bims-toxgon 2024-10-20 papers

bims-toxgon

Biomed News

on Toxoplasma gondii metabolism

Issue of 2024–10–20
28 papers selected by
Lakesh Kumar, BITS Pilani

Nuts and bolts of the behavioural manipulation by Toxoplasma gondii.
The invasion pore induced by Toxoplasma gondii.
The Structures, Functions, and Roles of Class III HDACs (Sirtuins) in Neuropsychiatric Diseases.
Lipophilic bisphosphonates reduced cyst burden and ameliorated hyperactivity of mice chronically infected with Toxoplasma gondii.
Nanospheres as the delivery vehicle: novel application of Toxoplasma gondii ribosomal protein S2 in PLGA and chitosan nanospheres against acute toxoplasmosis.
Toxoplasma-induced behavior changes - is microbial dysbiosis the missing link?
Adaptations and metabolic evolution of myzozoan protists across diverse lifestyles and environments.
Plasmodium falciparum protein phosphatase PP7 is required for early ring-stage development.
Genome Editing in Apicomplexan Parasites: Current Status, Challenges, and Future Possibilities.
H+-translocating pyrophosphatases in protozoan parasites.
Urban estuary serves as a critical nexus for the land-sea transfer of the terrestrial pathogen Toxoplasma gondii.
The role of SIRT1 in autophagy and drug resistance: unveiling new targets and potential biomarkers in cancer therapy.
A single Leishmania adenylate forming enzyme of the ANL superfamily generates both acetyl- and acetoacetyl-CoA.
Unraveling the complexities of ApiAP2 regulation in Plasmodium falciparum.
A Plasmodium falciparum MORC protein complex modulates epigenetic control of gene expression through interaction with heterochromatin.
Generation of a new DiCre expressing parasite strain for functional characterization of Plasmodium falciparum genes in blood stages.
SIRT2-mediated deacetylation of glutathione transferase alleviates oxidative damage and increases the heat tolerance of Pleurotus ostreatus.
Roles of Histone Acetylation and Deacetylation in Root Development.
Phosphorylation regulates the chromatin remodeler SMARCAD1 in nucleosome binding, ATP hydrolysis, and histone exchange.
Integration of 3D-QSAR, molecular docking, and machine learning techniques for rational design of nicotinamide-based SIRT2 inhibitors.
Design and optimization of novel Tetrahydro-β-carboline-based HDAC inhibitors with potent activities against tumor cell growth and metastasis.
A master regulator of central carbon metabolism directly activates virulence gene expression in attaching and effacing pathogens.
Sirtuin-dependent reversible lysine acetylation of the o-succinylbenzoyl-coenzyme A synthetase of Bacillus subtilis.
SIRT2 deacetylates and decreases the expression of FOXM1 in colon cancer.
Flow Cytometry FRET Reveals Posttranslational Modifications Drive Protein Phosphatase-5 Conformational Changes in Mammalian Cells.
Temporal regulation of acetylation status determines PARP1 role in DNA damage response and metabolic homeostasis.
Design, Synthesis, and Structural Evaluation of Acetylated Phenylthioketone Inhibitors of HDAC10.
Quantitative dynamics of intracellular NMN by genetically encoded biosensor.

Folia Parasitol (Praha). 2024 Sep 23. pii: 2024.017. [Epub ahead of print]71

Nuts and bolts of the behavioural manipulation by Toxoplasma gondii.

Ajai Vyas.

  In this review, I take the first-person perspective of a neuroscientist interested in Toxoplasma gondii (Nicolle et Manceaux, 1908). I reflect on the value of behavioural manipulation as a perturbation tool to understand the organisation of behaviour within the brain. Toxoplasma gondii infection reduces the aversion of rats to the olfactory cues of cat presence. This change in behaviour is one of the often-discussed exemplars of host-parasite coevolution, culminating in the manipulation of the host behaviour for the benefit of the parasite. Such coevolution also means that we can use host-parasite systems as tools to derive fundamental insights about the host brain itself.

Keywords:  Amygdala; Fear; Life-history; Parasite

DOI:  https://doi.org/10.14411/fp.2024.017
bioRxiv. 2024 Oct 13. pii: 2024.10.11.617945. [Epub ahead of print]

The invasion pore induced by Toxoplasma gondii.

Y Kegawa, F Male, I Jiménez-Munguía, P S Blank, E Mekhedov, G Ward, J Zimmerberg.

To survive, obligate intracellular apicomplexan parasites must invade host cells. For Toxoplasma gondii , a first indication of invasion is a transient breach in host cell permeability that precedes parasite entry. Here, a time-series analysis using novel filtering algorithms was performed on new electrophysiological data acquired at sub-200 μs time resolution. The analysis revealed an underlying structure to the parasite-induced conductance changes: conductance changes are consistent with a rapid insertion, then slower removal, blocking, or inactivation of quantal conductance elements. This quantal element was best described by a Gaussian distribution with mean of 0.26 nS (width 0.03 nS), which is like the conductance of another apicomplexan protein translocon, EXP2. The quantal conductance observed during interactions with parasites depleted of the rhoptry neck protein RON2, a central component of the moving junction between the parasite and the host cell during invasion, had a different Gaussian distribution (mean 0.19 nS, width 0.03 nS) supporting the hypothesis that RON2 contributes to the poration process or the passage of conductive elements through the pore.

DOI: https://doi.org/10.1101/2024.10.11.617945
Cells. 2024 Oct 02. pii: 1644. [Epub ahead of print]13(19):

The Structures, Functions, and Roles of Class III HDACs (Sirtuins) in Neuropsychiatric Diseases.

Robin E Bonomi, William Riordan, Juri G Gelovani.

  Over the past two decades, epigenetic regulation has become a rapidly growing and influential field in biology and medicine. One key mechanism involves the acetylation and deacetylation of lysine residues on histone core proteins and other critical proteins that regulate gene expression and cellular signaling. Although histone deacetylases (HDACs) have received significant attention, the roles of individual HDAC isoforms in the pathogenesis of psychiatric diseases still require further research. This is particularly true with regard to the sirtuins, class III HDACs. Sirtuins have unique functional activity and significant roles in normal neurophysiology, as well as in the mechanisms of addiction, mood disorders, and other neuropsychiatric abnormalities. This review aims to elucidate the differences in catalytic structure and function of the seven sirtuins as they relate to psychiatry.

Keywords:  HDACs; neuropsychiatric; sirtuins

DOI:  https://doi.org/10.3390/cells13191644
mBio. 2024 Oct 10. e0175624

Lipophilic bisphosphonates reduced cyst burden and ameliorated hyperactivity of mice chronically infected with Toxoplasma gondii.

Melissa A Sleda, Zaid F Pitafi, WenZhan Song, Eric Oldfield, Silvia N J Moreno.

  The current treatments for toxoplasmosis are only active against fast-growing tachyzoites, present in acute infections, with little effect on slow-growing bradyzoites within tissue cysts, present in latent chronic infections. The mitochondrion of Toxoplasma gondii is essential for its survival, and one of the major anti-parasitic drugs, atovaquone, inhibits the mitochondrial electron transport chain at the coenzyme Q:cytochrome c oxidoreductase site. Coenzyme Q (also known as ubiquinone [UQ]) consists of a quinone head and a lipophilic, isoprenoid tail that anchors UQ to membranes. The synthesis of the isoprenoid unit is essential for cell growth and is inhibited by lipophilic bisphosphonates, which inhibit the parasite growth. In this work, we investigated the effect of lipophilic bisphosphonates on the chronic stages of T. gondii. We discovered that three lipophilic bisphosphonates (BPH-1218, BPH-1236, and BPH-1238), effective for the acute infection, were also effective in controlling the development of chronic stages. We showed effectiveness by testing them against in vitro cysts and in vivo derived tissue cysts and, most importantly, these compounds reduced the cyst burden in the brains of chronically infected mice. We monitored the activity of infected mice non-invasively and continuously with a novel device termed the CageDot. A decrease in activity accompanied the acute phase, but mice recovered to normal activity and showed signs of hyperactivity when the chronic infection was established. Moreover, treatment with atovaquone or BPH-1218 ameliorated the hyperactivity observed during the chronic infection.IMPORTANCETreatment for toxoplasmosis is challenged by a lack of effective drugs to eradicate the chronic stages. Most of the drugs currently used are poorly distributed to the central nervous system, and they trigger allergic reactions in a large number of patients. There is a compelling need for safe and effective treatments for toxoplasmosis. Bisphosphonates (BPs) are analogs of inorganic pyrophosphate and are used for the treatment of bone disorders. BPs target the isoprenoid pathway and are effective against several experimental parasitic infections. Some lipophilic BPs can specifically inhibit the mitochondrial activity of Toxoplasma gondii by interfering with the mechanism by which ubiquinone is inserted into the inner mitochondrial membrane. In this work, we present the effect of three lipophilic BPs against T. gondii chronic stages. We also present a new strategy for the monitoring of animal activity during disease and treatment that is non-invasive and continuous.

Keywords:  Toxoplasma gondii; bisphosphonate; bradyzoite; hyperactivity

DOI:  https://doi.org/10.1128/mbio.01756-24
Front Immunol. 2024 ;15 1475280

Nanospheres as the delivery vehicle: novel application of Toxoplasma gondii ribosomal protein S2 in PLGA and chitosan nanospheres against acute toxoplasmosis.

WeiYu Qi, YouLi Yu, ChenChen Yang, XiaoJuan Wang, YuChen Jiang, Li Zhang, ZhengQing Yu.

  Toxoplasma gondii (T. gondii) is a zoonotic disease that poses great harm to humans and animals. So far, no effective T. gondii vaccine has been developed to provide fully protection against such parasites. Recently, numerous researches have focused on the use of poly-lactic-co-glycolic acid (PLGA) and chitosan (CS) for the vaccines against T. gondii infections. In this study, we employed PLGA and CS as the vehicles for T. gondii ribosome protein (TgRPS2) delivery. TgRPS2-PLGA and TgRPS2-CS nanospheres were synthesized by double emulsion solvent evaporation and ionic gelation technique as the nano vaccines. Before immunization in animals, the release efficacy and toxicity of the synthesized nanospheres were evaluated in vitro. Then, ICR mice were immunized intramuscularly, and immune protections of the synthesized nanospheres were assessed. The results showed that TgRPS2-PLGA and TgRPS2-CS nanospheres could induce higher levels of IgG and cytokines, activate dendritic cells, and promote the expression of histocompatibility complexes. The splenic lymphocyte proliferation and the enhancement in the proportion of CD4+ and CD8+ T lymphocytes were also observed in immunized animals. In addition, two types of nanospheres could significantly inhabit the replications of T. gondii in cardiac muscles and spleen tissues. All these obtained results in this study demonstrated that the TgRPS2 protein delivered by PLGA or CS nanospheres provided satisfactory immunoprotective effects in resisting T. gondii, and such formulations illustrated potential as prospective preventive agents for toxoplasmosis.

Keywords:  PLGA; Toxoplasma gondii; chitosan; immune protection; nano vaccine; ribosomal protein S2

DOI:  https://doi.org/10.3389/fimmu.2024.1475280
Front Cell Infect Microbiol. 2024 ;14 1415079

Toxoplasma-induced behavior changes - is microbial dysbiosis the missing link?

Emese Prandovszky, Emily G Severance, Victor W Splan, Hua Liu, Jianchun Xiao, Robert H Yolken.

  Toxoplasma gondii (T. gondii) is one of the most successful intracellular protozoa in that it can infect the majority of mammalian cell types during the acute phase of infection. Furthermore, it is able to establish a chronic infection for the host's entire lifespan by developing an encysted parasite form, primarily in the muscles and brain of the host, to avoid the host immune system. The infection affects one third of the world population and poses an increased risk for people with a suppressed immune system. Despite the dormant characteristics of chronic T. gondii infection, there is much evidence suggesting that this infection leads to specific behavior changes in both humans and rodents. Although numerous hypotheses have been put forth, the exact mechanisms underlying these behavior changes have yet to be understood. In recent years, several studies revealed a strong connection between the gut microbiome and the different organ systems that are affected in T. gondii infection. While it is widely studied and accepted that acute T. gondii infection can lead to a dramatic disruption of the host's normal, well-balanced microbial ecosystem (microbial dysbiosis), changes in the gut microbiome during the chronic stage of infection has not been well characterized. This review is intended to briefly inspect the different hypotheses that attempt to explain the behavior changes during T. gondii infection. Furthermore, this review proposes to consider the potential link between gut microbial dysbiosis, and behavior changes in T. gondii infection as a novel way to describe the underlying mechanism.

Keywords:  behavior; immune activation; microbiome; neurotransmitters; toxoplasma

DOI:  https://doi.org/10.3389/fcimb.2024.1415079
Microbiol Mol Biol Rev. 2024 Oct 10. e0019722

Adaptations and metabolic evolution of myzozoan protists across diverse lifestyles and environments.

Ross F Waller, Vern B Carruthers.

  SUMMARYMyzozoans encompass apicomplexans and dinoflagellates that manifest diverse lifestyles in highly varied environments. They show enormous propensity to employ different metabolic programs and exploit different nutrient resources and niches, and yet, they share much core biology that underlies this evolutionary success and impact. This review discusses apicomplexan parasites of medical significance and the traits and properties they share with non-pathogenic myzozoans. These include the versatility of myzozoan plastids, which scale from fully photosynthetic organelles to the site of very select key metabolic pathways. Pivotal evolutionary innovations, such as the apical complex, have allowed myzozoans to shift from predatory to parasitic and other symbiotic lifestyles multiple times in both apicomplexan and dinoflagellate branches of the myzozoan evolutionary tree. Such traits, along with shared mechanisms for nutrient acquisition, appear to underpin the prosperity of myzozoans in their varied habitats. Understanding the mechanisms of these shared traits has the potential to spawn new strategic interventions against medically and veterinary relevant parasites within this grouping.

Keywords:  Myzozoa; apical complex; apicomplexa; dinoflagellates; evolution; micropore; parasite; plastid; predator; symbiont

DOI:  https://doi.org/10.1128/mmbr.00197-22
mBio. 2024 Oct 10. e0253924

Plasmodium falciparum protein phosphatase PP7 is required for early ring-stage development.

Avnish Patel, Aline Fréville, Joshua A Rey, Helen R Flynn, Konstantinos Koussis, Mark J Skehel, Michael J Blackman, David A Baker.

  We previously reported that the Plasmodium falciparum putative serine/threonine protein phosphatase 7 (PP7) is a high-confidence substrate of the cAMP-dependent protein kinase (PKA). Here we explore the function of PP7 in asexual P. falciparum blood stage parasites. We show that conditional disruption of PP7 leads to a severe growth arrest. We show that PP7 is a calcium-dependent phosphatase that interacts with calmodulin and calcium-dependent protein kinase 1 (CDPK1), consistent with a role in calcium signaling. Notably, PP7 was found to be dispensable for erythrocyte invasion, but was crucial for ring-stage development, with PP7-null parasites arresting shortly following invasion and showing no transition to ameboid forms. Phosphoproteomic analysis revealed that PP7 may regulate certain PKAc substrates. Its interaction with calmodulin and CDPK1 further emphasizes a role in calcium signaling, while its impact on early ring development and PKAc substrate phosphorylation underscores its importance in parasite development.
IMPORTANCE: Plasmodium falciparum causes malaria and is responsible for more than 600,000 deaths each year. Although effective drugs are available to treat disease, the spread of drug-resistant parasites endangers their future efficacy. It is hoped that a better understanding of the biology of malaria parasites will help us to discover new drugs to tackle the resistance problem. Our work is focused on the cell signaling mechanisms that control the development of the parasite throughout its complex life cycle. All signal transduction pathways are ultimately regulated by reversible protein phosphorylation by protein kinase and protein phosphatase enzymes. In this study, we investigate the function of calcium-dependent protein phosphatase PP7 and show that it is essential for the development of ring-stage parasites following the invasion of human erythrocytes. Our results contribute to the understanding of the erythrocytic stages of the parasite life cycle that cause malaria pathology.

Keywords:  apicomplexan parasites; calcium signaling; malaria; serine/threonine phosphatases; signal transduction

DOI:  https://doi.org/10.1128/mbio.02539-24
CRISPR J. 2024 Oct 10.

Genome Editing in Apicomplexan Parasites: Current Status, Challenges, and Future Possibilities.

Ethel Webi, Hussein M Abkallo, George Obiero, Paul Ndegwa, Shengsong Xie, Shuhong Zhao, Vishvanath Nene, Lucilla Steinaa.

Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein (Cas) technology has revolutionized genome editing across various biological systems, including the Apicomplexa phylum. This review describes the status, challenges, and applications of CRISPR-Cas9 editing technology in apicomplexan parasites, such as Plasmodium, Toxoplasma, Theileria, Babesia, and Cryptosporidium. The discussion encompasses successfully implemented CRISPR-Cas9-based techniques in these parasites, highlighting the achieved milestones, from precise gene modifications to genome-wide screening. In addition, the review addresses the challenges hampering efficient genome editing, including the parasites' complex life cycles, multiple intracellular stages, and the lack of robust genetic tools. It further explores the ethical and policy considerations surrounding genome editing and the future perspectives of CRISPR-Cas applications in apicomplexan parasites.

DOI: https://doi.org/10.1089/crispr.2024.0032
Parasitol Res. 2024 Oct 18. 123(10): 353

H+-translocating pyrophosphatases in protozoan parasites.

Karina Araujo-Ruiz, Ricardo Mondragón-Flores.

  Integral membrane pyrophosphatases (mPPases) hydrolyze pyrophosphate. This enzymatic mechanism is coupled with the pumping of H + and/or Na + across membranes, which can be either K + -dependent or K + -independent. Inorganic proton-translocating pyrophosphatases (H + -PPases) can transport protons across cell membranes and are reported in various organisms such as plants, bacteria, and protozoan parasites. The evolutionary implications of these enzymes are of great interest for proposing approaches related to the treatment of parasitic of phytopathogenic diseases. This work presents a literature review on pyrophosphate, pyrophosphatases, their inhibitors and emphasizes H + -PPases found in various medically significant protozoan parasites such as Toxoplasma gondii, the causative agent of toxoplasmosis, and Plasmodium falciparum, the causative agent of malaria, as well as protozoan species that primarily affect animals, such as Eimeria maxima and Besnoitia besnoiti.

Keywords:  H + -PPase; Parasites; Protozoan; Pyrophosphatase; mPPase

DOI:  https://doi.org/10.1007/s00436-024-08362-3
Sci Total Environ. 2024 Oct 15. pii: S0048-9697(24)07140-7. [Epub ahead of print] 176983

Urban estuary serves as a critical nexus for the land-sea transfer of the terrestrial pathogen Toxoplasma gondii.

Xin-Kun Zhu, Hany M Elsheikha, Tao Yang, Man-Yao Li, Wei Cong.

  Terrestrial runoff is a key pathway for the transmission of the terrestrial pathogen Toxoplasma gondii from land to sea, posing a significant threat to marine ecosystems. Understanding the mechanisms by which T. gondii is transported from terrestrial to marine environment is crucial for developing effective prevention and control strategies for toxoplasmosis in marine organisms. This study investigates the transport of T. gondii through terrestrial runoff in the Sow River, a representative watershed in Weihai, China. Surface water, bottom water, and sediment samples were collected and analyzed for T. gondii DNA using PCR methods. Out of 1776 samples, the prevalence of T. gondii was found to be 8.61 % in surface water, 9.80 % in bottom water, and 16.61 % in sediment, with sediment identified as a significant reservoir. Additionally, estuarine zones showed a higher prevalence of T. gondii (16.80 %) compared to riverine areas (9.00 %). The study further revealed that seasonal climate variations, such as temperature and precipitation, had no significant impact on the distribution of T. gondii. However, there was significant spatial variability, with estuarine conditions facilitating increased pathogen transmission. These findings highlight the importance of estuaries and sediments as key conduits for T. gondii entry in marine food webs. The results provide a theoretical basis for designing infection prevention and control strategies aimed at protecting marine ecosystems.

Keywords:  Epidemiology; Estuary; Sediment; Terrestrial runoff; Toxoplasma gondii

DOI:  https://doi.org/10.1016/j.scitotenv.2024.176983
Front Pharmacol. 2024 ;15 1469830

The role of SIRT1 in autophagy and drug resistance: unveiling new targets and potential biomarkers in cancer therapy.

Yujing Tang, Wantao Ju, Yanjun Liu, Qin Deng.

  Cancer, the world's second leading cause of death after cardiovascular diseases, is characterized by hallmarks such as uncontrolled cell growth, metastasis, angiogenesis, hypoxia, and resistance to therapy. Autophagy, a cellular process that can both support and inhibit cancer progression, plays a critical role in cancer development and progression. This process involves the formation of autophagosomes that ultimately fuse with lysosomes to degrade cellular components. A key regulator of this process is Sirtuin 1 (SIRT1), which significantly influences autophagy. This review delves into the role of SIRT1 in modulating autophagy and its broader impacts on carcinogenesis. SIRT1 regulates crucial autophagy mediators, such as AMP-activated protein kinase (AMPK) and mammalian target of rapamycin (mTOR), effectively promoting or suppressing autophagy. Beyond its direct effects on autophagy, SIRT1's regulatory actions extend to other cell death processes, including apoptosis and ferroptosis, thereby influencing tumor cell proliferation, metastasis, and chemotherapy responses. These insights underscore the complex interplay between SIRT1 and autophagy, with significant implications for cancer therapy. Targeting SIRT1 and its associated pathways presents a promising strategy to manipulate autophagy in cancer treatment. This review underscores the potential of SIRT1 as a therapeutic target, opening new avenues for enhancing cancer treatment efficacy.

Keywords:  SIRT1; apoptosis; autophagy; drug resistance; ferroptosis; sirtuin family

DOI:  https://doi.org/10.3389/fphar.2024.1469830
J Biol Chem. 2024 Oct 10. pii: S0021-9258(24)02381-0. [Epub ahead of print] 107879

A single Leishmania adenylate forming enzyme of the ANL superfamily generates both acetyl- and acetoacetyl-CoA.

Andrew J Jezewski, Taiwo E Esan, Jonah Propp, Andrew J Fuller, Drashti G Daraji, Charles Lail, Bart L Staker, Elijah L Woodward, Linjun Liu, Kevin P Battaile, Scott Lovell, Timothy J Hagen, Damian J Krysan.

  Leishmania, a protozoan parasite, is responsible for significant morbidity and mortality worldwide, manifesting as cutaneous, mucocutaneous, and visceral leishmaniasis. These diseases pose a substantial burden, especially in impoverished regions with limited access to effective medical treatments. Current therapies are toxic, have low efficacy, and face growing resistance. Understanding the metabolic pathways of Leishmania, particularly those differing from its host, can unveil potential therapeutic targets. In this study, we investigated the acetyl-CoA synthetase (ACS) enzyme from Leishmania infantum (LiAcs1), which, unlike many organisms, also exhibits acetoacetyl-CoA synthetase (KBC) activity. This dual functionality is unique among ANL superfamily enzymes and crucial for the parasite's reliance on leucine catabolism, energy production and sterol biosynthesis. Our biochemical characterization of LiAcs1 revealed its ability to utilize both acetate and acetoacetate substrates. Additionally, LiAcs1 displayed a distinct CoA substrate inhibition pattern, partially alleviated by acetoacetate. Structural analysis provided insights into the substrate binding flexibility of LiAcs1, highlighting a more promiscuous substrate pocket compared to other ACS or KBC-specific enzymes. Substrate mimetics elucidated its ability to accommodate both small and large AMP-ester derivatives, contributing to its dual ACS/KBC functionality. These findings not only advance our understanding of Leishmania metabolism but also present LiAcs1 as a promising drug target. The dual functionality of LiAcs1 underscores the potential for developing selective inhibitors that could disrupt critical metabolic pathways across Leishmania spp. as it appears this enzyme is highly conserved across this genus. This paves the way for developing novel effective treatments against this devastating disease.

Keywords:  Leishmania; acetoacetate; acetyl‐CoA synthetase; metabolism; substrate specificity

DOI:  https://doi.org/10.1016/j.jbc.2024.107879
Trends Parasitol. 2024 Oct 16. pii: S1471-4922(24)00250-2. [Epub ahead of print]

Unraveling the complexities of ApiAP2 regulation in Plasmodium falciparum.

Ritwik Singhal, Isadora O Prata, Victoria A Bonnell, Manuel Llinás.

  The regulation of gene expression in Plasmodium spp., the causative agents of malaria, relies on precise transcriptional control. Malaria parasites encode a limited repertoire of sequence-specific transcriptional regulators dominated by the apicomplexan APETALA 2 (ApiAP2) protein family. ApiAP2 DNA-binding proteins play critical roles at all stages of the parasite life cycle. Recent studies have provided mechanistic insight into the functional roles of many ApiAP2 proteins. Two major areas that have advanced significantly are the identification of ApiAP2-containing protein complexes and the role of ApiAP2 proteins in malaria parasite sexual development. In this review, we present recent advances on the functional biology of ApiAP2 proteins and their role in regulating gene expression across the blood stages of the parasite life cycle.

Keywords:  DNA binding proteins; Plasmodium; apicomplexan APETALA2 (ApiAP2); gene regulation; malaria; transcription factors

DOI:  https://doi.org/10.1016/j.pt.2024.09.007
Elife. 2024 Oct 16. pii: RP92201. [Epub ahead of print]12

A Plasmodium falciparum MORC protein complex modulates epigenetic control of gene expression through interaction with heterochromatin.

Maneesh Kumar Singh, Victoria Ann Bonnell, Israel Tojal Da Silva, Verônica Feijoli Santiago, Miriam Santos Moraes, Jack Adderley, Christian Doerig, Giuseppe Palmisano, Manuel Llinas, Celia R S Garcia.

  Dynamic control of gene expression is critical for blood stage development of malaria parasites. Here, we used multi-omic analyses to investigate transcriptional regulation by the chromatin-associated microrchidia protein, MORC, during asexual blood stage development of the human malaria parasite Plasmodium falciparum. We show that PfMORC (PF3D7_1468100) interacts with a suite of nuclear proteins, including APETALA2 (ApiAP2) transcription factors (PfAP2-G5, PfAP2-O5, PfAP2-I, PF3D7_0420300, PF3D7_0613800, PF3D7_1107800, and PF3D7_1239200), a DNA helicase DS60 (PF3D7_1227100), and other chromatin remodelers (PfCHD1 and PfEELM2). Transcriptomic analysis of PfMORCHA-glmS knockdown parasites revealed 163 differentially expressed genes belonging to hypervariable multigene families, along with upregulation of genes mostly involved in host cell invasion. In vivo genome-wide chromatin occupancy analysis during both trophozoite and schizont stages of development demonstrates that PfMORC is recruited to repressed, multigene families, including the var genes in subtelomeric chromosomal regions. Collectively, we find that PfMORC is found in chromatin complexes that play a role in the epigenetic control of asexual blood stage transcriptional regulation and chromatin organization.

Keywords:  P. falciparum; PfMORC; Plasmodium falciparum; infectious disease; malaria; microbiology

DOI:  https://doi.org/10.7554/eLife.92201
Sci Rep. 2024 10 15. 14(1): 24076

Generation of a new DiCre expressing parasite strain for functional characterization of Plasmodium falciparum genes in blood stages.

Abhisheka Bansal, Manish Sharma, Himashree Choudhury.

  Conditional regulation is a highly beneficial system for studying the function of essential genes in Plasmodium falciparum and dimerizable Cre recombinase (DiCre) is a recently adapted conditional regulation system suitable for this purpose. In the DiCre system, two inactive fragments of Cre are reconstituted to form a functionally active enzyme in the presence of rapamycin. Different loci have been targeted to generate parasite lines that express the DiCre enzyme. Here, we have used marker-free CRISPR-Cas9 gene editing to integrate the DiCre cassette in a redundant cg6 locus. We have shown the utility of the newly generated ∆cg6DC4 parasites in mediating robust, rapid, and highly specific excision of exogenously encoded gfp sequence. The ∆cg6DC4 parasites are also capable of conditional excision of an endogenous parasite gene, PF3D7_1246000. Conditional deletion of PF3D7_1246000 did not cause any inhibition in the asexual proliferation of the parasites. Furthermore, the health and morphology of the mutant parasites were comparable to that of the control parasites in Giemsa smears. The availability of another stable DiCre parasite strain competent for conditional excision of target genes will expedite functional characterization and validation of novel drug and vaccine targets against malaria.

Keywords:  CRISPR-Cas9; Conditional regulation; Dimerizable cre recombinase; LoxP; Plasmodium; Rapamycin

DOI:  https://doi.org/10.1038/s41598-024-75657-x
Environ Res. 2024 Oct 13. pii: S0013-9351(24)02054-1. [Epub ahead of print]263(Pt 2): 120147

SIRT2-mediated deacetylation of glutathione transferase alleviates oxidative damage and increases the heat tolerance of Pleurotus ostreatus.

Huihui Li, Qianqian Chai, Xiukun Zheng, Qing Wen, Qing Liu, Yuan Cheng Qi, Fengqin Wang, Jinwen Shen, Yanru Hu.

  High-temperature stress (HS) severely threatens agricultural production. Pleurotus ostreatus is cultivated in many parts of the world, and its growth is strongly affected by HS. We previously reported that metabolic rearrangement occurred in HS, but the gene expression levels of several key enzymes remained unchanged. Therefore, in this study, we investigated the contribution of posttranslational modifications of proteins to HS resistance in P. ostreatus. We found that the level of acetylation of P. ostreatus decreased under short-term HS treatment and increased as the duration of HS treatment increased. Acetylation omics revealed that almost all metabolic enzymes were acetylated. We found that deacetylation under HS can improve the growth recovery ability of mycelia, the activity of matrix-degrading enzyme, and the contents of antioxidants, such as nicotinamide adenine dinucleotide phosphate (NADPH) and glutathione (GSH), but can decreased H2O2 levels. In vitro acetylation experiments and point mutations revealed that the deacetylase SIRT2 increased the activity of glutathione transferases (GSTs) by deacetylating GST1 66K, GST2 206K, and GST2 233K. Together, SIRT2 is activated by short-term HS and improves its antioxidant activity by deacetylating GSTs, thereby improving the resistance of P. ostreatus to HS. In this study, we identified new non-histone substrate proteins and new lysine acetylation sites of SIRT2 under HS. We also discovered the role of non-histone acetylation in the adaptation of organisms to HS.

Keywords:  Acetylation; High-temperature stress; Pleurotus ostreatus; SIRT2

DOI:  https://doi.org/10.1016/j.envres.2024.120147
Plants (Basel). 2024 Oct 01. pii: 2760. [Epub ahead of print]13(19):

Roles of Histone Acetylation and Deacetylation in Root Development.

Christos Tersenidis, Stylianos Poulios, George Komis, Emmanuel Panteris, Konstantinos Vlachonasios.

  Roots are usually underground plant organs, responsible for anchoring to the soil, absorbing water and nutrients, and interacting with the rhizosphere. During root development, roots respond to a variety of environmental signals, contributing to plant survival. Histone post-translational modifications play essential roles in gene expression regulation, contributing to plant responses to environmental cues. Histone acetylation is one of the most studied post-translational modifications, regulating numerous genes involved in various biological processes, including development and stress responses. Although the effect of histone acetylation on plant responses to biotic and abiotic stimuli has been extensively reviewed, no recent reviews exist focusing on root development regulation by histone acetylation. Therefore, this review brings together all the knowledge about the impact of histone acetylation on root development in several plant species, mainly focusing on Arabidopsis thaliana. Here, we summarize the role of histone acetylation and deacetylation in numerous aspects of root development, such as stem cell niche maintenance, cell division, expansion and differentiation, and developmental zone determination. We also emphasize the gaps in current knowledge and propose new perspectives for research toward deeply understanding the role of histone acetylation in root development.

Keywords:  cell division; cell elongation; epidermis cell fate; epigenetic modifications; gene expression; histone acetylation; histone deacetylation; mitosis; quiescent center maintenance; root development

DOI:  https://doi.org/10.3390/plants13192760
J Biol Chem. 2024 Oct 16. pii: S0021-9258(24)02395-0. [Epub ahead of print] 107893

Phosphorylation regulates the chromatin remodeler SMARCAD1 in nucleosome binding, ATP hydrolysis, and histone exchange.

Briana L Aboulache, Nicole M Hoitsma, Karolin Luger.

  Maintaining the dynamic structure of chromatin is critical for regulating the cellular processes that require access to the DNA template, such as DNA damage repair, transcription, and replication. Histone chaperones and ATP-dependent chromatin remodeling factors facilitate transitions in chromatin structure by assembling and positioning nucleosomes through a variety of enzymatic activities. SMARCAD1 is a unique chromatin remodeler that combines the ATP-dependent ability to exchange histones, with the chaperone-like activity of nucleosome deposition. We have shown previously that phosphorylated SMARCAD1 exhibits reduced binding to nucleosomes. However, it is unknown how phosphorylation affects SMARCAD1's ability to perform its various enzymatic activities. Here we use mutational analysis, activity assays, and mass spectrometry, to probe SMARCAD1 regulation and to investigate the role of its flexible N-terminal region. We show that phosphorylation affects SMARCAD1 binding to nucleosomes, DNA, and histones H2A-H2B as well as ATP hydrolysis and histone exchange. Conversely, we report only a marginal effect of phosphorylation for histone H3-H4 binding and nucleosome assembly. In addition, the SMARCAD1 N-terminal region is revealed to be critical for nucleosome assembly and histone exchange. Together, this work examines the intricacies of how phosphorylation governs SMARCAD1 activity and provides insight into its complex regulation and diverse activities.

Keywords:  ATP hydrolysis; SMARCAD1; chromatin remodeling; histone chaperone; histone exchange; nucleosome; nucleosome assembly; phosphorylation; post-translational modification (PTM)

DOI:  https://doi.org/10.1016/j.jbc.2024.107893
Comput Biol Chem. 2024 Oct 10. pii: S1476-9271(24)00230-5. [Epub ahead of print]113 108242

Integration of 3D-QSAR, molecular docking, and machine learning techniques for rational design of nicotinamide-based SIRT2 inhibitors.

Aleksandra Ilic, Nemanja Djokovic, Teodora Djikic, Katarina Nikolic.

  Selective inhibitors of sirtuin-2 (SIRT2) are increasingly recognized as potential therapeutics for cancer and neurodegenerative diseases. Derivatives of 5-((3-amidobenzyl)oxy)nicotinamides have been identified as some of the most potent and selective SIRT2 inhibitors reported to date (Ai et al., 2016; Ai et al., 2023, Baroni et al., 2007). In this study, a 3D-QSAR (3D-Quantitative Structure-Activity Relationship) model was developed using a dataset of 86 nicotinamide-based SIRT2 inhibitors from the literature, along with GRIND-derived pharmacophore models for selected inhibitors. External validation parameters emphasized the reliability of the 3D-QSAR model in predicting SIRT2 inhibition within the defined applicability domain. The interpretation of the 3D-QSAR model facilitated the generation of GRIND-derived pharmacophore models, which in turn enabled the design of novel SIRT2 inhibitors. Furthermore, based on molecular docking results for the SIRT1-3 isoforms, two classification models were developed: a SIRT1/2 model using the Naive Bayes algorithm and a SIRT2/3 model using the k-nearest neighbors algorithm, to predict the selectivity of inhibitors for SIRT1/2 and SIRT2/3. External validation parameters of the selectivity models confirmed their predictive power. Ultimately, the integration of 3D-QSAR, selectivity models and prediction of ADMET properties facilitated the identification of the most promising selective SIRT2 inhibitors for further development.

Keywords:  3D-QSAR; ADMET; Machine learning; Molecular docking; SIRT2 inhibitors

DOI:  https://doi.org/10.1016/j.compbiolchem.2024.108242
Bioorg Med Chem Lett. 2024 Oct 10. pii: S0960-894X(24)00388-3. [Epub ahead of print]114 129986

Design and optimization of novel Tetrahydro-β-carboline-based HDAC inhibitors with potent activities against tumor cell growth and metastasis.

Shule Fan, Zeyi Wan, Yuhua Qu, Wenxia Lu, Xiangzhi Li, Feifei Yang, Hua Zhang.

  Histone deacetylases (HDACs) are validated drug targets for various therapeutic applications. A series of Tetrahydro-β-carboline-based hydroxamate derivatives, designed as HDAC inhibitors (HDACis), were synthesized. Compound 11g exhibited strong inhibitory activity against HDAC1 and the A549 cancer cell line. Additionally, this compound increased the levels of acetylated histone H3 and H4. Notably, 11g effectively arrested A549 cells in the G2/M phase and also increased ROS production and DNA damage, thereby inducing apoptosis. Further molecular docking experiments illustrated the potential interactions between compound 11g and HDAC1. These findings suggested that the novel Tetrahydro-β-carboline-based HDACis could serve as a promising framework for further optimization as anticancer agents.

Keywords:  Antitumor; HDAC inhibitors; Hydroxamate; Tetrahydro-β-carboline

DOI:  https://doi.org/10.1016/j.bmcl.2024.129986
PLoS Pathog. 2024 Oct 15. 20(10): e1012451

A master regulator of central carbon metabolism directly activates virulence gene expression in attaching and effacing pathogens.

Kabo R Wale, Nicky O'Boyle, Rebecca McHugh, Ester Serrano, David Mark, Gillian R Douce, James P R Connolly, Andrew J Roe.

The ability of the attaching and effacing pathogens enterohaemorrhagic Escherichia coli (EHEC) and Citrobacter rodentium to overcome colonisation resistance is reliant on a type 3 secretion system used to intimately attach to the colonic epithelium. This crucial virulence factor is encoded on a pathogenicity island known as the Locus of Enterocyte Effacement (LEE) but its expression is regulated by several core-genome encoded transcription factors. Here, we unveil that the core transcription factor PdhR, traditionally known as a regulator of central metabolism in response to cellular pyruvate levels, is a key activator of the LEE. Through genetic and molecular analyses, we demonstrate that PdhR directly binds to a specific motif within the LEE master regulatory region, thus activating type 3 secretion directly and enhancing host cell adhesion. Deletion of pdhR in EHEC significantly impacted the transcription of hundreds of genes, with pathogenesis and protein secretion emerging as the most affected functional categories. Furthermore, in vivo studies using C. rodentium, a murine model for EHEC infection, revealed that PdhR is essential for effective host colonization and maximal LEE expression within the host. Our findings provide new insights into the complex regulatory networks governing bacterial pathogenesis. This research highlights the intricate relationship between virulence and metabolic processes in attaching and effacing pathogens, demonstrating how core transcriptional regulators can be co-opted to control virulence factor expression in tandem with the cell's essential metabolic circuitry.

DOI: https://doi.org/10.1371/journal.ppat.1012451
Microbiol Spectr. 2024 Oct 18. e0201124

Sirtuin-dependent reversible lysine acetylation of the o-succinylbenzoyl-coenzyme A synthetase of Bacillus subtilis.

Rachel M Burckhardt, Jorge C Escalante-Semerena.

  Reversible lysine acylation (RLA) is a conserved posttranslational modification that cells of all domains of life use to regulate the biological function of proteins, some of which have enzymatic activity. Many AMP-forming organic acid:CoA ligases are regulated via acylation in prokaryotes and eukaryotes. Here, we report the acetylation of the o-succinylbenzoyl-CoA synthetase (EC 6.2.1.26) of Bacillus subtilis (BsMenE) by the GCN5-related acetyltransferase (GNAT) AcuA enzyme of this bacterium. BsMenE is part of the metabolic pathway that assembles menaquinone (MK), an essential component of the electron transport chain in B. subtilis. We demonstrate that the active-site lysine 471 (K471) of BsMenE is acetylated specifically by BsAcuA, and that acetylated BsMenE (BsMenEAc) is deacetylated by the NAD+-dependent sirtuin (BsSrtN) of this bacterium. The in vivo analyses performed in this study were done in an Escherichia coli ΔmenE strain because the enzymatic activity of MenE is essential in B. subtilis, but not in E. coli. The use of a heterologous system allowed us to assess the effect of acetylation on BsMenE function under MK-dependent growth conditions. Based on our in vivo data, we suggest that regulation of BsMenE by RLA reduces MK production, negatively affecting the growth rate and yield of the culture.IMPORTANCEReversible lysine acylation (RLA) is a posttranslational modification used by all cells to rapidly control the biological function of proteins. Herein, we identify an acetyltransferase and deacetylase in the soil bacterium Bacillus subtilis that can modify/demodify an enzyme required for the synthesis of menaquinone (MK), an essential electron carrier involved in respiration in cells of all domains of life. Based on our data, we suggest that under some as-yet-undefined physiological conditions, B. subtilis modulates MK biosynthesis, which changes the flux of electrons through the electron transport chain of this bacterium. To our knowledge, this is the first example of control of respiration by RLA.

Keywords:  Bacillus subtilis metabolism; Gcn5-related acetyltransferases; OSB-CoA synthetase; menaquinone biosynthesis; metabolic stress; proton motive force control; sirtuin deacylase

DOI:  https://doi.org/10.1128/spectrum.02011-24
J Biochem Mol Toxicol. 2024 Nov;38(11): e70018

SIRT2 deacetylates and decreases the expression of FOXM1 in colon cancer.

Baris Yildiz, Ramazan Demirel, Jonas J Staudacher, Hatice Beseren, Gulden Yildiz, Ali Emre Akpinar, Seong-Hoon Park, Ozkan Ozden.

  New FOXM1-specific inhibitors with the potential to be used for therapeutic purposes are under extensive research. We hypothesized that deacetylation of FOXM1 would decrease protein expression, thus providing novel therapeutic management of colon cancers. Immunostaining was used to determine FOXM1 and SIRT2 expressions in human colon cancer tissue microarrays (n = 90) from Stage I to Stage IV. SIRT2-FOXM1 interaction was evaluated in colon cancer cells using immunoprecipitation. Deacetylation of FOXM1 via SIRT2 was determined using in vitro deacetylation assays. FOXM1 could be hyper-acetylated when p300 and pCAF histone acetyltransferases were administered alongside deacetylase inhibitors. We detected that SIRT2 and FOXM1 physically interacted, and SIRT2 deacetylated FOXM1 in vitro. SIRT2 overexpression led to a significant decrease while knockdown of SIRT2 increased the FOXM1 expression in HCT116 human colon carcinoma cells. In the analysis of 90 human colorectal cancer samples, high SIRT2 expression was observed in about 49% of colorectal cancer, intermediate in 29%, and low or no staining in 22%. Strong SIRT2 expression was found to be negatively associated with the FOXM1 staining in our clinical cohort. This study reveals a molecular interaction and association between SIRT2 and FOXM1 expression in colon cancer cell lines and human colon cancer samples, and suggests that targeting SIRT2 activity using small molecule modulators may be a promising therapeutic approach for colorectal cancer.

Keywords:  CRC; FOXM1; SirReal2; deacetylation; posttranslational regulation; resveratrol; sirtuin

DOI:  https://doi.org/10.1002/jbt.70018
Cell Stress Chaperones. 2024 Oct 10. pii: S1355-8145(24)00119-6. [Epub ahead of print]

Flow Cytometry FRET Reveals Posttranslational Modifications Drive Protein Phosphatase-5 Conformational Changes in Mammalian Cells.

Rebecca A Sager, Sarah J Backe, Jennifer Heritz, Mark R Woodford, Dimitra Bourboulia, Mehdi Mollapour.

  The serine/threonine protein phosphatase 5 (PP5) plays an essential role in regulating hormone and stress-induced signaling networks as well as extrinsic apoptotic pathways in cells. Unlike other protein phosphatases, PP5 possesses both regulatory and catalytic domains, and its function is further modulated through post-translational modifications (PTMs). PP5 contains a tetratricopeptide repeat (TPR) domain, which usually inhibits its phosphatase activity by blocking the active site (closed conformation). Certain activators bind to the PP5-TPR domain, alleviating this inhibition and allowing the catalytic domain to adopt an active (open) conformation. While this mechanism has been proposed based on structural and biophysical studies, PP5 conformational changes and activity has yet to be observed in cells. Here, we designed and developed a flow cytometry-based fluorescence resonance energy transfer (FC-FRET) method, enabling real-time observation of PP5 autoinhibition and activation within live mammalian cells. By quantifying FRET efficiency using sensitized emission, we established a standardized and adaptable data acquisition workflow. Our findings revealed that, in a cellular context, PP5 exists in multiple conformational states, none of which alone fully predict its activity. Additionally, we have demonstrated that PTMs such as phosphorylation and SUMOylation impact PP5 conformational changes, representing a significant advancement in our understanding of its regulatory mechanisms.

Keywords:  PP5; Phosphorylation; SUMOylation; Serine/threonine protein phosphatase-5; flow cytometry; fluorescence resonance energy transfer (FRET); post translational modification

DOI:  https://doi.org/10.1016/j.cstres.2024.10.002
Sci Adv. 2024 Oct 18. 10(42): eado7720

Temporal regulation of acetylation status determines PARP1 role in DNA damage response and metabolic homeostasis.

Witty Tyagi, Sanjeev Das.

Poly(ADP-ribose) polymerase 1 (PARP1) is an abundant nuclear protein involved in DNA repair, chromatin structure, and transcription. However, the regulation of its different functions remains poorly understood. Here, we report the role of PARP1 acetylation status in modulating its DNA repair and transactivation functions. We demonstrate that histone deacetylase 5 (HDAC5) determines PARP1 acetylation at Lys498 and Lys521 sites. HDAC5-mediated deacetylation at Lys498 site regulates PARP1 DNA damage response and facilitates efficient recruitment of DNA repair factors at damaged sites, thereby promoting cell survival. Additionally, HDAC5-mediated deacetylation at Lys521 site promotes PARP1 coactivator function, resulting in induction of proliferative and metabolic genes in an activating transcription factor 4-dependent manner. Thus, PARP1 induces metabolic adaptation to spur malignant phenotype. Our studies in mouse tumor models suggest that pharmacological inhibition of PARP1 enzymatic activity does not block tumor progression robustly as transactivation function remains unperturbed. These findings provide key mechanistic insights into PARP1 regulation and expand its role in tumor development.

DOI: https://doi.org/10.1126/sciadv.ado7720
ACS Med Chem Lett. 2024 Oct 10. 15(10): 1715-1723

Design, Synthesis, and Structural Evaluation of Acetylated Phenylthioketone Inhibitors of HDAC10.

Juana Goulart Stollmaier, Paris R Watson, David W Christianson.

Histone deacetylase 10 (HDAC10) is unique among the greater HDAC family due to its unusually narrow substrate specificity as a polyamine deacetylase, specifically as an N 8-acetylspermidine hydrolase. Polyamines are essential for cell growth and proliferation; consequently, inhibition of polyamine deacetylation represents a possible strategy for cancer chemotherapy. In this work, we have designed six acetylated phenylthioketone inhibitors of HDAC10 containing positively charged para- and meta-substituted amino groups designed to target interactions with E274, the gatekeeper that recognizes the positively charged ammonium group of the substrate N 8-acetylspermidine. We prepared each of these inhibitors through a short synthetic route of six steps. By adapting a low-cost colorimetric activity assay, we measured low-micromolar IC50 values for these compounds against a humanized construct of zebrafish HDAC10 (A24E-D94A HDAC10). Selected inhibitors were cocrystallized with A24E-D94A zebrafish HDAC10 and zebrafish HDAC6 to provide insight into class IIb isozyme affinity and selectivity.

DOI: https://doi.org/10.1021/acsmedchemlett.4c00293
Biosens Bioelectron. 2024 Oct 10. pii: S0956-5663(24)00849-2. [Epub ahead of print]267 116842

Quantitative dynamics of intracellular NMN by genetically encoded biosensor.

Liuqing Chen, Pei Wang, Guan Huang, Wenxiang Cheng, Kaijing Liu, Qiuliyang Yu.

  Nicotinamide mononucleotide (NMN) is the direct precursor and a major booster of NAD+ with increasing applications in NAD+- and aging-related pathologies. However, measuring live cell NMN dynamics was not possible, leaving key questions in NMN uptake and intracellular regulation unanswered. Here we developed genetically encoded bioluminescent and fluorescent sensors to quantify subcellular NMN in live cells by engineering specific NMN-responsive protein scaffolds fused to luciferase and fluorescent proteins. The sensor dissected the multimechanistic uptake of exogenous NMN and nicotinamide riboside (NR) in live cells and further measured the NMN levels across different subcellular compartments, as well as the perturbed NMN/NAD+ ratios by external supplements. Moreover, we measured the NMN regulation by NAD(H) hydrolase Nudts and peroxisomal carrier Pxmp2 and identified Slc25a45 as a potential mitochondrial NMN regulator for its unique fingerprint on the local NMN/NAD+ ratio. Collectively, the genetically encoded sensors provide a useful tool for visualizing NMN metabolism.

Keywords:  Biosensor; Metabolism; NAD(+); NMN; Subcellular

DOI:  https://doi.org/10.1016/j.bios.2024.116842