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1.
Mol Cell ; 74(6): 1123-1137.e6, 2019 06 20.
Article in English | MEDLINE | ID: mdl-31053472

ABSTRACT

Abnormal processing of stressed replication forks by nucleases can cause fork collapse, genomic instability, and cell death. Despite its importance, it is poorly understood how the cell properly controls nucleases to prevent detrimental fork processing. Here, we report a signaling pathway that controls the activity of exonuclease Exo1 to prevent aberrant fork resection during replication stress. Our results indicate that replication stress elevates intracellular Ca2+ concentration ([Ca2+]i), leading to activation of CaMKK2 and the downstream kinase 5' AMP-activated protein kinase (AMPK). Following activation, AMPK directly phosphorylates Exo1 at serine 746 to promote 14-3-3 binding and inhibit Exo1 recruitment to stressed replication forks, thereby avoiding unscheduled fork resection. Disruption of this signaling pathway results in excessive ssDNA, chromosomal instability, and hypersensitivity to replication stress inducers. These findings reveal a link between [Ca2+]i and the replication stress response as well as a function of the Ca2+-CaMKK2-AMPK signaling axis in safeguarding fork structure to maintain genome stability.


Subject(s)
AMP-Activated Protein Kinases/genetics , Calcium-Calmodulin-Dependent Protein Kinase Kinase/genetics , Calcium/metabolism , DNA Repair Enzymes/genetics , DNA Repair , DNA Replication , Exodeoxyribonucleases/genetics , 14-3-3 Proteins/genetics , 14-3-3 Proteins/metabolism , AMP-Activated Protein Kinases/metabolism , Animals , Calcium Signaling/genetics , Calcium-Calmodulin-Dependent Protein Kinase Kinase/metabolism , Cell Line, Tumor , Checkpoint Kinase 1/genetics , Checkpoint Kinase 1/metabolism , Chromatin/chemistry , Chromatin/metabolism , DNA Damage , DNA Repair Enzymes/metabolism , DNA, Single-Stranded/genetics , DNA, Single-Stranded/metabolism , Exodeoxyribonucleases/metabolism , Fibroblasts/cytology , Fibroblasts/metabolism , HEK293 Cells , HeLa Cells , Humans , Isoenzymes/genetics , Isoenzymes/metabolism , Mice , Osteoblasts/cytology , Osteoblasts/metabolism , Phosphorylation , Recombinant Proteins/genetics , Recombinant Proteins/metabolism
2.
Proc Natl Acad Sci U S A ; 121(28): e2322066121, 2024 Jul 09.
Article in English | MEDLINE | ID: mdl-38968125

ABSTRACT

The Wnt/Wingless signaling pathway plays critical roles in metazoan development and energy metabolism, but its role in regulating lipid homeostasis remains not fully understood. Here, we report that the activation of canonical Wnt/Wg signaling promotes lipolysis while concurrently inhibiting lipogenesis and fatty acid ß-oxidation in both larval and adult adipocytes, as well as cultured S2R+ cells, in Drosophila. Using RNA-sequencing and CUT&RUN (Cleavage Under Targets & Release Using Nuclease) assays, we identified a set of Wnt target genes responsible for intracellular lipid homeostasis. Notably, active Wnt signaling directly represses the transcription of these genes, resulting in decreased de novo lipogenesis and fatty acid ß-oxidation, but increased lipolysis. These changes lead to elevated free fatty acids and reduced triglyceride (TG) accumulation in adipocytes with active Wnt signaling. Conversely, downregulation of Wnt signaling in the fat body promotes TG accumulation in both larval and adult adipocytes. The attenuation of Wnt signaling also increases the expression of specific lipid metabolism-related genes in larval adipocytes, wing discs, and adult intestines. Taken together, these findings suggest that Wnt signaling-induced transcriptional repression plays an important role in regulating lipid homeostasis by enhancing lipolysis while simultaneously suppressing lipogenesis and fatty acid ß-oxidation.


Subject(s)
Drosophila Proteins , Wnt Signaling Pathway , Animals , Drosophila Proteins/metabolism , Drosophila Proteins/genetics , Adipocytes/metabolism , Lipid Mobilization , Drosophila melanogaster/metabolism , Drosophila melanogaster/genetics , Wnt1 Protein/metabolism , Wnt1 Protein/genetics , Lipolysis , Lipogenesis/genetics , Triglycerides/metabolism , Lipid Metabolism/genetics , Larva/metabolism , Larva/genetics , Transcription, Genetic , Homeostasis
3.
Proc Natl Acad Sci U S A ; 120(45): e2313787120, 2023 Nov 07.
Article in English | MEDLINE | ID: mdl-37903275

ABSTRACT

The manchette is a crucial transient structure involved in sperm development, with its composition and regulation still not fully understood. This study focused on investigating the roles of CAMSAP1 and CAMSAP2, microtubule (MT) minus-end binding proteins, in regulating manchette MTs, spermiogenesis, and male fertility. The loss of CAMSAP1, but not CAMSAP2, disrupts the well-orchestrated process of spermiogenesis, leading to abnormal manchette elongation and delayed removal, resulting in deformed sperm nuclei and tails resembling oligoasthenozoospermia symptoms. We investigated the underlying molecular mechanisms by purifying manchette assemblies and comparing them through proteomic analysis, and results showed that the absence of CAMSAP1 disrupted the proper localization of key proteins (CEP170 and KIF2A) at the manchette minus end, compromising its structural integrity and hindering MT depolymerization. These findings highlight the significance of maintaining homeostasis in manchette MT minus-ends for shaping manchette morphology during late spermiogenesis, offering insights into the molecular mechanisms underlying infertility and sperm abnormalities.


Subject(s)
Proteomics , Semen , Humans , Male , Spermatogenesis/physiology , Microtubules/metabolism , Fertility
4.
Plant Cell ; 34(9): 3383-3399, 2022 08 25.
Article in English | MEDLINE | ID: mdl-35708659

ABSTRACT

Photosynthesis and the biosynthesis of many important metabolites occur in chloroplasts. In these semi-autonomous organelles, the chloroplast genome encodes approximately 100 proteins. The remaining chloroplast proteins, close to 3,000, are encoded by nuclear genes whose products are translated in the cytosol and imported into chloroplasts. However, there is still no consensus on the composition of the protein import machinery including its motor proteins and on how newly imported chloroplast proteins are refolded. In this study, we have examined the function of orf2971, the largest chloroplast gene of Chlamydomonas reinhardtii. The depletion of Orf2971 causes the accumulation of protein precursors, partial proteolysis and aggregation of proteins, increased expression of chaperones and proteases, and autophagy. Orf2971 interacts with the TIC (translocon at the inner chloroplast envelope) complex, catalyzes ATP (adenosine triphosphate) hydrolysis, and associates with chaperones and chaperonins. We propose that Orf2971 is intimately connected to the protein import machinery and plays an important role in chloroplast protein quality control.


Subject(s)
Chloroplasts , Plant Proteins , Cell Nucleus , Chloroplast Proteins , Molecular Chaperones , Protein Transport
5.
Plant Cell ; 34(4): 1308-1325, 2022 03 29.
Article in English | MEDLINE | ID: mdl-34999895

ABSTRACT

Endoreduplication, a process in which DNA replication occurs in the absence of mitosis, is found in all eukaryotic kingdoms, especially plants, where it is assumed to be important for cell growth and cell fate maintenance. However, a comprehensive understanding of the mechanism regulating endoreduplication is still lacking. We previously reported that UBIQUITIN-SPECIFIC PROTEASE14 (UBP14), encoded by DA3, acts upstream of CYCLIN-DEPENDENT KINASE B1;1 (CDKB1;1) to influence endoreduplication and cell growth in Arabidopsis thaliana. The da3-1 mutant possesses large cotyledons with enlarged cells due to high ploidy levels. Here, we identified a suppressor of da3-1 (SUPPRESSOR OF da3-1 6; SUD6), encoding CYCLIN-DEPENDENT KINASE G2 (CDKG2), which promotes endoreduplication and cell growth. CDKG2/SUD6 physically associates with CDKB1;1 in vivo and in vitro. CDKB1;1 directly phosphorylates SUD6 and modulates its stability. Genetic analysis indicated that SUD6 acts downstream of DA3 and CDKB1;1 to control ploidy level and cell growth. Thus, our study establishes a regulatory cascade for UBP14/DA3-CDKB1;1-CDKG2/SUD6-mediated control of endoreduplication and cell growth in Arabidopsis.


Subject(s)
Arabidopsis Proteins , Arabidopsis , Arabidopsis/genetics , Arabidopsis Proteins/genetics , Cell Cycle Proteins/genetics , Cyclin-Dependent Kinases/genetics , Endoreduplication/genetics , Ubiquitin/genetics
6.
Mol Cell Proteomics ; 22(7): 100582, 2023 07.
Article in English | MEDLINE | ID: mdl-37225018

ABSTRACT

Carbon metabolism is central to photosynthetic organisms and involves the coordinated operation and regulation of numerous proteins. In cyanobacteria, proteins involved in carbon metabolism are regulated by multiple regulators including the RNA polymerase sigma factor SigE, the histidine kinases Hik8, Hik31 and its plasmid-borne paralog Slr6041, and the response regulator Rre37. To understand the specificity and the cross-talk of such regulations, we simultaneously and quantitatively compared the proteomes of the gene knockout mutants for the regulators. A number of proteins showing differential expression in one or more mutants were identified, including four proteins that are unanimously upregulated or downregulated in all five mutants. These represent the important nodes of the intricate and elegant regulatory network for carbon metabolism. Moreover, serine phosphorylation of PII, a key signaling protein sensing and regulating in vivo carbon/nitrogen (C/N) homeostasis through reversible phosphorylation, is massively increased with a concomitant significant decrease in glycogen content only in the hik8-knockout mutant, which also displays impaired dark viability. An unphosphorylatable PII S49A substitution restored the glycogen content and rescued the dark viability of the mutant. Together, our study not only establishes the quantitative relationship between the targets and the corresponding regulators and elucidated their specificity and cross-talk but also unveils that Hik8 regulates glycogen accumulation through negative regulation of PII phosphorylation, providing the first line of evidence that links the two-component system with PII-mediated signal transduction and implicates them in the regulation of carbon metabolism.


Subject(s)
Carbon , Synechocystis , Phosphorylation , Carbon/metabolism , Proteomics , Synechocystis/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Glycogen/metabolism , Nitrogen , Gene Expression Regulation, Bacterial
7.
Traffic ; 23(3): 140-157, 2022 03.
Article in English | MEDLINE | ID: mdl-34994051

ABSTRACT

The extremely dynamic life cycle of gap junction connections requires highly efficient intracellular trafficking system especially designed for gap junction proteins, but the underlying mechanisms are largely unknown. Here, we identified that the COPII-associated proteins ERGIC2 (ER-Golgi intermediate compartment) and ERGIC3 are specifically required for the efficient intracellular transport of gap junction proteins in both Caenorhabditis elegans and mice. In the absence of Ergic2 or Ergic3, gap junction proteins accumulate in the ER and Golgi apparatus and the size of endogenous gap junction plaques is reduced. Knocking out the Ergic2 or Ergic3 in mice results in heart enlargement and cardiac malfunction accompanied by reduced number and size of connexin 43 (Cx43) gap junctions. Invertebrates' gap junction protein innexins share no sequence similarity with vertebrates' connexins. However, ERGIC2 and ERGIC3 could bind to gap junction proteins in both worms and mice. Characterization of the highly specialized roles of ERGIC2 and ERGIC3 in metazoans reveals how the early secretory pathway could be adapted to facilitate the efficient transport for gap junction proteins in vivo.


Subject(s)
Connexins , Golgi Apparatus , Animals , Connexins/metabolism , Gap Junctions/metabolism , Golgi Apparatus/metabolism , Mice , Secretory Pathway , Vesicular Transport Proteins
8.
New Phytol ; 243(3): 936-950, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38831647

ABSTRACT

Glycosyltransferases (GTs) are enzymes that transfer sugars to various targets. They play important roles in diverse biological processes, including photosynthesis, cell motility, exopolysaccharide biosynthesis, and lipid metabolism; however, their involvement in regulating carbon metabolism in Synechocystis sp. PCC 6803 has not been reported. We identified a novel GT protein, Slr1064, involved in carbon metabolism. The effect of slr1064 deletion on the growth of Synechocystis cells and functional mechanisms of Slr1064 on carbon metabolism were thoroughly investigated through physiological, biochemistry, proteomic, and metabolic analyses. We found that this GT, which is mainly distributed in the membrane compartment, is essential for the growth of Synechocystis under heterotrophic and mixotrophic conditions, but not under autotrophic conditions. The deletion of slr1064 hampers the turnover rate of Gap2 under mixotrophic conditions and disrupts the assembly of the PRK/GAPDH/CP12 complex under dark culture conditions. Additionally, UDP-GlcNAc, the pivotal metabolite responsible for the O-GlcNAc modification of GAPDH, is downregulated in the Δslr1064. Our work provides new insights into the role of GTs in carbon metabolism in Synechocystis and elucidate the mechanism by which carbon metabolism is regulated in this important model organism.


Subject(s)
Bacterial Proteins , Carbon , Glycosyltransferases , Synechocystis , Uridine Diphosphate N-Acetylglucosamine , Synechocystis/metabolism , Synechocystis/genetics , Synechocystis/growth & development , Carbon/metabolism , Glycosyltransferases/metabolism , Glycosyltransferases/genetics , Bacterial Proteins/metabolism , Bacterial Proteins/genetics , Uridine Diphosphate N-Acetylglucosamine/metabolism , Gene Expression Regulation, Bacterial , Gene Deletion
9.
Plant Cell ; 33(8): 2883-2898, 2021 08 31.
Article in English | MEDLINE | ID: mdl-34015125

ABSTRACT

Endoplasmic reticulum-associated degradation (ERAD) is known to regulate plant responses to diverse stresses, yet its underlying molecular mechanisms and links to various stress signaling pathways are poorly understood. Here, we show that the ERAD component ubiquitin-conjugating enzyme UBC32 positively regulates drought tolerance in Arabidopsis thaliana by targeting the aquaporins PIP2;1 and PIP2;2 for degradation. Furthermore, we demonstrate that the RING-type ligase Rma1 acts together with UBC32 and that the E2 activity of UBC32 is essential for the ubiquitination of Rma1. This complex ubiquitinates a phosphorylated form of PIP2;1 at Lys276 to promote its degradation, thereby enhancing plant drought tolerance. Extending these molecular insights into crops, we show that overexpression of Arabidopsis UBC32 also improves drought tolerance in rice (Oryza sativa). Thus, beyond uncovering the molecular basis of an ERAD-regulated stress response, our study suggests multiple potential strategies for engineering crops with improved drought tolerance.


Subject(s)
Aquaporins/metabolism , Arabidopsis Proteins/metabolism , Arabidopsis/physiology , Oryza/physiology , Ubiquitin-Conjugating Enzymes/metabolism , Abscisic Acid/metabolism , Aquaporins/genetics , Arabidopsis Proteins/genetics , Dehydration , Droughts , Endoplasmic Reticulum-Associated Degradation , Lysine/metabolism , Mass Spectrometry , Membrane Proteins/genetics , Membrane Proteins/metabolism , Oryza/genetics , Oryza/growth & development , Phosphorylation , Plants, Genetically Modified , Protein Stability , Ubiquitin-Conjugating Enzymes/genetics , Ubiquitination
10.
EMBO Rep ; 23(3): e52669, 2022 02 03.
Article in English | MEDLINE | ID: mdl-35132760

ABSTRACT

The size of lipid droplets varies greatly in vivo and is determined by both intrinsic and extrinsic factors. From an RNAi screen in Drosophila, we found that knocking down subunits of COP9 signalosome (CSN) results in enlarged lipid droplets under high-fat, but not normal, conditions. We identified CG2064, a retinol dehydrogenase (RDH) homolog, as the proteasomal degradation target of CSN in regulating lipid droplet size. RDH/CG2064 interacts with the lipid droplet-resident protein Plin2 and the RDH/CG2064-Plin2 axis acts to reduce the overall level and lipid droplet localization of Bmm/ATGL lipase. This axis is important for larval survival under prolonged starvation. Thus, we discovered an RDH-Plin2 axis modulates lipid droplet size.


Subject(s)
Drosophila , Lipase , Lipid Droplets , Perilipin-2 , Animals , Drosophila/genetics , Drosophila/metabolism , Drosophila Proteins/genetics , Drosophila Proteins/metabolism , Larva/genetics , Larva/metabolism , Lipase/genetics , Lipase/metabolism , Lipid Droplets/metabolism , Perilipin-2/metabolism
11.
J Org Chem ; 89(1): 101-110, 2024 Jan 05.
Article in English | MEDLINE | ID: mdl-38071750

ABSTRACT

Sodium carbonate-promoted facile synthesis of 5-amino-1,2,4-thiadiazoles and 5-amino-1,2,4-selenadiazoles with elemental sulfur and selenium, respectively, was developed. This method was carried out with O2 in the air as the green oxidant, and it has several advantages, including low cost, low toxicity, and stable sulfur and selenium sources, good to excellent yields with water as the sole byproduct, simple operation, and a broad substrate scope. Preliminary mechanistic studies indicate that the formation of the 1,2,4-thiadiazole ring and the 1,2,4-selenadiazole ring undergoes different processes.

12.
BMC Infect Dis ; 24(1): 602, 2024 Jun 19.
Article in English | MEDLINE | ID: mdl-38898407

ABSTRACT

BACKGROUND: Invasive pneumococcal disease (IPD) is a significant health concern in children worldwide. In this study, we aimed to analyze the clinical features, antibiotic resistance, and risk variables for poor outcomes in patients with IPD in Hangzhou. METHODS: A retrospective single-centre study was performed using the pediatric intensive care (PIC) database from 2010 to 2018. The clinical characteristics, laboratory data, antimicrobial resistance, and risk factors for in-hospital mortality and sepsis in patients with IPD in intensive care units (ICUs) were analyzed systematically. RESULTS: A total of 178 IPD patients were included in the study. The majority of the IPD children were 2-10 years old. Antimicrobial resistance tests of S. pneumoniae isolates revealed high resistance to erythromycin, tetracycline and compound sulfamethoxazole (SMZ-Co). All the isolates were sensitive to vancomycin, linezolid, moxifloxacin, telithromycin, ofloxacin, and levofloxacin. IPD patients may experience poor outcomes, including death and sepsis. The in-hospital mortality was 3.93%, and 34.27% of patients suffered from sepsis. Temperature (OR 3.80, 95% CI 1.62-8.87; P = 0.0021), Partial Pressure of Oxygen in Arterial Blood (PaO2) (OR 0.99, 95% CI 0.98-1.00; P = 0.0266), and albumin (OR 0.89, 95% CI 0.80-0.99; P = 0.0329) were found to be independent risk factors for sepsis in children with IPD. CONCLUSION: Pediatric IPD deserves attention in China. Appropriate surveillance and antibiotic selection are crucial in managing resistant strains. Early identification of high-risk individuals with risk factors contributes to the development of appropriate treatment strategies.


Subject(s)
Anti-Bacterial Agents , Hospital Mortality , Pneumococcal Infections , Streptococcus pneumoniae , Humans , China/epidemiology , Pneumococcal Infections/microbiology , Pneumococcal Infections/drug therapy , Pneumococcal Infections/mortality , Pneumococcal Infections/epidemiology , Child , Male , Risk Factors , Retrospective Studies , Female , Child, Preschool , Streptococcus pneumoniae/drug effects , Streptococcus pneumoniae/isolation & purification , Anti-Bacterial Agents/therapeutic use , Anti-Bacterial Agents/pharmacology , Infant , Microbial Sensitivity Tests , Sepsis/microbiology , Sepsis/drug therapy , Sepsis/mortality , Sepsis/epidemiology , Adolescent , Intensive Care Units, Pediatric/statistics & numerical data , Drug Resistance, Bacterial
13.
Cell Mol Biol (Noisy-le-grand) ; 70(3): 233-240, 2024 Mar 31.
Article in English | MEDLINE | ID: mdl-38650128

ABSTRACT

Skin photoaging affects appearance and is associated with a variety of skin diseases, even skin cancer. Therefore, the prevention and treatment of skin photoaging is very important. However, there is a lack of effective evaluation methods, so it is an urgent problem to explore a comprehensive, non-invasive and in vivo evaluation method. Adipose-derived mesenchymal stem cells (ADSCs) are widely used to improve skin conditions as easier to obtain and positive effects. Recently, as the development of ultrasound technology, skin ultrasound has been widely used. Changes in skin layer and structure can be observed by high-frequency ultrasound (HFUS). In addition, Shear wave elastography (SWE) technology can be used to monitor the change of skin hardness. However, it is necessary to further explore the ultrasound parameters in interpreting histological changes. We simulate the progression and treatment process of human skin photoaging by using UVB-induced nude mice skin photoaging model and ADSCs injection. The analysis of the degree and therapeutic effect of skin photoaging was conducted by HFUS, SWE and to verify with histopathology. Our study aims to clarify the value of HFUS combined SWE techniques in evaluating the degree and therapeutic efficacy of skin photoaging, which provides theoretical basis for diagnosis and treatment evaluation systems.


Subject(s)
Mesenchymal Stem Cells , Mice, Nude , Skin Aging , Skin , Ultraviolet Rays , Animals , Skin Aging/radiation effects , Mesenchymal Stem Cells/cytology , Humans , Skin/radiation effects , Skin/pathology , Adipose Tissue/cytology , Elasticity Imaging Techniques , Mesenchymal Stem Cell Transplantation/methods , Mice , Female
14.
Mol Cell Proteomics ; 21(12): 100440, 2022 12.
Article in English | MEDLINE | ID: mdl-36356940

ABSTRACT

Ascorbate peroxidase (APEX)-based proximity labeling coupled with mass spectrometry has a great potential for spatiotemporal identification of proteins proximal to a protein complex of interest. Using this approach is feasible to define the proteome neighborhood of important protein complexes in a popular photosynthetic model cyanobacterium Synechocystis sp. PCC6803 (hereafter named as Synechocystis). To this end, we developed a robust workflow for APEX2-based proximity labeling in Synechocystis and used the workflow to identify proteins proximal to the photosystem II (PS II) oxygen evolution complex (OEC) through fusion APEX2 with a luminal OEC subunit, PsbO. In total, 38 integral membrane proteins (IMPs) and 93 luminal proteins were identified as proximal to the OEC. A significant portion of these proteins are involved in PS II assembly, maturation, and repair, while the majority of the rest were not previously implicated with PS II. The IMPs include subunits of PS II and cytochrome b6/f, but not of photosystem I (except for PsaL) and ATP synthases, suggesting that the latter two complexes are spatially separated from the OEC with a distance longer than the APEX2 labeling radius. Besides, the topologies of six IMPs were successfully predicted because their lumen-facing regions exclusively contain potential APEX2 labeling sites. The luminal proteins include 66 proteins with a predicted signal peptide and 57 proteins localized also in periplasm, providing important targets to study the regulation and selectivity of protein translocation. Together, we not only developed a robust workflow for the application of APEX2-based proximity labeling in Synechocystis and showcased the feasibility to define the neighborhood proteome of an important protein complex with a short radius but also discovered a set of the proteins that potentially interact with and regulate PS II structure and function.


Subject(s)
Photosystem II Protein Complex , Synechocystis , Photosystem II Protein Complex/metabolism , Proteome/metabolism , Oxygen/metabolism , Photosystem I Protein Complex/metabolism , Synechocystis/metabolism
15.
Mol Cell Proteomics ; 21(8): 100261, 2022 08.
Article in English | MEDLINE | ID: mdl-35738554

ABSTRACT

Brain development and function are governed by precisely regulated protein expressions in different regions. To date, multiregional brain proteomes have been systematically analyzed only for adult human and mouse brains. To understand the underpinnings of brain development and function, we generated proteomes from six regions of the postnatal brain at three developmental stages of domestic dogs (Canis familiaris), which are special among animals in terms of their remarkable human-like social cognitive abilities. Quantitative analysis of the spatiotemporal proteomes identified region-enriched synapse types at different developmental stages and differential myelination progression in different brain regions. Through integrative analysis of inter-regional expression patterns of orthologous proteins and genome-wide cis-regulatory element frequencies, we found that proteins related with myelination and hippocampus were highly correlated between dog and human but not between mouse and human, although mouse is phylogenetically closer to human. Moreover, the global expression patterns of neurodegenerative disease and autism spectrum disorder-associated proteins in dog brain more resemble human brain than in mouse brain. The high similarity of myelination and hippocampus-related pathways in dog and human at both proteomic and genetic levels may contribute to their shared social cognitive abilities. The inter-regional expression patterns of disease-associated proteins in the brain of different species provide important information to guide mechanistic and translational study using appropriate animal models.


Subject(s)
Autism Spectrum Disorder , Neurodegenerative Diseases , Adult , Animals , Brain , Dogs , Humans , Mice , Proteome , Proteomics
16.
Proc Natl Acad Sci U S A ; 118(18)2021 05 04.
Article in English | MEDLINE | ID: mdl-33926963

ABSTRACT

Stomata in leaves regulate gas exchange between the plant and its atmosphere. Various environmental stimuli elicit abscisic acid (ABA); ABA leads to phosphoactivation of slow anion channel 1 (SLAC1); SLAC1 activity reduces turgor pressure in aperture-defining guard cells; and stomatal closure ensues. We used electrophysiology for functional characterizations of Arabidopsis thaliana SLAC1 (AtSLAC1) and cryoelectron microscopy (cryo-EM) for structural analysis of Brachypodium distachyon SLAC1 (BdSLAC1), at 2.97-Å resolution. We identified 14 phosphorylation sites in AtSLAC1 and showed nearly 330-fold channel-activity enhancement with 4 to 6 of these phosphorylated. Seven SLAC1-conserved arginines are poised in BdSLAC1 for regulatory interaction with the N-terminal extension. This BdSLAC1 structure has its pores closed, in a basal state, spring loaded by phenylalanyl residues in high-energy conformations. SLAC1 phosphorylation fine-tunes an equilibrium between basal and activated SLAC1 trimers, thereby controlling the degree of stomatal opening.


Subject(s)
Arabidopsis Proteins/genetics , Arabidopsis/genetics , Membrane Proteins/genetics , Plant Leaves/genetics , Plant Stomata/genetics , Abscisic Acid/metabolism , Anions/metabolism , Arabidopsis/ultrastructure , Arabidopsis Proteins/ultrastructure , Brachypodium/genetics , Brachypodium/ultrastructure , Carbon Dioxide/metabolism , Cryoelectron Microscopy , Ion Transport/genetics , Membrane Proteins/ultrastructure , Phosphorylation/genetics , Plant Leaves/ultrastructure , Plant Stomata/ultrastructure , Protein Conformation , Signal Transduction/genetics
17.
Molecules ; 29(10)2024 May 09.
Article in English | MEDLINE | ID: mdl-38792091

ABSTRACT

Methyl 4-(1,3a,6a-triazapentalen-3-yl)benzoate (TAP1) shows interesting properties as a small molecule fluorophore. In the search for post-functionalization methods, palladium-catalyzed arylation reactions were demonstrated. Direct CH arylation reactions of TAP1 with various aryl halides resulted in 3,6-diaryltriazapentalenes TAP4, although mostly in poor yields. Bromination of TAP1 followed by Suzuki coupling, on the other hand, requires a more delicate procedure, but gave arylated products with the same regiochemistry (TAP4) in moderate to good yields. The structure of 6-phenyltriazapentalene TAP4a was confirmed by crystallographic analysis. In addition, the effect of the C6 arylation on the fluorescent properties of 3-aryl-1,3a,6a-triazapentalenes was studied in dichloromethane at room temperature and in 2-methyltetrahydrofuran at 77 K, while the photophysical properties of two saponified derivatives were measured in acetonitrile.

18.
Sci Eng Ethics ; 30(3): 26, 2024 Jun 10.
Article in English | MEDLINE | ID: mdl-38856788

ABSTRACT

The rapid development of computer vision technologies and applications has brought forth a range of social and ethical challenges. Due to the unique characteristics of visual technology in terms of data modalities and application scenarios, computer vision poses specific ethical issues. However, the majority of existing literature either addresses artificial intelligence as a whole or pays particular attention to natural language processing, leaving a gap in specialized research on ethical issues and systematic solutions in the field of computer vision. This paper utilizes bibliometrics and text-mining techniques to quantitatively analyze papers from prominent academic conferences in computer vision over the past decade. It first reveals the developing trends and specific distribution of attention regarding trustworthy aspects in the computer vision field, as well as the inherent connections between ethical dimensions and different stages of visual model development. A life-cycle framework regarding trustworthy computer vision is then presented by making the relevant trustworthy issues, the operation pipeline of AI models, and viable technical solutions interconnected, providing researchers and policymakers with references and guidance for achieving trustworthy CV. Finally, it discusses particular motivations for conducting trustworthy practices and underscores the consistency and ambivalence among various trustworthy principles and technical attributes.


Subject(s)
Artificial Intelligence , Humans , Artificial Intelligence/ethics , Artificial Intelligence/trends , Trust , Natural Language Processing , Data Mining/ethics , Bibliometrics
19.
J Proteome Res ; 22(4): 1255-1269, 2023 04 07.
Article in English | MEDLINE | ID: mdl-36930737

ABSTRACT

Spatial proteome reorganization in response to a changing environment represents a different layer of adaptation mechanism in addition to differential expression of a subset of stress responsive genes in photosynthetic organisms. Profiling such reorganization events is critically important to extend our understanding how photosynthetic organisms adapt to adverse environments. Thus, we treated a unicellular photosynthetic model cyanobacterium, Synechocystis sp. PCC 6803 (hereafter referred to as Synechocystis), with five different types of abiotic stresses including nitrogen starvation, iron deficiency, cold, heat, and darkness, and systematically identified proteins showing stress-induced differential expression and/or redistribution between the membrane and the soluble fractions using a quantitative proteomics approach. A number of proteins showing such a redistribution in response to a single or multiple types of abiotic stresses were identified. These include 12 ribosomal proteins displaying unanimous cold-induced redistribution to the membrane and the protein FurA, a master regulator of iron acquisition, displaying iron deficiency- and nitrogen starvation-induced redistribution to the membrane. Such findings shed light on a novel regulatory mechanism underlying the corresponding stress responses, and establish the results in the present study as an important resource for future studies intended to understand how photosynthetic organisms cope with adverse environments.


Subject(s)
Iron Deficiencies , Synechocystis , Humans , Proteome/genetics , Proteome/metabolism , Stress, Physiological , Synechocystis/genetics , Synechocystis/metabolism , Nitrogen/metabolism , Bacterial Proteins/genetics , Bacterial Proteins/metabolism
20.
J Biol Chem ; 298(9): 102341, 2022 09.
Article in English | MEDLINE | ID: mdl-35931119

ABSTRACT

Human papillomaviruses (HPVs) cause a subset of head and neck squamous cell carcinomas (HNSCCs). Previously, we demonstrated that HPV16 oncogene E6 or E6/E7 transduction increases the abundance of O-linked ß-N-acetylglucosamine (O-GlcNAc) transferase (OGT), but OGT substrates affected by this increase are unclear. Here, we focus on the effects of O-GlcNAcylation on HPV-positive HNSCCs. We found that upon HPV infection, Unc-51-like kinase 1 (ULK1), an autophagy-initiating kinase, is hyper-O-GlcNAcylated, stabilized, and linked with autophagy elevation. Through mass spectrometry, we identified that ULK1 is O-GlcNAcylated at Ser409, which is distinct from the previously reported Thr635/Thr754 sites. It has been demonstrated that PKCα mediates phosphorylation of ULK1 at Ser423, which attenuates its stability by shunting ULK1 to the chaperone-mediated autophagy (CMA) pathway. Using biochemical assays, we demonstrate that ULK1 Ser409Ser410 O-GlcNAcylation antagonizes its phosphorylation at Ser423. Moreover, mutations of Ser409A and its neighboring site Ser410A (2A) render ULK1 less stable by promoting interaction with the CMA chaperone HSC70 (heat shock cognate 70 kDa protein). Furthermore, ULK1-2A mutants attenuate the association of ULK1 with STX17, which is vital for the fusion between autophagosomes and lysosomes. Analysis of The Cancer Genome Atlas (TCGA) database reveals that ULK1 is upregulated in HPV-positive HNSCCs, and its level positively correlates with HNSCC patient survival. Overall, our work demonstrates that O-GlcNAcylation of ULK1 is altered in response to environmental changes. O-GlcNAcylation of ULK1 at Ser409 and perhaps Ser410 stabilizes ULK1, which might underlie the molecular mechanism of HPV-positive HNSCC patient survival.


Subject(s)
Acetylglucosamine , Autophagy-Related Protein-1 Homolog , Chaperone-Mediated Autophagy , Head and Neck Neoplasms , Intracellular Signaling Peptides and Proteins , Papillomavirus Infections , Protein Kinase C-alpha , Squamous Cell Carcinoma of Head and Neck , Acetylglucosamine/metabolism , Autophagy-Related Protein-1 Homolog/genetics , Autophagy-Related Protein-1 Homolog/metabolism , Enzyme Stability , Glycosylation , Head and Neck Neoplasms/metabolism , Head and Neck Neoplasms/virology , Humans , Intracellular Signaling Peptides and Proteins/genetics , Intracellular Signaling Peptides and Proteins/metabolism , N-Acetylglucosaminyltransferases/metabolism , Papillomavirus Infections/metabolism , Protein Kinase C-alpha/metabolism , Squamous Cell Carcinoma of Head and Neck/metabolism , Squamous Cell Carcinoma of Head and Neck/virology
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