-
EMBO Reports Dec 2023Mitochondrial and peroxisomal anchored protein ligase (MAPL) is a dual ubiquitin and small ubiquitin-like modifier (SUMO) ligase with roles in mitochondrial quality...
Mitochondrial and peroxisomal anchored protein ligase (MAPL) is a dual ubiquitin and small ubiquitin-like modifier (SUMO) ligase with roles in mitochondrial quality control, cell death and inflammation in cultured cells. Here, we show that MAPL function in the organismal context converges on metabolic control, as knockout mice are viable, insulin-sensitive, and protected from diet-induced obesity. MAPL loss leads to liver-specific activation of the integrated stress response, inducing secretion of stress hormone FGF21. MAPL knockout mice develop fully penetrant spontaneous hepatocellular carcinoma. Mechanistically, the peroxisomal bile acid transporter ABCD3 is a primary MAPL interacting partner and SUMOylated in a MAPL-dependent manner. MAPL knockout leads to increased bile acid production coupled with defective regulatory feedback in liver in vivo and in isolated primary hepatocytes, suggesting cell-autonomous function. Together, our findings establish MAPL function as a regulator of bile acid synthesis whose loss leads to the disruption of bile acid feedback mechanisms. The consequences of MAPL loss in liver, along with evidence of tumor suppression through regulation of cell survival pathways, ultimately lead to hepatocellular carcinogenesis.
Topics: Animals; Mice; Bile; Bile Acids and Salts; Liver; Mice, Knockout; Mitochondrial Proteins; Ubiquitin-Protein Ligases; Ubiquitins
PubMed: 37962001
DOI: 10.15252/embr.202357972 -
Natural Product Reports May 2020Covering: up to the end of 2019Diverse natural product small molecules have allowed critical insights into processes that govern eukaryotic cells' ability to secrete... (Review)
Review
Covering: up to the end of 2019Diverse natural product small molecules have allowed critical insights into processes that govern eukaryotic cells' ability to secrete cytosolically synthesized secretory proteins into their surroundings or to insert newly synthesized integral membrane proteins into the lipid bilayer of the endoplasmic reticulum. In addition, many components of the endoplasmic reticulum, required for protein homeostasis or other processes such as lipid metabolism or maintenance of calcium homeostasis, are being investigated for their potential in modulating human disease conditions such as cancer, neurodegenerative conditions and diabetes. In this review, we cover recent findings up to the end of 2019 on natural products that influence protein secretion or impact ER protein homeostasis, and serve as powerful chemical tools to understand protein flux through the mammalian secretory pathway and as leads for the discovery of new therapeutics.
Topics: Animals; Biological Products; Calcium; Endoplasmic Reticulum Stress; Eukaryotic Cells; Humans; Protein Transport; Proteins; RNA Splicing
PubMed: 32067014
DOI: 10.1039/c9np00066f -
Ticks and Tick-borne Diseases Mar 2024Ticks are blood-sucking ectoparasites that secrete immunomodulatory substances in saliva to hosts during engorging. Cystatins, a tick salivary protein and natural... (Review)
Review
Ticks are blood-sucking ectoparasites that secrete immunomodulatory substances in saliva to hosts during engorging. Cystatins, a tick salivary protein and natural inhibitor of Cathepsins, are attracting growing interest globally because of the immunosuppressive activities and the feasibility as an antigen for developing anti-tick vaccines. This review outlines the classification and the structure of tick Cystatins, and focuses on the anti-inflammatory effects and molecular mechanisms. Tick Cystatins can be divided into four families based on structures and cystatin 1 and cystatin 2 are the most abundant. They are injected into hosts during blood feeding and effectively mitigate the host inflammatory response. Mechanically, tick Cystatins exert anti-inflammatory properties through the inhibition of TLR-NF-κb, JAK-STAT and p38 MAPK signaling pathways. Further investigations are crucial to confirm the reduction of inflammation in other cell types like neutrophils and mast cells, and fully elucidate the underlying mechanism (like the structural mechanism) to make Cystatin a potential candidate for the development of novel anti-inflammation agents.
Topics: Humans; Animals; Ticks; Cystatins; Saliva; Anti-Inflammatory Agents
PubMed: 38070274
DOI: 10.1016/j.ttbdis.2023.102289 -
Proceedings of the National Academy of... Nov 2022Neuron-immune interaction through secreted factors contributes significantly to the complex microenvironment in the central nervous system that could alter cell...
Neuron-immune interaction through secreted factors contributes significantly to the complex microenvironment in the central nervous system that could alter cell functionalities and fates in both physiological and pathological conditions, which remains poorly characterized at the single-cell level. Herein, using a spatially patterned antibody barcode microchip, we realized the mapping of 12 different secretomes, covering cytokines, neurotrophic factors (NFs), and neuron-derived exosomes (NDEs) from high-throughput, paired single cells (≥ 600) simultaneously under normal conditions and an Alzheimer's disease (AD) model induced with amyloid beta protein 1-42 (Aβ). We applied the platform to analyze the secretion profiles from paired neuron-macrophage and neuron-microglia single cells with human cell lines. We found that pairwise neuron-macrophage interaction would trigger immune responses and attenuate neuron cells' secretion, while neuron-microglia interaction generally results in opposite outcomes in secretion. When neuron cells are induced with Aβ protein into the AD model, both neuron-macrophage and neuron-microglia interactions lead to increased cytokines and NDEs and decreased NFs. Further analysis of AD patients' serum showed that NDEs were significantly higher in patients' samples than in the control group, validating our observation from the interaction assay. Furthermore, we resolved previously undifferentiated heterogeneity underlying the secretions from single-neuron cells. We found that the NDE and NF secretion was less dependent on the paracrine signaling between one another and that secretions from neuron cells would attenuate after differentiation with Aβ. This study demonstrates the mapping of the different secretomes from paired neuron-immune single cells, providing avenues for understanding how neurons and immune cells interact through the complex secretome network.
Topics: Humans; Amyloid beta-Peptides; Secretome; Alzheimer Disease; Neurons; Microglia; Cytokines; Macrophages; Nerve Growth Factors
PubMed: 36288285
DOI: 10.1073/pnas.2200944119 -
BMC Biology Apr 2023Circular RNAs (circRNAs) are a large class of mammalian RNAs. Several protein products translated by circRNAs have been reported to be involved in the development of...
BACKGROUND
Circular RNAs (circRNAs) are a large class of mammalian RNAs. Several protein products translated by circRNAs have been reported to be involved in the development of various tissues and systems; however, their physiological functions in male reproduction have yet not been explored.
RESULTS
Here, we report an endogenous circRNA (circRsrc1) that encodes a novel 161-amino-acid protein which we named Rsrc1-161aa through circRNA sequencing coupled with mass spectrometry analysis on mouse testicular tissues. Deletion of Rsrc1-161aa in mice impaired male fertility with a significant decrease in sperm count and motility due to dysfunctions of mitochondrial energy metabolism. A series of in vitro rescue experiments revealed that circRsrc1 regulates mitochondrial functions via its encoded protein Rsrc1-161aa. Mechanistically, Rsrc1-161aa directly interacts with mitochondrial protein C1qbp and enhances its binding activity to mitochondrial mRNAs, thereby regulating the assembly of mitochondrial ribosomes and affecting the translation of oxidative phosphorylation (OXPHOS) proteins and mitochondrial energy metabolism.
CONCLUSIONS
Our studies reveal that Rsrc1-161aa protein encoded by circRsrc1 regulates mitochondrial ribosome assembly and translation during spermatogenesis, thereby affecting male fertility.
Topics: Male; Animals; Mice; Mitochondrial Ribosomes; RNA, Circular; Semen; Spermatogenesis; Mitochondria; Mitochondrial Proteins; Mammals; Protein Biosynthesis
PubMed: 37095490
DOI: 10.1186/s12915-023-01597-z -
Frontiers in Cellular and Infection... 2022The endoplasmic reticulum (ER) of higher eukaryotic cells forms an intricate membranous network that serves as the main processing facility for folding and assembling of... (Review)
Review
The endoplasmic reticulum (ER) of higher eukaryotic cells forms an intricate membranous network that serves as the main processing facility for folding and assembling of secreted and membrane proteins. The ER is a highly dynamic organelle that interacts with other intracellular structures, as well as endosymbiotic pathogenic and non-pathogenic microorganisms. A strict ER quality control (ERQC) must work to ensure that proteins entering the ER are folded and processed correctly. Unfolded or misfolded proteins are usually identified, selected, and addressed to Endoplasmic Reticulum-Associated Degradation (ERAD) complex. Conversely, when there is a large demand for secreted proteins or ER imbalance, the accumulation of unfolded or misfolded proteins activates the Unfold Protein Response (UPR) to restore the ER homeostasis or, in the case of persistent ER stress, induces the cell death. Pathogenic trypanosomatids, such as , and are the etiological agents of important neglected diseases. These protozoans have a complex life cycle alternating between vertebrate and invertebrate hosts. The ER of trypanosomatids, like those found in higher eukaryotes, is also specialized for secretion, and depends on the ERAD and non-canonical UPR to deal with the ER stress. Here, we reviewed the basic aspects of ER biology, organization, and quality control in trypanosomatids. We also focused on the unusual way by which , , and spp. respond to ER stress, emphasizing how these parasites' ER-unrevealed roads might be an attractive target for chemotherapy.
Topics: Unfolded Protein Response; Endoplasmic Reticulum-Associated Degradation; Endoplasmic Reticulum; Endoplasmic Reticulum Stress; Proteins; Leishmania
PubMed: 36439218
DOI: 10.3389/fcimb.2022.1057774 -
Nature Chemistry Sep 2022The composition of soluble toxic protein aggregates formed in vivo is currently unknown in neurodegenerative diseases, due to their ultra-low concentration in human...
The composition of soluble toxic protein aggregates formed in vivo is currently unknown in neurodegenerative diseases, due to their ultra-low concentration in human biofluids and their high degree of heterogeneity. Here we report a method to capture amyloid-containing aggregates in human biofluids in an unbiased way, a process we name amyloid precipitation. We use a structure-specific chemical dimer, a Y-shaped, bio-inspired small molecule with two capture groups, for amyloid precipitation to increase affinity. Our capture molecule for amyloid precipitation (CAP-1) consists of a derivative of Pittsburgh Compound B (dimer) to target the cross β-sheets of amyloids and a biotin moiety for surface immobilization. By coupling CAP-1 to magnetic beads, we demonstrate that we can target the amyloid structure of all protein aggregates present in human cerebrospinal fluid, isolate them for analysis and then characterize them using single-molecule fluorescence imaging and mass spectrometry. Amyloid precipitation enables unbiased determination of the molecular composition and structural features of the in vivo aggregates formed in neurodegenerative diseases.
Topics: Amyloid; Amyloid beta-Peptides; Bodily Secretions; Humans; Protein Aggregates
PubMed: 35798951
DOI: 10.1038/s41557-022-00976-3 -
Translational Vision Science &... Dec 2022To screen and compare the differential proteins in meibomian gland secretions between patients with blepharokeratoconjunctivitis (BKC) and healthy individuals and to...
PURPOSE
To screen and compare the differential proteins in meibomian gland secretions between patients with blepharokeratoconjunctivitis (BKC) and healthy individuals and to identify target proteins that may participate in the occurrence and development of BKC.
METHODS
Thirteen patients diagnosed with BKC in Shenzhen Eye Hospital and five healthy volunteers were included in this study. Meibomian gland secretions and clinical traits were collected before and after 1 month of standard BKC treatment. Label-free mass spectrometry was used for proteomic detection of meibomian gland secretions. Weighted protein coexpression network analysis (WPCNA) and several different protein analyses were performed to identify hub proteins associated with BKC and its clinical characteristics.
RESULTS
Patients with BKC had significantly lower cleanliness of the eyelid margin, higher palpebral margin scores, more serious clinical manifestations of secretions, and more damaged meibomian gland morphology compared with the healthy controls. One hundred fifteen differential proteins were associated with the clinical traits, which included diagnosis, sex, age, severity, corneal neovascularization, disease course, eyelid margin cleanliness, palpebral margin score, secretion characteristics, and meibomian gland morphology. Four hub proteins related to inflammation and the immune response (namely, S100A8, S100A9, ANXA3, and LCN2) were increased in BKC and remained increased after 1 month of treatment. The cleanliness, blepharon eyelid score, and secretion characteristics were improved after BKC treatment.
CONCLUSIONS
S100A8, S100A9, ANXA3, and LCN2 are BKC-associated proteins probably involved in the chronic inflammation of BKC.
TRANSLATIONAL RELEVANCE
Hub proteins probably involved in chronic inflammation of BKC were identified by proteomic methods.
Topics: Humans; Meibomian Glands; Proteomics; Bodily Secretions; Calgranulin A; Calgranulin B; Inflammation
PubMed: 36458945
DOI: 10.1167/tvst.11.12.4 -
BMC Bioinformatics Jun 2021In eukaryotes, proteins targeted for secretion contain a signal peptide, which allows them to proceed through the conventional ER/Golgi-dependent pathway. However, an...
MOTIVATION
In eukaryotes, proteins targeted for secretion contain a signal peptide, which allows them to proceed through the conventional ER/Golgi-dependent pathway. However, an important number of proteins lacking a signal peptide can be secreted through unconventional routes, including that mediated by exosomes. Currently, no method is available to predict protein secretion via exosomes.
RESULTS
Here, we first assembled a dataset including the sequences of 2992 proteins secreted by exosomes and 2961 proteins that are not secreted by exosomes. Subsequently, we trained different random forests models on feature vectors derived from the sequences in this dataset. In tenfold cross-validation, the best model was trained on dipeptide composition, reaching an accuracy of 69.88% ± 2.08 and an area under the curve (AUC) of 0.76 ± 0.03. In an independent dataset, this model reached an accuracy of 75.73% and an AUC of 0.840. After these results, we developed ExoPred, a web-based tool that uses random forests to predict protein secretion by exosomes.
CONCLUSION
ExoPred is available for free public use at http://imath.med.ucm.es/exopred/ . Datasets are available at http://imath.med.ucm.es/exopred/datasets/ .
Topics: Exosomes; Golgi Apparatus; Protein Sorting Signals; Protein Transport; Proteins
PubMed: 34134630
DOI: 10.1186/s12859-021-04219-z -
Metabolic Engineering Nov 2022Yeasts and especially Pichia pastoris (syn Komagataella spp.) are popular microbial expression systems for the production of recombinant proteins. One of the key...
Yeasts and especially Pichia pastoris (syn Komagataella spp.) are popular microbial expression systems for the production of recombinant proteins. One of the key advantages of yeast host systems is their ability to secrete the recombinant protein into the culture media. However, secretion of some recombinant proteins is less efficient. These proteins include antibody fragments such as Fabs or scFvs. We have recently identified translocation of nascent Fab fragments from the cytosol into the endoplasmic reticulum (ER) as one major bottleneck. Conceptually, this bottleneck requires engineering to increase the flux of recombinant proteins at the translocation step by pushing on the cytosolic side and pulling on the ER side. This engineering strategy is well-known in the field of metabolic engineering. To apply the push-and-pull strategy to recombinant protein secretion, we chose to modulate the cytosolic and ER Hsp70 cycles, which have a key impact on the translocation process. After identifying the relevant candidate factors of the Hsp70 cycles, we combined the push-and-pull factors in a single strain and achieved synergistic effects for antibody fragment secretion. With this concept we were able to successfully engineer strains and improve protein secretion up to 5-fold for different model protein classes. Overall, titers of more than 1.3 g/L Fab and scFv were reached in bioreactor cultivations.
Topics: Pichia; Secretory Pathway; Recombinant Proteins; Protein Transport; Metabolic Engineering
PubMed: 36057427
DOI: 10.1016/j.ymben.2022.08.010