bims-toxgon 2023-09-24 papers

bims-toxgon

Biomed News

on Toxoplasma gondii metabolism

Issue of 2023–09–24
sixteen papers selected by
Lakesh Kumar, BITS Pilani

F-actin and myosin F control apicoplast elongation dynamics which drive apicoplast-centrosome association in Toxoplasma gondii.
Phytohormones regulate asexual Toxoplasma gondii replication.
Where is the EXIT? Phenotypic screens for new egress factors in apicomplexan parasites.
Toxoplasma gondii autophagy-related protein ATG7 maintains apicoplast inheritance by stabilizing and lipidating ATG8.
Gene editing of putative cAMP and Ca2+ -regulated proteins using an efficient cloning-free CRISPR/Cas9 system in Trypanosoma cruzi.
Label-free quantitative proteomic analyses of mouse astrocytes provides insight into the host response mechanism at different developmental stages of Toxoplasma gondii.
Nasal vaccination of six squirrel monkeys (Saimiri sciureus): Improved immunization protocol against Toxoplasma gondii with a nanoparticle-born vaccine.
Connections between metabolism and epigenetic modifications in cancer.
Ovine placental explants: A new ex vivo model to study host‒pathogen interactions in reproductive pathogens.
Disruption of the inositol phosphorylceramide synthase gene affects Trypanosoma cruzi differentiation and infection capacity.
Critical interdependencies between Plasmodium nutrient flux and drugs.
PARylated PDHE1α generates acetyl-CoA for local chromatin acetylation and DNA damage repair.
Histone Acetylation and Deacetylation - Mechanistic Insights from Structural Biology.
Acetylation in pathogenesis: Revealing emerging mechanisms and therapeutic prospects.
Identification of SIRT3 as an eraser of H4K16la.
Epigenetic meets metabolism: novel vulnerabilities to fight cancer.

mBio. 2023 Sep 21. e0164023

F-actin and myosin F control apicoplast elongation dynamics which drive apicoplast-centrosome association in Toxoplasma gondii.

Parvathi Madhavi Devarakonda, Valeria Sarmiento, Aoife T Heaslip.

  Toxoplasma gondii contains an essential plastid organelle called the apicoplast that is necessary for fatty acid, isoprenoid, and heme synthesis. Perturbations affecting apicoplast function or inheritance lead to parasite death. The apicoplast is a single copy organelle and, therefore, must be divided so that each daughter parasite inherits an apicoplast during cell division. In this study, we identify new roles for F-actin and an unconventional myosin motor, TgMyoF, in this process. First, loss of TgMyoF and actin lead to an accumulation of apicoplast vesicles in the cytosol indicating a role for this actomyosin system in apicoplast protein trafficking or morphological integrity of the organelle. Second, live cell imaging reveals that during division the apicoplast is highly dynamic, exhibiting branched, U-shaped and linear morphologies that are dependent on TgMyoF and actin. In parasites where movement was inhibited by the depletion of TgMyoF, the apicoplast fails to associate with the parasite centrosomes. Thus, this study provides crucial new insight into mechanisms controlling apicoplast-centrosome association, a vital step in the apicoplast division cycle, which ensures that each daughter inherits a single apicoplast. IMPORTANCE Toxoplasma gondii and most other parasites in the phylum Apicomplexa contain an apicoplast, a non-photosynthetic plastid organelle required for fatty acid, isoprenoid, iron-sulfur cluster, and heme synthesis. Perturbation of apicoplast function results in parasite death. Thus, parasite survival critically depends on two cellular processes: apicoplast division to ensure every daughter parasite inherits a single apicoplast, and trafficking of nuclear encoded proteins to the apicoplast. Despite the importance of these processes, there are significant knowledge gaps in regards to the molecular mechanisms which control these processes; this is particularly true for trafficking of nuclear-encoded apicoplast proteins. This study provides crucial new insight into the timing of apicoplast protein synthesis and trafficking to the apicoplast. In addition, this study demonstrates how apicoplast-centrosome association, a key step in the apicoplast division cycle, is controlled by the actomyosin cytoskeleton.

Keywords:  Toxoplasma gondii; actin; apicomplexan parasites; apicoplast; centrosomes; myosin; vesicle transport

DOI:  https://doi.org/10.1128/mbio.01640-23
Parasitol Res. 2023 Sep 19.

Phytohormones regulate asexual Toxoplasma gondii replication.

Tina Wagner, Berit Bangoura, Stefanie Wiedmer, Arwid Daugschies, Ildiko Rita Dunay.

  The protozoan Toxoplasma gondii (T. gondii) is a zoonotic disease agent causing systemic infection in warm-blooded intermediate hosts including humans. During the acute infection, the parasite infects host cells and multiplies intracellularly in the asexual tachyzoite stage. In this stage of the life cycle, invasion, multiplication, and egress are the most critical events in parasite replication. T. gondii features diverse cell organelles to support these processes, including the apicoplast, an endosymbiont-derived vestigial plastid originating from an alga ancestor. Previous studies have highlighted that phytohormones can modify the calcium-mediated secretion, e.g., of adhesins involved in parasite movement and cell invasion processes. The present study aimed to elucidate the influence of different plant hormones on the replication of asexual tachyzoites in a human foreskin fibroblast (HFF) host cell culture. T. gondii replication was measured by the determination of T. gondii DNA copies via qPCR. Three selected phytohormones, namely abscisic acid (ABA), gibberellic acid (GIBB), and kinetin (KIN) as representatives of different plant hormone groups were tested. Moreover, the influence of typical cell culture media components on the phytohormone effects was assessed. Our results indicate that ABA is able to induce a significant increase of T. gondii DNA copies in a typical supplemented cell culture medium when applied in concentrations of 20 ng/μl or 2 ng/μl, respectively. In contrast, depending on the culture medium composition, GIBB may potentially serve as T. gondii growth inhibitor and may be further investigated as a potential treatment for toxoplasmosis.

Keywords:  Abscisic acid; Apicomplexa; Coccidia; Gibberellic acid; Multiplication

DOI:  https://doi.org/10.1007/s00436-023-07968-3
Mol Microbiol. 2023 Sep 22.

Where is the EXIT? Phenotypic screens for new egress factors in apicomplexan parasites.

Elena Jimenéz-Ruiz, Wei Li, Markus Meissner.

  Apicomplexans, such as Plasmodium and Toxoplasma are obligate intracellular parasites that invade, replicate and finally EXIT their host cell. During replication within a parasitophorous vacuole (PV), the parasites establish an extensive F-actin-containing network that connects individual parasites and is required for material exchange, recycling and the final steps of daughter cell assembly. After multiple rounds of replication, the parasites exit the host cell involving multiple signalling cascades, disassembly of the network, secretion of microneme proteins and activation of the acto-myosin motor. Blocking the host cell EXIT process leads to the formation of large PVs, making the screening for genes involved in exiting the cell relatively straightforward. Given that apicomplexans are highly diverse from other eukaryotes, approximately 30% of all genes are annotated as hypothetical, some apicomplexan-specific factors are likely to be critical during EXIT. This motivated several labs to design and perform forward genetic and phenotypic screens using various approaches, such as random insertion mutagenesis, temperature-sensitive mutants and, more recently, CRISPR/Cas9-mediated targeted editing and conditional mutagenesis. Here we will provide an overview of the technological developments over recent years and the most successful stories that led to the identification of new critical factors in Toxoplasma gondii.

Keywords:  CRISPR/Cas9 screens; apicomplexan parasites; egress factors; forward genetic screens

DOI:  https://doi.org/10.1111/mmi.15166
Biochim Biophys Acta Mol Basis Dis. 2023 Sep 20. pii: S0925-4439(23)00257-0. [Epub ahead of print] 166891

Toxoplasma gondii autophagy-related protein ATG7 maintains apicoplast inheritance by stabilizing and lipidating ATG8.

Mimi Wu, Jiaqi Ying, Xuejing Lin, Chao Xu, Xiaozi Zheng, Yi Zheng, Zhouxi Fang, Baolong Yan, Nu Zhang, Yani Mou, Feng Tan.

  ATG8/LC3-mediated autophagosome formation is a key rate-limiting step in the process of autophagy. The parasitic protist Toxoplasma gondii possesses a single ATG8 homolog (TgATG8), which can localize to either cytosolic autophagosome involved in delivery of autophagic material in bradyzoites, or the outermost membrane of apicoplast, a nonphotosynthetic plastid-like organelle, responsible for maintaining homeostasis in tachyzoites. However, mechanisms that regulate TgATG8 remain insufficiently understood. Here, a TgATG7 conditional knockdown line that we have generated is severely impaired in parasite's growth and exhibits significant defects in the organelle level, strikingly with a fragmentation of the mitochondrial network and a loss of the apicoplast. Specific TgATG7C1133S point mutant complemented line showed that these defects were associated with its E1-type enzyme activity. Both depletion of TgATG7 and mutation of its catalytic cysteine 1133 hindered TgATG8 lipidation and apicoplast localization. Unexpectedly, we also found that depletion of TgATG7 reduced the unlipidated TgATG8 protein level. Subsequently, we determined that TgATG7 was able to interact with TgATG8 directly via its C-terminal domain and multi-monoubiquitination stimulated proteasome-dependent degradation of TgATG8, while TgATG7 could inhibit the degradation through stabilization of TgATG8. Additionally, we identified a putative TgATG8 interacting fragment of TgATG7, 1281-1290aa. Depletion of the fragment impaired the parasite growth and apicoplast inheritance. To our knowledge, our study is the first to elucidate the role of TgATG7 and the ubiquitin-proteasome system in synergistically regulating the non-lipidated pool of TgATG8, suggesting a potential homeostatic mechanism responsible for balancing autophagic activity in T. gondii.

Keywords:  ATG7; ATG8; Apicoplast; Autophagy; Toxoplasma gondii; Ubiquitination

DOI:  https://doi.org/10.1016/j.bbadis.2023.166891
J Eukaryot Microbiol. 2023 Sep 19. e12999

Gene editing of putative cAMP and Ca2+ -regulated proteins using an efficient cloning-free CRISPR/Cas9 system in Trypanosoma cruzi.

Miguel A Chiurillo, Milad Ahmed, César González, Aqsa Raja, Noelia Lander.

  Trypanosoma cruzi, the agent of Chagas disease, must adapt to a diversity of environmental conditions that it faces during its life cycle. The adaptation to these changes is mediated by signaling pathways that coordinate the cellular responses to the new environmental settings. Cyclic AMP (cAMP) and Calcium (Ca2+ ) signaling pathways regulate critical cellular processes in this parasite, such as differentiation, osmoregulation, host cell invasion and cell bioenergetics. Although the use of CRISPR/Cas9 technology prompted reverse genetics approaches for functional analysis in T. cruzi, it is still necessary to expand the toolbox for genome editing in this parasite, as for example to perform multigene analysis. Here we used an efficient T7RNAP/Cas9 strategy to tag and delete three genes predicted to be involved in cAMP and Ca2+ signaling pathways: a putative Ca2+ /calmodulin-dependent protein kinase (CAMK), Flagellar Member 6 (FLAM6) and Cyclic nucleotide-binding domain/C2 domain-containing protein (CC2CP). We endogenously tagged these three genes and determined the subcellular localization of the tagged proteins. Furthermore, the strategy used to knockout these genes allows us to presume that TcCC2CP is an essential gene in T. cruzi epimastigotes. Our results will open new venues for future research on the role of these proteins in T. cruzi.

Keywords:  calcium ions; cyclic AMP; essential genes; genome editing; trypanosomes

DOI:  https://doi.org/10.1111/jeu.12999
PLoS Negl Trop Dis. 2023 Sep 18. 17(9): e0011102

Label-free quantitative proteomic analyses of mouse astrocytes provides insight into the host response mechanism at different developmental stages of Toxoplasma gondii.

Huanhuan Xie, Hang Sun, Hongjie Dong, Lisha Dai, Haozhi Xu, Lixin Zhang, Qi Wang, Junmei Zhang, Guihua Zhao, Chao Xu, Kun Yin.

Toxoplasma gondii (T. gondii) is an opportunistic parasite that can infect the central nervous system (CNS), causing severe toxoplasmosis and behavioral cognitive impairment. Mortality is high in immunocompromised individuals with toxoplasmosis, most commonly due to reactivation of infection in the CNS. There are still no effective vaccines and drugs for the prevention and treatment of toxoplasmosis. There are five developmental stages for T. gondii to complete life cycle, of which the tachyzoite and bradyzoite stages are the key to the acute and chronic infection. In this study, to better understanding of how T. gondii interacts with the host CNS at different stages of infection, we constructed acute and chronic infection models of T. gondii in astrocytes, and used label-free proteomics to detect the proteome changes before and after infection, respectively. A total of 4676 proteins were identified, among which 163 differentially expressed proteins (fold change ≥ 1.5 or ≤ 0.67 and p-value ≤ 0.05) including 109 up-regulated proteins and 54 down-regulated proteins in C8-TA vs C8 group, and 719 differentially expressed proteins including 495 up-regulated proteins and 224 down-regulated proteins in C8-BR vs C8-TA group. After T. gondii tachyzoites infected astrocytes, differentially expressed proteins were enriched in immune-related biological processes to promote the formation of bradyzoites and maintain the balance of T. gondii, CNS and brain. After T. gondii bradyzoites infected astrocytes, the differentially expressed proteins up-regulated the host's glucose metabolism, and some up-regulated proteins were strongly associated with neurodegenerative diseases. These findings not only provide new insights into the psychiatric pathogenesis of T. gondii, but also provide potential targets for the treatment of acute and chronic Toxoplasmosis.

DOI: https://doi.org/10.1371/journal.pntd.0011102
Int J Parasitol Parasites Wildl. 2023 Dec;22 69-74

Nasal vaccination of six squirrel monkeys (Saimiri sciureus): Improved immunization protocol against Toxoplasma gondii with a nanoparticle-born vaccine.

François Fasquelle, Angelo Scuotto, Anaïs-Camille Vreulx, Thierry Petit, Thomas Charpentier, Didier Betbeder.

Toxoplasma gondii is an intracellular protozoon found worldwide, which completes its life cycle between felids (its definitive host) and other warm-blooded animals. While the infection rarely leads to severe complications in humans, many animal species are very susceptible to this infection, for example the squirrel monkey (Saimiri sciureus) which is the subject of this study. Toxoplasmosis is lethal for 80% of cases in this species, and fatal outbreaks are frequently reported in zoological parks. No efficient treatment exists, but a new vaccine prepared with maltodextrin nanoparticles containing killed T. gondii antigens has been tested recently in French zoos. The animals were immunized through heterologous administrations, with two nasal doses at one-month interval, followed by nasal/subcutaneous boosts thereafter. No death has been reported since the beginning of this vaccination campaign, but we felt the protocol could be simplified. Here, an improved and less-invasive immunization protocol was evaluated on 6 Saimiri sciureus in the French zoo La Palmyre. It consisted of two nasal administrations at one-month interval, followed by a nasal boost at 6 months. A specific memory T-cell immunity was observed by ELISPOT after two administrations in all the animals, without humoral responses. The results suggest that 2 nasal administrations induce a protective immune response against T. gondii infection and might be sufficient to induce a strong Tcell memory, further improving immunity.

DOI: https://doi.org/10.1016/j.ijppaw.2023.09.002
Med Rev (Berl). 2021 Dec;1(2): 199-221

Connections between metabolism and epigenetic modifications in cancer.

Guangchao Wang, Jingdong J Han.

  How cells sense and respond to environmental changes is still a key question. It has been identified that cellular metabolism is an important modifier of various epigenetic modifications, such as DNA methylation, histone methylation and acetylation and RNA N6-methyladenosine (m6A) methylation. This closely links the environmental nutrient availability to the maintenance of chromatin structure and gene expression, and is crucial to regulate cellular homeostasis, cell growth and differentiation. Cancer metabolic reprogramming and epigenetic alterations are widely observed, and facilitate cancer development and progression. In cancer cells, oncogenic signaling-driven metabolic reprogramming modifies the epigenetic landscape via changes in the key metabolite levels. In this review, we briefly summarized the current evidence that the abundance of key metabolites, such as S-adenosyl methionine (SAM), acetyl-CoA, α-ketoglutarate (α-KG), 2-hydroxyglutarate (2-HG), uridine diphospho-N-acetylglucosamine (UDP-GlcNAc) and lactate, affected by metabolic reprogramming plays an important role in dynamically regulating epigenetic modifications in cancer. An improved understanding of the roles of metabolic reprogramming in epigenetic regulation can contribute to uncover the underlying mechanisms of metabolic reprogramming in cancer development and identify the potential targets for cancer therapies.

Keywords:  DNA methylation; RNA m6A; cancer metabolic reprogramming; epigenetic modifications; histone acetylation; histone methylation

DOI:  https://doi.org/10.1515/mr-2021-0015
Theriogenology. 2023 Sep 15. pii: S0093-691X(23)00368-0. [Epub ahead of print]212 157-171

Ovine placental explants: A new ex vivo model to study host‒pathogen interactions in reproductive pathogens.

Pilar Horcajo, Luis Miguel Ortega-Mora, Julio Benavides, Roberto Sánchez-Sánchez, Rafael Amieva, Esther Collantes-Fernández, Iván Pastor-Fernández.

  Reproductive failure is one of the main performance constraints in ruminant livestock. Transmissible agents such as Toxoplasma gondii and Neospora caninum are commonly involved in the occurrence of abortion in ruminants, but little is known about the mechanisms involved. While in vivo models are optimal for the study of abortion pathogenesis, they have a high economic cost and come with ethical concerns. Unfortunately, alternative in vitro models fail to replicate the complex in vivo placental structure. To overcome the limitations of currently available models, we developed an ex vivo model based on the cultivation of fresh and cryopreserved sheep placental explants, enabling the biobanking of tissues. Reproducible and simple markers of tissue integrity (histology, RNA concentrations), viability (resazurin reduction), and functionality (synthesis of steroid hormones) were also investigated, allowing a clear quality assessment of the model. This work shows that, similar to fresh explants, tissues cryopreserved in ethylene glycol using slow freezing rates maintain not only their structure and function but also their receptivity to T. gondii and N. caninum infection. In addition, the findings demonstrate that explant lifespan is mainly limited by the culture method, with protocols requiring improvements to extend it beyond 2 days. These findings suggest that cryopreserved tissues can be exploited to study the initial host‒pathogen interactions taking place in the placenta, thus deepening the knowledge of the specific mechanisms that trigger reproductive failure in sheep. Importantly, this work paves the way for the development of similar models in related species and contributes to the reduction of experimental animal use in the future.

Keywords:  Ex vivo model; Neospora caninum; Ovine; Placental explant; Reproductive failure; Toxoplasma gondii

DOI:  https://doi.org/10.1016/j.theriogenology.2023.09.009
PLoS Negl Trop Dis. 2023 Sep 20. 17(9): e0011646

Disruption of the inositol phosphorylceramide synthase gene affects Trypanosoma cruzi differentiation and infection capacity.

Nailma S Aprigio-Santos, Carlos F Estevez-Castro, Juan P Macedo, Daniela F Chame, Thiago Castro-Gomes, Mariana Santos-Cardoso, Gabriela A Burle-Caldas, Courtney N Covington, Patrick G Steel, Terry K Smith, Paul W Denny, Santuza M R Teixeira.

Sphingolipids (SLs) are essential components of all eukaryotic cellular membranes. In fungi, plants and many protozoa, the primary SL is inositol-phosphorylceramide (IPC). Trypanosoma cruzi is a protozoan parasite that causes Chagas disease (CD), a chronic illness for which no vaccines or effective treatments are available. IPC synthase (IPCS) has been considered an ideal target enzyme for drug development because phosphoinositol-containing SL is absent in mammalian cells and the enzyme activity has been described in all parasite forms of T. cruzi. Furthermore, IPCS is an integral membrane protein conserved amongst other kinetoplastids, including Leishmania major, for which specific inhibitors have been identified. Using a CRISPR-Cas9 protocol, we generated T. cruzi knockout (KO) mutants in which both alleles of the IPCS gene were disrupted. We demonstrated that the lack of IPCS activity does not affect epimastigote proliferation or its susceptibility to compounds that have been identified as inhibitors of the L. major IPCS. However, disruption of the T. cruzi IPCS gene negatively affected epimastigote differentiation into metacyclic trypomastigotes as well as proliferation of intracellular amastigotes and differentiation of amastigotes into tissue culture-derived trypomastigotes. In accordance with previous studies suggesting that IPC is a membrane component essential for parasite survival in the mammalian host, we showed that T. cruzi IPCS null mutants are unable to establish an infection in vivo, even in immune deficient mice.

DOI: https://doi.org/10.1371/journal.pntd.0011646
Trends Parasitol. 2023 Sep 14. pii: S1471-4922(23)00212-X. [Epub ahead of print]

Critical interdependencies between Plasmodium nutrient flux and drugs.

Isabelle G Henshall, Tobias Spielmann.

  Nutrient import and waste efflux are critical dependencies for intracellular Plasmodium falciparum parasites. Nutrient transport proteins are often lineage specific and can provide unique targets for antimalarial drug development. P. falciparum nutrient transport pathways can be a double-edged sword for the parasite, not only mediating the import of nutrients and excretion of waste products but also providing an access route for drugs. Here we briefly summarise the nutrient acquisition pathways of intracellular P. falciparum blood-stage parasites and then highlight how these pathways influence many aspects relevant to antimalarial drugs, resulting in complex and often underappreciated interdependencies.

Keywords:  Plasmodium; drugs; malaria; nutrients; resistance; waste

DOI:  https://doi.org/10.1016/j.pt.2023.08.008
Nat Struct Mol Biol. 2023 Sep 21.

PARylated PDHE1α generates acetyl-CoA for local chromatin acetylation and DNA damage repair.

Jun Zhang, Feng Chen, Yuan Tian, Wenchao Xu, Qian Zhu, Zhenhai Li, Lingyu Qiu, Xiaopeng Lu, Bin Peng, Xiangyu Liu, Haiyun Gan, Baohua Liu, Xingzhi Xu, Wei-Guo Zhu.

Chromatin relaxation is a prerequisite for the DNA repair machinery to access double-strand breaks (DSBs). Local histones around the DSBs then undergo prompt changes in acetylation status, but how the large demands of acetyl-CoA are met is unclear. Here, we report that pyruvate dehydrogenase 1α (PDHE1α) catalyzes pyruvate metabolism to rapidly provide acetyl-CoA in response to DNA damage. We show that PDHE1α is quickly recruited to chromatin in a polyADP-ribosylation-dependent manner, which drives acetyl-CoA generation to support local chromatin acetylation around DSBs. This process increases the formation of relaxed chromatin to facilitate repair-factor loading, genome stability and cancer cell resistance to DNA-damaging treatments in vitro and in vivo. Indeed, we demonstrate that blocking polyADP-ribosylation-based PDHE1α chromatin recruitment attenuates chromatin relaxation and DSB repair efficiency, resulting in genome instability and restored radiosensitivity. These findings support a mechanism in which chromatin-associated PDHE1α locally generates acetyl-CoA to remodel the chromatin environment adjacent to DSBs and promote their repair.

DOI: https://doi.org/10.1038/s41594-023-01107-3
Gene. 2023 Sep 17. pii: S0378-1119(23)00639-X. [Epub ahead of print] 147798

Histone Acetylation and Deacetylation - Mechanistic Insights from Structural Biology.

Avinash Patel, Yuan He, Ishwar Radhakrishnan.

Histones are subject to a diverse array of post-translational modifications. Among them, lysine acetylation is not only the most pervasive and dynamic modification but also highly consequential for regulating gene transcription. Although enzymes responsible for the addition and removal of acetyl groups were discovered almost 30 years ago, high-resolution structures of the enzymes in the context of their native complexes are only now beginning to become available, thanks to revolutionary technologies in protein structure determination and prediction. Here, we will review our current understanding of the molecular mechanisms of acetylation and deacetylation engendered by chromatin-modifying complexes, compare and contrast shared features, and discuss some of the pressing questions for future studies.

DOI: https://doi.org/10.1016/j.gene.2023.147798
Biomed Pharmacother. 2023 Sep 18. pii: S0753-3322(23)01317-3. [Epub ahead of print]167 115519

Acetylation in pathogenesis: Revealing emerging mechanisms and therapeutic prospects.

Nan Jiang, Wenyong Li, Shuanglin Jiang, Ming Xie, Ran Liu.

  Protein acetylation modifications play a central and pivotal role in a myriad of biological processes, spanning cellular metabolism, proliferation, differentiation, apoptosis, and beyond, by effectively reshaping protein structure and function. The metabolic state of cells is intricately connected to epigenetic modifications, which in turn influence chromatin status and gene expression patterns. Notably, pathological alterations in protein acetylation modifications are frequently observed in diseases such as metabolic syndrome, cardiovascular disorders, and cancer. Such abnormalities can result in altered protein properties and loss of function, which are closely associated with developing and progressing related diseases. In recent years, the advancement of precision medicine has highlighted the potential value of protein acetylation in disease diagnosis, treatment, and prevention. This review includes provocative and thought-provoking papers outlining recent breakthroughs in acetylation modifications as they relate to cardiovascular disease, mitochondrial metabolic regulation, liver health, neurological health, obesity, diabetes, and cancer. Additionally, it covers the molecular mechanisms and research challenges in understanding the role of acetylation in disease regulation. By summarizing novel targets and prognostic markers for the treatment of related diseases, we aim to contribute to the field. Furthermore, we discuss current hot topics in acetylation research related to health regulation, including N4-acetylcytidine and liquid-liquid phase separation. The primary objective of this review is to provide insights into the functional diversity and underlying mechanisms by which acetylation regulates proteins in disease contexts.

Keywords:  Epigenetic modifications; Molecular mechanism; Precision medicine; Protein acetylation; Therapeutic targets

DOI:  https://doi.org/10.1016/j.biopha.2023.115519
iScience. 2023 Oct 20. 26(10): 107757

Identification of SIRT3 as an eraser of H4K16la.

Zhuming Fan, Zhiyang Liu, Nan Zhang, Wenyu Wei, Ke Cheng, Hongyan Sun, Quan Hao.

  Lysine lactylation (Kla) is a novel histone post-translational modification discovered in late 2019. Later, HDAC1-3, were identified as the robust Kla erasers. While the Sirtuin family proteins showed weak eraser activities toward Kla, as reported. However, the catalytic mechanisms and physiological functions of HDACs and Sirtuins are not identical. In this study, we observed that SIRT3 exhibits a higher eraser activity against the H4K16la site than the other human Sirtuins. Crystal structures revealed the detailed binding mechanisms between lactyl-lysine peptides and SIRT3. Furthermore, a chemical probe, p-H4K16laAlk, was developed to capture potential Kla erasers from cell lysates. SIRT3 was captured by this probe and detected via proteomic analysis. And another chemical probe, p-H4K16la-NBD, was developed to detect the eraser-Kla delactylation processes directly via fluorescence indication. Our findings and chemical probes provide new directions for further investigating Kla and its roles in gene transcription regulation.

Keywords:  Enzymology; Molecular interaction; Protein; Structural biology

DOI:  https://doi.org/10.1016/j.isci.2023.107757
Cell Commun Signal. 2023 Sep 21. 21(1): 249

Epigenetic meets metabolism: novel vulnerabilities to fight cancer.

Domenica Scumaci, Qingfei Zheng.

  Histones undergo a plethora of post-translational modifications (PTMs) that regulate nucleosome and chromatin dynamics and thus dictate cell fate. Several evidences suggest that the accumulation of epigenetic alterations is one of the key driving forces triggering aberrant cellular proliferation, invasion, metastasis and chemoresistance pathways. Recently a novel class of histone "non-enzymatic covalent modifications" (NECMs), correlating epigenome landscape and metabolic rewiring, have been described. These modifications are tightly related to cell metabolic fitness and are able to impair chromatin architecture. During metabolic reprogramming, the high metabolic flux induces the accumulation of metabolic intermediate and/or by-products able to react with histone tails altering epigenome homeostasis. The accumulation of histone NECMs is a damaging condition that cancer cells counteracts by overexpressing peculiar "eraser" enzymes capable of removing these modifications preserving histones architecture. In this review we explored the well-established NECMs, emphasizing the role of their corresponding eraser enzymes. Additionally, we provide a parterre of drugs aiming to target those eraser enzymes with the intent to propose novel routes of personalized medicine based on the identification of epi-biomarkers which might be selectively targeted for therapy. Video Abstract.

Keywords:  Cancer onset and progression; Histone non-enzymatic covalent modification; Histone post-translational modification; Metabolic reprogramming

DOI:  https://doi.org/10.1186/s12964-023-01253-7