bims-toxgon Biomed News
on Toxoplasma gondii metabolism
Issue of 2024‒07‒28
24 papers selected by
Lakesh Kumar, BITS Pilani
  1. Functional Characterization of Six Eukaryotic Translation Initiation Factors of Toxoplasma gondii Using the CRISPR-Cas9 System.
  2. Recent Advances in Toxoplasma gondii Infection and Toxoplasmosis.
  3. Mutual regulations between Toxoplasma gondii and type I interferon.
  4. γ-tubulin complex controls the nucleation of tubulin-based structures in Apicomplexa.
  5. Nuclear pyruvate dehydrogenase complex regulates histone acetylation and transcriptional regulation in the ethylene response.
  6. The Toxoplasma Effector GRA4 Hijacks Host TBK1 to Oppositely Regulate Anti-T. Gondii Immunity and Tumor Immunotherapy.
  7. Toxoplasma gondii suppress human cord blood cell differentiation to the NK cell population.
  8. Citrate metabolism controls the senescent microenvironment via the remodeling of pro-inflammatory enhancers.
  9. A Micronemal Protein, Scot1, Is Essential for Apicoplast Biogenesis and Liver Stage Development in Plasmodium berghei.
  10. Genetics of MDH in humans.
  11. SIRT1: a novel regulator in colorectal cancer.
  12. A Review of the Bromodomain and Extraterminal Domain Epigenetic Reader Proteins: Function on Virus Infection and Cancer.
  13. Seroprevalence and Association of Toxoplasma gondii with Bone Health in a Cohort of Osteopenia and Osteoporosis Patients.
  14. Roles of Lysine Methylation in Glucose and Lipid Metabolism: Functions, Regulatory Mechanisms, and Therapeutic Implications.
  15. Histone (de)acetylation in epigenetic regulation of Phytophthora pathobiology.
  16. General ADP-Ribosylation Mechanism Based on the Structure of ADP-Ribosyltransferase-Substrate Complexes.
  17. How mass spectrometry can be exploited to study AMPK.
  18. Automated Immunoprecipitation Workflow for Comprehensive Acetylome Analysis.
  19. SIRT5 mutants reveal the role of conserved asparagine and glutamine residues in the NAD+-binding pocket.
  20. Structural insights into autoinhibition and activation of defense-associated sirtuin protein.
  21. Targeting POLD1 to suppress the proliferation and migration of breast cancer MDA-MB-231 cell lines by downregulation of SIRT1.
  22. Lysine Methylation and Histone Modifications during Cold Stress of Insects: Freeze-Tolerant Eurosta solidaginis and Freeze-Avoiding Epiblema scudderiana.
  23. [Progress in research and application of the biotin ligase BirA and its mutants in pathogen-host interaction].
  24. Fluorogenic Rhodamine-Based Chemigenetic Biosensor for Monitoring Cellular NADPH Dynamics.
  1. Int J Mol Sci. 2024 Jul 17. pii: 7834. [Epub ahead of print]25(14):
    Functional Characterization of Six Eukaryotic Translation Initiation Factors of Toxoplasma gondii Using the CRISPR-Cas9 System.
    Yong-Jie Kou, Jin Gao, Rui Li, Zhi-Ya Ma, Hany M Elsheikha, Xiao-Jing Wu, Xiao-Nan Zheng, Meng Wang, Xing-Quan Zhu.
      Eukaryotic translation initiation factors (eIFs) are crucial for initiating protein translation and ensuring the correct assembly of mRNA-ribosomal subunit complexes. In this study, we investigated the effects of deleting six eIFs in the apicomplexan parasite Toxoplasma gondii using the CRISPR-Cas9 system. We determined the subcellular localization of these eIFs using C-terminal endogenous tagging and immunofluorescence analysis. Four eIFs (RH::315150-6HA, RH::286090-6HA, RH::249370-6HA, and RH::211410-6HA) were localized in the cytoplasm, while RH::224235-6HA was localized in the apicoplast. Additionally, RH::272640-6HA was found in both the basal complex and the cytoplasm of T. gondii. Functional characterization of the six RHΔeIFs strains was conducted using plaque assay, cell invasion assay, intracellular growth assay and egress assay in vitro, and virulence assay in mice. Disruption of five eIF genes (RHΔ315150, RHΔ272640, RHΔ249370, RHΔ211410, and RHΔ224235) did not affect the ability of the T. gondii RH strain to invade, replicate, form plaques and egress in vitro, or virulence in Kunming mice (p > 0.05). However, the RHΔ286090 strain showed slightly reduced invasion efficiency and virulence (p < 0.01) compared to the other five RHΔeIFs strains and the wild-type strain. The disruption of the TGGT1_286090 gene significantly impaired the ability of tachyzoites to differentiate into bradyzoites in both type I RH and type II Pru strains. These findings reveal that the eukaryotic translation initiation factor TGGT1_286090 is crucial for T. gondii bradyzoite differentiation and may serve as a potential target for drug development and an attenuated vaccine against T. gondii.
    Keywords:  CRISPR-Cas9; Toxoplasma gondii; differentiation; eukaryotic protein translation initiation factors
    DOI:  https://doi.org/10.3390/ijms25147834
  2. Trop Med Infect Dis. 2024 Jul 18. pii: 160. [Epub ahead of print]9(7):
    Recent Advances in Toxoplasma gondii Infection and Toxoplasmosis.
    Vinícius Longo Ribeiro Vilela, Thais Ferreira Feitosa.
      Toxoplasmosis, caused by the protozoan Toxoplasma gondii, affects nearly all warm-blooded animals, including humans, domestic animals, and both terrestrial and marine wildlife [...].
    DOI:  https://doi.org/10.3390/tropicalmed9070160
  3. Front Immunol. 2024 ;15 1428232
    Mutual regulations between Toxoplasma gondii and type I interferon.
    Lingling Song, Ruoyu Wang, Yuanyuan Cao, Li Yu.
      In the decades since the discovery, Type I interferon (IFN-I) has been intensively studied for their antiviral activity. However, increasing evidences suggest that it may also play an important role in the infection of Toxoplasma gondii, a model organism for intracellular parasites. Recent studies demonstrated that the induction of IFN-I by the parasite depends on cell type, strain genotype, and mouse strain. IFN-I can inhibit the proliferation of T. gondii, but few studies showed that it is beneficial to the growth of the parasite. Meanwhile, T. gondii also can secrete proteins that impact the pathway of IFN-I production and downstream induced interferon-stimulated genes (ISGs) regulation, thereby escaping immune destruction by the host. This article reviews the major findings and progress in the production, function, and regulation of IFN-I during T. gondii infection, to thoroughly understand the innate immune mechanism of T. gondii infection, which provides a new target for subsequent intervention and treatment.
    Keywords:  IFN-I; T.gondii; immune evasion; innate immunity; treatment
    DOI:  https://doi.org/10.3389/fimmu.2024.1428232
  4. Mol Biol Cell. 2024 Jul 24. mbcE24030100
    γ-tubulin complex controls the nucleation of tubulin-based structures in Apicomplexa.
    Romuald Haase, Annet Puthenpurackal, Bohumil Maco, Amandine Guérin, Dominique Soldati-Favre.
      Apicomplexan parasites rely on tubulin structures throughout their cell and life cycles, particularly in the polymerization of spindle microtubules to separate the replicated nucleus into daughter cells. Additionally, tubulin structures, including conoid and subpellicular microtubules, provide the necessary rigidity and structure for dissemination and host cell invasion. However, it is unclear whether these tubulin structures are nucleated via a highly conserved γ-tubulin complex or through a specific process unique to apicomplexans. This study demonstrates that Toxoplasma γ-tubulin is responsible for nucleating spindle microtubules, akin to higher eukaryotes, facilitating nucleus division in newly formed parasites. Interestingly, γ-tubulin colocalizes with nascent conoid and subpellicular microtubules during division, potentially nucleating these structures as well. Loss of γ-tubulin results in significant morphological defects due to impaired nucleus scission and the loss of conoid and subpellicular microtubule nucleation, crucial for parasite shape and rigidity. Additionally, the nucleation process of tubulin structures involves a concerted action of γ-tubulin and Gamma Tubulin Complex proteins (GCPs), recapitulating the localization and phenotype of γ-tubulin. This study also introduces new molecular markers for cytoskeletal structures and applies iterative expansion microscopy to reveal microtubule-based architecture in Cryptosporidium parvum sporozoites, further demonstrating the conserved localization and probable function of γ-tubulin in Cryptosporidium.
    DOI:  https://doi.org/10.1091/mbc.E24-03-0100
  5. Sci Adv. 2024 Jul 26. 10(30): eado2825
    Nuclear pyruvate dehydrogenase complex regulates histone acetylation and transcriptional regulation in the ethylene response.
    Zhengyao Shao, Liangqiao Bian, Shyon K Ahmadi, Tyler J Daniel, Miguel A Belmonte, Jackson G Burns, Prashanth Kotla, Yang Bi, Zhouxin Shen, Shou-Ling Xu, Zhi-Yong Wang, Steven P Briggs, Hong Qiao.
      Ethylene plays its essential roles in plant development, growth, and defense responses by controlling the transcriptional reprograming, in which EIN2-C-directed regulation of histone acetylation is the first key step for chromatin to perceive ethylene signaling. But how the nuclear acetyl coenzyme A (acetyl CoA) is produced to ensure the ethylene-mediated histone acetylation is unknown. Here we report that ethylene triggers the accumulation of the pyruvate dehydrogenase complex (PDC) in the nucleus to synthesize nuclear acetyl CoA to regulate ethylene response. PDC is identified as an EIN2-C nuclear partner, and ethylene triggers its nuclear accumulation. Mutations in PDC lead to an ethylene hyposensitivity that results from the reduction of histone acetylation and transcription activation. Enzymatically active nuclear PDC synthesizes nuclear acetyl CoA for EIN2-C-directed histone acetylation and transcription regulation. These findings uncover a mechanism by which PDC-EIN2 converges the mitochondrial enzyme-mediated nuclear acetyl CoA synthesis with epigenetic and transcriptional regulation for plant hormone response.
    DOI:  https://doi.org/10.1126/sciadv.ado2825
  6. Adv Sci (Weinh). 2024 Jun 21. e2400952
    The Toxoplasma Effector GRA4 Hijacks Host TBK1 to Oppositely Regulate Anti-T. Gondii Immunity and Tumor Immunotherapy.
    Zhiqiang Hu, Yufen Zhang, Yingchao Xie, Jianwu Yang, Haotian Tang, Bolin Fan, Ke Zeng, Zhongxin Han, Jiansen Lu, Huaji Jiang, Wenqiang Peng, Hongyu Li, Huadan Chen, Sha Wu, Bang Shen, Zhao-Rong Lun, Xiao Yu.
      Toxoplasma gondii (T. gondii)-associated polymorphic effector proteins are crucial in parasite development and regulating host anti-T. gondii immune responses. However, the mechanism remains obscure. Here, it is shown that Toxoplasma effector dense granules 4 (GRA4) restricts host IFN-I activation. Infection with Δgra4 mutant T. gondii strain induces stronger IFN-I responses and poses a severe threat to host health. Mechanistically, GRA4 binds to phosphorylated TBK1 to promote TRIM27-catalyzed K48-ubiquitination at Lys251/Lys372 residues, which enhances its recognition by autophagy receptor p62, ultimately leading to TBK1 autophagic degradation. Furthermore, an avirulent Δgra4 strain (ME49Δompdc/gra4) is constructed for tumor immunotherapy due to its ability to enhance IFN-I production. Earlier vaccination with ME49Δompdc/gra4 confers complete host resistance to the tumor compared with the classical ME49Δompdc treatment. Notably, ME49Δompdc/gra4 vaccination induces a specific CD64+MAR-1+CD11b+ dendritic cell subset, thereby enhancing T cell anti-tumor responses. Overall, these findings identify the negative role of T. gondii GRA4 in modulating host IFN-I signaling and suggest that GRA4 can be a potential target for the development of T. gondii vaccines and tumor immunotherapy.
    Keywords:  attenuated T. gondii; selective autophagy; toxoplasmosis; tumor therapy; type I interferon
    DOI:  https://doi.org/10.1002/advs.202400952
  7. Immun Inflamm Dis. 2024 Jun;12(6): e1329
    Toxoplasma gondii suppress human cord blood cell differentiation to the NK cell population.
    Sepideh Mahmoudzadeh, Khadijeh Dizaji Asl, Hojjatollah Nozad Charoudeh, Reza Rahbarghazi, Mahdi Ahmadi, Morteza Heidarzadeh, Adel Spotin, Ehsan Ahmadpour.
      BACKGROUND: Toxoplasma gondii is an obligate intracellular protozoan parasite that can invade all mammalian cells. It is well established that natural killer (NK) cells have critical protective roles in innate immunity during infections by intracellular pathogens. In the current study, we conducted an in vitro experiment to evaluate NK cell differentiation and activation from human umbilical cord blood mononuclear cells (UCB-MNCs) after infection with T. gondii tachyzoites.METHODS: UCB-MNCs were infected by fresh tachyzoites of type I (RH) or type II (PTG) strains of T. gondii pre-expanded in mesenchymal stem cells for 2 weeks in a medium enriched with stem cell factor, Flt3, IL-2, and IL-15. Flow cytometry analysis and western blot analysis were performed to measure the CD57+, CD56+, and Granzyme A (GZMA).
    RESULTS: Data revealed that incubation of UCB-MNCs with NK cell differentiation medium increased the CD57+, CD56+, and GZMA. UCB-MNCs cocultured with PTG tachyzoites showed a significant reduction of CD56+ and GZMA, but nonsignificant changes, in the levels of CD56+ compared to the control UCB-MNCs (p > .05). Noteworthy, 2-week culture of UCB-MNCs with type I (RH) tachyzoites significantly suppressed CD57+, CD56+, and GZMA, showing reduction of NK cell differentiation from cord blood cells.
    CONCLUSION: Our findings suggest that virulent T. gondii tachyzoites with cytopathic effects inhibit NK cell activation and eliminate innate immune responses during infection, and consequently enable the parasite to continue its survival in the host body.
    Keywords:  NK cells; Toxoplasma gondii; differentiation; functional activity; maturation; umbilical cord blood mononuclear cells
    DOI:  https://doi.org/10.1002/iid3.1329
  8. Cell Rep. 2024 Jul 17. pii: S2211-1247(24)00825-8. [Epub ahead of print] 114496
    Citrate metabolism controls the senescent microenvironment via the remodeling of pro-inflammatory enhancers.
    Kan Etoh, Hirotaka Araki, Tomoaki Koga, Yuko Hino, Kanji Kuribayashi, Shinjiro Hino, Mitsuyoshi Nakao.
      The senescent microenvironment and aged cells per se contribute to tissue remodeling, chronic inflammation, and age-associated dysfunction. However, the metabolic and epigenomic bases of the senescence-associated secretory phenotype (SASP) remain largely unknown. Here, we show that ATP-citrate lyase (ACLY), a key enzyme in acetyl-coenzyme A (CoA) synthesis, is essential for the pro-inflammatory SASP, independent of persistent growth arrest in senescent cells. Citrate-derived acetyl-CoA facilitates the action of SASP gene enhancers. ACLY-dependent de novo enhancers augment the recruitment of the chromatin reader BRD4, which causes SASP activation. Consistently, specific inhibitions of the ACLY-BRD4 axis suppress the STAT1-mediated interferon response, creating the pro-inflammatory microenvironment in senescent cells and tissues. Our results demonstrate that ACLY-dependent citrate metabolism represents a selective target for controlling SASP designed to promote healthy aging.
    Keywords:  ACLY; CP: Cell biology; CP: Metabolism; H3K27 acetylation; SASP; acetyl-CoA; citrate metabolism; senescence; senostatics
    DOI:  https://doi.org/10.1016/j.celrep.2024.114496
  9. ACS Infect Dis. 2024 Jul 22.
    A Micronemal Protein, Scot1, Is Essential for Apicoplast Biogenesis and Liver Stage Development in Plasmodium berghei.
    Ankit Ghosh, Akancha Mishra, Raksha Devi, Sunil Kumar Narwal, Nirdosh, Pratik Narain Srivastava, Satish Mishra.
      Plasmodium sporozoites invade hepatocytes, transform into liver stages, and replicate into thousands of merozoites that infect erythrocytes and cause malaria. Proteins secreted from micronemes play an essential role in hepatocyte invasion, and unneeded micronemes are subsequently discarded for replication. The liver-stage parasites are potent immunogens that prevent malarial infection. Late liver stage-arresting genetically attenuated parasites (GAPs) exhibit greater protective efficacy than early GAP. However, the number of late liver-stage GAPs for generating GAPs with multiple gene deletions is limited. Here, we identified Scot1 (Sporozoite Conserved Orthologous Transcript 1), which was previously shown to be upregulated in sporozoites, and by endogenous tagging with mCherry, we demonstrated that it is expressed in the sporozoite and liver stages in micronemes. Using targeted gene deletion in Plasmodium berghei, we showed that Scot1 is essential for late liver-stage development. Scot1 KO sporozoites grew normally into liver stages but failed to initiate blood-stage infection in mice due to impaired apicoplast biogenesis and merozoite formation. Bioinformatic studies suggested that Scot1 is a metal-small-molecule carrier protein. Remarkably, supplementation with metals in the culture of infected Scot1 KO cells did not rescue their phenotype. Immunization with Scot1 KO sporozoites in C57BL/6 mice confers protection against malaria via infection. These proof-of-concept studies will enable the generation of P. falciparum Scot1 mutants that could be exploited to generate GAP malaria vaccines.
    Keywords:  GAP; Plasmodium; liver stage; malaria; microneme; preerythrocytic; protection; sporozoite; vaccine
    DOI:  https://doi.org/10.1021/acsinfecdis.4c00362
  10. Essays Biochem. 2024 Jul 22. pii: EBC20230078. [Epub ahead of print]
    Genetics of MDH in humans.
    Adam Haberman, Celeste N Peterson.
      Malate dehydrogenase (MDH) performs key roles in metabolism, but little is known about its function specifically in human health and disease. In this minireview, we describe the incomplete state of our knowledge of human MDH genetics. Humans have three MDH genes with a total of four validated isoforms. MDH1 and MDH2 are widely expressed, while MDH1B is only expressed in a small subset of tissues. Many mutations in MDH1 and MDH2 have been identified in patients, but only a few have been studied to determine what symptoms they cause. MDH1 has been associated with cancer and a neurodevelopmental disorder. MDH2 has been associated with diabetes, neurodevelopmental disorders, and cancer.
    Keywords:  MDH; gene expression and regulation; mutation
    DOI:  https://doi.org/10.1042/EBC20230078
  11. Biomed Pharmacother. 2024 Jul 24. pii: S0753-3322(24)01060-6. [Epub ahead of print]178 117176
    SIRT1: a novel regulator in colorectal cancer.
    Weiwei Dong, Jinjing Lu, You Li, Juan Zeng, Xiaoyun Du, Ao Yu, Xuechan Zhao, Feng Chi, Zhuo Xi, Shuo Cao.
      The class-III histone deacetylase SIRT1 is the most extensively investigated sirtuin deacetylase. It is resistant to the broad deacetylase inhibitor trichostatin A and depends on oxidized nicotinamide adenine nucleotide (NAD+). SIRT1 plays a crucial role in the tumorigenesis of numerous types of cancers, including colorectal cancer (CRC). Accumulating evidence indicates that SIRT1 is a therapeutic target for CRC; however, the function and underlying mechanism of SIRT1 in CRC still need to be elucidated. Herein, we provide a detailed and updated review to illustrate that SIRT1 regulates many processes that go awry in CRC cells, such as apoptosis, autophagy, proliferation, migration, invasion, metastasis, oxidative stress, resistance to chemo-radio therapy, immune evasion, and metabolic reprogramming. Moreover, we closely link our review to the clinical practice of CRC treatment, summarizing the mechanisms and prospects of SIRT1 inhibitors in CRC therapy. SIRT1 inhibitors as monotherapy in CRC or in combination with chemotherapy, radiotherapy, and immune therapies are comprehensively discussed. From epigenetic regulation to its potential therapeutic effect, we hope to offer novel insights and a comprehensive understanding of SIRT1's role in CRC.
    Keywords:  Colorectal cancer (CRC); Epigenetics; Histone deacetylases; SIRT1
    DOI:  https://doi.org/10.1016/j.biopha.2024.117176
  12. Viruses. 2024 Jul 08. pii: 1096. [Epub ahead of print]16(7):
    A Review of the Bromodomain and Extraterminal Domain Epigenetic Reader Proteins: Function on Virus Infection and Cancer.
    Mengli Wu, Guiquan Guan, Hong Yin, Qingli Niu.
      The BET (bromodomain and extraterminal domain) family of proteins, particularly BRD4 (bromodomain-containing protein 4), plays a crucial role in transcription regulation and epigenetic mechanisms, impacting key cellular processes such as proliferation, differentiation, and the DNA damage response. BRD4, the most studied member of this family, binds to acetylated lysines on both histones and non-histone proteins, thereby regulating gene expression and influencing diverse cellular functions such as the cell cycle, tumorigenesis, and immune responses to viral infections. Given BRD4's involvement in these fundamental processes, it is implicated in various diseases, including cancer and inflammation, making it a promising target for therapeutic development. This review comprehensively explores the roles of the BET family in gene transcription, DNA damage response, and viral infection, discussing the potential of targeted small-molecule compounds and highlighting BET proteins as promising candidates for anticancer therapy.
    Keywords:  BET family; cancer; inhibitors; transcription; viral infection
    DOI:  https://doi.org/10.3390/v16071096
  13. Biomedicines. 2024 Jun 24. pii: 1400. [Epub ahead of print]12(7):
    Seroprevalence and Association of Toxoplasma gondii with Bone Health in a Cohort of Osteopenia and Osteoporosis Patients.
    Indulekha Karunakaran, Jayagopi Surendar, Pia Ransmann, Marius Brühl, Silvia Kowalski, Victoria Frische, Jamil Hmida, Sabine Nachtsheim, Achim Hoerauf, Dieter C Wirtz, Marc P Hübner, Andreas C Strauss, Frank A Schildberg.
      Considering the fact that Toxoplasma is a common parasite of humans and Toxoplasma bradyzoites can reside in skeletal muscle, T. gondii-mediated immune responses may modulate the progression and pathophysiology of another musculoskeletal disorder, osteoporosis. In the current study, we investigated the association of bone health and Toxoplasma gondii infection status. A total of 138 patients living in Germany with either osteopenia or osteoporosis were included in the study, and they were categorized into two groups, T. gondii uninfected (n = 74) and infected (n = 64), based on the presence of T. gondii-specific IgG antibodies. The demographic and clinical details of the study subjects were collected from the medical records. Logistic regression analysis was performed to delineate the association of bone health parameters with the infection status. The prevalence of toxoplasmosis was 46.4% in the study participants. The infected individuals with osteopenia and osteoporosis showed higher levels of mean spine and femoral T score, Z score, and bone mineral density (BMD), indicating improved bone health compared to the uninfected group. Logistic regression analysis showed that subjects with T. gondii infection displayed increased odds of having a higher mean femur T score, femur BMD, and femur Z score even after adjusting for age, creatinine, and urea levels. However, when the duration of drug intake for osteoporosis was taken into account, the association lost statistical significance. In summary, in this study, an improvement in osteopenia and osteoporosis was observed in Toxoplasma-infected patients, which may be partly due to the longer duration of drug intake for osteoporosis in the infected patient group.
    Keywords:  Toxoplasma gondii; bone health; musculoskeletal disease; osteopenia; osteoporosis; seroprevalence
    DOI:  https://doi.org/10.3390/biomedicines12071400
  14. Biomolecules. 2024 Jul 19. pii: 862. [Epub ahead of print]14(7):
    Roles of Lysine Methylation in Glucose and Lipid Metabolism: Functions, Regulatory Mechanisms, and Therapeutic Implications.
    Zhen Wang, Huadong Liu.
      Glucose and lipid metabolism are essential energy sources for the body. Dysregulation in these metabolic pathways is a significant risk factor for numerous acute and chronic diseases, including type 2 diabetes (T2DM), Alzheimer's disease (AD), obesity, and cancer. Post-translational modifications (PTMs), which regulate protein structure, localization, function, and activity, play a crucial role in managing cellular glucose and lipid metabolism. Among these PTMs, lysine methylation stands out as a key dynamic modification vital for the epigenetic regulation of gene transcription. Emerging evidence indicates that lysine methylation significantly impacts glucose and lipid metabolism by modifying key enzymes and proteins. This review summarizes the current understanding of lysine methylation's role and regulatory mechanisms in glucose and lipid metabolism. We highlight the involvement of methyltransferases (KMTs) and demethylases (KDMs) in generating abnormal methylation signals affecting these metabolic pathways. Additionally, we discuss the chemical biology and pharmacology of KMT and KDM inhibitors and targeted protein degraders, emphasizing their clinical implications for diseases such as diabetes, obesity, neurodegenerative disorders, and cancers. This review suggests that targeting lysine methylation in glucose and lipid metabolism could be an ideal therapeutic strategy for treating these diseases.
    Keywords:  glucose metabolism; lipid metabolism; lysine methylation
    DOI:  https://doi.org/10.3390/biom14070862
  15. Mol Plant Pathol. 2024 Jul;25(7): e13497
    Histone (de)acetylation in epigenetic regulation of Phytophthora pathobiology.
    Yufeng Guan, Joanna Gajewska, Jolanta Floryszak-Wieczorek, Umesh Kumar Tanwar, Ewa Sobieszczuk-Nowicka, Magdalena Arasimowicz-Jelonek.
      Phytophthora species are oomycetes that have evolved a broad spectrum of biological processes and improved strategies to cope with host and environmental challenges. A growing body of evidence indicates that the high pathogen plasticity is based on epigenetic regulation of gene expression linked to Phytophthora's rapid adjustment to endogenous cues and various stresses. As 5mC DNA methylation has not yet been identified in Phytophthora, the reversible processes of acetylation/deacetylation of histone proteins seem to play a pivotal role in the epigenetic control of gene expression in oomycetes. To explore this issue, we review the structure, diversity, and phylogeny of histone acetyltransferases (HATs) and histone deacetylases (HDACs) in six plant-damaging Phytophthora species: P. capsici, P. cinnamomi, P. infestans, P. parasitica, P. ramorum, and P. sojae. To further integrate and improve our understanding of the phylogenetic classification, evolutionary relationship, and functional characteristics, we supplement this review with a comprehensive view of HATs and HDACs using recent genome- and proteome-level databases. Finally, the potential functional role of transcriptional reprogramming mediated by epigenetic changes during Phytophthora species saprophytic and parasitic phases under nitro-oxidative stress is also briefly discussed.
    Keywords:  Phytophthora spp.; epigenetic modifications; histone acetyltransferases; histone deacetylases; nitro‐oxidative stress; oomycetes
    DOI:  https://doi.org/10.1111/mpp.13497
  16. Toxins (Basel). 2024 Jul 11. pii: 313. [Epub ahead of print]16(7):
    General ADP-Ribosylation Mechanism Based on the Structure of ADP-Ribosyltransferase-Substrate Complexes.
    Hideaki Tsuge, Noriyuki Habuka, Toru Yoshida.
      ADP-ribosylation is a ubiquitous modification of proteins and other targets, such as nucleic acids, that regulates various cellular functions in all kingdoms of life. Furthermore, these ADP-ribosyltransferases (ARTs) modify a variety of substrates and atoms. It has been almost 60 years since ADP-ribosylation was discovered. Various ART structures have been revealed with cofactors (NAD+ or NAD+ analog). However, we still do not know the molecular mechanisms of ART. It needs to be better understood how ART specifies the target amino acids or bases. For this purpose, more information is needed about the tripartite complex structures of ART, the cofactors, and the substrates. The tripartite complex is essential to understand the mechanism of ADP-ribosyltransferase. This review updates the general ADP-ribosylation mechanism based on ART tripartite complex structures.
    Keywords:  ADP-ribosylation; ADP-ribosyltransferase; complex; substrate recognition
    DOI:  https://doi.org/10.3390/toxins16070313
  17. Essays Biochem. 2024 Jul 26. pii: EBC20240009. [Epub ahead of print]
    How mass spectrometry can be exploited to study AMPK.
    Mark H Rider, Didier Vertommen, Manuel Johanns.
      AMP-activated protein kinase (AMPK) is a key regulator of metabolism and a recognised target for the treatment of metabolic diseases such as Type 2 diabetes (T2D). Here, we review how mass spectrometry (MS) can be used to study short-term control by AMPK via protein phosphorylation and long-term control due to changes in protein expression. We discuss how MS can quantify AMPK subunit levels in tissues from different species. We propose hydrogen-deuterium exchange (HDX)-MS to investigate molecular mechanisms of AMPK activation and thermoproteomic profiling (TPP) to assess off-target effects of pharmacological AMPK activators/inhibitors. Lastly, because large MS data sets are generated, we consider different approaches that can be used for their interpretation.
    Keywords:  AMPK; Phosphoproteomics; mass spectrometry; proteomics
    DOI:  https://doi.org/10.1042/EBC20240009
  18. Methods Mol Biol. 2024 ;2823 173-191
    Automated Immunoprecipitation Workflow for Comprehensive Acetylome Analysis.
    Marina A Gritsenko, Chia-Feng Tsai, Hyeyoon Kim, Tao Liu.
      Immunoprecipitation is one of the most effective methods for enrichment of lysine-acetylated peptides for comprehensive acetylome analysis using mass spectrometry. Manual acetyl peptide enrichment method using non-conjugated antibodies and agarose beads has been developed and applied in various studies. However, it is time-consuming and can introduce contaminants and variability that leads to potential sample loss and decreased sensitivity and robustness of the analysis. Here we describe a fast, automated enrichment protocol that enables reproducible and comprehensive acetylome analysis using a magnetic bead-based immunoprecipitation reagent.
    Keywords:   Acetyl peptide enrichment; Acetylome; Automation; Immunoprecipitation; Magnetic beads; Mass spectrometry; Post-translational modification; Proteomics; Lysine acetylation
    DOI:  https://doi.org/10.1007/978-1-0716-3922-1_12
  19. FEBS Lett. 2024 Jun 20.
    SIRT5 mutants reveal the role of conserved asparagine and glutamine residues in the NAD+-binding pocket.
    Takeshi Yokoyama, Yuki Takayama, Mineyuki Mizuguchi, Yuko Nabeshima, Katsuhiro Kusaka.
      SIRT5, one of the mammalian sirtuins, specifically recognizes succinyl-lysine residues on proteins and catalyzes the desuccinylation reaction. In this study, we characterized SIRT5 mutants with hydrophobic amino acid substitutions at Q140 and N141, in addition to the catalytic residue H158, known as an active site residue, by the Michaelis-Menten analysis and X-ray crystallography. Kinetic analysis showed that the catalytic efficiency (kcat/Km) of the Q140L and N141V mutants decreased to 0.02 times and 0.0038 times that of the wild-type SIRT5, respectively, with the activity of the N141V mutant becoming comparable to that of the H158M mutant. Our findings indicate that N141 contributes significantly to the desuccinylation reaction.
    Keywords:  SIRT5; desuccinylation; protein crystallography; proton transfer; steady‐state kinetics
    DOI:  https://doi.org/10.1002/1873-3468.14961
  20. Int J Biol Macromol. 2024 Jul 24. pii: S0141-8130(24)04950-X. [Epub ahead of print] 134145
    Structural insights into autoinhibition and activation of defense-associated sirtuin protein.
    Xu Yang, Yiqun Wang, Jianting Zheng.
      Bacterial defense-associated sirtuin 2 (DSR2) proteins harbor an N-terminal sirtuin (SIR2) domain degrading NAD+. DSR2 from Bacillus subtilis 29R is autoinhibited and unable to hydrolyze NAD+ in the absence of phage infection. A tail tube protein (TTP) of phage SPR activates the DSR2 while a DSR2-inhibiting protein of phage SPbeta, known as DSAD1 (DSR anti-defense 1), inactivates the DSR2. Although DSR2 structures in complexed with TTP and DSAD1, respectively, have been reported recently, the autoinhibition and activation mechanisms remain incompletely understood. Here, we present cryo-electron microscopy structures of the DSR2-NAD+ complex in autoinhibited state and the in vitro assembled DSR2-TFD (TTP tube-forming domain) complex in activated state. The DSR2-NAD+ complex reveals that the autoinhibited DSR2 assembles into an inactive tetramer, binding NAD+ through a distinct pocket situated outside active site. Binding of TFD into cavities within the sensor domains of DSR2 triggers a conformational change in SIR2 regions, activating its NADase activity, whereas the TTP β-sandwich domain (BSD) is flexible and does not contribute to the activation process. The activated form of DSR2 exists as tetramers and dimers, with the tetramers exhibiting more NADase activity. Overall, our results extend the current understanding of autoinhibition and activation of DSR2 immune proteins.
    Keywords:  DSR2; NADase activity; SIR2
    DOI:  https://doi.org/10.1016/j.ijbiomac.2024.134145
  21. Toxicol Res (Camb). 2024 Aug;13(4): tfae111
    Targeting POLD1 to suppress the proliferation and migration of breast cancer MDA-MB-231 cell lines by downregulation of SIRT1.
    Areege Ibrahim Salih, Basma Talib Al-Sudani, Bahir Abdul-Razzaq Mshimesh.
      Background: The resistant and aggressive nature of triple-negative breast cancer (TNBC) renders it mostly incurable even following extensive multimodal treatment. Therefore, more studies are required to understand the underlying molecular mechanisms of its pathogenesis. SIRT1 is a class III histone deacetylase NAD + -dependent enzyme that is interlinked in tumor progression, apoptosis, metastasis, and other mechanisms of tumorigenesis, while DNA polymerase delta 1 (POLD1) functions as a gene coding for p125, which plays an important role in genome stability and DNA replication.Objective: We aimed to investigate the downstream signaling pathway of EX-527, a potent and selective SIRT1 inhibitor, in MDA-MB-231 breast cancer cell lines, and the crosstalk between SIRT1 and POLD1, which is essential for the activities of polymerase δ.
    Methods: The antiproliferative and apoptotic effects of EX-527 on MDA-MB-231 cells were assessed by MTT and annexin V/PI double staining assays. Migration and invasion activity of MDA-MB-231 cells were assessed by wound-healing scratch and transwell assays. Protein expressions were examined using Western Blot analysis.
    Results: MDA-MB-231 cells treatment with IC50 values of 45.3 μM EX-527 significantly suppressed cell proliferation and induced apoptosis by down-regulating SIRT1. Also, it significantly repressed migration and invasion of MDA-MB-231 cells as evaluated by wound healing and transwell invasion assays. Western blot results showed that decreased expression of SIRT1 is positively correlated with expression of p53 along with down-regulating POLD1.
    Conclusion: SIRT1 could have an oncogenic role in breast cancer development and progression via activating POLD1. These conclusions present new insights into the underlying mechanisms of TNBC.
    Keywords:  Breast cancer; EX-527; MDA-MB-231; POLD1; SIRT1 inhibitor
    DOI:  https://doi.org/10.1093/toxres/tfae111
  22. Insects. 2024 Jul 04. pii: 498. [Epub ahead of print]15(7):
    Lysine Methylation and Histone Modifications during Cold Stress of Insects: Freeze-Tolerant Eurosta solidaginis and Freeze-Avoiding Epiblema scudderiana.
    Zhijun Yu, Tingwei Pei, Han Wang, Chunyuan Wang, Jingze Liu, Kenneth B Storey.
      Overwintering survival by insects, whether of the freeze-tolerant or freeze-avoiding types, is typically associated with a strong suppression of metabolic rate (e.g., entry into diapause) that involves the differential expression of many genes with regulation at the transcriptional, translational or post-translational levels. Epigenetic modifications have been suggested to play a vital role in regulating cold responses of insects. However, knowledge of the roles of epigenetic mechanisms in modulating gene expression for winter survival of the larvae of two goldenrod gall formers, the freeze-tolerant dipteran Eurosta solidaginis and the freeze-avoiding lepidopteran Epiblema scudderiana, remain unknown. The current study evaluates the role of cold-induced lysine methylation and histone modifications, with enzymes of lysine methylation (SETD8, SETD7, SUV39H1, SMYD2 and ASH2L), as well as relative levels of histone H3 acetylation (H3K9ac, H3K18ac, H3K27ac, H3K56ac) and methylation (H3K4me1, H3K9me3, H3K36me2) examined in two insects. Significant (p < 0.05) reductions were observed in most of the targets of histone methylation/acetylation for decreasing temperatures of Ep. scudderiana larvae, whereas selected histone methylation/acetylation targets were conversely elevated (p < 0.05) in E. solidaginis, particularly under conditions of 5 °C for 4 h. Histone H3 expression was found to be variable without statistical differences in larval goldenrod gall moths and gall flies. These results provide basic information on the patterns of epigenetic regulation involved in insect cold hardiness.
    Keywords:  cold stress; diapause; epigenetics; histone acetylation; histone methylation
    DOI:  https://doi.org/10.3390/insects15070498
  23. Sheng Wu Gong Cheng Xue Bao. 2024 Jul 25. 40(7): 1981-1996
    [Progress in research and application of the biotin ligase BirA and its mutants in pathogen-host interaction].
    Hanyu Zhang, Pengfei Li, Zheyu Liao, Mengjia Zhang, Yumei Sun, Min Zhang, Qigai He, Wentao Li.
      Proteins serve as the primary executors of cellular activities in organisms, and thus investigating the subcellular localization and interactions of proteins is crucial for understanding protein functions and elucidating the molecular mechanisms in organisms. Proximity labeling is a recently developed effective method for detecting protein-protein interactions in live cells. Compared with the conventional methods for studying protein-protein interactions, proximity labeling demonstrates high sensitivity, strong specificity, and low background and is widely employed in the research of protein-protein interactions between pathogens and hosts. This article reviews the recent progress in the development and applications of the biotin ligase BirA and its mutants and elucidates the functioning principles of several classical biotin ligases. This review aims to clarify the role of proximity labeling based on BirA and its mutants in identifying protein-protein interactions between pathogens and hosts.
    Keywords:  BirA; biotin; interaction; protein; proximity labeling
    DOI:  https://doi.org/10.13345/j.cjb.230855
  24. J Am Chem Soc. 2024 Jul 22.
    Fluorogenic Rhodamine-Based Chemigenetic Biosensor for Monitoring Cellular NADPH Dynamics.
    Huimin Chang, Simon Clemens, Pingting Gao, Quanlin Li, Hanqing Zhao, Lehua Wang, Jingye Zhang, Pinghong Zhou, Kai Johnsson, Lu Wang.
      Ratiometric biosensors employing Förster Resonance Energy Transfer (FRET) enable the real-time tracking of metabolite dynamics. Here, we introduce an approach for generating a FRET-based biosensor in which changes in apparent FRET efficiency rely on the analyte-controlled fluorogenicity of a rhodamine rather than the commonly used distance change between donor-acceptor fluorophores. Our fluorogenic, rhodamine-based, chemigenetic biosensor (FOCS) relies on a synthetic, protein-tethered FRET probe, in which the rhodamine acting as the FRET acceptor switches in an analyte-dependent manner from a dark to a fluorescent state. This allows ratiometric sensing of the analyte concentration. We use this approach to generate a chemigenetic biosensor for nicotinamide adenine dinucleotide phosphate (NADPH). FOCS-NADPH exhibits a rapid and reversible response toward NAPDH with a good dynamic range, selectivity, and pH insensitivity. FOCS-NADPH allows real-time monitoring of cytosolic NADPH fluctuations in live cells during oxidative stress or after drug exposure. We furthermore used FOCS-NADPH to investigate NADPH homeostasis regulation through the pentose phosphate pathway of glucose metabolism. FOCS-NADPH is a powerful tool for studying NADPH metabolism and serves as a blueprint for the development of future fluorescent biosensors.
    DOI:  https://doi.org/10.1021/jacs.3c13137
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