bims-toxgon 2024-06-30 papers

bims-toxgon

Biomed News

on Toxoplasma gondii metabolism

Issue of 2024‒06‒30
25 papers selected by
Lakesh Kumar, BITS Pilani

Malate dehydrogenase in parasitic protozoans: roles in metabolism and potential therapeutic applications.
GRA47 is important for the morphology and permeability of the parasitophorous vacuole in Toxoplasma gondii.
Protective Efficacy of a Novel DNA Vaccine with a CL264 Molecular Adjuvant against Toxoplasma gondii in a Murine Model.
Efficacy of the bumped kinase inhibitor BKI-1708 against the cyst-forming apicomplexan parasites Toxoplasma gondii and Neospora caninum in vitro and in experimentally infected mice.
Brain -cyst-driven genes expression in Toxoplasma Gondii Tehran strain: a parasitic-immunogenicity assessment by dint of RNA-Seq.
Activation loop phosphorylation and cGMP saturation of PKG regulate egress of malaria parasites.
Mammalian placental explants: A tool for studying host-parasite interactions and placental biology.
Early immune response to Toxoplasma gondii lineage III isolates of different virulence phenotype.
Effect of 3-nitropropionic acid on sirtuin gene expression in Sirt3 deficient mice.
Histone deacetylases and inhibitors in diabetes mellitus and its complications.
SIRT1 signaling pathways in sarcopenia: Novel mechanisms and potential therapeutic targets.
Sirtuin 3 in renal diseases and aging: From mechanisms to potential therapies.
Elucidating the Unconventional Binding Mode of a DNA-Encoded Library Hit Provides a Blueprint for Sirtuin 6 Inhibitor Development.
Sirtulin-Ypk1 regulation axis governs the TOR signaling pathway and fungal pathogenicity in Cryptococcus neoformans.
Versatile JMJD proteins: juggling histones and much more.
Resveratrol Induces Myotube Development by Altering Circadian Metabolism via the SIRT1-AMPK-PP2A Axis.
Replenishment of TCA cycle intermediates and long-noncoding RNAs regulation in breast cancer.
Lactate transported by MCT1 plays an active role in promoting mitochondrial biogenesis and enhancing TCA flux in skeletal muscle.
Quantitative analysis of the lysine acetylome reveals the role of SIRT3-mediated HSP60 deacetylation in suppressing intracellular Mycobacterium tuberculosis survival.
A homogeneous time-resolved fluorescence screen to identify SIRT2 deacetylase and defatty-acylase inhibitors.
Dynamic Alterations in Acetylation and Modulation of Histone Deacetylase Expression Evident in the Dentine-Pulp Complex during Dentinogenesis.
The role of sirtuins in intervertebral disc degeneration: Mechanisms and therapeutic potential.
Histone H3 N-Terminal Lysine Acetylation Governs Fungal Growth, Conidiation, and Pathogenicity through Regulating Gene Expression in Fusarium pseudograminearum.
Differentiating human phospholipase A2's activity toward phosphatidylinositol, phosphatidylinositol phosphate and phosphatidylinositol bisphosphate.
Plasmodium falciparum artemisinin resistance: something gained in translation.

Essays Biochem. 2024 Jun 28. pii: EBC20230075. [Epub ahead of print]

Malate dehydrogenase in parasitic protozoans: roles in metabolism and potential therapeutic applications.

Amy L Springer, Swati Agrawal, Eric P Chang.

  The role of malate dehydrogenase (MDH) in the metabolism of various medically significant protozoan parasites is reviewed. MDH is an NADH-dependent oxidoreductase that catalyzes interconversion between oxaloacetate and malate, provides metabolic intermediates for both catabolic and anabolic pathways, and can contribute to NAD+/NADH balance in multiple cellular compartments. MDH is present in nearly all organisms; isoforms of MDH from apicomplexans (Plasmodium falciparum, Toxoplasma gondii, Cryptosporidium spp.), trypanosomatids (Trypanosoma brucei, T. cruzi) and anaerobic protozoans (Trichomonas vaginalis, Giardia duodenalis) are presented here. Many parasitic species have complex life cycles and depend on the environment of their hosts for carbon sources and other nutrients. Metabolic plasticity is crucial to parasite transition between host environments; thus, the regulation of metabolic processes is an important area to explore for therapeutic intervention. Common themes in protozoan parasite metabolism include emphasis on glycolytic catabolism, substrate-level phosphorylation, non-traditional uses of common pathways like tricarboxylic acid cycle and adapted or reduced mitochondria-like organelles. We describe the roles of MDH isoforms in these pathways, discuss unusual structural or functional features of these isoforms relevant to activity or drug targeting, and review current studies exploring the therapeutic potential of MDH and related genes. These studies show that MDH activity has important roles in many metabolic pathways, and thus in the metabolic transitions of protozoan parasites needed for success as pathogens.

Keywords:  Apicomplexan; Kinetoplastid; MDH; parasitic protozoa

DOI:  https://doi.org/10.1042/EBC20230075
Int J Parasitol. 2024 Jun 25. pii: S0020-7519(24)00135-8. [Epub ahead of print]

GRA47 is important for the morphology and permeability of the parasitophorous vacuole in Toxoplasma gondii.

Xiao-Nan Zheng, Ting-Ting Li, Hany M Elsheikha, Meng Wang, Li-Xiu Sun, Xiao-Jing Wu, Bao-Quan Fu, Xing-Quan Zhu, Jin-Lei Wang.

  Establishing an intact intracellular parasitophorous vacuole (PV) that enables efficient nutrient uptake and protein trafficking is essential for the survival and proliferation of Toxoplasma gondii. Although the PV membrane (PVM)-localized dense granule protein 17 (GRA17) and GRA23 mediate the permeability of the PVM to small molecules, including nutrient uptake and excretion of metabolic by-products, the molecular mechanism by which T. gondii acquires nutrients remains unclear. In this study, we showed that the secreted protein GRA47 contributed to normal PV morphology, PVM permeability to small molecules, growth, and virulence in T. gondii. Co-immunoprecipitation analysis demonstrated potential interaction of GRA47 with GRA72, and the loss of GRA72 affected PV morphology, parasite growth and infectivity. To investigate the biological relationship among GRA47, GRA72, GRA17 and GRA23, attempts were made to construct strains with double gene deletion and overexpressing strains. Only Δgra23Δgra72 was successfully constructed. This strain exhibited a significant increase in the proportion of aberrant PVs compared with the Δgra23 strain. Overexpressing one of the three related GRAs partially rescued PVs with aberrant morphology in Δgra47, Δgra72 and Δgra17, while the expression of the Plasmodium falciparum PVM protein PfExp2, an ortholog of GRA17 and GRA23, fully rescued the PV morphological defect in all three Δgra strains. These results suggest that these three GRA proteins may not be functionally redundant but rather work in different ways to regulate nutrient acquisition. These findings highlight the versatility of the nutrient uptake mechanisms in T. gondii, which may contribute to the parasite's remarkable ability to grow in different cellular niches in a very broad range of hosts.

Keywords:  Dense granule proteins; Nutrient uptake; PVM permeability; Toxoplasma gondii; Virulence

DOI:  https://doi.org/10.1016/j.ijpara.2024.06.003
Vaccines (Basel). 2024 May 25. pii: 577. [Epub ahead of print]12(6):

Protective Efficacy of a Novel DNA Vaccine with a CL264 Molecular Adjuvant against Toxoplasma gondii in a Murine Model.

Kunping Ju, Yunnan Zhang, Zhaolin Xu, Lingyu Li, Xiaoyan Zhao, Huaiyu Zhou.

  Toxoplasmosis is a significant global zoonosis with devastating impacts, and an effective vaccine against toxoplasmosis for humans has not yet been developed. In this study, we designed and formulated a novel DNA vaccine encoding the inhibitor of STAT1 transcriptional activity (IST) of T. gondii utilizing the eukaryotic expression vector pEGFP-N1 for the first time, with CL264 being a molecular adjuvant. Following intramuscular injection of the vaccine into mice, the levels of antibodies and cytokines were assessed to evaluate the immune response. Additionally, mice were challenged with highly virulent RH-strain tachyzoites of T. gondii, and their survival time was observed. The results show that the levels of IgG in serum, the ratio of IgG2a/IgG1 and the levels of IFN-γ in splenocytes of mice were significantly higher in the pEGFP-TgIST group and the pEGFP-TgIST + CL264 group than in the control group. In addition, the proportion of CD4+/CD8+ T cells was higher in mice immunized with either the pEGFP-TgIST group (p < 0.001) or the pEGFP-TgIST + CL264 group (p < 0.05) compared to the three control groups. Notably, TgIST-immunized mice exhibited prolonged survival times after T. gondii RH strain infection (p < 0.05). Our findings collectively demonstrate that the TgIST DNA vaccine elicits a significant humoral and cellular immune response and offers partial protection against acute T. gondii infection in the immunized mice, which suggests that TgIST holds potential as a candidate for further development as a DNA vaccine.

Keywords:  DNA vaccine; IST; Toxoplasma gondii; adjuvant; immunity

DOI:  https://doi.org/10.3390/vaccines12060577
Int J Parasitol Drugs Drug Resist. 2024 Jun 19. pii: S2211-3207(24)00034-4. [Epub ahead of print]25 100553

Efficacy of the bumped kinase inhibitor BKI-1708 against the cyst-forming apicomplexan parasites Toxoplasma gondii and Neospora caninum in vitro and in experimentally infected mice.

Maria Cristina Ferreira de Sousa, Dennis Imhof, Kai Pascal Alexander Hänggeli, Ryan Choi, Matthew A Hulverson, Samuel L M Arnold, Wesley C Van Voorhis, Erkang Fan, Sánchez-Sánchez Roberto, Luis M Ortega-Mora, Andrew Hemphill.

  Toxoplasma gondii and Neospora caninum are major worldwide morbidity-causing pathogens. Bumped kinase inhibitors (BKIs) are a compound class that has been optimized to target the apicomplexan calcium-dependent protein kinase 1 (CDPK1) - and several members of this class have proven to be safe and highly active in vitro and in vivo. BKI-1708 is based on a 5-aminopyrazole-4-carboxamide scaffold, and exhibited in vitro IC50 values of 120 nM for T. gondii and 480 nM for N. caninum β-galactosidase expressing strains, and did not affect human foreskin fibroblast (HFF) viability at concentrations up to 25 μM. Electron microscopy established that exposure of tachyzoite-infected fibroblasts to 2.5 μM BKI-1708 in vitro induced the formation of multinucleated schizont-like complexes (MNCs), characterized by continued nuclear division and harboring newly formed intracellular zoites that lack the outer plasma membrane. These zoites were unable to finalize cytokinesis to form infective tachyzoites. BKI-1708 did not affect zebrafish (Danio rerio) embryo development during the first 96 h following egg hatching at concentrations up to 2 μM. Treatments of mice with BKI-1708 at 20 mg/kg/day during five consecutive days resulted in drug plasma levels ranging from 0.14 to 4.95 μM. In vivo efficacy of BKI-1708 was evaluated by oral application of 20 mg/kg/day from day 9-13 of pregnancy in mice experimentally infected with N. caninum (NcSpain-7) tachyzoites or T. gondii (TgShSp1) oocysts. This resulted in significantly decreased cerebral parasite loads and reduced vertical transmission in both models without drug-induced pregnancy interference.

Keywords:  Drug treatment; Electron microscopy; In vitro culture; In vivo efficacy; Mouse model; Neospora; PCR; Toxoplasma

DOI:  https://doi.org/10.1016/j.ijpddr.2024.100553
Vet Res Commun. 2024 Jun 25.

Brain -cyst-driven genes expression in Toxoplasma Gondii Tehran strain: a parasitic-immunogenicity assessment by dint of RNA-Seq.

Marzieh Asadi, Zahra Babaei, Ali Afgar, Mohammad Hossein Banabazi, Naser ZiaAli, Ahmad Daryani, Ehsan Aghajani, Milad Mahdavi, Mohamadreza Attari, Farzaneh Zarrinkar.

  Toxoplasma gondii (T. gondii) is an obligate intracellular parasite of warm-blooded vertebrates. At present, High-throughput RNA sequencing analysis have made it possible to determine the role of effective genes in host immune response. The aim of the present study is to global transcriptome analysis of the brain of mice infected with T. gondii Tehran strain for the first time and also to evaluate the expression of effective genes in the chronic form of infection. RNA was extracted from the samples and the library was prepared and sequenced using the IlluminaNovaSeq 6000 system. After analyzing gene expression changes, the results were confirmed by real-time method. We found 125 genes that were significantly differentially expressed between infected and non-infected samples (p < 0.0005). Gene ontology analysis revealed that the expression of many genes is critical for pathways such as T cell receptor signaling pathway, Natural Killer cell mediated cytotoxicity, Lysosome and Apoptosis of the host. As infection with Tehran strain leads to chronic infection in mice, therefore, we investigated the genes effective in creating the chronic form of Toxoplasma infection. The comparative analysis of genes showed increases in the expression of genes ctla4, ccl4, cd3e, c3, lcn2, gbp5, usp18, cyba, tap1 and samhd1 in the in the infected sample, which highlights their role in causing chronic infection. RNA-seq provides a valuable tool for analyzing host transcriptomes, better understanding the parasite-host interaction, and developing future drug and vaccine targets.

Keywords:   Toxoplasma gondii ; Chronic infection; Immunogenicity; RNA-seq

DOI:  https://doi.org/10.1007/s11259-023-10241-8
PLoS Pathog. 2024 Jun 27. 20(6): e1012360

Activation loop phosphorylation and cGMP saturation of PKG regulate egress of malaria parasites.

Konstantinos Koussis, Silvia Haase, Chrislaine Withers-Martinez, Helen R Flynn, Simone Kunzelmann, Evangelos Christodoulou, Fairouz Ibrahim, Mark Skehel, David A Baker, Michael J Blackman.

The cGMP-dependent protein kinase (PKG) is the sole cGMP sensor in malaria parasites, acting as an essential signalling hub to govern key developmental processes throughout the parasite life cycle. Despite the importance of PKG in the clinically relevant asexual blood stages, many aspects of malarial PKG regulation, including the importance of phosphorylation, remain poorly understood. Here we use genetic and biochemical approaches to show that reduced cGMP binding to cyclic nucleotide binding domain B does not affect in vitro kinase activity but prevents parasite egress. Similarly, we show that phosphorylation of a key threonine residue (T695) in the activation loop is dispensable for kinase activity in vitro but is essential for in vivo PKG function, with loss of T695 phosphorylation leading to aberrant phosphorylation events across the parasite proteome and changes to the substrate specificity of PKG. Our findings indicate that Plasmodium PKG is uniquely regulated to transduce signals crucial for malaria parasite development.

DOI: https://doi.org/10.1371/journal.ppat.1012360
Placenta. 2024 Jun 19. pii: S0143-4004(24)00291-1. [Epub ahead of print]

Mammalian placental explants: A tool for studying host-parasite interactions and placental biology.

Christian Castillo, Cintia Díaz-Luján, Ana Liempi, Ricardo Fretes, Ulrike Kemmerling.

  The placenta plays a critical role in host-pathogen interactions. Thus, ex vivo infection of mammalian placental explants is an excellent and simple method to study the mechanisms of cellular and tissue invasion by different pathogens in different mammalian species. These explants can be maintained in culture for several days, preserving the tissue architecture and resembling in-utero conditions under more physiological conditions than their isolated counterparts in isolated cell culture models. In addition, placental explants not only allow us to study how the placenta responds and defends itself against various infections but also provide a versatile platform for advancing our understanding of placental biology and the immune response. Furthermore, they serve as powerful tools for drug discovery, facilitating the screening of potential therapeutics for placental infections and for the identification of diagnostic markers. This review highlights the utility of mammalian placental explants in studying the host-pathogen interaction of two relevant protozoan parasites, Trypanosoma cruzi, the causative agent of Chagas disease, and Toxoplasma gondii, the etiological agent of Toxoplasmosis. Here, we discuss the different methodologies and technical aspects of the model, as well as the effect of both parasites on placental responses in human, canine, and ovine explants.

Keywords:  Host-pathogen interactions; Parasite infection; Placenta; Tissue explants; Toxoplasma gondii; Trypanosoma cruzi

DOI:  https://doi.org/10.1016/j.placenta.2024.06.016
Front Cell Infect Microbiol. 2024 ;14 1414067

Early immune response to Toxoplasma gondii lineage III isolates of different virulence phenotype.

Aleksandra Uzelac, Ivana Klun, Olgica Djurković-Djaković.

  Introduction: Toxoplasma gondii is an intracellular parasite of importance to human and veterinary health. The structure and diversity of the genotype population of T. gondii varies considerably with respect to geography, but three lineages, type I, II and III, are distributed globally. Lineage III genotypes are the least well characterized in terms of biology, host immunity and virulence. Once a host is infected with T.gondii, innate immune mechanisms are engaged to reduce the parasite burden in tissues and create a pro-inflammatory environment in which the TH1 response develops to ensure survival. This study investigated the early cellular immune response of Swiss-Webster mice post intraperitoneal infection with 10 tachyzoites of four distinct non-clonal genotypes of lineage III and a local isolate of ToxoDB#1. The virulence phenotype, cumulative mortality (CM) and allele profiles of ROP5, ROP16, ROP18 and GRA15 were published previously.Methods: Parasite dissemination in different tissues was analyzed by real-time PCR and relative expression levels of IFNγ, IL12-p40, IL-10 and TBX21 in the cervical lymph nodes (CLN), brain and spleen were calculated using the ΔΔCt method. Stage conversion was determined by detection of the BAG1 transcript in the brain.
Results: Tissue dissemination depends on the virulence phenotype but not CM, while the TBX21 and cytokine levels and kinetics correlate better with CM than virulence phenotype. The earliest detection of BAG1 was seven days post infection. Only infection with the genotype of high CM (69.4%) was associated with high T-bet levels in the CLN 24 h and high systemic IFNγ expression which was sustained over the first week, while infection with genotypes of lower CM (38.8%, 10.7% and 6.8%) is characterized by down-regulation and/or low systemic levels of IFNγ. The response intensity, as assessed by cytokine levels, to the genotype of high CM wanes over time, while it increases gradually to genotypes of lower CM.
Discussion: The results point to the conclusion that the immune response is not correlated with the virulence phenotype and/or allele profile, but an early onset, intense pro-inflammatory response is characteristic of genotypes with high CM. Additionally, high IFNγ level in the brain may hamper stage conversion.

Keywords:  Toxoplasma gondii; cytokines; genotypes; immune response; virulence

DOI:  https://doi.org/10.3389/fcimb.2024.1414067
Neurosci Lett. 2024 Jun 22. pii: S0304-3940(24)00260-X. [Epub ahead of print]836 137882

Effect of 3-nitropropionic acid on sirtuin gene expression in Sirt3 deficient mice.

Orsolya Horváth, Péter Klivényi.

  Huntington's disease (HD) is an autosomal inherited progressive neurodegenerative disorder which is caused by the CAG trinucleotide repeat in the huntingtin gene. The mutation induces mitochondrial dysfunction in neurons, which leads to striatal neuronal loss. The efficacy of the available therapies is limited, thus acquisition of more data about the pathomechanism of HD and development of new strategies is urgent. Sirtuins (Sirt1-7) belong to the histone deacetylase family, and interestingly they have been associated with HD, however, their role in HD is still not fully understood. To clarify the role of sirtuins in HD, we utilized a 3-nitropropionic acid (3-NP) induced HD model and assessed alterations in gene expression using RT-PCR. Moreover, we studied the extension of neurodegeneration in the striatum, and behavioural changes. Furthermore, we involved Sirt3 knockout (Sirt3KO) mice to investigate the impact of Sirt3 deficiency in the expression of the other sirtuins. Our results showed that with 3-NP treatment, the mRNA level of Sirt2,5,7 changed significantly in wild-type (WT) mice, whereas in Sirt3KO animals there was no change. Interestingly, Sirt3 deficiency did not exacerbate 3-NP-mediated striatal neuronal loss, while Sirt3KO animals showed higher mortality than WT littermates. However, the absence of Sirt3 did not affect the behaviour of animals. Finally, we demonstrated that the changes in the expression of sirtuins are age- and sex- dependent. According to our findings, there is evidence that Sirt3 has a major impact on the regulation of other sirtuin isoforms, survival and neuroprotection. However, this neuroprotective effect does not manifest in the behaviour.

Keywords:  3-Nitropropionic acid; Huntington’s disease; Neurodegeneration, Sirtuin3 knockout; Sirtuins

DOI:  https://doi.org/10.1016/j.neulet.2024.137882
Biomed Pharmacother. 2024 Jun 27. pii: S0753-3322(24)00894-1. [Epub ahead of print]177 117010

Histone deacetylases and inhibitors in diabetes mellitus and its complications.

Li Wang, Yuning Bai, Zhengmin Cao, Ziwei Guo, Yanjie Lian, Pan Liu, Yixian Zeng, Wenliang Lyu, Qiu Chen.

  Diabetes mellitus (DM) is a metabolic disorder characterized by hyperglycemia, with its prevalence linked to both genetic predisposition and environmental factors. Epigenetic modifications, particularly through histone deacetylases (HDACs), have been recognized for their significant influence on DM pathogenesis. This review focuses on the classification of HDACs, their role in DM and its complications, and the potential therapeutic applications of HDAC inhibitors. HDACs, which modulate gene expression without altering DNA sequences, are categorized into four classes with distinct functions and tissue specificity. HDAC inhibitors (HDACi) have shown efficacy in various diseases, including DM, by targeting these enzymes. The review highlights how HDACs regulate β-cell function, insulin sensitivity, and hepatic gluconeogenesis in DM, as well as their impact on diabetic cardiomyopathy, nephropathy, and retinopathy. Finally, we suggest that targeted histone modification is expected to become a key method for the treatment of diabetes and its complications. The study of HDACi offers insights into new treatment strategies for DM and its associated complications.

Keywords:  Complications; Diabetes Mellitus; Histone Deacetylases; Inhibitor

DOI:  https://doi.org/10.1016/j.biopha.2024.117010
Biomed Pharmacother. 2024 Jun 21. pii: S0753-3322(24)00801-1. [Epub ahead of print]177 116917

SIRT1 signaling pathways in sarcopenia: Novel mechanisms and potential therapeutic targets.

Luning Yang, Di Liu, Shide Jiang, Hengzhen Li, Lin Chen, Yuxiang Wu, Anko Elijah Essien, Michael Opoku, Shinen Naranmandakh, ShuGuang Liu, Qin Ru, Yusheng Li.

  Sarcopenia is an aging-related skeletal disease characterized by decreased muscle mass, strength, and physical function, severely affecting the quality of life (QoL) of the elderly population. Sirtuin 1 (SIRT1), as a nicotinamide adenine dinucleotide (NAD+)-dependent histone deacetylases, has been reported to participate in various aging-related signaling pathways and exert protective effect on many human diseases. SIRT1 functioned as an important role in the occurrence and progression of sarcopenia through regulating key pathways related to protein homeostasis, apoptosis, mitochondrial dysfunction, insulin resistance and autophagy in skeletal muscle, including SIRT1/Forkhead Box O (FoxO), AMP-activated protein kinase (AMPK)/SIRT1/nuclear factor κB (NF-κB), SIRT1/p53, AMPK/SIRT1/peroxisome proliferator-activated receptor gamma coactivator-1α (PGC-1α), and SIRT1/live kinase B1 (LKB1)/AMPK pathways. However, the specific mechanisms of these processes have not been fully illuminated. Currently, several SIRT1-mediated interventions on sarcopenia have been preliminarily developed, such as SIRT1 activator polyphenolic compounds, exercising and calorie restriction. In this review, we summarized the predominant mechanisms of SIRT1 involved in sarcopenia and therapeutic modalities targeting the SIRT1 signaling pathways for the prevention and prognosis of sarcopenia.

Keywords:  Aging; Prevention; Sarcopenia; Sirtuin 1

DOI:  https://doi.org/10.1016/j.biopha.2024.116917
Pharmacol Res. 2024 Jun 23. pii: S1043-6618(24)00206-8. [Epub ahead of print]206 107261

Sirtuin 3 in renal diseases and aging: From mechanisms to potential therapies.

Xuan Peng, Haiqiang Ni, Baicheng Kuang, Zhiheng Wang, Shuaiheng Hou, Shiqi Gu, Nianqiao Gong.

  The longevity protein sirtuins (SIRTs) belong to a family of nicotinamide adenine dinucleotide (NAD+)-dependent deacetylases. In mammals, SIRTs comprise seven members (SIRT1-7) which are localized to different subcellular compartments. As the most prominent mitochondrial deacetylases, SIRT3 is known to be regulated by various mechanisms and participate in virtually all aspects of mitochondrial homeostasis and metabolism, exerting significant impact on multiple organs. Notably, the kidneys possess an abundance of mitochondria that provide substantial energy for filtration and reabsorption. A growing body of evidence now supports the involvement of SIRT3 in several renal diseases, including acute kidney injury, chronic kidney disease, and diabetic nephropathy; notably, these diseases are all associated with aging. In this review, we summarize the emerging role of SIRT3 in renal diseases and aging, and highlights the intricate mechanisms by which SIRT3 exerts its effects. In addition, we highlight the potential therapeutic significance of modulating SIRT3 and provide valuable insights into the therapeutic role of SIRT3 in renal diseases to facilitate clinical application.

Keywords:  Mitochondrial homeostasis; Potential therapies; Renal aging; Renal diseases; Sirtuin 3

DOI:  https://doi.org/10.1016/j.phrs.2024.107261
ChemMedChem. 2024 Jun 28. e202400273

Elucidating the Unconventional Binding Mode of a DNA-Encoded Library Hit Provides a Blueprint for Sirtuin 6 Inhibitor Development.

Weijie You, Alba L Montoya, Srikanta Dana, Raphael M Franzini, Clemens Steegborn.

  Sirtuin 6 (Sirt6), an NAD+-dependent deacylase, has emerged as a promising target for aging-related diseases and cancer. Advancing the medicinal chemistry of Sirt6 modulators is crucial for the development of chemical probes aimed at unraveling the intricate biological functions of Sirt6 and unlocking its therapeutic potential. A proprietary DNA-encoded library yielded Sirt6 inhibitor 2-Pr, displaying remarkable inhibitory activity and isoform-selectivity, and featuring a chemical structure distinct from reported Sirt6 modulators. In this study, we explore the inhibitory mechanism of 2-Pr, evaluating the impact of chemical modifications and presenting a crystal structure of the Sirt6/ADP-ribose/2-Pr complex. Notably, co-crystal structure analysis reveals an unexpected and unprecedented binding mode of Sirt6, with 2-Pr spanning the acyl channel of the enzyme, extending into the acetyl-lysine binding pocket, and reaching toward the C-site. This unique binding mode guides potential avenues for developing potent and selective Sirt6 inhibitors.

Keywords:  Acyl binding pocket; Crystal structure; DNA-Encoded Chemical Libraries; Deacylase; Sirt6 Inhibition

DOI:  https://doi.org/10.1002/cmdc.202400273
Microbiol Spectr. 2024 Jun 24. e0003824

Sirtulin-Ypk1 regulation axis governs the TOR signaling pathway and fungal pathogenicity in Cryptococcus neoformans.

Zhenghua Chai, Yanjian Li, Jing Zhang, Chen Ding, Xiujuan Tong, Zhijie Zhang.

  Cryptococcus neoformans is a life-threatening fungal pathogen that is a causative agent for pulmonary infection and meningoencephalitis in both immunocompetent and immunodeficient individuals. Recent studies have elucidated the important function of the target of rapamycin (TOR) signaling pathway in the modulation of C. neoformans virulence factor production and pathogenicity in animal infection models. Herein, we discovered that Ypk1, a critical component of the TOR signaling pathway, acts as a critical modulator in fungal pathogenicity through post-translational modifications (PTMs). Mass spectrometry analysis revealed that Ypk1 is subject to protein acetylation at lysines 315 and 502, and both sites are located within kinase functional domains. Inhibition of the C. neoformans TOR pathway by rapamycin activates the deacetylation process for Ypk1. The YPK1Q strain, a hyper-acetylation of Ypk1, exhibited increased sensitivity to rapamycin, decreased capsule formation ability, reduced starvation tolerance, and diminished fungal pathogenicity, indicating that deacetylation of Ypk1 is crucial for responding to stress. Deacetylase inhibition assays have shown that sirtuin family proteins are critical to the Ypk1 deacetylation mechanism. After screening deacetylase mutants, we found that Dac1 and Dac7 directly interact with Ypk1 to facilitate the deacetylation modification process via a protein-protein interaction. These findings provide new insights into the molecular basis for regulating the TORC-Ypk1 axis and demonstrate an important function of protein acetylation in modulating fungal pathogenicity.IMPORTANCE: Cryptococcus neoformans is an important opportunistic fungal pathogen in humans. While there are currently few effective antifungal treatments, the absence of novel molecular targets in fungal pathogenicity hinders the development of new drugs. There is increasing evidence that protein post-translational modifications (PTMs) can modulate the pathogenicity of fungi. In this study, we discovered that the pathogenicity of C. neoformans was significantly impacted by the dynamic acetylation changes of Ypk1, the immediate downstream target of the TOR complex. We discovered that Ypk1 is acetylated at lysines 315 and 502, both of which are within kinase functional domains. Deacetylation of Ypk1 is necessary for formation of the capsule structure, the response to the TOR pathway inhibitor rapamycin, nutrient utilization, and host infection. We also demonstrate that the sirtuin protein family is involved in the Ypk1 deacetylation mechanism. We anticipate that the sirtuin-Ypk1 regulation axis could be used as a potential target for the development of antifungal medications.

Keywords:  Cryptococcus neoformans; acetylation; deacetylase; fungal infection; fungal pathogenicity

DOI:  https://doi.org/10.1128/spectrum.00038-24
Trends Biochem Sci. 2024 Jun 25. pii: S0968-0004(24)00152-X. [Epub ahead of print]

Versatile JMJD proteins: juggling histones and much more.

Sangphil Oh, Ralf Janknecht.

  Jumonji C domain-containing (JMJD) proteins are found in bacteria, fungi, animals, and plants. They belong to the 2-oxoglutarate-dependent oxygenase superfamily and are endowed with various enzymatic activities, including demethylation of histones and hydroxylation of non-histone proteins. Many JMJD proteins are involved in the epigenetic control of gene expression, yet they also modulate a myriad other cellular processes. In this review we focus on the 33 human JMJD proteins and their established and controversial catalytic properties, survey their epigenetic and non-epigenetic functions, emphasize their contribution to sex-specific disease differences, and highlight how they sense metabolic changes. All this underlines not only their key roles in development and homeostasis, but also that JMJD proteins are destined to become drug targets in multiple diseases.

Keywords:  demethylase; epigenetics; metabolism; oxygenase; protein hydroxylase; sex bias

DOI:  https://doi.org/10.1016/j.tibs.2024.06.009
Cells. 2024 Jun 20. pii: 1069. [Epub ahead of print]13(12):

Resveratrol Induces Myotube Development by Altering Circadian Metabolism via the SIRT1-AMPK-PP2A Axis.

Natalie Avital-Cohen, Nava Chapnik, Oren Froy.

  Resveratrol is a polyphenol known to have metabolic as well as circadian effects. However, there is little information regarding the metabolic and circadian effect of resveratrol on muscle cells. We sought to investigate the metabolic impact of resveratrol throughout the circadian cycle to clarify the associated signaling pathways. C2C12 myotubes were incubated with resveratrol in the presence of increasing concentrations of glucose, and metabolic and clock proteins were measured for 24 h. Resveratrol led to SIRT1, AMPK and PP2A activation. Myotubes treated with increasing glucose concentrations showed higher activation of the mTOR signaling pathway. However, resveratrol did not activate the mTOR signaling pathway, except for P70S6K and S6. In accordance with the reduced mTOR activity, resveratrol led to advanced circadian rhythms and reduced levels of pBMAL1 and CRY1. Resveratrol increased myogenin expression and advanced its rhythms. In conclusion, resveratrol activates the SIRT1-AMPK-PP2A axis, advances circadian rhythms and induces muscle development.

Keywords:  PP2A; circadian; clock; mTOR; metabolism; muscle; resveratrol

DOI:  https://doi.org/10.3390/cells13121069
Mol Cell Endocrinol. 2024 Jun 25. pii: S0303-7207(24)00177-1. [Epub ahead of print] 112321

Replenishment of TCA cycle intermediates and long-noncoding RNAs regulation in breast cancer.

Xuewei Zheng, ShunShun Zhang, HaoDi Ma, Yirui Dong, Jiayu Zheng, Li Zeng, Jiangbo Liu, Yanzhenzi Dai, Qinan Yin.

  The tricarboxylic acid (TCA) cycle is an essential interface that coordinates cellular metabolism and is as a primary route determining the fate of a variety of fuel sources, including glucose, fatty acid and glutamate. The crosstalk of nutrients replenished TCA cycle regulates breast cancer (BC) progression by changing substrate levels-induced epigenetic alterations, especially the methylation, acetylation, succinylation and lactylation. Long non-coding RNAs (lncRNA) have dual roles in inhibiting or promoting energy reprogramming, and so altering the metabolic flux of fuel sources to the TCA cycle, which may regulate epigenetic modifications at the cellular level of BC. This narrative review discussed the central role of the TCA cycle in interconnecting numerous fuels and the induced epigenetic modifications, and the underlying regulatory mechanisms of lncRNAs in BC.

Keywords:  Epigenetic modifications; TCA cycle; breast cancer; long-noncoding RNAs

DOI:  https://doi.org/10.1016/j.mce.2024.112321
Sci Adv. 2024 Jun 28. 10(26): eadn4508

Lactate transported by MCT1 plays an active role in promoting mitochondrial biogenesis and enhancing TCA flux in skeletal muscle.

Lingling Zhang, Chenhao Xin, Shuo Wang, Shixuan Zhuo, Jing Zhu, Zi Li, Yuyi Liu, Lifeng Yang, Yan Chen.

Once considered as a "metabolic waste," lactate is now recognized as a major fuel for tricarboxylic acid (TCA) cycle. Our metabolic flux analysis reveals that skeletal muscle mainly uses lactate to fuel TCA cycle. Lactate is transported through the cell membrane via monocarboxylate transporters (MCTs) in which MCT1 is highly expressed in the muscle. We analyzed how MCT1 affects muscle functions using mice with specific deletion of MCT1 in skeletal muscle. MCT1 deletion enhances running performance, increases oxidative fibers while decreasing glycolytic fibers, and enhances flux of glucose to TCA cycle. MCT1 deficiency increases the expression of mitochondrial proteins, augments cell respiration rate, and elevates mitochondrial activity in the muscle. Mechanistically, the protein level of PGC-1α, a master regulator of mitochondrial biogenesis, is elevated upon loss of MCT1 via increases in cellular NAD+ level and SIRT1 activity. Collectively, these results demonstrate that MCT1-mediated lactate shuttle plays a key role in regulating muscle functions by modulating mitochondrial biogenesis and TCA flux.

DOI: https://doi.org/10.1126/sciadv.adn4508
Microbiol Spectr. 2024 Jun 25. e0074924

Quantitative analysis of the lysine acetylome reveals the role of SIRT3-mediated HSP60 deacetylation in suppressing intracellular Mycobacterium tuberculosis survival.

Chuanzhi Zhu, Yuheng Duan, Jing Dong, Hongyan Jia, Lanyue Zhang, Aiying Xing, Zihui Li, Boping Du, Qi Sun, Yinxia Huang, Zongde Zhang, Liping Pan.

  Protein acetylation and deacetylation are key epigenetic modifications that regulate the initiation and development of several diseases. In the context of infection with Mycobacterium tuberculosis (M. tb), these processes are essential for host-pathogen interactions and immune responses. However, the specific effects of acetylation and deacetylation on cellular functions during M. tb infection are not fully understood. This study employed Tandem Mass Tag (TMT) labeling for quantitative proteomic profiling to examine the acetylproteome (acetylome) profiles of noninfected and M. tb-infected macrophages. We identified 715 acetylated peptides from 1,072 proteins and quantified 544 lysine acetylation sites (Kac) in 402 proteins in noninfected and M. tb-infected macrophages. Our research revealed a link between acetylation events and metabolic changes during M. tb infection. Notably, the deacetylation of heat shock protein 60 (HSP60), a key chaperone protein, was significantly associated with this process. Specifically, the deacetylation of HSP60 at K96 by sirtuin3 (SIRT3) enhances macrophage apoptosis, leading to the elimination of intracellular M. tb. These findings underscore the pivotal role of the SIRT3-HSP60 axis in the host immune response to M. tb. This study offers a new perspective on host protein acetylation and suggests that targeting host-directed therapies could be a promising approach for tuberculosis immunotherapy.IMPORTANCE: Protein acetylation is crucial for the onset, development, and outcome of tuberculosis (TB). Our study comprehensively investigated the dynamics of lysine acetylation during M. tb infection, shedding light on the intricate host-pathogen interactions that underlie the pathogenesis of tuberculosis. Using an advanced quantitative lysine proteomics approach, different profiles of acetylation sites and proteins in macrophages infected with M. tb were identified. Functional enrichment and protein-protein network analyses revealed significant associations between acetylated proteins and key cellular pathways, highlighting their critical role in the host response to M. tb infection. Furthermore, the deacetylation of HSP60 and its influence on macrophage-mediated clearance of M. tb underscore the functional significance of acetylation in tuberculosis pathogenesis. In conclusion, this study provides valuable insights into the regulatory mechanisms governing host immune responses to M. tb infection and offers promising avenues for developing novel therapeutic interventions against TB.

Keywords:  Mycobacterium tuberculosis; acetylome; apoptosis; heat shock proteins 60; sirtuin 3

DOI:  https://doi.org/10.1128/spectrum.00749-24
PLoS One. 2024 ;19(6): e0305000

A homogeneous time-resolved fluorescence screen to identify SIRT2 deacetylase and defatty-acylase inhibitors.

Jie Yang, Joel Cassel, Brian C Boyle, Daniel Oppong, Young-Hoon Ahn, Brian P Weiser.

Human sirtuin-2 (SIRT2) has emerged as an attractive drug target for a variety of diseases. The enzyme is a deacylase that can remove chemically different acyl modifications from protein lysine residues. Here, we developed a high-throughput screen based on a homogeneous time-resolved fluorescence (HTRF) binding assay to identify inhibitors of SIRT2's demyristoylase activity, which is uncommon among many ligands that only affect its deacetylase activity. From a test screen of 9600 compounds, we identified a small molecule that inhibited SIRT2's deacetylase activity (IC50 = 7 μM) as well as its demyristoylase activity (IC50 = 37 μM). The inhibitor was composed of two small fragments that independently inhibited SIRT2: a halogenated phenol fragment inhibited its deacetylase activity, and a tricyclic thiazolobenzimidazole fragment inhibited its demyristoylase activity. The high-throughput screen also detected multiple deacetylase-specific SIRT2 inhibitors.

DOI: https://doi.org/10.1371/journal.pone.0305000
Int J Mol Sci. 2024 Jun 14. pii: 6569. [Epub ahead of print]25(12):

Dynamic Alterations in Acetylation and Modulation of Histone Deacetylase Expression Evident in the Dentine-Pulp Complex during Dentinogenesis.

Yukako Yamauchi, Emi Shimizu, Henry F Duncan.

  Epigenetic modulation, including histone modification, alters gene expression and controls cell fate. Histone deacetylases (HDACs) are identified as important regulators of dental pulp cell (DPC) mineralisation processes. Currently, there is a paucity of information regarding the nature of histone modification and HDAC expression in the dentine-pulp complex during dentinogenesis. The aim of this study was to investigate post-translational histone modulation and HDAC expression during DPC mineralisation and the expression of Class I/II HDACs during tooth development and in adult teeth. HDAC expression (isoforms -1 to -6) was analysed in mineralising primary rat DPCs using qRT-PCR and Western blot with mass spectrometry being used to analyse post-translational histone modifications. Maxillary molar teeth from postnatal and adult rats were analysed using immunohistochemical (IHC) staining for HDACs (1-6). HDAC-1, -2, and -4 protein expression increased until days 7 and 11, but decreased at days 14 and 21, while other HDAC expression increased continuously for 21 days. The Class II mineralisation-associated HDAC-4 was strongly expressed in postnatal sample odontoblasts and DPCs, but weakly in adult teeth, while other Class II HDACs (-5, -6) were relatively strongly expressed in postnatal DPCs and adult odontoblasts. Among Class I HDACs, HDAC-1 showed high expression in postnatal teeth, notably in ameloblasts and odontoblasts. HDAC-2 and -3 had extremely low expression in the rat dentine-pulp complex. Significant increases in acetylation were noted during DPC mineralisation processes, while trimethylation H3K9 and H3K27 marks decreased, and the HDAC-inhibitor suberoylanilide hydroxamic acid (SAHA) enhanced H3K27me3. These results highlight a dynamic alteration in histone acetylation during mineralisation and indicate the relevance of Class II HDAC expression in tooth development and regenerative processes.

Keywords:  dentinogenesis; epigenetics; histone deacetylases; odontoblasts; pulp biology; tooth development

DOI:  https://doi.org/10.3390/ijms25126569
J Cell Physiol. 2024 Jun 24.

The role of sirtuins in intervertebral disc degeneration: Mechanisms and therapeutic potential.

Heng Tu, Qian Gao, Yumeng Zhou, Li Peng, Dan Wu, Demao Zhang, Jing Yang.

  Intervertebral disc degeneration (IDD) is one of the main causes of low back pain, which affects the patients' quality of life and health and imposes a significant socioeconomic burden. Despite great efforts made by researchers to understand the pathogenesis of IDD, effective strategies for preventing and treating this disease remain very limited. Sirtuins are a highly conserved family of (NAD+)-dependent deacetylases in mammals that are involved in a variety of metabolic processes in vivo. In recent years, sirtuins have attracted much attention owing to their regulatory roles in IDD on physiological activities such as inflammation, apoptosis, autophagy, aging, oxidative stress, and mitochondrial function. At the same time, many studies have explored the therapeutic effects of sirtuins-targeting activators or micro-RNA in IDD. This review summarizes the molecular pathways of sirtuins involved in IDD, and summarizes the therapeutic role of activators or micro-RNA targeting Sirtuins in IDD, as well as the current limitations and challenges, with a view to provide possible solutions for the treatment of IDD.

Keywords:  apoptosis; intervertebral disc degeneration; mitochondrial dysfunction; oxidative stress; sirtuins

DOI:  https://doi.org/10.1002/jcp.31328
J Fungi (Basel). 2024 May 25. pii: 379. [Epub ahead of print]10(6):

Histone H3 N-Terminal Lysine Acetylation Governs Fungal Growth, Conidiation, and Pathogenicity through Regulating Gene Expression in Fusarium pseudograminearum.

Hang Jiang, Lifang Yuan, Liguo Ma, Kai Qi, Yueli Zhang, Bo Zhang, Guoping Ma, Junshan Qi.

  The acetylation of histone lysine residues regulates multiple life processes, including growth, conidiation, and pathogenicity in filamentous pathogenic fungi. However, the specific function of each lysine residue at the N-terminus of histone H3 in phytopathogenic fungi remains unclear. In this study, we mutated the N-terminal lysine residues of histone H3 in Fusarium pseudograminearum, the main causal agent of Fusarium crown rot of wheat in China, which also produces deoxynivalenol (DON) toxins harmful to humans and animals. Our findings reveal that all the FpH3K9R, FpH3K14R, FpH3K18R, and FpH3K23R mutants are vital for vegetative growth and conidiation. Additionally, FpH3K14 regulates the pathogen's sensitivity to various stresses and fungicides. Despite the slowed growth of the FpH3K9R and FpH3K23R mutants, their pathogenicity towards wheat stems and heads remains unchanged. However, the FpH3K9R mutant produces more DON. Furthermore, the FpH3K14R and FpH3K18R mutants exhibit significantly reduced virulence, with the FpH3K18R mutant producing minimal DON. In the FpH3K9R, FpH3K14R, FpH3K18R, and FpH3K23R mutants, there are 1863, 1400, 1688, and 1806 downregulated genes, respectively, compared to the wild type. These downregulated genes include many that are crucial for growth, conidiation, pathogenicity, and DON production, as well as some essential genes. Gene ontology (GO) enrichment analysis indicates that genes downregulated in the FpH3K14R and FpH3K18R mutants are enriched for ribosome biogenesis, rRNA processing, and rRNA metabolic process. This suggests that the translation machinery is abnormal in the FpH3K14R and FpH3K18R mutants. Overall, our findings suggest that H3 N-terminal lysine residues are involved in regulating the expression of genes with important functions and are critical for fungal development and pathogenicity.

Keywords:  Fusarium crown rot; H3 N-terminal lysine residues; gene expression; histone acetylation; phytopathogen

DOI:  https://doi.org/10.3390/jof10060379
Biochim Biophys Acta Mol Cell Biol Lipids. 2024 Jun 23. pii: S1388-1981(24)00077-5. [Epub ahead of print]1869(7): 159527

Differentiating human phospholipase A2's activity toward phosphatidylinositol, phosphatidylinositol phosphate and phosphatidylinositol bisphosphate.

Daiki Hayashi, Edward A Dennis.

  Phospholipase A2's (PLA2's) constitute a superfamily of enzymes that hydrolyze the sn-2 fatty acyl chain on glycerophospholipids. We have previously reported that each PLA2 Type shows a unique substrate specificity for the molecular species it hydrolyzes, especially the acyl chain that is cleaved from the sn-2 position and to some extent the polar group. However, phosphatidylinositol (PI) and PI phosphates (PIPs) have not been as well studied as substrates as other phospholipids because the PIPs require adaptation of the standard analysis methods, but they are important in vivo. We determined the in vitro activity of the three major types of human PLA2's, namely the cytosolic (c), calcium-independent (i), and secreted (s) PLA2's toward PI, PI-4-phosphate (PI(4)P), and PI-4,5-bisphosphate (PI(4,5)P2). The in vitro assay revealed that Group IVA cPLA2 (GIVA cPLA2) showed relatively high activity toward PI and PI(4)P among the tested PLA2's; nevertheless, the highly hydrophilic headgroup disrupted the interaction between the lipid surface and the enzyme. GIVA cPLA2 and GVIA iPLA2 showed detectable activity toward PI(4,5)P2, but it appeared to be a poorer substrate for all of the PLA2's tested. Furthermore, molecular dynamics (MD) simulations demonstrated that Thr416 and Glu418 of GIVA cPLA2 contribute significantly to accommodating the hydrophilic head groups of PI and PI(4)P, which could explain some selectivity for PI and PI(4)P. These results indicated that GIVA cPLA2 can accommodate PI and PI(4)P in its active site and hydrolyze them, suggesting that the GIVA cPLA2 may best account for the PI and PIP hydrolysis in living cells.

Keywords:  Lipidomics; Phosphatidylinositides; Phosphatidylinositol; Phospholipase A(2)

DOI:  https://doi.org/10.1016/j.bbalip.2024.159527
Trends Parasitol. 2024 Jun 22. pii: S1471-4922(24)00144-2. [Epub ahead of print]

Plasmodium falciparum artemisinin resistance: something gained in translation.

Katie R Hughes, Andrew P Waters.

  Small-Saunders et al. uncovered a new facet of artemisinin resistance in Plasmodium in which parasites use a previously underexplored arm of stress response mechanisms. Through altered epitranscriptomic modifications on tRNA, changed translation patterns adapt resistant cells to facilitate entry into a quiescent-like state which provides the parasite an escape from many drugs.

Keywords:  artemisinin; drug resistance; epitranscriptomics; malaria; tRNA modification; translation

DOI:  https://doi.org/10.1016/j.pt.2024.06.004