bims-toxgon Biomed News
on Toxoplasma gondii metabolism
Issue of 2024–04–28
twenty papers selected by
Lakesh Kumar, BITS Pilani
  1. Phosphoproteomic analysis reveals changes in A-Raf-related protein phosphorylation in response to Toxoplasma gondii infection in porcine macrophages.
  2. Oral Sex as a Potential Route for Toxoplasma Gondii Transmission: Experiment with Human Semen and Laboratory Mice Model.
  3. Ontological representation, modeling, and analysis of parasite vaccines.
  4. Global profiling of protein S-palmitoylation in the second-generation merozoites of Eimeria tenella.
  5. Toxoplasma gondii suppresses proliferation and migration of breast cancer cells by regulating their transcriptome.
  6. A comprehensive assessment of toxoplasmosis and its dormant impact on psychotic disorders (Review).
  7. Evaluation of In Vitro Cytotoxic and Apoptotic Effects of Miltefosine on the Toxoplasma gondii RH Strain.
  8. Acetyl-CoA metabolic accumulation promotes hepatocellular carcinoma metastasis via enhancing CXCL1-dependent infiltration of tumor-associated neutrophils.
  9. The α-tubulin acetyltransferase ATAT1: structure, cellular functions, and its emerging role in human diseases.
  10. Investigating Potential Cancer Therapeutics: Insight into Histone Deacetylases (HDACs) Inhibitions.
  11. Let it glow: genetically encoded fluorescent reporters in Plasmodium.
  12. Biophysical insights into the dimer formation of human Sirtuin 2.
  13. The SWI/SNF chromatin remodeling complex: a critical regulator of metabolism.
  14. Muscle-Specific Pyruvate Kinase Isoforms, Pkm1 and Pkm2, Regulate Mammalian SWI/SNF Proteins and Histone 3 Phosphorylation During Myoblast Differentiation.
  15. Neutrophil Elastase Degrades Histone Deacetylases and Sirtuin 1 in Primary Human Monocyte Derived Macrophages.
  16. Lysine acetylation of Hsp16.3: Effect on its structure, chaperone function and influence towards the growth of Mycobacterium tuberculosis.
  17. USP3: Key deubiquitylation enzyme in human diseases.
  18. Structural basis for α-tubulin-specific and modification state-dependent glutamylation.
  19. Deacylases-structure, function, and relationship to diseases.
  20. The acetylation of MDH1 and IDH1 is associated with energy metabolism in acute liver failure.
  1. Parasit Vectors. 2024 Apr 20. 17(1): 191
    Phosphoproteomic analysis reveals changes in A-Raf-related protein phosphorylation in response to Toxoplasma gondii infection in porcine macrophages.
    Dingzeyang Su, Shifan Zhu, Kangzhi Xu, Zhaofeng Hou, Fuxing Hao, Fan Xu, Yifan Lin, Yuyang Zhu, Dandan Liu, Qiangde Duan, Xinjun Zhang, Yuguo Yuan, Jinjun Xu, Jianping Tao.
       BACKGROUND: Toxoplasma gondii is an obligate intracellular protozoan parasite that causes severe threats to humans and livestock. Macrophages are the cell type preferentially infected by T. gondii in vivo. Protein phosphorylation is an important posttranslational modification involved in diverse cellular functions. A rapidly accelerated fibrosarcoma kinase (A-Raf) is a member of the Raf family of serine/threonine protein kinases that is necessary for MAPK activation. Our previous research found that knockout of A-Raf could reduce T. gondii-induced apoptosis in porcine alveolar macrophages (3D4/21 cells). However, limited information is available on protein phosphorylation variations and the role of A-Raf in macrophages infected with T. gondii.
    METHODS: We used immobilized metal affinity chromatography (IMAC) in combination with liquid chromatography tandem mass spectrometry (LC-MS/MS) to profile changes in phosphorylation in T. gondii-infected 3D4/21 and 3D4/21-ΔAraf cells.
    RESULTS: A total of 1647 differentially expressed phosphorylated proteins (DEPPs) with 3876 differentially phosphorylated sites (DPSs) were identified in T. gondii-infected 3D4/21 cells (p3T group) when compared with uninfected 3D4/21 cells (pho3 group), and 959 DEPPs with 1540 DPSs were identified in the p3T group compared with infected 3D4/21-ΔAraf cells (p3KT group). Venn analysis revealed 552 DPSs corresponding to 406 DEPPs with the same phosphorylated sites when comparing p3T/pho3 versus p3T/p3KT, which were identified as DPSs and DEPPs that were directly or indirectly related to A-Raf.
    CONCLUSIONS: Our results revealed distinct responses of macrophages to T. gondii infection and the potential roles of A-Raf in fighting infection via phosphorylation of crucial proteins.
    Keywords:   Toxoplasma gondii ; 3D4/21; A-Raf; Apoptosis; Host cells; Phosphorylation
    DOI:  https://doi.org/10.1186/s13071-024-06273-x
  2. Acta Parasitol. 2024 Apr 25.
    Oral Sex as a Potential Route for Toxoplasma Gondii Transmission: Experiment with Human Semen and Laboratory Mice Model.
    Jana Ullmann, Petr Kodym, Jaroslav Flegr, Dagmar Berenová, Simona Jirsová, Šárka Kaňková.
       PURPOSE: Toxoplasma gondii is one of the most widespread parasites in the human population globally. Several modes of its transmission have been proposed: some are well-researched and confirmed, others remain unconfirmed. One unconfirmed hypothesis pertains to potential transmission of Toxoplasma gondii via oral sex (fellatio) in humans. A recent study found tissue cysts in the semen of men with latent toxoplasmosis. Therefore, we aimed to test the hypothesis of Toxoplasma gondii transmission through oral sex experimentally.
    METHODS: Eighty-two laboratory mice were orally administered semen samples from 41 men with latent toxoplasmosis. These semen samples were examined for the presence of Toxoplasma gondii DNA using PCR.
    RESULTS: We detected Toxoplasma gondii DNA in three of the 41 semen samples from men with latent toxoplasmosis. Oral administration of semen samples to laboratory mice did not result in parasite transmission.
    CONCLUSION: We have not demonstrated the transmission of Toxoplasma to mice by oral exposure to semen from infected men. While this does not conclusively rule out the possibility of such transmission in humans, the results suggest that, if it does occur, this mode of transmission is likely infrequent.
    Keywords:  Ejaculate; Fellatio; Latent toxoplasmosis; Parasitic disease; Sexual transmission; Sperm
    DOI:  https://doi.org/10.1007/s11686-024-00848-5
  3. J Biomed Semantics. 2024 Apr 25. 15(1): 4
    Ontological representation, modeling, and analysis of parasite vaccines.
    Anthony Huffman, Xumeng Zhang, Meghana Lanka, Jie Zheng, Anna Maria Masci, Yongqun He.
       BACKGROUND: Pathogenic parasites are responsible for multiple diseases, such as malaria and Chagas disease, in humans and livestock. Traditionally, pathogenic parasites have been largely an evasive topic for vaccine design, with most successful vaccines only emerging recently. To aid vaccine design, the VIOLIN vaccine knowledgebase has collected vaccines from all sources to serve as a comprehensive vaccine knowledgebase. VIOLIN utilizes the Vaccine Ontology (VO) to standardize the modeling of vaccine data. VO did not model complex life cycles as seen in parasites. With the inclusion of successful parasite vaccines, an update in parasite vaccine modeling was needed.
    RESULTS: VIOLIN was expanded to include 258 parasite vaccines against 23 protozoan species, and 607 new parasite vaccine-related terms were added to VO since 2022. The updated VO design for parasite vaccines accounts for parasite life stages and for transmission-blocking vaccines. A total of 356 terms from the Ontology of Parasite Lifecycle (OPL) were imported to VO to help represent the effect of different parasite life stages. A new VO class term, 'transmission-blocking vaccine,' was added to represent vaccines able to block infectious transmission, and one new VO object property, 'blocks transmission of pathogen via vaccine,' was added to link vaccine and pathogen in which the vaccine blocks the transmission of the pathogen. Additionally, our Gene Set Enrichment Analysis (GSEA) of 140 parasite antigens used in the parasitic vaccines identified enriched features. For example, significant patterns, such as signal, plasma membrane, and entry into host, were found in the antigens of the vaccines against two parasite species: Plasmodium falciparum and Toxoplasma gondii. The analysis found 18 out of the 140 parasite antigens involved with the malaria disease process. Moreover, a majority (15 out of 54) of P. falciparum parasite antigens are localized in the cell membrane. T. gondii antigens, in contrast, have a majority (19/24) of their proteins related to signaling pathways. The antigen-enriched patterns align with the life cycle stage patterns identified in our ontological parasite vaccine modeling.
    CONCLUSIONS: The updated VO modeling and GSEA analysis capture the influence of the complex parasite life cycles and their associated antigens on vaccine development.
    Keywords:  Parasite vaccine; VIOLIN vaccine knowledgebase; Vaccine Ontology
    DOI:  https://doi.org/10.1186/s13326-024-00307-0
  4. Parasitol Res. 2024 Apr 22. 123(4): 190
    Global profiling of protein S-palmitoylation in the second-generation merozoites of Eimeria tenella.
    Zigang Qu, Yuqiong Li, Wenhui Li, Nianzhang Zhang, Joshua Seun Olajide, Xiaoyun Mi, Baoquan Fu.
      The intracellular protozoan Eimeria tenella is responsible for avian coccidiosis which is characterized by host intestinal damage. During developmental cycle, E. tenella undergoes versatile transitional stages such as oocyst, sporozoites, merozoites, and gametocytes. These developmental transitions involve changes in cell shape and cell size requiring cytoskeletal remodeling and changes in membrane proteins, which may require transcriptional and translational regulations as well as post-translational modification of proteins. Palmitoylation is a post-translational modification (PTM) of protein that orchestrates protein targeting, folding, stability, regulated enzymatic activity and even epigenetic regulation of gene expression. Previous research revealed that protein palmitoylation play essential role in Toxoplasma gondii, Trypanosoma cruzi, Trichomonas vaginalis, and several Plasmodium parasites. Until now, there is little information on the enzymes related to palmitoylation and role of protein acylation or palmitoylation in E. tenella. Therefore, palmitome of the second-generation merozoite of E. tenella was investigated. We identified a total of 2569 palmitoyl-sites that were assigned to 2145 palmitoyl-peptides belonging to 1561 protein-groups that participated in biological processes including parasite morphology, motility and host cell invasion. In addition, RNA biosynthesis, protein biosynthesis, folding, proteasome-ubiquitin degradation, and enzymes involved in PTMs, carbohydrate metabolism, glycan biosynthesis, and mitochondrial respiratory chain as well as vesicle trafficking were identified. The study allowed us to decipher the broad influence of palmitoylation in E. tenella biology, and its potential roles in the pathobiology of E. tenella infection. Raw data are publicly available at iProX with the dataset identifier PXD045061.
    Keywords:   E. tenella ; Bioiological process; Protein acylation; The second-generation merozoites
    DOI:  https://doi.org/10.1007/s00436-024-08204-2
  5. Cancer Cell Int. 2024 Apr 23. 24(1): 144
    Toxoplasma gondii suppresses proliferation and migration of breast cancer cells by regulating their transcriptome.
    Hengming Ye, Xiaotao Zhou, Bike Zhu, Tiantian Xiong, Weile Huang, Feng He, Hui Li, Lihua Chen, Luying Tang, Zefang Ren.
       BACKGROUND: Breast cancer is the most common cancer in women worldwide. Toxoplasma gondii (T. gondii) has shown anticancer activity in breast cancer mouse models, and exerted beneficial effect on the survival of breast cancer patients, but the mechanism was unclear.
    METHODS: The effect of tachyzoites of T. gondii (RH and ME49 strains) on human breast cancer cells (MCF-7 and MDA-MB-231 cells) proliferation and migration was assessed using cell growth curve and wound healing assays. Dual RNA-seq was performed for T. gondii-infected and non-infected cells to determine the differentially expressed genes (DEGs). Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Protein-Protein Interaction Networks analysis (PPI) were performed to explore the related signaling pathway and hub genes. Hub genes were validated using the Kaplan-Meier plotter database, and Pathogen Host Interaction (PHI-base) database. The results were verified by qRT-PCR.
    RESULTS: The tachyzoites of T. gondii decreased the expression of Ki67 and increased the expression of E-cadherin, resulting in suppressing the proliferation and migration of infected human breast cancer cells. The inhibitory effect of T. gondii on breast cancer cells showed a significant dose-response relationship. Compared with the control group, 2321 genes were transcriptionally regulated in MCF-7 cells infected with T. gondii, while 169 genes were transcriptionally regulated in infected MDA-MB-231 cells. Among these genes, 698 genes in infected MCF-7 cells and 67 genes in infected MDA-MB-231 cells were validated by the publicly available database. GO and KEGG analyses suggested that several pathways were involved in anticancer function of T. gondii, such as ribosome, interleukin-17 signaling, coronavirus disease pathway, and breast cancer pathway. BRCA1, MYC and IL-6 were identified as the top three hub genes in infected-breast cancer cells based on the connectivity of PPI analysis. In addition, after interacting with breast cancer cells, the expression of ROP16 and ROP18 in T. gondii increased, while the expression of crt, TgIST, GRA15, GRA24 and MIC13 decreased.
    CONCLUSIONS: T. gondii transcriptionally regulates several signaling pathways by altering the hub genes such as BRCA1, MYC and IL-6, which can inhibit the breast tumor growth and migration, hinting at a potential therapeutic strategy.
    Keywords:   Toxoplasma gondii ; Breast cancer; Migration; Proliferation; Transcriptome
    DOI:  https://doi.org/10.1186/s12935-024-03333-1
  6. Biomed Rep. 2024 Jun;20(6): 86
    A comprehensive assessment of toxoplasmosis and its dormant impact on psychotic disorders (Review).
    Aliss Madalina Mares, Corina Ioana Varlam, Floris Petru Iliuta, Radu Mihail Lacau, Mihnea Costin Manea.
      Toxoplasmosis is a pathological condition induced by the parasite, Toxoplasma gondii (T. gondii), which has a notable affinity for the cellular components of the central nervous system. Over the decades, the relationship between toxoplasmosis and the development of psychiatric disorders has generated profound interest within the scientific community. Whether considering immunocompetent or immunocompromised patients, epidemiological studies suggest that exposure to T. gondii may be associated with a higher risk of certain psychiatric disorders. However, there are extensive debates regarding the exact nature of this association and how T. gondii is involved in the pathogenesis of these disorders. Toxoplasmosis has long been considered an asymptomatic infection among immunocompetent patients. However, there appears to be an association between chronic brain infection with T. gondii and alterations in patient neuronal architecture, neurochemistry and behavior. The present review aimed to compile statements and pathophysiological hypotheses regarding the potential association between toxoplasmosis and psychotic disorders. Further research is necessary for understanding the potential relationship of T. gondii infection and psychotic disorders.
    Keywords:  gene-environment interactions; pathophysiology; psychosis; risk factors; toxoplasma; toxoplasmosis
    DOI:  https://doi.org/10.3892/br.2024.1774
  7. Iran J Parasitol. 2024 Jan-Mar;19(1):19(1): 52-60
    Evaluation of In Vitro Cytotoxic and Apoptotic Effects of Miltefosine on the Toxoplasma gondii RH Strain.
    Shahram Khademvatan, Elham Yousefi, Negar Asadi, Esmaeil Abasi.
       Background: We aimed to investigate the cytotoxic and apoptotic effects of miltefosine on Toxoplasma gondii RH strain by various techniques.
    Methods: The study was conducted at the Department of Parasitology and Mycology, Urmia University of Medical Sciences, Iran in 2020. Four groups of five BALB/c mice were selected. The cytotoxicity test was conducted by adding miltefosine to T. gondii tachyzoites; control tachyzoites received PBS and MTT assay was done on each suspension. For evaluating the Th1-type immune responses, the serum levels of IFN-γ and nitric oxide (NO) were assessed in mice after injecting tachyzoites and miltefosine, respectively. The flow cytometry technique was performed on T. gondii tachyzoites challenged with IC50 and IC90 doses of miltefosine and unchallenged cells. DNA fragments in T. gondii tachyzoites were detected by Terminal dUTPnick-end labeling (TUNEL) method.
    Results: Overall, 256, 64, 32, and 16 μg concentrations of miltefosine, respectively could kill more than 50% of viable T. gondii tachyzoites. The infected mice group, treated with miltefosine, significantly produced more IFN-γ relative to other groups (P< 0.001). Moreover, a significant difference was found in inducible NO synthase between the experimental and control groups (P<0.05). The flow cytometry results demonstrated a concentration-dependent apoptosis rate in tachyzoites incubated with miltefosine, though the necrosis rate was non-significant. DNA fragmentation analysis indicated oligonucleotides (18-200 bp) in tachyzoites treated with 11μg of miltefosine for 24, 48 and 72 h. However, this pattern was not observed in untreated control microorganisms.
    Conclusion: Miltefosine could be a favorable candidate for use as a new treatment for toxoplasmosis.
    Keywords:  Interferon-gamma; Miltefosine; Nitric oxide; Tachyzoite; Toxoplasma gondii
    DOI:  https://doi.org/10.18502/ijpa.v19i1.15204
  8. Cancer Lett. 2024 Apr 24. pii: S0304-3835(24)00296-9. [Epub ahead of print] 216903
    Acetyl-CoA metabolic accumulation promotes hepatocellular carcinoma metastasis via enhancing CXCL1-dependent infiltration of tumor-associated neutrophils.
    Jun-Jie Pan, Sun-Zhe Xie, Xin Zheng, Jian-Feng Xu, Hao Xu, Rui-Qi Yin, Yun-Ling Luo, Li Shen, Zheng-Ru Chen, Yi-Ran Chen, Shi-Zhe Yu, Lu Lu, Wen-Wei Zhu, Ming Lu, Lun-Xiu Qin.
      High levels of acetyl-CoA are considered a key metabolic feature of metastatic cancers. However, the impacts of acetyl-CoA metabolic accumulation on cancer microenvironment remodeling are poorly understood. In this study, using human hepatocellular carcinoma (HCC) tissues and orthotopic xenograft models, we found a close association between high acetyl-CoA levels in HCCs, increased infiltration of tumor-associated neutrophils (TANs) in the cancer microenvironment and HCC metastasis. Cytokine microarray and enzyme-linked immunosorbent assays (ELISA) revealed the crucial role of the chemokine (C-X-C motif) ligand 1(CXCL1). Mechanistically, acetyl-CoA accumulation induces H3 acetylation-dependent upregulation of CXCL1 gene expression. CXCL1 recruits TANs, leads to neutrophil extracellular traps (NETs) formation and promotes HCC metastasis. Collectively, our work linked the accumulation of acetyl-CoA in HCC cells and TANs infiltration, and revealed that the CXCL1-CXC receptor 2 (CXCR2)-TANs-NETs axis is a potential target for HCCs with high acetyl-CoA levels.
    Keywords:  Acetyl-CoA; cancer metastasis; histone acetylation; neutrophil extracellular traps; tumor-associated neutrophils
    DOI:  https://doi.org/10.1016/j.canlet.2024.216903
  9. Cell Mol Life Sci. 2024 Apr 23. 81(1): 193
    The α-tubulin acetyltransferase ATAT1: structure, cellular functions, and its emerging role in human diseases.
    Angela Iuzzolino, Francesca Romana Pellegrini, Dante Rotili, Francesca Degrassi, Daniela Trisciuoglio.
      The acetylation of α-tubulin on lysine 40 is a well-studied post-translational modification which has been associated with the presence of long-lived stable microtubules that are more resistant to mechanical breakdown. The discovery of α-tubulin acetyltransferase 1 (ATAT1), the enzyme responsible for lysine 40 acetylation on α-tubulin in a wide range of species, including protists, nematodes, and mammals, dates to about a decade ago. However, the role of ATAT1 in different cellular activities and molecular pathways has been only recently disclosed. This review comprehensively summarizes the most recent knowledge on ATAT1 structure and substrate binding and analyses the involvement of ATAT1 in a variety of cellular processes such as cell motility, mitosis, cytoskeletal organization, and intracellular trafficking. Finally, the review highlights ATAT1 emerging roles in human diseases and discusses ATAT1 potential enzymatic and non-enzymatic roles and the current efforts in developing ATAT1 inhibitors.
    Keywords:  Acetyltransferase; Cancer; Cytoskeleton; Microtubules; Neurological diseases; Tubulin acetylation
    DOI:  https://doi.org/10.1007/s00018-024-05227-x
  10. Pharmaceuticals (Basel). 2024 Mar 29. pii: 444. [Epub ahead of print]17(4):
    Investigating Potential Cancer Therapeutics: Insight into Histone Deacetylases (HDACs) Inhibitions.
    Basharat Ahmad, Aamir Saeed, Ahmed Al-Amery, Ismail Celik, Iraj Ahmed, Muhammad Yaseen, Imran Ahmad Khan, Dhurgham Al-Fahad, Mashooq Ahmad Bhat.
      Histone deacetylases (HDACs) are enzymes that remove acetyl groups from ɛ-amino of histone, and their involvement in the development and progression of cancer disorders makes them an interesting therapeutic target. This study seeks to discover new inhibitors that selectively inhibit HDAC enzymes which are linked to deadly disorders like T-cell lymphoma, childhood neuroblastoma, and colon cancer. MOE was used to dock libraries of ZINC database molecules within the catalytic active pocket of target HDACs. The top three hits were submitted to MD simulations ranked on binding affinities and well-occupied interaction mechanisms determined from molecular docking studies. Inside the catalytic active site of HDACs, the two stable inhibitors LIG1 and LIG2 affect the protein flexibility, as evidenced by RMSD, RMSF, Rg, and PCA. MD simulations of HDACs complexes revealed an alteration from extended to bent motional changes within loop regions. The structural deviation following superimposition shows flexibility via a visual inspection of movable loops at different timeframes. According to PCA, the activity of HDACs inhibitors induces structural dynamics that might potentially be utilized to define the nature of protein inhibition. The findings suggest that this study offers solid proof to investigate LIG1 and LIG2 as potential HDAC inhibitors.
    Keywords:  histone deacetylases; molecular docking; molecular dynamic simulation; neuroblastoma
    DOI:  https://doi.org/10.3390/ph17040444
  11. Malar J. 2024 Apr 20. 23(1): 114
    Let it glow: genetically encoded fluorescent reporters in Plasmodium.
    Pia J Thiele, Raquel Mela-Lopez, Stéphanie A Blandin, Dennis Klug.
      The use of fluorescent proteins (FPs) in Plasmodium parasites has been key to understand the biology of this obligate intracellular protozoon. FPs like the green fluorescent protein (GFP) enabled to explore protein localization, promoter activity as well as dynamic processes like protein export and endocytosis. Furthermore, FP biosensors have provided detailed information on physiological parameters at the subcellular level, and fluorescent reporter lines greatly extended the malariology toolbox. Still, in order to achieve optimal results, it is crucial to know exactly the properties of the FP of choice and the genetic scenario in which it will be used. This review highlights advantages and disadvantages of available landing sites and promoters that have been successfully applied for the ectopic expression of FPs in Plasmodium berghei and Plasmodium falciparum. Furthermore, the properties of newly developed FPs beyond DsRed and EGFP, in the visualization of cells and cellular structures as well as in the sensing of small molecules are discussed.
    Keywords:   Plasmodium ; Apicomplexa; Fluorescent protein; GFP; Malaria; Parasite
    DOI:  https://doi.org/10.1186/s12936-024-04936-9
  12. Protein Sci. 2024 May;33(5): e4994
    Biophysical insights into the dimer formation of human Sirtuin 2.
    Noa Suzuki, Tsuyoshi Konuma, Takahisa Ikegami, Satoko Akashi.
      Sirtuin 2 (SIRT2) is a class III histone deacetylase that is highly conserved from bacteria to mammals. We prepared and characterized the wild-type (WT) and mutant forms of the histone deacetylase (HDAC) domain of human SIRT2 (hSIRT2) using various biophysical methods and evaluated their deacetylation activity. We found that WT hSIRT2 HDAC (residues 52-357) forms a homodimer in a concentration-dependent manner with a dimer-monomer dissociation constant of 8.3 ± 0.5 μM, which was determined by mass spectrometry. The dimer was disrupted into two monomers by binding to the HDAC inhibitors SirReal1 and SirReal2. We also confirmed dimer formation of hSIRT2 HDAC in living cells using a NanoLuc complementation reporter system. Examination of the relationship between dimer formation and deacetylation activity using several mutants of hSIRT2 HDAC revealed that some non-dimerizing mutants exhibited deacetylation activity for the N-terminal peptide of histone H3, similar to the wild type. The hSIRT2 HDAC mutant Δ292-306, which lacks a SIRT2-specific disordered loop region, was identified to exist as a monomer with slightly reduced deacetylation activity; the X-ray structure of the mutant Δ292-306 was almost identical to that of the WT hSIRT2 HDAC bound to an inhibitor. These results indicate that hSIRT2 HDAC forms a dimer, but this is independent of deacetylation activity. Herein, we discuss insights into the dimer formation of hSIRT2 based on our biophysical experimental results.
    Keywords:  HDAC domain; Sirtuin 2; dimer; inhibitor; native MS
    DOI:  https://doi.org/10.1002/pro.4994
  13. Biochem Soc Trans. 2024 Apr 26. pii: BST20231141. [Epub ahead of print]
    The SWI/SNF chromatin remodeling complex: a critical regulator of metabolism.
    Michael C Church, Jerry L Workman.
      The close relationship between chromatin and metabolism has been well-studied in recent years. Many metabolites have been found to be cofactors used to modify chromatin, and these modifications can in turn affect gene transcription. One chromatin-associated factor responsible for regulating transcription is the SWI/SNF complex, an ATP-dependent chromatin remodeler conserved throughout eukaryotes. SWI/SNF was originally described in yeast as regulating genes involved in carbon source metabolism and mating type switching, and its mammalian counterpart has been extensively studied for its role in diseases such as cancer. The yeast SWI/SNF complex is closely associated with activation of stress response genes, many of which have metabolic functions. It is now recognized that this is a conserved function of the complex, and recent work has shown that mammalian SWI/SNF is also a key regulator of metabolic transcription. Emerging evidence suggests that loss of SWI/SNF introduces vulnerabilities to cells due to this metabolic influence, and that this may present opportunities for treatment of SWI/SNF-deficient cancers.
    Keywords:  chromatin; metabolism; transcription
    DOI:  https://doi.org/10.1042/BST20231141
  14. bioRxiv. 2024 Apr 11. pii: 2024.04.10.588959. [Epub ahead of print]
    Muscle-Specific Pyruvate Kinase Isoforms, Pkm1 and Pkm2, Regulate Mammalian SWI/SNF Proteins and Histone 3 Phosphorylation During Myoblast Differentiation.
    Monserrat Olea-Flores, Tapan Sharma, Odette Verdejo-Torres, Imaru DiBartolomeo, Paul R Thompson, Teresita Padilla-Benavides, Anthony N Imbalzano.
      Pyruvate kinase is a glycolytic enzyme that converts phosphoenolpyruvate and ADP into pyruvate and ATP. There are two genes that encode pyruvate kinase in vertebrates; Pkm and Pkl encode muscle- and liver/erythrocyte-specific forms, respectively. Each gene encodes two isoenzymes due to alternative splicing. Both muscle-specific enzymes, Pkm1 and Pkm2, function in glycolysis, but Pkm2 also has been implicated in gene regulation due to its ability to phosphorylate histone 3 threonine 11 (H3T11) in cancer cells. Here, we examined the roles of Pkm1 and Pkm2 during myoblast differentiation. RNA-seq analysis revealed that Pkm2 promotes the expression of Dpf2/Baf45d and Baf250a/Arid1A . Dpf2 and Baf250a are subunits that identify a specific sub-family of the mammalian SWI/SNF (mSWI/SNF) of chromatin remodeling enzymes that is required for activation of myogenic gene expression during differentiation. Pkm2 also mediated the incorporation of Dpf2 and Baf250a into the regulatory sequences controlling myogenic gene expression. Pkm1 did not affect expression but was required for nuclear localization of Dpf2. Additionally, Pkm2 was required not only for the incorporation of phosphorylated H3T11 in myogenic promoters, but also for the incorporation of phosphorylated H3T6 and H3T45 at myogenic promoters via regulation of AKT and protein kinase C isoforms that phosphorylate those amino acids. Our results identify multiple unique roles for Pkm2 and a novel function for Pkm1 in gene expression and chromatin regulation during myoblast differentiation.
    DOI:  https://doi.org/10.1101/2024.04.10.588959
  15. Int J Mol Sci. 2024 Apr 12. pii: 4265. [Epub ahead of print]25(8):
    Neutrophil Elastase Degrades Histone Deacetylases and Sirtuin 1 in Primary Human Monocyte Derived Macrophages.
    Shuo Zheng, Gamze B Bulut, Apparao B Kummarapurugu, Jonathan Ma, Judith A Voynow.
      Neutrophil elastase (NE) is taken up by macrophages, retains intracellular protease activity, and induces a pro-inflammatory phenotype. However, the mechanism of NE-induced pro-inflammatory polarization of macrophages is not well understood. We hypothesized that intracellular NE degrades histone deacetylases (HDAC) and Sirtuins, disrupting the balance of lysine acetylation and deacetylation and resulting in nuclear to cytoplasmic translocation of a major alarmin, High Mobility Group Box 1 (HMGB1), a pro-inflammatory response in macrophages. Human blood monocytes were obtained from healthy donors or from subjects with cystic fibrosis (CF) or chronic obstructive pulmonary disease (COPD). Monocytes were differentiated into blood monocyte derived macrophages (BMDMs) in vitro. Human BMDMs were exposed to NE or control vehicle, and the abundance of HDACs and Sirtuins was determined by Western blotting of total cell lysates or nuclear extracts or determined by ELISA. HDAC, Sirtuin, and Histone acetyltransferase (HAT) activities were measured. NE degraded most HDACs and Sirtuin (Sirt)1, resulting in decreased HDAC and sirtuin activities, with minimal change in HAT activity. We then evaluated whether the NE-induced loss of Sirt activity or loss of HDAC activities would alter the cellular localization of HMGB1. NE treatment or treatment with Trichostatin A (TSA), a global HDAC inhibitor, both increased HMGB1 translocation from the nucleus to the cytoplasm, consistent with HMGB1 activation. NE significantly degraded Class I and II HDAC family members and Sirt 1, which shifted BMDMs to a pro-inflammatory phenotype.
    Keywords:  COPD; HDACs; HMGB1; Sirtuin; cystic fibrosis; macrophage; neutrophil elastase
    DOI:  https://doi.org/10.3390/ijms25084265
  16. Int J Biol Macromol. 2024 Apr 22. pii: S0141-8130(24)02568-6. [Epub ahead of print] 131763
    Lysine acetylation of Hsp16.3: Effect on its structure, chaperone function and influence towards the growth of Mycobacterium tuberculosis.
    Subhashree Barik, Alok Kumar Panda, Viplov Kumar Biswas, Sheetal Das, Ayon Chakraborty, Shibangini Beura, Rahul Modak, Sunil Kumar Raghav, Rajiv K Kar, Ashis Biswas.
      Hsp16.3 plays a vital role in the slow growth of Mycobacterium tuberculosis via its chaperone function. Many secretory proteins, including Hsp16.3 undergo acetylation in vivo. Seven lysine (K) residues (K64, K78, K85, K114, K119, K132 and K136) in Hsp16.3 are acetylated inside pathogen. However, how lysine acetylation affects its structure, chaperone function and pathogen's growth is still elusive. We examined these aspects by executing in vitro chemical acetylation (acetic anhydride modification) and by utilizing a lysine acetylation mimic mutant (K64Q/K78Q/K85Q/K114Q/K119Q/K132Q/K136Q). Far- and near-UV CD measurements revealed that the chemically acetylated proteins(s) and acetylation mimic mutant has altered secondary and tertiary structure than unacetylated/wild-type protein. The chemical modification and acetylation mimic mutation also disrupted the oligomeric assembly, increased surface hydrophobicity and reduced stability of Hsp16.3, as revealed by GF-HPLC, 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid binding and urea denaturation experiments, respectively. These structural changes collectively led to an enhancement in chaperone function (aggregation and thermal inactivation prevention ability) of Hsp16.3. Moreover, when the H37Rv strain expressed the acetylation mimic mutant protein, its growth was slower in comparison to the strain expressing the wild-type/unacetylated Hsp16.3. Altogether, these findings indicated that lysine acetylation improves the chaperone function of Hsp16.3 which may influence pathogen's growth in host environment.
    Keywords:  Lysine acetylation; Molecular chaperone; Mycobacterium tuberculosis Hsp16.3; Small heat shock proteins (sHsps); Tuberculosis
    DOI:  https://doi.org/10.1016/j.ijbiomac.2024.131763
  17. Cancer Sci. 2024 Apr 23.
    USP3: Key deubiquitylation enzyme in human diseases.
    Hongyan Zhang, Wenjing Liu, Yingying Wu, Ceshi Chen.
      Ubiquitination and deubiquitylation are pivotal posttranslational modifications essential for regulating cellular protein homeostasis and are implicated in the development of human diseases. Ubiquitin-specific protease 3 (USP3), a member of the ubiquitin-specific protease family, serves as a key deubiquitylation enzyme, playing a critical role in diverse cellular processes including the DNA damage response, cell cycle regulation, carcinogenesis, tumor cell proliferation, migration, and invasion. Despite notable research efforts, our current understanding of the intricate and context-dependent regulatory networks governing USP3 remains incomplete. This review aims to comprehensively synthesize existing published works on USP3, elucidating its multifaceted roles, functions, and regulatory mechanisms, while offering insights for future investigations. By delving into the complexities of USP3, this review strives to provide a foundation for a more nuanced understanding of its specific roles in various cellular processes. Furthermore, the exploration of USP3's regulatory networks may uncover novel therapeutic strategies targeting this enzyme in diverse human diseases, thereby holding promising clinical implications. Overall, an in-depth comprehension of USP3's functions and regulatory pathways is crucial for advancing our knowledge and developing targeted therapeutic approaches for human diseases.
    Keywords:  DNA damage; USP3; cancer; deubiquitylation; posttranslation modification
    DOI:  https://doi.org/10.1111/cas.16178
  18. Nat Chem Biol. 2024 Apr 24.
    Structural basis for α-tubulin-specific and modification state-dependent glutamylation.
    Kishore K Mahalingan, Danielle A Grotjahn, Yan Li, Gabriel C Lander, Elena A Zehr, Antonina Roll-Mecak.
      Microtubules have spatiotemporally complex posttranslational modification patterns. Tubulin tyrosine ligase-like (TTLL) enzymes introduce the most prevalent modifications on α-tubulin and β-tubulin. How TTLLs specialize for specific substrate recognition and ultimately modification-pattern generation is largely unknown. TTLL6, a glutamylase implicated in ciliopathies, preferentially modifies tubulin α-tails in microtubules. Cryo-electron microscopy, kinetic analysis and single-molecule biochemistry reveal an unprecedented quadrivalent recognition that ensures simultaneous readout of microtubule geometry and posttranslational modification status. By binding to a β-tubulin subunit, TTLL6 modifies the α-tail of the longitudinally adjacent tubulin dimer. Spanning two tubulin dimers along and across protofilaments (PFs) ensures fidelity of recognition of both the α-tail and the microtubule. Moreover, TTLL6 reads out and is stimulated by glutamylation of the β-tail of the laterally adjacent tubulin dimer, mediating crosstalk between α-tail and β-tail. This positive feedback loop can generate localized microtubule glutamylation patterns. Our work uncovers general principles that generate tubulin chemical and topographic complexity.
    DOI:  https://doi.org/10.1038/s41589-024-01599-0
  19. FEBS Lett. 2024 Apr 21.
    Deacylases-structure, function, and relationship to diseases.
    Shuxian Wang, Xiaoke Xing, Jialin Ma, Sihao Zheng, Qibin Song, Pingfeng Zhang.
      Reversible S-acylation plays a pivotal role in various biological processes, modulating protein functions such as subcellular localization, protein stability/activity, and protein-protein interactions. These modifications are mediated by acyltransferases and deacylases, among which the most abundant modification is S-palmitoylation. Growing evidence has shown that this rivalrous pair of modifications, occurring in a reversible cycle, is essential for various biological functions. Aberrations in this process have been associated with various diseases, including cancer, neurological disorders, and immune diseases. This underscores the importance of studying enzymes involved in acylation and deacylation to gain further insights into disease pathogenesis and provide novel strategies for disease treatment. In this Review, we summarize our current understanding of the structure and physiological function of deacylases, highlighting their pivotal roles in pathology. Our aim is to provide insights for further clinical applications.
    Keywords:  ABHD family; APT1/2; PPT1/2; S‐acylation; deacylases
    DOI:  https://doi.org/10.1002/1873-3468.14885
  20. iScience. 2024 May 17. 27(5): 109678
    The acetylation of MDH1 and IDH1 is associated with energy metabolism in acute liver failure.
    Chunxia Shi, Yanqiong Zhang, Qian Chen, Yukun Wang, Danmei Zhang, Jin Guo, Qingqi Zhang, Wenbin Zhang, Zuojiong Gong.
      The liver is the main organ associated with metabolism. In our previous studies, we identified that the metabolic enzymes malate dehydrogenase 1 (MDH1) and isocitrate dehydrogenase 1 (IDH1) were differentially expressed in ALF. The aim of this study was to explore the changes in the acetylation of MDH1 and IDH1 and the therapeutic effect of histone deacetylase (HDAC) inhibitor in acute liver failure (ALF). Decreased levels of many metabolites were observed in ALF patients. MDH1 and IDH1 were decreased in the livers of ALF patients. The HDAC inhibitor ACY1215 improved the expression of MDH1 and IDH1 after treatment with MDH1-siRNA and IDH1-siRNA. Transfection with mutant plasmids and adeno-associated viruses, identified MDH1 K118 acetylation and IDH1 K93 acetylation as two important sites that regulate metabolism in vitro and in vivo.
    Keywords:  Hepatology; Human metabolism; Molecular biology
    DOI:  https://doi.org/10.1016/j.isci.2024.109678
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