bims-toxgon 2024-09-01 papers

bims-toxgon

Biomed News

on Toxoplasma gondii metabolism

Issue of 2024‒09‒01
sixteen papers selected by
Lakesh Kumar, BITS Pilani

Enzymatically enhanced ultrastructure expansion microscopy unlocks expansion of in vitro Toxoplasma gondii cysts.
Host cell-specific metabolism of linoleic acid controls Toxoplasma gondii growth in cell culture.
Calcium tunneling through the ER and transfer to other organelles for optimal signaling in Toxoplasma gondii.
Single cell expression and chromatin accessibility of the Toxoplasma gondii lytic cycle identifies AP2XII-8 as an essential ribosome regulon driver.
AMPK: The energy sensor at the crossroads of aging and cancer.
Research Progress on the Mechanism and Function of Histone Acetylation Regulating the Interaction between Pathogenic Fungi and Plant Hosts.
Endocytosis in malaria parasites: An ultrastructural perspective of membrane interplay in a unique infection model.
Gut microbiota mediates anxiety-like behaviors induced by chronic infection of Toxoplasma gondii in mice.
Does AMPK bind glycogen in skeletal muscle or is the relationship correlative?
Acetylation of PGK1 at lysine 323 promotes glycolysis, cell proliferation, and metastasis in luminal A breast cancer cells.
Osteoclasts control endochondral ossification via regulating acetyl-CoA availability.
Stack-HDAC3i: A high-precision identification of HDAC3 inhibitors by exploiting a stacked ensemble-learning framework.
The Role of Sirtuin-1 Isoforms in Regulating Mitochondrial Function.
Conjoint analysis of succinylome and phosphorylome reveals imbalanced HDAC phosphorylation-driven succinylayion dynamic contibutes to lung cancer.
Nuclear ATP-citrate lyase regulates chromatin-dependent activation and maintenance of the myofibroblast gene program.
Emerging interactions between mitochondria and NAD+ metabolism in cardiometabolic diseases.

mSphere. 2024 Aug 27. e0032224

Enzymatically enhanced ultrastructure expansion microscopy unlocks expansion of in vitro Toxoplasma gondii cysts.

Kseniia Bondarenko, Floriane Limoge, Kayvon Pedram, Mathieu Gissot, Joanna C Young.

  Expansion microscopy (ExM) is an innovative approach to achieve super-resolution images without using super-resolution microscopes, based on the physical expansion of the sample. The advent of ExM has unlocked the detail of super-resolution images for a broader scientific circle, lowering the cost and entry skill requirements for the field. One of its branches, ultrastructure expansion microscopy (U-ExM), has become popular among research groups studying apicomplexan parasites, including the acute stage of Toxoplasma gondii infection. Here, we show that the chronic cyst-forming stage of Toxoplasma, however, resists U-ExM expansion, impeding precise protein localization. We then solve the in vitro cyst's resistance to denaturation required for successful U-ExM. As the cyst's main structural protein CST1 contains a mucin domain, we added an enzymatic digestion step using the pan-mucinase StcE prior to the expansion protocol. This allowed full expansion of the cysts in fibroblasts and primary neuronal cell culture without disrupting immunofluorescence analysis of parasite proteins. Using StcE-enhanced U-ExM, we clarified the localization of the GRA2 protein, which is important for establishing a normal cyst, observing GRA2 granules spanning across the CST1 cyst wall. The StcE-U-ExM protocol allows accurate pinpointing of proteins in the bradyzoite cyst, which will greatly facilitate investigation of the underlying biology of cyst formation and its vulnerabilities.IMPORTANCE: Toxoplasma gondii is an intracellular parasite capable of establishing long-term chronic infection in nearly all warm-blooded animals. During the chronic stage, parasites encapsulate to form cysts predominantly in neurons and skeletal muscle. Current anti-Toxoplasma drugs do not eradicate chronic parasites, leaving a reservoir of infection. The cyst is critical for disease transmission and pathology, yet it is harder to study, with the function of many chronic-stage proteins still unknown. Ultrastructure expansion microscopy, a new method to overcome the light microscopy's diffraction limit by physically expanding the sample, allowed in-depth studies of acute Toxoplasma infection. We show that Toxoplasma cysts resist expansion using standard protocol, but an additional enzymatic digestion with the mucinase StcE allows full expansion. This protocol offers new avenues for examining the chronic stage, including precise spatial organization of cyst-specific proteins, linking these locations to morphological structures, and detailed investigations of components of the durable cyst wall.

Keywords:  Toxoplasma; apicomplexan parasites; chronic infection; expansion microscopy; host–parasite relationship

DOI:  https://doi.org/10.1128/msphere.00322-24
Infect Immun. 2024 Aug 28. e0029924

Host cell-specific metabolism of linoleic acid controls Toxoplasma gondii growth in cell culture.

Nicole D Hryckowian, Carlos J Ramírez-Flores, Caitlin Zinda, Sung Chul Park, Martin T Kelty, Laura J Knoll.

  The obligate intracellular parasite Toxoplasma gondii can infect and replicate in any warm-blooded cell tested to date, but much of our knowledge about T. gondii cell biology comes from just one host cell type: human foreskin fibroblasts (HFFs). To expand our knowledge of host-parasite lipid interactions, we studied T. gondii in intestinal epithelial cells, the first site of host-parasite contact following oral infection and the exclusive site of parasite sexual development in feline hosts. We found that highly metabolic Caco-2 cells are permissive to T. gondii growth even when treated with high levels of linoleic acid (LA), a polyunsaturated fatty acid (PUFA) that kills parasites in HFFs. Caco-2 cells appear to sequester LA away from the parasite, preventing membrane disruptions and lipotoxicity that characterize LA-induced parasite death in HFFs. Our work is an important step toward understanding host-parasite interactions in feline intestinal epithelial cells, an understudied but important cell type in the T. gondii life cycle.

Keywords:  Toxoplasma gondii; enterocytes; linoleic acid; lipid droplet; lipotoxicity; polyunsaturated fatty acid

DOI:  https://doi.org/10.1128/iai.00299-24
bioRxiv. 2024 Aug 15. pii: 2024.08.15.608087. [Epub ahead of print]

Calcium tunneling through the ER and transfer to other organelles for optimal signaling in Toxoplasma gondii.

Zhu-Hong Li, Beejan Asady, Le Chang, Miryam Andrea Hortua Triana, Catherine Li, Isabelle Coppens, Silvia N J Moreno.

  Ca2+ signaling in cells begins with the opening of Ca2+ channels in either the plasma membrane (PM) or the endoplasmic reticulum (ER) and results in a dramatic increase in the physiologically low (<100 nM) cytosolic Ca2+ level. The temporal and spatial Ca2+ levels are well regulated to enable precise and specific activation of critical biological processes. Ca2+ signaling regulates pathogenic features of apicomplexan parasites like Toxoplasma gondii which infects approximately one-third of the world's population. T. gondii relies on Ca2+ signals to stimulate traits of its infection cycle and several Ca2+ signaling elements play essential roles in its parasitic cycle. Active egress, an essential step for the infection cycle of T. gondii is preceded by a large increase in cytosolic Ca2+ most likely by release from intracellular stores. Intracellular parasites take up Ca2+ from the host cell during host Ca2+ signaling events to replenish intracellular stores. In this work, we investigated the mechanism by which intracellular stores are replenished with Ca2+ and demonstrated a central role for the SERCA-Ca2+-ATPase to keep not only the ER filled with Ca2+ but also acidic stores. We also show mitochondrial Ca2+ uptake, by transfer of Ca2+ from the ER most likely through membrane contact sites. We propose a central role for the ER in tunneling of calcium from the extracellular milieu through the ER to other organelles.

Keywords:  Calcium; SERCA-Ca2+-ATPase; Toxoplasma gondii; calcium tunneling; endoplasmic reticulum; membrane contact sites

DOI:  https://doi.org/10.1101/2024.08.15.608087
Nat Commun. 2024 Aug 28. 15(1): 7419

Single cell expression and chromatin accessibility of the Toxoplasma gondii lytic cycle identifies AP2XII-8 as an essential ribosome regulon driver.

Jingjing Lou, Yasaman Rezvani, Argenis Arriojas, Yihan Wu, Nachiket Shankar, David Degras, Caroline D Keroack, Manoj T Duraisingh, Kourosh Zarringhalam, Marc-Jan Gubbels.

Sequential lytic cycles driven by cascading transcriptional waves underlie pathogenesis in the apicomplexan parasite Toxoplasma gondii. This parasite's unique division by internal budding, short cell cycle, and jumbled up classically defined cell cycle stages have restrained in-depth transcriptional program analysis. Here, unbiased transcriptome and chromatin accessibility maps throughout the lytic cell cycle are established at the single-cell level. Correlated pseudo-timeline assemblies of expression and chromatin profiles maps transcriptional versus chromatin level transition points promoting the cell division cycle. Sequential clustering analysis identifies functionally related gene groups promoting cell cycle progression. Promoter DNA motif mapping reveals patterns of combinatorial regulation. Pseudo-time trajectory analysis reveals transcriptional bursts at different cell cycle points. The dominant burst in G1 is driven largely by transcription factor AP2XII-8, which engages a conserved DNA motif, and promotes the expression of 44 ribosomal proteins encoding regulon. Overall, the study provides integrated, multi-level insights into apicomplexan transcriptional regulation.

DOI: https://doi.org/10.1038/s41467-024-51011-7
Semin Cancer Biol. 2024 Aug 26. pii: S1044-579X(24)00060-9. [Epub ahead of print]106-107 15-27

AMPK: The energy sensor at the crossroads of aging and cancer.

Vasudevarao Penugurti, Rajesh Kumar Manne, Ling Bai, Rajni Kant, Hui-Kuan Lin.

  AMP-activated protein kinase (AMPK) is a protein kinase that plays versatile roles in response to a variety of physiological stresses, including glucose deprivation, hypoxia, and ischemia. As a kinase with pleiotropic functions, it plays a complex role in tumor progression, exhibiting both tumor-promoting and tumor-suppressing activities. On one hand, AMPK enhances cancer cell proliferation and survival, promotes cancer metastasis, and impairs anti-tumor immunity. On the other hand, AMPK inhibits cancer cell growth and survival and stimulates immune responses in a context-dependent manner. Apart from these functions, AMPK plays a key role in orchestrating aging and aging-related disorders, including cardiovascular diseases (CVD), Osteoarthritis (OA), and Diabetes. In this review article, we summarized the functions of AMPK pathway based on its oncogenic and tumor-suppressive roles and highlighted the importance of AMPK pathway in regulating cellular aging. We also spotlighted the significant role of various signaling pathways, activators, and inhibitors of AMPK in serving as therapeutic strategies for anti-cancer and anti-aging therapy.

Keywords:  AICAR; AMP-activated protein Kinase (AMPK); Aging; Autophagy; Longevity; Metformin; Tumorigenesis; mTOR

DOI:  https://doi.org/10.1016/j.semcancer.2024.08.002
J Fungi (Basel). 2024 Jul 26. pii: 522. [Epub ahead of print]10(8):

Research Progress on the Mechanism and Function of Histone Acetylation Regulating the Interaction between Pathogenic Fungi and Plant Hosts.

Xiaokang Zhang, Yuzhu Zhou, Yangzhi Liu, Boqiang Li, Shiping Tian, Zhanquan Zhang.

  Histone acetylation is a crucial epigenetic modification, one that holds the key to regulating gene expression by meticulously modulating the conformation of chromatin. Most histone acetylation enzymes (HATs) and deacetylation enzymes (HDACs) in fungi were originally discovered in yeast. The functions and mechanisms of HATs and HDACs in yeast that have been documented offer us an excellent entry point for gaining insights into these two types of enzymes. In the interaction between plants and pathogenic fungi, histone acetylation assumes a critical role, governing fungal pathogenicity and plant immunity. This review paper delves deep into the recent advancements in understanding how histone acetylation shapes the interaction between plants and fungi. It explores how this epigenetic modification influences the intricate balance of power between these two kingdoms of life, highlighting the intricate network of interactions and the subtle shifts in these interactions that can lead to either mutual coexistence or hostile confrontation.

Keywords:  disease resistance; fungal pathogenicity; histone acetylation; histone acetylation enzymes; histone deacetylation enzymes

DOI:  https://doi.org/10.3390/jof10080522
Curr Top Membr. 2024 ;pii: S1063-5823(24)00002-4. [Epub ahead of print]93 27-49

Endocytosis in malaria parasites: An ultrastructural perspective of membrane interplay in a unique infection model.

Camila Wendt, Kildare Miranda.

  Malaria remains a major global threat, representing a severe public health problem worldwide. Annually, it is responsible for a high rate of morbidity and mortality in many tropical developing countries where the disease is endemic. The causative agent of malaria, Plasmodium spp., exhibits a complex life cycle, alternating between an invertebrate vector, which transmits the disease, and the vertebrate host. The disease pathology observed in the vertebrate host is attributed to the asexual development of Plasmodium spp. inside the erythrocyte. Once inside the red blood cell, malaria parasites cause extensive changes in the host cell, increasing membrane rigidity and altering its normal discoid shape. Additionally, during their intraerythrocytic development, malaria parasites incorporate and degrade up to 70 % of host cell hemoglobin. This mechanism is essential for parasite development and represents an important drug target. Blocking the steps related to hemoglobin endocytosis or degradation impairs parasite development and can lead to its death. The ultrastructural analysis of hemoglobin endocytosis on Plasmodium spp. has been broadly explored along the years. However, it is only recently that the proteins involved in this process have started to emerge. Here, we will review the most important features related to hemoglobin endocytosis and catabolism on malaria parasites. A special focus will be given to the recent analysis obtained through 3D visualization approaches and to the molecules involved in these mechanisms.

Keywords:  Cytostome; Electron microscopy; Electron tomography; Endocytosis; Food vacuole; Hemoglobin; Hemozoin; Malaria; Plasmodium

DOI:  https://doi.org/10.1016/bs.ctm.2024.05.001
Gut Microbes. 2024 Jan-Dec;16(1):16(1): 2391535

Gut microbiota mediates anxiety-like behaviors induced by chronic infection of Toxoplasma gondii in mice.

Xiaotong Luo, Xiaoying Yang, Shimin Tan, Yongsheng Zhang, Yunqiu Liu, Xiaokang Tian, Yingting Huang, Yuying Zhou, Cheng He, Kun Yin, Daxiang Xu, Xiangyang Li, Fenfen Sun, Renxian Tang, Jianping Cao, Kuiyang Zheng, Yinghua Yu, Wei Pan.

  BACKGROUND: Chronic infection with the neurotropic parasite Toxoplasma gondii (T. gondii) can cause anxiety and gut microbiota dysbiosis in hosts. However, the potential role of gut microbiota in anxiety induced by the parasite remains unclear.METHODS: C57BL/6J mice were infected with 10 cysts of T. gondii. Antibiotic depletion of gut microbiota and fecal microbiota transplantation experiments were utilized to investigate the causal relationship between gut microbiota and anxiety. Anxiety-like behaviors were examined by the elevated plus maze test and the open field test; blood, feces, colon and amygdala were collected to evaluate the profiles of serum endotoxin (Lipopolysaccharide, LPS) and serotonin (5-hydroxytryptamine, 5-HT), gut microbiota composition, metabolomics, global transcriptome and neuroinflammation in the amygdala. Furthermore, the effects of Diethyl butylmalonate (DBM, an inhibitor of mitochondrial succinate transporter, which causes the accumulation of endogenous succinate) on the disorders of the gut-brain axis were evaluated.
RESULTS: Here, we found that T. gondii chronic infection induced anxiety-like behaviors and disturbed the composition of the gut microbiota in mice. In the amygdala, T. gondii infection triggered the microglial activation and neuroinflammation. In the colon, T. gondii infection caused the intestinal dyshomeostasis including elevated colonic inflammation, enhanced bacterial endotoxin translocation to blood and compromised intestinal barrier. In the serum, T. gondii infection increased the LPS levels and decreased the 5-HT levels. Interestingly, antibiotics ablation of gut microbiota alleviated the anxiety-like behaviors induced by T. gondii infection. More importantly, transplantation of the fecal microbiota from T. gondii-infected mice resulted in anxiety and the transcriptomic alteration in the amygdala of the antibiotic-pretreated mice. Notably, the decreased abundance of succinate-producing bacteria and the decreased production of succinate were observed in the feces of the T. gondii-infected mice. Moreover, DBM administration ameliorated the anxiety and gut barrier impairment induced by T. gondii infection.
CONCLUSIONS: The present study uncovers a novel role of gut microbiota in mediating the anxiety-like behaviors induced by chronic T. gondii infection. Moreover, we show that DBM supplementation has a beneficial effect on anxiety. Overall, these findings provide new insights into the treatment of T. gondii-related mental disorders.

Keywords:  Diethyl butylmalonate; Toxoplasma gondii; anxiety; fecal microbiota transplantation; gut microbiota; succinate

DOI:  https://doi.org/10.1080/19490976.2024.2391535
Essays Biochem. 2024 Aug 28. pii: EBC20240006. [Epub ahead of print]

Does AMPK bind glycogen in skeletal muscle or is the relationship correlative?

Barnaby P Frankish, Robyn M Murphy.

  Since its discovery over five decades ago, an emphasis on better understanding the structure and functional role of AMPK has been prevalent. In that time, the role of AMPK as a heterotrimeric enzyme that senses the energy state of various cell types has been established. Skeletal muscle is a dynamic, plastic tissue that adapts to both functional and metabolic demands of the human body, such as muscle contraction or exercise. With a deliberate focus on AMPK in skeletal muscle, this review places a physiological lens to the association of AMPK and glycogen that has been established biochemically. It discusses that, to date, no in vivo association of AMPK with glycogen has been shown and this is not altered with interventions, either by physiological or biochemical utilisation of glycogen in skeletal muscle. The reason for this is likely due to the persistent phosphorylation of Thr148 in the β-subunit of AMPK which prevents AMPK from binding to carbohydrate domains. This review presents the correlative data that suggests AMPK senses glycogen utilisation through a direct interaction with glycogen, the biochemical data showing that AMPK can bind carbohydrate in vitro, and highlights that in a physiological setting of rodent skeletal muscle, AMPK does not directly bind to glycogen.

Keywords:  AMPK; glycogen; skeletal muscle

DOI:  https://doi.org/10.1042/EBC20240006
BMC Cancer. 2024 Aug 27. 24(1): 1054

Acetylation of PGK1 at lysine 323 promotes glycolysis, cell proliferation, and metastasis in luminal A breast cancer cells.

Xiuli Gao, Ting Pan, Yu Gao, Wenbin Zhu, Likun Liu, Wenbo Duan, Cuicui Han, Bo Feng, Wenjing Yan, Qiuhang Song, Yunlong Liu, Liling Yue.

  BACKGROUND: In prior research employing iTRAQ (Isobaric Tags for Relative and Absolute Quantitation) technology, we identified a range of proteins in breast cancer tissues exhibiting high levels of acetylation. Despite this advancement, the specific functions and implications of these acetylated proteins in the context of cancer biology have yet to be elucidated. This study aims to systematically investigate the functional roles of these acetylated proteins with the objective of identifying potential therapeutic targets within breast cancer pathophysiology.METHODS: Acetylated targets were identified through bioinformatics, with their expression and acetylation subsequently confirmed. Proteomic analysis and validation studies identified potential acetyltransferases and deacetylases. We evaluated metabolic functions via assays for catalytic activity, glucose consumption, ATP levels, and lactate production. Cell proliferation and metastasis were assessed through viability, cycle analysis, clonogenic assays, PCNA uptake, wound healing, Transwell assays, and MMP/EMT marker detection.
RESULTS: Acetylated proteins in breast cancer were primarily involved in metabolism, significantly impacting glycolysis and the tricarboxylic acid cycle. Notably, PGK1 showed the highest acetylation at lysine 323 and exhibited increased expression and acetylation across breast cancer tissues, particularly in T47D and MCF-7 cells. Notably, 18 varieties acetyltransferases or deacetylases were identified in T47D cells, among which p300 and Sirtuin3 were validated for their interaction with PGK1. Acetylation at 323 K enhanced PGK1's metabolic role by boosting its activity, glucose uptake, ATP production, and lactate output. This modification also promoted cell proliferation, as evidenced by increased viability, S phase ratio, clonality, and PCNA levels. Furthermore, PGK1-323 K acetylation facilitated metastasis, improving wound healing, cell invasion, and upregulating MMP2, MMP9, N-cadherin, and Vimentin while downregulating E-cadherin.
CONCLUSION: PGK1-323 K acetylation was significantly elevated in T47D and MCF-7 luminal A breast cancer cells and this acetylation could be regulated by p300 and Sirtuin3. PGK1-323 K acetylation promoted cell glycolysis, proliferation, and metastasis, highlighting novel epigenetic targets for breast cancer therapy.

Keywords:  Acetyltransferase and deacetylase; Breast cancer; Cell proliferation and metastasis; Glycolysis; PGK1 acetylation

DOI:  https://doi.org/10.1186/s12885-024-12792-8
Bone Res. 2024 Aug 28. 12(1): 49

Osteoclasts control endochondral ossification via regulating acetyl-CoA availability.

Daizhao Deng, Xianming Liu, Wenlan Huang, Sirui Yuan, Genming Liu, Shanshan Ai, Yijie Fu, Haokun Xu, Xinyi Zhang, Shihai Li, Song Xu, Xiaochun Bai, Yue Zhang.

Osteoclast is critical in skeletal development and fracture healing, yet the impact and underlying mechanisms of their metabolic state on these processes remain unclear. Here, by using osteoclast-specific small GTPase Rheb1-knockout mice, we reveal that mitochondrial respiration, rather than glycolysis, is essential for cathepsin K (CTSK) production in osteoclasts and is regulated by Rheb1 in a mechanistic target of rapamycin complex 1 (mTORC1)-independent manner. Mechanistically, we find that Rheb1 coordinates with mitochondrial acetyl-CoA generation to fuel CTSK, and acetyl-CoA availability in osteoclasts is the central to elevating CTSK. Importantly, our findings demonstrate that the regulation of CTSK by acetyl-CoA availability is critical and may confer a risk for abnormal endochondral ossification, which may be the main cause of poor fracture healing on alcohol consumption, targeting Rheb1 could successfully against the process. These findings uncover a pivotal role of mitochondria in osteoclasts and provide a potent therapeutic opportunity in bone disorders.

DOI: https://doi.org/10.1038/s41413-024-00360-6
Methods. 2024 Aug 25. pii: S1046-2023(24)00184-1. [Epub ahead of print]230 147-157

Stack-HDAC3i: A high-precision identification of HDAC3 inhibitors by exploiting a stacked ensemble-learning framework.

Watshara Shoombuatong, Ittipat Meewan, Lawankorn Mookdarsanit, Nalini Schaduangrat.

  Epigenetics involves reversible modifications in gene expression without altering the genetic code itself. Among these modifications, histone deacetylases (HDACs) play a key role by removing acetyl groups from lysine residues on histones. Overexpression of HDACs is linked to the proliferation and survival of tumor cells. To combat this, HDAC inhibitors (HDACi) are commonly used in cancer treatments. However, pan-HDAC inhibition can lead to numerous side effects. Therefore, isoform-selective HDAC inhibitors, such as HDAC3i, could be advantageous for treating various medical conditions while minimizing off-target effects. To date, computational approaches that use only the SMILES notation without any experimental evidence have become increasingly popular and necessary for the initial discovery of novel potential therapeutic drugs. In this study, we develop an innovative and high-precision stacked-ensemble framework, called Stack-HDAC3i, which can directly identify HDAC3i using only the SMILES notation. Using an up-to-date benchmark dataset, we first employed both molecular descriptors and Mol2Vec embeddings to generate feature representations that cover multi-view information embedded in HDAC3i, such as structural and contextual information. Subsequently, these feature representations were used to train baseline models using nine popular ML algorithms. Finally, the probabilistic features derived from the selected baseline models were fused to construct the final stacked model. Both cross-validation and independent tests showed that Stack-HDAC3i is a high-accuracy prediction model with great generalization ability for identifying HDAC3i. Furthermore, in the independent test, Stack-HDAC3i achieved an accuracy of 0.926 and Matthew's correlation coefficient of 0.850, which are 0.44-6.11% and 0.83-11.90% higher than its constituent baseline models, respectively.

Keywords:  Feature selection; HDAC3 inhibitor; Machine learning; Mol2vec, feature encoding; Stacking strategy

DOI:  https://doi.org/10.1016/j.ymeth.2024.08.003
Curr Issues Mol Biol. 2024 Aug 14. 46(8): 8835-8851

The Role of Sirtuin-1 Isoforms in Regulating Mitochondrial Function.

Pankaj Patyal, Fathima S Ameer, Ambika Verma, Xiaomin Zhang, Gohar Azhar, Jyotsna Shrivastava, Shakshi Sharma, Rachel Zhang, Jeanne Y Wei.

  The sirtuin-1 (SIRT1) gene contains multiple exons that usually undergo alternative splicing. The exclusion of one or more exons causes domain loss in the alternatively spliced isoforms and may change their functions. However, it is not completely established to what extent the loss of a non-catalytic domain could affect its regulatory function. Using muscle cells and SIRT1-knockout cells, we examined the function of the constitutively spliced isoform (SIRT1-v1) versus the alternatively spliced isoforms SIRT1-v2 and SIRT1-v3 that had lost part of the N-terminal region. Our data indicate that partial loss of the N-terminal domains in SIRT1-v2 and SIRT1-v3 attenuated their function. The full-length SIRT1-v1 significantly increased the oxidative phosphorylation and ATP production rate. Furthermore, SIRT1-v1 specifically upregulated the mitochondrial respiratory complex I without affecting the activity of complexes II, III, and IV. Additionally, domain loss affected the regulation of site-specific lysine acetylation in the histone H4 protein, the gene expression of respiratory complex I subunits, and the metabolic balance of oxidative phosphorylation versus glycolysis. Since alternatively spliced isoforms tend to increase with advancing age, the impact of SIRT1 isoforms on mitochondrial respiratory complexes warrants further investigation.

Keywords:  acetylation; bioenergetics; domain loss; histone-H4; mitochondria; sirtuin-1

DOI:  https://doi.org/10.3390/cimb46080522
Brief Bioinform. 2024 Jul 25. pii: bbae415. [Epub ahead of print]25(5):

Conjoint analysis of succinylome and phosphorylome reveals imbalanced HDAC phosphorylation-driven succinylayion dynamic contibutes to lung cancer.

Yifan Guo, Haoyu Wen, Zongwei Chen, Mengxia Jiao, Yuchen Zhang, Di Ge, Ronghua Liu, Jie Gu.

  Cancerous genetic mutations result in a complex and comprehensive post-translational modification (PTM) dynamics, in which protein succinylation is well known for its ability to reprogram cell metabolism and is involved in the malignant evolution. Little is known about the regulatory interactions between succinylation and other PTMs in the PTM network. Here, we developed a conjoint analysis and systematic clustering method to explore the intermodification communications between succinylome and phosphorylome from eight lung cancer patients. We found that the intermodification coorperation in both parallel and series. Besides directly participating in metabolism pathways, some phosphosites out of mitochondria were identified as an upstream regulatory modification directing succinylome dynamics in cancer metabolism reprogramming. Phosphorylated activation of histone deacetylase (HDAC) in lung cancer resulted in the removal of acetylation and favored the occurrence of succinylation modification of mitochondrial proteins. These results suggest a tandem regulation between succinylation and phosphorylation in the PTM network and provide HDAC-related targets for intervening mitochondrial succinylation and cancer metabolism reprogramming.

Keywords:  lung cancer; metabolism; phosphorylation; proteome; succinylation

DOI:  https://doi.org/10.1093/bib/bbae415
Nat Cardiovasc Res. 2024 Jul;3(7): 869-882

Nuclear ATP-citrate lyase regulates chromatin-dependent activation and maintenance of the myofibroblast gene program.

Michael P Lazaropoulos, Andrew A Gibb, Douglas J Chapski, Abheya A Nair, Allison N Reiter, Rajika Roy, Deborah M Eaton, Kenneth C Bedi, Kenneth B Margulies, Kathryn E Wellen, Conchi Estarás, Thomas M Vondriska, John W Elrod.

Differentiation of cardiac fibroblasts to myofibroblasts is necessary for matrix remodeling and fibrosis in heart failure. We previously reported that mitochondrial calcium signaling drives α-ketoglutarate-dependent histone demethylation, promoting myofibroblast formation. Here we investigate the role of ATP-citrate lyase (ACLY), a key enzyme for acetyl-CoA biosynthesis, in histone acetylation regulating myofibroblast fate and persistence in cardiac fibrosis. We show that inactivation of ACLY prevents myofibroblast differentiation and reverses myofibroblasts towards quiescence. Genetic deletion of Acly in post-activated myofibroblasts prevents fibrosis and preserves cardiac function in pressure-overload heart failure. TGFβ stimulation enhances ACLY nuclear localization and ACLY-SMAD2/3 interaction, and increases H3K27ac at fibrotic gene loci. Pharmacological inhibition of ACLY or forced nuclear expression of a dominant-negative ACLY mutant prevents myofibroblast formation and H3K27ac. Our data indicate that nuclear ACLY activity is necessary for myofibroblast differentiation and persistence by maintaining histone acetylation at TGFβ-induced myofibroblast genes. These findings provide targets to prevent and reverse pathological fibrosis.

DOI: https://doi.org/10.1038/s44161-024-00502-3
Trends Endocrinol Metab. 2024 Aug 27. pii: S1043-2760(24)00191-7. [Epub ahead of print]

Emerging interactions between mitochondria and NAD+ metabolism in cardiometabolic diseases.

Azadeh Nasuhidehnavi, Weronika Zarzycka, Ignacy Górecki, Ying Ann Chiao, Chi Fung Lee.

Nicotinamide adenine dinucleotide (NAD+) is an essential coenzyme for redox reactions and regulates cellular catabolic pathways. An intertwined relationship exists between NAD+ and mitochondria, with consequences for mitochondrial function. Dysregulation in NAD+ homeostasis can lead to impaired energetics and increased oxidative stress, contributing to the pathogenesis of cardiometabolic diseases. In this review, we explore how disruptions in NAD+ homeostasis impact mitochondrial function in various cardiometabolic diseases. We discuss emerging studies demonstrating that enhancing NAD+ synthesis or inhibiting its consumption can ameliorate complications of this family of pathological conditions. Additionally, we highlight the potential role and therapeutic promise of mitochondrial NAD+ transporters in regulating cellular and mitochondrial NAD+ homeostasis.

DOI: https://doi.org/10.1016/j.tem.2024.07.010