein β-tubulin. Potential interactions between chemical inhibitors and pSS on protein expression and phosphorylation were analyzed by two-way ANOVA. Results: After 24 hours of pSS exposure, total eNOS levels were significantly (p<0.05) increased in hLMVECs, although the p-eNOS/eNOS ratio was not changed (p=0.85). Conversely, 24 hours of pSS exposure increased the p-Akt/Akt ratio (p<0.05) but did not increase total Akt levels (p=0.88). Inhibition of VEGFR2 activity with SU5416 attenuated pSS-induced changes in total eNOS levels (p<0.05 for interaction) but did not attenuate pSS-induced increases in the p-Akt/Akt ratio (p=0.91 for interaction). Inhibition of PI3K activity using LY294002 did not modify the effects of pSS on total eNOS levels (p=0.25 for interaction) or p-Akt/Akt ratio (p=0.47 for interaction). Conclusions: We conclude that VEGFR2 activity is necessary for pSS-mediated increases in eNOS protein levels, but not PI3K activity, in hLMVECs. Furthermore, neither VEGFR2 nor PI3K activity appear to be required for pSS-mediated eNOS phosphorylation in these cells. Collectively, these data suggest that shear stress regulates hLMVEC eNOS signaling via multiple signaling pathways. This complex regulation may have important implications for local nitric oxide bioavailability under pathological conditions that modify shear stress (e.g., pulmonary embolism, pulmonary hypertension). This work is supported by NIH grants HL126514 and HL159906. This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Selective prosaposin expression in Langerhans islets of the mouse pancreas

The islets of Langerhans are clusters of endocrine cells surrounded by exocrine acinar cells in the pancreas. Prosaposin is a housekeeping protein required for normal lysosomal function, but its expression level is significantly different among tissues. Prosaposin also exists in various body fluids including serum. Intracellularly, prosaposin activates lysosomes and may support autophagy, and extracellularly, prosaposin promotes survival of neurons via G protein-coupled receptors. In this study, prosaposin and its mRNA expression were examined in endocrine cells of the islets as well as in exocrine acinar cells in the pancreas of mice by in situ hybridization and immunostaining. High expression levels of prosaposin were found in Alpha, Beta and Delta cells in the islets, whereas prosaposin mRNA expression was faint or negative and prosaposin immunoreactivity was negative in exocrine acinar cells. The high expression levels of prosaposin in endocrine cells may indicate that prosaposin plays a crucial role in crinophagy, which is a characteristic autophagy in peptide-secreting endocrine cells, and/or that prosaposin is secreted from pancreatic islets. Since prosaposin has been reported in serum, this study suggests a new possible function of the Langerhans islets.

P05 Identifying novel drug targets of the ESKAPE pathogen Pseudomonas aeruginosa

Abstract The Gram-negative ESKAPE pathogen Pseudomonas aeruginosa is currently listed top of the priority one pathogens by the WHO that require urgent research and development of new antimicrobials. Currently, microbiologists and clinicians face an ever-growing challenge in treating MDR bacterial infections, for this, and other pathogens, using conventional antibiotics. With a limited number of antibiotics currently in clinical trials and a general stagnation in the discovery of promising antimicrobials, new drug targets are desperately needed, and recent investigations include targeting bacterial virulence factors. Targeting bacterial virulence factors should reduce the pathogenesis of an organism, slow its infection progression and prevent vital virulence processes such as biofilm formation as well as potentially increasing a strain’s susceptibility to antibiotics. However, given the incredible diversity of bacteria, virulence mechanisms vary massively, meaning that identifying a broad-spectrum virulence target presents a major challenge. This important point has brought researchers to a fascinating group of enzymes that are ubiquitous in nature, and possess a plethora of biological roles, including acting as virulence factors. The macrophage infectivity potentiators (Mips) belong to the ubiquitous FK506 binding protein (FKBPs) family of peptidyl-prolyl cis/trans isomerases (PPIases). FKBPs are found in all bacteria serving as general house-keeping proteins involved in protein folding and chaperoning. However, a small subset has been identified as virulence proteins. Mips have been characterized in several Gram-negative pathogens including Legionella pneumophila and Burkholderia pseudomallei and were shown to be essential for invasion of macrophages, both in vitro and in murine-infection models, and for other virulence determinants. Pseudomonas aeruginosa also possess three Mip virulence factors, PaMip1, PaMip2 and PaMip3, which are required for the full virulence of P. aeruginosa in in vivo and ex vivo models. Virulence can be addressed in a pharmacological manner using bacterial natural products.

An antibody-free evaluation of an mRNA COVID-19 vaccine

This manuscript describes the use of an analytical assay that combines transfection of mammalian cells and isotope dilution mass spectrometry (IDMS) for accurate quantification of antigen expression. Expired mRNA COVID-19 vaccine material was stored at 4 °C, room temperature (∼25 °C), and 56 °C over a period of 5 weeks. The same vaccine was also exposed to 5 freeze-thaw cycles. Every week, the spike protein antigenic expression in mammalian (BHK-21) cells was evaluated. Housekeeping proteins, β-actin and GAPDH, were simultaneously quantified to account for the variation in cell counts that occurs during maintenance and growth of cell cultures. Data show that vaccine stored at elevated temperatures results in reduced spike protein expression. Also, maintaining the vaccine in ultracold conditions or exposing the vaccine to freeze-thaw cycles had less effect on the vaccine's ability to produce the antigen in mammalian cells. We describe the use of IDMS as an antibody-free means to accurately quantify expressed protein from mammalian cells transfected with mRNA vaccine.

Rapid detection of heat stress biomarkers in Atlantic salmon (Salmo salar) liver using targeted proteomics

AbstractMost fish are ectothermic; therefore, their physiology is significantly affected by temperature. Aquaculture fish have limited ability to avoid elevated water temperatures, with impacts increasing as a result of climate change. To date, quantifying gene expression has been proposed to monitor heat stress in salmon liver. This study aimed to establish a faster multiplexed proteomics method to measure the abundance of thermal stress biomarkers in liver of salmon reared at 15°C or 20°C. Moreover, this study aimed to determine the effects that sample pooling, and data normalisation using housekeeping (HK) protein peptides would exert over the statistical significance of these thermal stress markers. A multiple reaction monitoring (MRM) mass spectrometry method, comprised 45 peptides derived from thermal stress markers and 10 peptides from HK proteins, was applied to measure these markers in liver of salmon reared at 15°C or 20°C. When samples were processed individually, 34 peptides were significant between salmon livers at 15°C or 20°C. In pooled samples, this decreased to five significant peptides. Peptides hprt1_HYADDLDR (hypoxanthine phosphoribosyl transferase) and gapdh_VPTPNVSVVDLTVR (glyceraldehyde‐3‐phosphate dehydrogenase) were the most stable and unstable HK protein peptides, respectively. When data was normalised with hprt1_HYADDLDR, 16 peptides were significant in individual samples and 13 in pooled samples. Significant peptides serpinh1a_ADLSNISGK, SerpinH1_TNSILFIGR, ela2_VVGGEDVR and gapdh_VPTPNVSVVDLTVR were common regardless of data strategy. A fast and reliable MRM method was established to validate thermal stress markers in salmon liver, where individual samples yielded better results than pooled samples. Sample pooling was only better when combined with normalisation as it validated twice the number of markers than sample pooling alone. This method could be applied to monitoring stress response in experiments involving feeding additives designed to mitigate thermal stress or in selective breeding programs to help understanding family variance in thermal tolerance.

Pharmacokinetic Parameters of Recombinant Human Cyclophilin A in Mice.

Cyclophilin A (CypA) is an isomerase that functions as a chaperone, housekeeping protein, and cyclosporine A (CsA) ligand. Secreted CypA is a proinflammatory factor, chemoattractant, immune regulator, and factor of antitumor immunity. Experimental data suggest clinical applications of recombinant human CypA (rhCypA) as a biotherapeutic for cancer immunotherapy, stimulation of tissue regeneration, treatment of brain pathologies, and as a supportive treatment for CsA-based therapies. The objective of this study is to analyze the pharmacokinetics of rhCypA in a mouse model. rhCypA was isotope-labeled with 125I and injected intraperitoneally (i.p.) or subcutaneously (s/c) into female mice as a single dose of 100μg per mouse, equivalent to the estimated first-in-human dose. Analysis of 125I-rhCypA biodistribution and excretion was performed by direct radiometry of the blood, viscera, and urine of mice 0.5-72h following its administration. rhCypA showed rapid and even tissue-organ distribution, with the highest tropism (fT=1.56) and accumulation (maximum concentration,Cmax=137-167μg/g) in the kidneys, its primary excretory organ. rhCypA showed the lowest tropism to the bone marrow and the brain (fT = 0.07) but the longest retention in these organs [mean retention time (MRT)=25-28h]. This study identified promising target organs for rhCypA's potential therapeutic effects. The mode of rhCypA accumulation and retention in organs could be primarily due to the expression of its receptors in them. For the first time, rhCypA was shown to cross the blood-brain barrier and accumulate in the brain. These rhCypA pharmacokinetic data could be extrapolated to humans as preliminary data for possible clinical trials.

Enzyme kinetics of deoxyuridine triphosphatase from Western corn rootworm

ObjectiveThe Western corn rootworm (WCR), Diabrotica virgifera virgifera, is a highly adaptable insect pest that has evolved resistance to a variety of control strategies, including insecticides. Therefore, it is interesting to examine how housekeeping proteins in WCR have been changed under WCR-controlling strategies. In this study, we focused on one of such proteins in WCR, a ubiquitous enzyme 5'-triphosphate nucleotidohydrolase (dUTPase). In the thymidine synthetic pathway, dUTPase hydrolyzes deoxyuridine triphosphate (dUTP) and supplies the substrate, deoxyuridine monophosphate, for the thymidylate synthase (TS). It decreases the cellular content of uracil, reducing uracil misincorporation into DNA. Suppressing the dUTPase activity, therefore, contributes to thymineless death. In this study, we investigated the enzymatic properties of dUTPase.ResultsThe WCR dUTPase gene (DUT) was synthesized with the addition of His-tag corresponding DNA sequence and then cloned and expressed in Escherichia coli, and the protein product was purified. The product of WCR DUT hydrolyzed dUTP and was designated as dUTPase. WCR dUTPase did not hydrolyze dATP, dTTP, dCTP, or dGTP. WCR dUTPase was analyzed via size-exclusion chromatography and exhibited a molecular weight corresponding to that of trimer. The present format can be interpreted as nuclear trimer type. Possible isomers will be examined once transcriptome analyses are conducted.

Bioaerosols in swine confinement buildings: A metaproteomic view.

Swine confinement buildings represent workplaces with high biological air pollution. It is suspected that individual components of inhalable air are causatives of chronic respiratory disease that are regularly detected among workers. In order to understand the relationship between exposure and stress, it is necessary to study the components of bioaerosols in more detail. For this purpose, bioaerosols from pig barns were collected on quartz filters and analysed via a combinatorial approach of 16S rRNA amplicon sequencing and metaproteomics. The study reveals the presence of peptides from pigs, their feed and microorganisms. The proportion of fungal peptides detected is considered to be underrepresented compared to bacterial peptides. In addition, the metaproteomic workflow enabled functional predictions about the discovered peptides. Housekeeping proteins were found in particular, but also evidence for the presence of bacterial virulence factors (e.g., serralysin-like metalloprotease) as well as plant (e.g., chitinase) and fungal allergens (e.g., alt a10). Metaproteomic analyses can thus be used to identify factors that may be relevant to the health of pig farmers. Accordingly, such studies could be used in the future to assess the adverse health potential of an occupationally relevant bioaerosol and help consider defined protective strategies for workers.

2-DE-based and shotgun proteomics approach in the analysis of the seed proteome of a low phytic acid rice (Oryza sativa, ssp. japonica) mutant

A low phytic acid (lpa) rice mutant line, denoted as Os-lpa-XS110-2, was developed through gamma irradiation (Liu et al., 2007). Subsequently, this mutant line was cultivated alongside its parental wild-type counterpart, Xiushui 110, in four distinct field trials conducted in China. The primary objective of this research was to conduct a comparative proteomic analysis between the parental and mutant lines, aiming to detect and compare protein species with varying levels of relative abundance and their potential involvement in phytic acid biosynthesis. To elucidate the molecular underpinnings of this alteration, proteome analyses were conducted on both the parental and mutant lines, employing LC-MS/MS in conjunction with 2-dimensional gel electrophoresis. Only, 7 proteins consistently exhibited significant differential abundance across all trial locations, suggesting that the regulation of these proteins is less susceptible to environmental influences. In a broader context, among the 700 detected proteins, 56 displayed noteworthy up- or down-regulation across diverse geographical regions. Notably, storage and housekeeping proteins emerged as the most frequently identified protein categories, with globulin and glutelin demonstrating prominent differences in abundance. However, based on our current understanding, none of the identified proteins appear to have direct roles in phytic acid biosynthesis.

Readthrough Approach Using NV Translational Readthrough-Inducing Drugs (TRIDs): A Study of the Possible Off-Target Effects on Natural Termination Codons (NTCs) on TP53 and Housekeeping Gene Expression.

Nonsense mutations cause several genetic diseases such as cystic fibrosis, Duchenne muscular dystrophy, β-thalassemia, and Shwachman-Diamond syndrome. These mutations induce the formation of a premature termination codon (PTC) inside the mRNA sequence, resulting in the synthesis of truncated polypeptides. Nonsense suppression therapy mediated by translational readthrough-inducing drugs (TRIDs) is a promising approach to correct these genetic defects. TRIDs generate a ribosome miscoding of the PTC named "translational readthrough" and restore the synthesis of full-length and potentially functional proteins. The new oxadiazole-core TRIDs NV848, NV914, and NV930 (NV) showed translational readthrough activity in nonsense-related in vitro systems. In this work, the possible off-target effect of NV molecules on natural termination codons (NTCs) was investigated. Two different in vitro approaches were used to assess if the NV molecule treatment induces NTC readthrough: (1) a study of the translational-induced p53 molecular weight and functionality; (2) the evaluation of two housekeeping proteins' (Cys-C and β2M) molecular weights. Our results showed that the treatment with NV848, NV914, or NV930 did not induce any translation alterations in both experimental systems. The data suggested that NV molecules have a specific action for the PTCs and an undetectable effect on the NTCs.

Antioxioxidant and antiapoptotic effects of Thymosin β4 in Aβ-induced SH-SY5Y cells via the 5-HTR1A/ERK axis.

Alzheimer's disease (AD) is a common amnestic cognitive impairment characterised by β-amyloid (Aβ) plaques deposit in the brain of the elderly. AD is a yet incurable disease due to its unknown exact pathogenesis and unavailability of effective remedies in clinical application. Thymosin β4 (Tβ4) is a housekeeping protein that plays important role in cell proliferation, migration and differentiation. It has the ability to protect and repair neurons however it is still unclear involvement in AD. Therefore, the aim of this study is to elucidate the role and mechanism of Tβ4 in mediating the improvement of AD. AD-like cell model was constructed in neuroblastoma cell line SH-SY5Y treated with Aβ. Overexpression of Tβ4 were done using lentivirus infection and downregulation through siRNA transfection. We performed western blot and flow cytometry to study the apoptosis and standard kits to measure the oxidative stress-associated biomarkers. There is significant increased in viability and decreased apoptosis in Tβ4 overexpression group compared to control. Furthermore, overexpression of Tβ4 suppressed the expression of pro-apoptotic markers such as Caspase-3, Caspase-8, and Bax meanwhile upregulated the expression of anti-apoptotic gene Bcl-2. Tβ4 alleviated oxidative damage by reducing MDA, LDH and ROS and increasing SOD and GSH-PX in Aβ-treated SH-SY5Y cells. We found that Tβ4 inhibit ERK/p38 MAPK pathway and intensify the expression of 5-HTR1A. Additionally, we showed that upregulation of 5-HTR1A dampened the Tβ4 to activate ERK signalling. In conclusion, our study revealed the neuroprotective role of Tβ4 in AD which may open up new therapeutic applications in AD treatment.