Candidate Proteins Research Articles

Characterization of Potential Plastic-Degradation Enzymes from Marine Bacteria.

Polyethylene terephthalate (PET) and polyethylene (PE) are prominent polymer materials that comprise a significant portion of commercial plastic waste. Their durability and slow degradation rate have resulted in significant accumulation of plastic on Earth. In a recent study, macrotranscriptomic profiling of a reconstituted marine bacterial community identified 10 putative enzymes capable of directly acting on PE or PET (PEases or PETases). Among these enzymes, three recombinant proteins were reported to possess PE degradation activity. To select potential plastic degrading enzyme candidates for protein engineering efforts, we expressed and purified eight out of the 10 candidates, excluding two due to poor expression and/or solubility. Notably, several candidate proteins displayed significant esterase activity on p-nitrophenyl butyrate and exhibited unexpected thermostability despite their marine origin. Additionally, we observed dose- and time-dependent hydrolytic activity on the PET trimer substrate. Structural analysis and mutagenesis of a candidate protein confirmed the presence of catalytic triad residues, classifying it as an esterase. Furthermore, we elucidated the structural importance of the two disulfide bonds. Through point mutation experiments, we observed an enhanced hydrolytic activity of a selected enzyme candidate on PET nanoparticles. Our findings challenge the classification of the enzymes directly acting on PE and highlight the significance and complexity of validating PE degradation enzymes identified through metagenomic analysis.

RDH12 allows cone photoreceptors to regenerate opsin visual pigments from a chromophore precursor to escape competition with rods

Capture of a photon by an opsin visual pigment isomerizes its 11-cis-retinaldehyde (11cRAL) chromophore to all-trans-retinaldehyde (atRAL), which subsequently dissociates. To restore light sensitivity, the unliganded apo-opsin combines with another 11cRAL to make a new visual pigment. Two enzyme pathways supply chromophore to photoreceptors. The canonical visual cycle in retinal pigment epithelial cells supplies 11cRAL at low rates. The photic visual cycle in Müller cells supplies cones with 11-cis-retinol (11cROL) chromophore precursor at high rates. Although rods can only use 11cRAL to regenerate rhodopsin, cones can use 11cRAL or 11cROL to regenerate cone visual pigments. We performed a screen in zebrafish retinas and identified ZCRDH as a candidate for the enzyme that converts 11cROL to 11cRAL in cone inner segments. Retinoid analysis of eyes from Zcrdh-mutant zebrafish showed reduced 11cRAL and increased 11cROL levels, suggesting impaired conversion of 11cROL to 11cRAL. By microspectrophotometry, isolated Zcrdh-mutant cones lost the capacity to regenerate visual pigments from 11cROL. ZCRDH therefore possesses all predicted properties of the cone 11cROL dehydrogenase. The human protein most similar to ZCRDH is RDH12. By immunocytochemistry, ZCRDH was abundantly present in cone inner segments, similar to the reported distribution of RDH12. Finally, RDH12 was the only mammalian candidate protein to exhibit 11cROL-oxidase catalytic activity. These observations suggest that RDH12 in mammals is the functional ortholog of ZCRDH, which allows cones, but not rods, to regenerate visual pigments from 11cROL provided by Müller cells. This capacity permits cones to escape competition from rods for visual chromophore in daylight-exposed retinas.

Regulation of Proline Accumulation and Protein Secretion in Sorghum under Combined Osmotic and Heat Stress.

Plants reprogramme their proteome to alter cellular metabolism for effective stress adaptation. Intracellular proteomic responses have been extensively studied, and the extracellular matrix stands as a key hub where peptide signals are generated/processed to trigger critical adaptive signal transduction cascades inaugurated at the cell surface. Therefore, it is important to study the plant extracellular proteome to understand its role in plant development and stress response. This study examined changes in the soluble extracellular sub-proteome of sorghum cell cultures exposed to a combination of sorbitol-induced osmotic stress and heat at 40 °C. The combined stress significantly reduced metabolic activity and altered protein secretion. While cells treated with osmotic stress alone had elevated proline content, the osmoprotectant in the combined treatment remained unchanged, confirming that sorghum cells exposed to combined stress utilise adaptive processes distinct from those invoked by the single stresses applied separately. Reactive oxygen species (ROS)-metabolising proteins and proteases dominated differentially expressed proteins identified in cells subjected to combined stress. ROS-generating peroxidases were suppressed, while ROS-degrading proteins were upregulated for protection from oxidative damage. Overall, our study provides protein candidates that could be used to develop crops better suited for an increasingly hot and dry climate.

Proteome-wide analysis identifies plasma immune regulators of amyloid-beta progression

While immune function is known to play a mechanistic role in Alzheimer’s disease (AD), whether immune proteins in peripheral circulation influence the rate of amyloid-β (Aβ) progression – a central feature of AD – remains unknown. In the Baltimore Longitudinal Study of Aging, we quantified 942 immunological proteins in plasma and identified 32 (including CAT [catalase], CD36 [CD36 antigen], and KRT19 [keratin 19]) associated with rates of cortical Aβ accumulation measured with positron emission tomography (PET). Longitudinal changes in a subset of candidate proteins also predicted Aβ progression, and the mid- to late-life (20-year) trajectory of one protein, CAT, was associated with late-life Aβ-positive status in the Atherosclerosis Risk in Communities (ARIC) study. Genetic variation that influenced plasma levels of CAT, CD36 and KRT19 predicted rates of Aβ accumulation, including causal relationships with Aβ PET levels identified with two-sample Mendelian randomization. In addition to associations with tau PET and plasma AD biomarker changes, as well as expression patterns in human microglia subtypes and neurovascular cells in AD brain tissue, we showed that 31 % of candidate proteins were related to mid-life (20-year) or late-life (8-year) dementia risk in ARIC. Our findings reveal plasma proteins associated with longitudinal Aβ accumulation, and identify specific peripheral immune mediators that may contribute to the progression of AD pathophysiology.

Exogenous serpin B1 restricts immune complex-mediated NET formation via inhibition of a chymotrypsin-like protease and enhances microbial phagocytosis

Immune complex (IC)-driven formation of neutrophil extracellular traps (NETs) is a major contributing factor to the pathogenesis of autoimmune diseases including systemic lupus erythematosus (SLE). Exogenous recombinant human serpin B1 (rhsB1) can regulate NET formation; however, its mechanism(s) of action is currently unknown as is its ability to regulate IC-mediated NET formation and other neutrophil effector functions. To investigate this, we engineered or post-translationally modified rhsB1 proteins that possessed specific neutrophil protease inhibitory activities and pretreated isolated neutrophils with them prior to inducing NET formation with ICs derived from patients with SLE, PMA, or the calcium ionophore A23187. Neutrophil activation and phagocytosis assays were also performed with rhsB1 pretreated and IC-activated neutrophils. rhsB1 dose-dependently inhibited NET formation by all three agents in a process dependent on its chymotrypsin-like inhibitory activity, most likely cathepsin G. Only one variant (rhsB1 C344A) increased surface levels of neutrophil adhesion/activation markers on IC-activated neutrophils and boosted intracellular ROS production. Further, rhsB1 enhanced complement-mediated neutrophil phagocytosis of opsonized bacteria but not ICs. In conclusion, we have identified a novel mechanism of action by which exogenously administered rhsB1 inhibits IC, PMA, and A2138-mediated NET formation. Cathepsin G is a well-known contributor to autoimmune disease but to our knowledge, this is the first report implicating it as a potential driver of NET formation. We identified the rhsB1 C334A variant as a candidate protein that can suppress IC-mediated NET formation, boost microbial phagocytosis, and potentially impact additional neutrophil effector functions including ROS-mediated microbial killing in phagolysosomes.

Tibial cortex transverse transport surgery improves wound healing in patients with severe type 2 DFUs by activating a systemic immune response: a cross-sectional study.

Tibial cortex transverse transport (TTT) surgery has become an ideal treatment for patients with type 2 severe diabetic foot ulcerations (DFUs) while conventional treatments are ineffective. Based on our clinical practice experience, the protective immune response from TTT surgery may play a role against infections to promote wound healing in patients with DFUs. Therefore, this research aimed to systematically study the specific clinical efficacy and the mechanism of TTT surgery. Between June 2022 and September 2023, 68 patients with type 2 severe DFUs were enrolled and therapized by TTT surgery in this cross-sectional and experimental study. Major clinical outcomes including limb salvage rate and antibiotics usage rate were investigated. Ten clinical characteristics and laboratory features of glucose metabolism and kidney function were statistically analyzed. Blood samples from 6 key time points of TTT surgery were collected for label-free proteomics and clinical immune biomarker analysis. Besides, tissue samples from 3 key time points were for spatially resolved metabolomics and transcriptomics analysis, as well as applied to validate the key TTT-regulated molecules by RT-qPCR. Notably, 64.7% of patients did not use antibiotics during the entire TTT surgery. TTT surgery can achieve a high limb salvage rate of 92.6% in patients with unilateral or bilateral DFUs. Pathway analysis of a total of 252 differentially expressed proteins (DEPs) from the proteomic revealed that the immune response induced by TTT surgery at different stages was first comprehensively verified through multi-omics combined with immune biomarker analysis. The function of upward transport was activating the systemic immune response, and wound healing occurs with downward transport. The spatial metabolic characteristics of skin tissue from patients with DFUs indicated downregulated levels of stearoylcarnitine and the glycerophospholipid metabolism pathway in skin tissue from patients with severe DFUs. Finally, the expressions of PRNP (prion protein) to activate the immune response, PLCB3 (PLCB3, phospholipase C beta 3) and VE-cadherin to play roles in neovascularization, and PPDPF (pancreatic progenitor cell differentiation and proliferation factor), LAMC2 (laminin subunit gamma 2) and SPRR2G (small proline rich protein 2G) to facilitate the developmental process mainly keratinocyte differentiation were statistically significant in skin tissues through transcriptomic and RT-qPCR analysis. Tibial cortex transverse transport (TTT) surgery demonstrates favorable outcomes for patients with severe type 2 DFUs by activating a systemic immune response, contributing to anti-infection, ulcer recurrence, and the limb salvage rate for unilateral or bilateral DFUs. The specific clinical immune responses, candidate proteins, genes, and metabolic characteristics provide directions for in-depth mechanistic research on TTT surgery. Further research and public awareness are needed to optimize TTT surgery in patients with severe type 2 DFUs.

Species-specific variation in mental gland secretions of turtles revealed by proteomic and lipidomic profiling

Chemical signaling through pheromones is an ancient and widespread mode of communication. Turtles and tortoises (chelonians) secrete pheromones via mental (chin) glands and have superior olfactory capacities rendering them a promising group to study the evolution and function of chemical communication in vertebrates. Here, we use state-of-the art proteomics and lipidomics techniques to identify and explore the possible functions of proteins and lipids secreted by mental glands in turtles. We examined four turtle species all from the family Geoemydidae, to understand among-species as well as sexual variation in the composition of mental gland secretions. Differential expression of a relatively small number (ca. 65) of proteins explained a large portion of the proteome variation across species, highlighting the existence of specific signals evolving even in closely related species. Lipidomic analysis revealed high inter-individual variation, but species differences could be attributed to five different lipid classes. The lipids found in mental glands could have a dietary origin or be related to individual condition, but may nonetheless be used in communication. We also examined sex-specific differences in the proteome of a single species (Mauremys leprosa) and found that males expressed a much larger array of proteins than females. Our findings establish a group of candidate proteins potentially involved in chemical signaling in freshwater geoemydid turtles. Alternatively, differently expressed proteins in mental glands could have an indirect link to chemical communication, being involved in pheromone transport and/or antioxidant protection.

Proteome-wide association studies have predicted that the protein abundance of LSM6, GMPPB, ICA1L, and CISD2 is associated with attention-deficit/hyperactivity disorder.

Identification of changes in protein abundance for attention-deficit/hyperactivity disorder (ADHD) is important for potential disease mechanisms and therapeutic study for ADHD. In order to identify candidate proteins that confer risk for ADHD, a proteome-wide association study (PWAS) for ADHD was conducted by integrating two human brain proteome datasets and the ADHD genome-wide association study (GWAS) summary statistics released by the Psychiatric Genomics Consortium (PGC). A total of 11 risk proteins were identified as significant candidates that passed the bonferroni corrected proteome-wide significant (PWS) level. The predicted protein abundance level of LSM6, GMPPB, ICA1L and CISD2 are shown significantly associated with ADHD in both proteome datasets, highlighting their potential role in ADHD pathogenesis. A transcriptome-wide association study (TWAS) of ADHD was also conducted, and 13 genes with predicted expression changes related to ADHD were identified. GMPPB, ICA1L and NAT6 were supported by both TWAS and PWASs analysis. This study uncovers the predicted protein abundance changes that confer risk for ADHD and pinpoints a number of high-confidence protein candidates (e.g. LSM6, GMPPB, ICA1L, CISD2) for further functional exploration studies and drug development targeting these proteins.

Machine learning and 4D-LFQ quantitative proteomic analysis explore the molecular mechanism of kidney stone formation

BackgroundNephrolithiasis, a common and chronic urological condition, exerts significant pressure on both the general public and society as a whole. The precise mechanisms of nephrolith formation remain inadequately comprehended. Nevertheless, the utilization of proteomics methods has not been employed to examine the development of renal calculi in order to efficiently hinder and manage the creation and reappearance of nephrolith. Nowadays, with the rapid development of proteomics techniques, more efficient and more accurate proteomics technique is utilized to uncover the mechanisms underlying diseases. The objective of this study was to investigate the possible alterations of HK-2 cells when exposed to varying amounts of calcium oxalate (CaOx). The aim was to understand the precise development of stone formation and recurrence, in order to find effective preventive and treatment methods. MethodsTo provide a complete view of the proteins involved in the development of nephrolithiasis, we utilized an innovative proteomics method called 4D-LFQ proteomic quantitative techniques. HK-2 cells were selected as our experimental subjects. Three groups (n = 3) of HK-2 cells were treated with intervention solutions containing 0 (negative control, NC), 1 mM, and 2 mM CaOx, respectively. For the proteins that showed differential expression, various analyses were conducted including examination of Gene Ontology (GO), Clusters of Orthologous Groups of proteins (KOG), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, enrichment analysis of protein domains, and hierarchical clustering analysis. The STRING database was used to identify the interaction network of the chosen proteins. Candidate proteins were validated using parallel reaction monitoring (PRM) in the end. ResultsAll three groups verified the repeatability of samples. According to the results of 4D-LFQ proteomic quantitative analysis, there were 120, 262, and 81 differentially expressed proteins (DEPs) in the 1 mM-VS-NC, 2 mM-VS-NC, and 2 mM-VS-1mM conditions, respectively. According to GO annotation, the functional enrichment analysis indicates that the differentially expressed proteins (DEPs) were notably enriched in promoting cell migration and the extracellular matrix, among other functions. Analysis of enrichment, based on the KEGG pathway, revealed significant enrichment of DEPs in complement and coagulation cascades, as well as in ECM-receptor (extracellular matrix-receptor) interaction and other related pathways. 14 DEPs of great interest were selected as candidate proteins, including FN1, TFRC, ITGA3, FBN1, HYOU1, SPP1, HSPA5, COL6A1, MANF, HIP1R, JUP, AXL, CTNNB1 and DSG2.The data from PRM demonstrated the variation trend of 14 DEPs was identical as 4D-LFQ proteomic quantitative analysis. ConclusionProteomics studies of CaOx-induced HK-2 cells using 4D-LFQ proteomic quantitative analysis and PRM may help to provide crucial potential target proteins and signaling pathways for elucidating the mechanism of nephrolithiasis and better treating nephrolithiasis.

Design of multi-epitope vaccine candidate based on OmpA, CarO and ZnuD proteins against multi-drug resistant Acinetobacter baumannii

Acinetobacter baumannii has been identified as a major cause of nosocomial infections. Acinetobacter infections are often difficult to treat with multidrug resistant phenotypes. One of the most effective ways to combat infectious diseases is through vaccination. In this study, an attempt was made to select the most protective and potent immunostimulatory epitopes based on the epitope-rich domains of the ZnuD, OmpA and CarO proteins of Acinetobacter baumannii to design a vaccine that can protect against this infection. After predicting the epitope of B- and T-cells, seven antigenic regions of three proteins CarO, ZnuD and OmpA, were selected. These regions were bound by a GGGS linker. The binding affinity and molecular interactions of the vaccine with the immune receptors TLR2 and TLR4 were studied using molecular docking analysis. This vaccine design was subjected to in silico immune simulations using C-ImmSim. The designed vaccine was highly antigenic, non-allergenic and stable. TLR2 and TLR4 were selected to analyze the ability of the modeled chimeric protein to interact with immune system receptors. The results showed strong interaction between the designed protein vaccine with TLR2 (−18.8 kcal mol-1) and TLR4 (−15.1 kcal mol-1). To verify the stability of the interactions and the structure of the designed protein, molecular dynamics (MD) simulations were performed for 200 ns. Various analyses using MD showed that the protein structure is stable alone and in interaction with TLR2 and TLR4. The ability of the vaccine candidate protein to stimulate the immune system to produce the necessary cytokines and antibodies against Acinetobacter baumannii was also demonstrated by the ability of the protein designed using the C-ImmSim web server to induce an immune response. Therefore, the designed protein vaccine may be a suitable candidate for in vivo as well as in vitro studies against Acinetobacter baumannii infections.

Identifying regulatory elements and their RNA-binding proteins in the 3' untranslated regions of papillomavirus late mRNAs.

Human papillomaviruses (HPVs) infect cutaneous and mucosal epithelia to cause benign (warts) and malignant lesions (e.g. cervical cancer). Bovine papillomaviruses (BPVs) infect fibroblasts to cause fibropapillomas but can also infect cutaneous epithelial cells. For HPV-1, -16, -31 and BPV-1, cis-acting RNA elements in the late 3' untranslated region (3'UTR) control expression of virus proteins by binding host cell proteins. The present study compared the effects on gene expression of the cis-acting elements of seven PV late 3'UTRs (HPV-6b, -11, -16, -31 and BPV-1, -3 and -4) representing a range of different genera and species and pathological properties. pSV-beta-galactosidase reporter plasmids containing the late 3'UTRs from seven PVs were transiently transfected into cervical adenocarcinoma HeLa cells, and reporter gene expression quantified by reverse transcription-quantitative PCR and a beta-galactosidase assay. All elements inhibited gene expression in keratinocytes. Cancer-related types HPV-16 and -31, had the greatest inhibitory activity whereas the lowest inhibition was found in the non-cancer related types, BPV-3 and HPV-11. Using RBPmap version 1.1, bioinformatics predictions of factors binding the elements identified proteins which function mainly in mRNA splicing. Markedly, in terms of protein binding motifs, BPV late 3'UTR elements were similar to those of HPV-1a but not to other HPVs. Using HPV-1a as a model and siRNA depletion, the bioinformatics predictions were tested and it was found that PABPC4 was responsible for some of the 3'UTR repressive activity. The data revealed candidate proteins that could control PV late gene expression.

Plasma GPI and PGD are associated with vascular normalization and may serve as novel prognostic biomarkers for lung adenocarcinoma: Multi-omics and multi-dimensional analysis

The aim of this study was to explore potential novel plasma protein biomarkers for lung adenocarcinoma (LUAD). A plasma proteomics analysis was carried out and candidate protein biomarkers were validated in 102 LUAD cases and 102 matched healthy controls. The same LUAD tumor tissues were detected to explore the correlation between the expression of candidate proteins in tissues and plasma and vascular normalization. A LUAD active metastasis mice model was constructed to explore the role of candidate proteins for lung metastasis. GPI and PGD were verified to be upregulated in plasma from LUAD patients, and the expression of GPI in tumor tissue was positively correlated with the expression of GPI in plasma and negatively correlated with the normalization of tumor blood vessels. Meanwhile, a negative correlation between the expression of GPI and PGD in plasma and tumor vascular normalization was discovered. In the LUAD active metastasis model, the lowest levels of vascular normalization and the highest expression of GPI and PGD were found in mice with lung metastases. This study found that GPI and PGD may be potential plasma biomarkers for LUAD, and monitoring those may infer the risk of metastasis and malignancy of the tumor. SignificantWe identified GPI and PGD as potential novel diagnostic and prognostic biomarkers for LUAD. PGD and GPI can be used as diagnostic biomarkers in combination with other available strategies to assist in the screening and diagnosis of LUAD, and as prognostic biomarkers aid in predict the risk of tumor metastasis and malignancy in patients with LUAD.

The combination of RNA-seq transcriptomics and data-independent acquisition proteomics reveal the mechanisms and function of different gooses testicular development at different stages of laying cycle

Egg production performance is an important economic trait in the poultry industry. In previous studies, attention has often been paid to the growth and development of the ovaries, while there has been less research on the testicular tissue of male goose. Due to various factors, there are usually significant differences in the process of testicular spermatogenesis among different goose breeds. The Jilin white goose (JL) is a high-production local goose species in China, domesticated from Anser cygnoides, which has a high egg-laying performance and the egg-laying period can last from February to July. In the production of goose within Jilin Province, the female goose of Jilin White goose is considered as an important maternal parent of synthetic lines, and ganders from Hungarian white goose (HU), Wanxi white goose (WX) and Jilin white goose are the main male parents. Each year, all 3 gander species begin to exhibit breeding capacity in February and reach the peak of reproductive capacity by April, marked by high fertilization rates. With the gradual increase in temperature, the testicular tissue of Hungarian and Wanxi goose gradually diminishes in its ability to produce sperm. the testicular tissue undergoes significant shrinkage by the end of June, resulting in a near loss of sperm production capability, thereby yielding low fertilization rates. However, the Jilin White goose demonstrates the ability to maintain a stable sperm production capacity. Individuals with low sperm motility contribute to increased seed production costs and pose constraints on the industrial development of livestock and poultry varieties. In this study, transcriptomics and proteomics data from gooses testicular of 3 different goose breeds inclouding Jilin white goose, Wanxi white gooseand Hungary white goose sampled in 2 stages, peak of laying cycle (PLC) and end of laying cycle (ELC). In a comparative analysis between PLC and ELC groups (ELC vs. PLC) of 3 breeds, we identified 401,340,6651 differentially expressed genes (DEGs) and 18,225,323 differentially expressed proteins (DEPs), respectively. Differentially expressed genes and proteins were significantly enriched in Gene Ontology (GO) terms such as phosphotransferase activity, cytoskeletal protein binding, microtubule motor activity, channel activity and carbohydrate metabolic process. The KEGG enrichment analysis of the DEGs in testicular showed that most differentially expressed mRNAs participate in the KEGG pathways, including ECM-receptor interaction, MAPK signaling pathway, carbon metabolism, Cell cycle, VEGF signaling pathway, Lipoic acid metabolism and p53 signaling pathway. The differential expression of 4 selected DEGs (SPAG6, NEK2, HSPA4L, SERF1A) was verified by qRT-PCR, and the results were consistent with RNA-seq data. In conclusion, this study reveals the differences in gene expression regulation in testicular tissues of different goose species, and screening candidate genes and proteins related to spermatogenesis.

Zebrafish do not have calprotectin.

The protein heterodimer calprotectin and its component proteins, S100A8 and S100A9, play important antibacterial and proinflammatory roles in the mammalian innate immune response. Gaining mechanistic insights into the regulation and biological function of calprotectin will help facilitate patient diagnostics and therapy and further our understanding of the host-microbe interface. Recent literature has identified zebrafish s100a10b as zebrafish calprotectin based on sequence similarity, genomic context, and transcriptional upregulation during the immune response to bacterial infections. The field would benefit from expanding the breadth of calprotectin studies into a zebrafish innate immunity model. Here, we carefully evaluated the possibility that zebrafish possess a calprotectin. We found that zebrafish do not possess an ortholog of mammalian S100A8 or S100A9. We then identified four zebrafish s100 proteins- including s100a10b-that are expressed in immune cells and upregulated during the immune response. We recombinantly expressed and purified these proteins and measured the antimicrobial and proinflammatory characteristics. We found that none of the zebrafish proteins exhibited activity comparable to mammalian calprotectin. Our work demonstrates conclusively that zebrafish have no ortholog of calprotectin, and the most plausible candidate proteins have not convergently evolved similar functions.

Molecular evolution of the mammalian kinetochore complex.

Mammalian centromeres are satellite-rich chromatin domains that serve as sites for kinetochore complex assembly. Centromeres are highly variable in sequence and satellite organization across species, but the processes that govern the co-evolutionary dynamics between rapidly evolving centromeres and their associated kinetochore proteins remain poorly understood. Here, we pursue a course of phylogenetic analyses to investigate the molecular evolution of the complete kinetochore complex across primate and rodent species with divergent centromere repeat sequences and features. We show that many protein components of the core centromere associated network (CCAN) harbor signals of adaptive evolution, consistent with their intimate association with centromere satellite DNA and roles in the stability and recruitment of additional kinetochore proteins. Surprisingly, CCAN and outer kinetochore proteins exhibit comparable rates of adaptive divergence, suggesting that changes in centromere DNA can ripple across the kinetochore to drive adaptive protein evolution within distant domains of the complex. Our work further identifies kinetochore proteins subject to lineage-specific adaptive evolution, including rapidly evolving proteins in species with centromere satellites characterized by higher-order repeat structure and lacking CENP-B boxes. Thus, features of centromeric chromatin beyond the linear DNA sequence may drive selection on kinetochore proteins. Overall, our work spotlights adaptively evolving proteins with diverse centromere-associated functions, including centromere chromatin structure, kinetochore protein assembly, kinetochore-microtubule association, cohesion maintenance, and DNA damage response pathways. These adaptively evolving kinetochore protein candidates present compelling opportunities for future functional investigations exploring how their concerted changes with centromere DNA ensure the maintenance of genome stability.

Evaluating the associations between intelligence quotient and multi-tissue proteome from the brain, CSF and plasma.

Intelligence quotient is a vital index to evaluate the ability of an individual to think rationally, learn from experience and deal with the environment effectively. However, limited efforts have been paid to explore the potential associations of intelligence quotient traits with the tissue proteins from the brain, CSF and plasma. The information of protein quantitative trait loci was collected from a recently released genome-wide association study conducted on quantification data of proteins from the tissues including the brain, CSF and plasma. Using the individual-level genotypic data from the UK Biobank cohort, we calculated the polygenic risk scores for each protein based on the protein quantitative trait locus data sets above. Then, Pearson correlation analysis was applied to evaluate the relationships between intelligence quotient traits (including 120 330 subjects for 'fluid intelligence score' and 38 949 subjects for 'maximum digits remembered correctly') and polygenic risk scores of each protein in the brain (17 protein polygenic risk scores), CSF (116 protein polygenic risk scores) and plasma (59 protein polygenic risk scores). The Bonferroni corrected P-value threshold was P < 1.30 × 10-4 (0.05/384). Finally, Mendelian randomization analysis was conducted to test the causal relationships between 'fluid intelligence score' and pre-specific proteins from correlation analysis results. Pearson correlation analysis identified significant association signals between the protein of macrophage-stimulating protein and fluid intelligence in brain and CSF tissues (P brain = 1.21 × 10-8, P CSF = 1.10 × 10-7), as well as between B-cell lymphoma 6 protein and fluid intelligence in CSF (P CSF = 1.23 × 10-4). Other proteins showed close-to-significant associations with the trait of 'fluid intelligence score', such as plasma protease C1 inhibitor (P CSF = 4.19 × 10-4, P plasma = 6.97 × 10-4), and with the trait of 'maximum digits remembered correctly', such as tenascin (P plasma = 3.42 × 10-4). Additionally, Mendelian randomization analysis results suggested that macrophage-stimulating protein (Mendelian randomization-Egger: β = 0.54, P = 1.64 × 10-61 in the brain; β = 0.09, P = 1.60 × 10-12 in CSF) had causal effects on fluid intelligence score. We observed functional relevance of specific tissue proteins to intelligence quotient and identified several candidate proteins, such as macrophage-stimulating protein. This study provided a novel insight to the relationship between tissue proteins and intelligence quotient traits.

Investigating SARS-CoV-2 virus-host interactions and mRNA expression: Insights using three models of D. melanogaster

Responsible for COVID-19, SARS-CoV-2 is a coronavirus in which contagious variants continue to appear. Therefore, some population groups have demonstrated greater susceptibility to contagion and disease progression. For these reasons, several researchers have been studying the SARS-CoV-2/human interactome to understand the pathophysiology of COVID-19 and develop new pharmacological strategies. D. melanogaster is a versatile animal model with approximately 90 % human protein orthology related to SARS-CoV-2/human interactome and is widely used in metabolic studies. In this context, our work assessed the potential interaction between human proteins (ZNF10, NUP88, BCL2L1, UBC9, and RBX1) and their orthologous proteins in D. melanogaster (gl, Nup88, Buffy, ubc9, and Rbx1a) with proteins from SARS-CoV-2 (nsp3, nsp9, E, ORF7a, N, and ORF10) using computational approaches. Our results demonstrated that all the proteins have the potential to interact, and we compared the binding sites between humans and fruit flies. The stability and consistency in the structure of the gl_nsp3 complex, specifically, could be crucial for its specific biological functions. Lastly, to enhance the understanding of the influence of host factors on coronavirus infection, we also analyse the mRNA expression of the five genes (mbo, gl, lwr, Buffy, and Roc1a) responsible for encoding the fruit fly proteins. Briefly, we demonstrated that those genes were differentially regulated according to diets, sex, and age. Two groups showed higher positive gene regulation than others: females in the HSD group and males in the aging group, which could imply a higher virus-host susceptibility. Overall, while preliminary, our work contributes to the understanding of host defense mechanisms and potentially identifies candidate proteins and genes for in vivo viral studies against SARS-CoV-2.

Single-cell proteomics differentiates Arabidopsis root cell types.

Single-cell proteomics (SCP) is an emerging approach to resolve cellular heterogeneity within complex tissues of multi-cellular organisms. Here, we demonstrate the feasibility of SCP on plant samples using the model plant Arabidopsis thaliana. Specifically, we focused on examining isolated single cells from the cortex and endodermis, which are two adjacent root cell types derived from a common stem cell lineage. From 756 root cells, we identified 3763 proteins and 1118 proteins/cell. Ultimately, we focus on 3217 proteins quantified following stringent filtering. Of these, we identified 596 proteins whose expression is enriched in either the cortex or endodermis and are able to differentiate these closely related plant cell types. Collectivity, this study demonstrates that SCP can resolve neighboring cell types with distinct functions, thereby facilitating the identification of biomarkers and candidate proteins to enable functional genomics.

Nucleotide sequence characterization, amino acid variations and 3D structural analysis of HN protein of the NDV VIId genotype.

Haemagglutinin-neuraminidase (HN) is one of the membrane proteins of Newcastle disease virus (NDV) that plays a significant role during host viral infection. Therefore, antibodies against HN are vital for the host's ability to protect itself against NDV infection due to their critical functions in viral infection. As a result, HN has been a candidate protein in vaccine development against the Newcastle disease virus. This report used the full-length sequence of the HN protein of NDV isolated in Iran (VIId subgenotype). We characterize and identify amino acid substitutions in comparison to other more prevalent NDV genotypes, VII subgenotypes and vaccine strains. Furthermore, bioinformatics tools were applied to determine the three-dimensional structure, molecular dynamics simulation and prediction of B-cell antigenic epitopes. The results showed that the antigenic regions of our isolate are quite comparable to the other VII subgenotypes of NDV isolated from different geographical places. Moreover, by employing the final 3D structure of our HN protein, the amino acid residues are proposed as a B-cell epitope by epitope prediction servers, which leads to the introduction of linear and conformational antigenic sites. Immunoinformatic vaccine design principles currently exhibit tremendous potential for developing a new generation of candidate vaccines quickly and economically to eradicate infectious viruses, including the NDV. In order to accomplish this, focus is directed on residues that might be considered antigenic.

Autophagic signaling promotes systems-wide remodeling in skeletal muscle upon oncometabolic stress by D2-HG

ObjectivesCachexia is a metabolic disorder and comorbidity with cancer and heart failure. The syndrome impacts more than thirty million people worldwide, accounting for 20% of all cancer deaths. In acute myeloid leukemia, somatic mutations of the metabolic enzyme isocitrate dehydrogenase 1 and 2 cause the production of the oncometabolite D2-hydroxyglutarate (D2-HG). Increased production of D2-HG is associated with heart and skeletal muscle atrophy, but the mechanistic links between metabolic and proteomic remodeling remain poorly understood. Therefore, we assessed how oncometabolic stress by D2-HG activates autophagy and drives skeletal muscle loss. MethodsWe quantified genomic, metabolomic, and proteomic changes in cultured skeletal muscle cells and mouse models of IDH-mutant leukemia using RNA sequencing, mass spectrometry, and computational modeling. ResultsD2-HG impairs NADH redox homeostasis in myotubes. Increased NAD+ levels drive activation of nuclear deacetylase Sirt1, which causes deacetylation and activation of LC3, a key regulator of autophagy. Using LC3 mutants, we confirm that deacetylation of LC3 by Sirt1 shifts its distribution from the nucleus into the cytosol, where it can undergo lipidation at pre-autophagic membranes. Sirt1 silencing or p300 overexpression attenuated autophagy activation in myotubes. In vivo, we identified increased muscle atrophy and reduced grip strength in response to D2-HG in male vs. female mice. In male mice, glycolytic intermediates accumulated, and protein expression of oxidative phosphorylation machinery was reduced. In contrast, female animals upregulated the same proteins, attenuating the phenotype in vivo. Network modeling and machine learning algorithms allowed us to identify candidate proteins essential for regulating oncometabolic adaptation in mouse skeletal muscle. ConclusionsOur multi-omics approach exposes new metabolic vulnerabilities in response to D2-HG in skeletal muscle and provides a conceptual framework for identifying therapeutic targets in cachexia.