bims-toxgon Biomed News
on Toxoplasma gondii metabolism
Issue of 2026–05–24
fourteen papers selected by
Lakesh Kumar, BITS Pilani
  1. Proliferating toward sex: characterization of cell division of Toxoplasma gondii's pre-sexual stages.
  2. Dense granule proteins: key mediators of Toxoplasma gondii pathogenesis and therapeutic targets.
  3. Beyond deacetylation: crosstalk mechanisms and context-dependent regulation of sirtuin non-classical enzymatic functions in disease.
  4. Author Correction: Structure, assembly and inhibition of the Toxoplasma gondii respiratory chain supercomplex.
  5. NRSF regulation of OPRM1 through histone acetylation.
  6. Stage-specific differential gene expression leads to adaptive changes in the promastigote and amastigote stages of Leishmania donovani.
  7. SIRT2 mediates integrated stress response by deacetylating and stabilizing 4E-BP1 to suppress translation.
  8. Chromatin context-dependent deacetylation by the asymmetric Rpd3L.
  9. "SelO"ective NAD+ hydrolysis regulates mitochondrial NAD+ and homeostasis.
  10. An updated patent review of histone deacetylase 6 inhibitors in neurodegenerative diseases (2020-2025).
  11. HDAC7-Induced Epigenetic Repression Modulates ATF3 Functional Plasticity in Colorectal Cancer Pathogenesis.
  12. Computational Design, Synthesis, and In Vitro Evaluation of Novel Piperazine-Based HDAC Inhibitors as Potential Breast Cancer Therapeutics.
  13. Methionine concentration regulates LSD1 acetylation in glioma cells.
  14. Global impact on metabolic capacity of yeast cell factories by optogenetic control of the cAMP-PKA axis.
  1. mBio. 2026 May 19. e0244025
    Proliferating toward sex: characterization of cell division of Toxoplasma gondii's pre-sexual stages.
    Florencia Sena, Mohamed-Ali Hakimi, Maria E Francia.
      Toxoplasmosis is a disease of worldwide distribution, causing high morbidity and mortality in humans, as well as heavily impacting animal health and the economy. Toxoplasma gondii, the causative agent, is an intracellular parasite with a complex life cycle whose completion entails asexual, pre-sexual, and sexual stage conversions. Pre-sexual and sexual differentiation take place only within the intestinal epithelium of felines. Recently, several transcriptional factors and epigenetic components crucial to trigger parasite stage transitions within the cat have been identified, allowing, through precise genetic manipulation, obtaining pre-sexual stages known as merozoites in vitro. Through conditional depletion of two pre-sexual stage-specific gene silencing transcription factors, AP2XII-1 and AP2XII-2, we have characterized the interplay between cell division and the sequence of events leading up to differentiation of tachyzoites into merozoites. We explored genome duplication, assembly of daughter cells, karyokinesis, and cytokinesis, characterizing the differential cell division modes and kinetics undergone by critical structures along the differentiation axis. Building onto the pre-existing body of knowledge, primarily describing the underpinnings of these forms of division by transmission electron microscopy, our work contributes previously unexplored temporal and spatial resolution to the transitions between endodyogeny and endopolygeny, providing a conceptual framework for understanding and exploring T. gondii's route of sexual differentiation.IMPORTANCESexual development in Toxoplasma gondii is essential for transmission, but remains poorly understood, largely because pre-sexual stages are restricted to the feline intestine and have only recently become experimentally accessible. Here, we leverage an in vitro differentiation system to resolve how parasites transition toward merozoite formation at the cellular level. By combining expansion microscopy, stage-specific markers, and quantitative analyses, we define the temporal sequence of nuclear division and daughter cell assembly during merogony, addressing longstanding ambiguity regarding division modes in these stages. Our findings reveal that parasites can adopt alternative division strategies emerging from a polyploid intermediate, highlighting an unexpected degree of flexibility in how cell division is executed during differentiation. Beyond refining this developmental framework, this work establishes a foundation for future mechanistic studies of pre-sexual biology and provides broader insight into the diversity of eukaryotic cell division strategies.
    Keywords:  Toxoplasma gondii; apicomplexan; cell division; endopolygeny; expansion microscopy; merozoite; pre-sexual
    DOI:  https://doi.org/10.1128/mbio.02440-25
  2. Front Med (Lausanne). 2026 ;13 1770993
    Dense granule proteins: key mediators of Toxoplasma gondii pathogenesis and therapeutic targets.
    Ruiming Zeng, Hammad Bacha, Shams Uz Zaman, Mohammed Abohashrh, Rasha Alonaizan, Khalid J Alzahrani, Khalaf F Alsharif, Fuad M Alzahrani, Abdul Qadeer, Qingming Fu.
      Toxoplasma gondii (T. gondii) is an apicomplexan parasite that infects most warm-blooded animals, including approximately one-third of the human population worldwide. Dense granule proteins (GRAs), secreted from specialized organelles and trafficked to multiple compartments, including the parasitophorous vacuole (PV), parasitophorous vacuole membrane (PVM), host cytosol, and host cell nucleus following host cell invasion, have emerged as critical mediators of host-parasite interactions. This review provides a comprehensive analysis of our current knowledge of GRA proteins in toxoplasmosis pathogenesis and establishes a framework for developing novel interventions against this globally significant parasitic disease. Key GRA proteins form pore complexes that regulate PVM permeability, while GRA effectors manipulate host immunity to evade invasion. GRA proteins are essential for tissue cyst formation and bradyzoite differentiation, enabling lifelong chronic infection. The exceptional immunogenicity of GRA antigens has positioned them as promising candidates for diagnostic applications and vaccine development. Additionally, GRA proteins are attractive therapeutic targets through either the direct inhibition of effector-host protein interactions or by the disruption of effector export.
    Keywords:  Toxoplasma gondii; dense granule proteins; immune modulation; parasitophorous vacuole; pathogenesis
    DOI:  https://doi.org/10.3389/fmed.2026.1770993
  3. Mol Med. 2026 May 20.
    Beyond deacetylation: crosstalk mechanisms and context-dependent regulation of sirtuin non-classical enzymatic functions in disease.
    Yiran Ma, Junli Chen, Ruixiao Song, Xiaolong Yu.
      The sirtuin (SIRT) family, long regarded as NAD⁺-dependent lysine deacetylases, is now recognized as a diverse superfamily of lysine deacylases with high substrate selectivity. Beyond classical deacetylation, sirtuin isoforms catalyze various non-classical enzymatic activities, including demyristoylation, desuccinylation, delactylation, and mono-ADP-ribosylation, and regulate cellular signaling via non-catalytic protein interactions. While the classification of sirtuins as a lysine deacylase superfamily is well-established, their integration into complex disease networks remains fragmented. This review synthesizes the context-dependent mechanisms of these non-classical functions across five major disease areas: metabolic syndrome, cancer, aging, neurodegeneration, and cardiovascular disease. We emphasize that the same non-classical sirtuin activity exerts context-dependent bidirectional effects, either protective or pathogenic, influenced by tissue type, cellular microenvironment, and substrate availability. We illustrate synergistic and antagonistic crosstalk among sirtuin members that supports precise metabolic regulation. We also summarize emerging therapeutic strategies targeting non-classical sirtuin activities, including small molecules, natural products, and biologics, and highlight key challenges: improving substrate selectivity, minimizing off-target effects, and promoting clinical translation. Finally, we propose three critical research directions: clarifying dynamic mechanisms of substrate selectivity, developing condition-specific targeting approaches, and advancing high-resolution detection of post-translational modifications. This review provides a paradigm shift in understanding sirtuin biology and lays the molecular foundation for precision therapies against metabolic and age-related diseases.
    Keywords:  Crosstalk mechanisms; Metabolic homeostasis; Non-classical enzymatic functions; Post-translational modifications; Signal transduction; Sirtuins
    DOI:  https://doi.org/10.1186/s10020-026-01503-7
  4. Nat Struct Mol Biol. 2026 May 22.
    Author Correction: Structure, assembly and inhibition of the Toxoplasma gondii respiratory chain supercomplex.
    Andrew E MacLean, Shikha Shikha, Mariana Ferreira Silva, Max J Gramelspacher, Aaron Nilsen, Katherine M Liebman, Sovitj Pou, Rolf W Winter, Amit Meir, Michael K Riscoe, J Stone Doggett, Lilach Sheiner, Alexander Mühleip.
      
    DOI:  https://doi.org/10.1038/s41594-026-01824-5
  5. Clin Epigenetics. 2026 May 19.
    NRSF regulation of OPRM1 through histone acetylation.
    Ryan Thompson, Christina Chan.
      The Neuron Restrictive Silencer Factor (NRSF) is a master transcriptional regulator of neuronal differentiation. Dysregulation of NRSF in neurons contributes to multiple neurological disorder. Following peripheral nerve injury, NRSF is upregulated and has been implicated in the establishment and maintenance of neuropathic pain. While the molecular and genetic changes in nerves occur during neuropathic pain are numerous and complex, a key downstream consequence of NRSF activation is repression of the mu-opioid receptor gene (OPRM1), a critical mediator of nociception and opioid responsiveness. NRSF controls repression of gene expression through recruitment of histone deacetylases (HDACs) to target genes. Here, we demonstrate that pharmacological inhibition of HDACs with valproic acid (VPA) is able to de-repress expression of OPRM1 in iPSC-derived neurons. To produce more targeted epigenetic changes to specific genomic loci, we further employed a CRISPR based epigenetic editing strategy using dCas9 fused to the histone acetyltransferase p300. Targeted acetylation of the OPRM1 gene promoter region with dCas9-p300 upregulated OPRM1 gene expression. Restoring OPRM1 expression in neurons is able to alter its responsiveness to mu-opioid receptor agonist, as evidenced by changes in calcium signaling. This study demonstrated targeted epigenetic acetylation with dCas9-p300 is a powerful strategy to reverse NRSF-medicated gene repression and restore opioid receptor function, highlighting a potential therapeutic avenue for neuropathic pain.
    Keywords:  HDACi; NRSF; Neuron restrictive silencer factor; OPRM1; Opioid receptor; acetylation; calcium signaling; cas9; epigenetics; histone deacetylase; neuropathic pain; p300
    DOI:  https://doi.org/10.1186/s13148-026-02146-5
  6. Mol Biochem Parasitol. 2026 May 17. pii: S0166-6851(26)00036-8. [Epub ahead of print]267 111757
    Stage-specific differential gene expression leads to adaptive changes in the promastigote and amastigote stages of Leishmania donovani.
    Ishana Jha, Basant K Tiwary.
      Leishmania donovani exists in two distinct environments to complete its life cycle. It exists as a non-motile infective amastigote state in humans and as a motile promastigote state in the sandfly gut. Although the differences in gene expression between life-cycle stages have been extensively studied, the contribution of variability of gene expression to parasite adaptation remains poorly understood. Here, we have explored transcriptional changes in L. donovani using bulk RNA-seq data, using the amastigote as a reference. After the differential expression analysis, we calculated the gene-wise Wasserstein distance to capture shifts in the expression distribution across the stages. We found that amastigotes show overall lower transcriptional changes than promastigotes, but greater heterogeneity in genes related to stress responses, membrane proteins, and regulation. Importantly, we identified a subset of genes exhibiting high distributional shifts despite minimal changes in mean expression, which were not detected by conventional differential expression analysis. This suggests that deeper regulatory mechanisms may be masked by mean-based differential expression analyses. Furthermore, the poorly annotated genes in both stages were annotated, and many were found to have specific roles that help the parasite survive within host cells and vectors. Overall, our results provide exploratory insights into gene expression variability, revealing genes with stable mean expression but altered distributional patterns across life stages of L. donovani. Together, these findings suggest that transcriptional heterogeneity may constitute an underappreciated regulatory layer that contributes to parasite adaptation during the transition between vector and host environments.
    Keywords:  Amastigote; Differential gene expression; Hypothetical genes; Promastigote; Wasserstein distance
    DOI:  https://doi.org/10.1016/j.molbiopara.2026.111757
  7. EMBO Rep. 2026 May 18.
    SIRT2 mediates integrated stress response by deacetylating and stabilizing 4E-BP1 to suppress translation.
    Yanlin Zi, Jiaqi Zhao, Miao Wang, Dan Hou, Richard A Cerione, Hening Lin.
      The ability to adapt to nutrient stress, such as amino acid limitation, is crucial for cell survival. The mTORC1 complex and integrated stress response (ISR) are two mechanisms that sense the availability of amino acids and regulate protein synthesis. Here, we reveal a new SIRT2-mediated pathway, downstream of the ISR, that is activated under amino acids limitation to suppress global translation. Under amino acid deprivation, SIRT2 protein level is upregulated translationally by its upstream open reading frame (uORF). SIRT2 in turn suppresses translation, which helps cells to survive amino acid limitation. We identify eukaryotic translation initiation factor 4E (eIF4E) binding protein 1 (4E-BP1), which binds to eIF4E and inhibits translation, as a substrate of SIRT2. SIRT2 deacetylates 4E-BP1 at lysine 69 and stabilizes 4E-BP1 by protecting it from proteasomal degradation, leading to suppression of global translation. Our study uncovers a role for SIRT2 in regulating translation and identifies a new regulatory mechanism of 4E-BP1 in cells.
    DOI:  https://doi.org/10.1038/s44319-026-00803-7
  8. Nucleic Acids Res. 2026 May 05. pii: gkag443. [Epub ahead of print]54(9):
    Chromatin context-dependent deacetylation by the asymmetric Rpd3L.
    Heyu Zhao, Huadong Li, Chi Wang, Xuechen Yang, Binqian Zou, Shuqi Dong, Nan Zhang, Yuxing Zhou, Li Yi, Ying Zhang, Yixuan Xie, Dajiang Qin, William Chong Hang Chao, Duanqing Pei, Jun He.
      The regulation of gene expression requires precise control of chromatin-associated complexes that respond to diverse structural and epigenetic cues. The Rpd3 Large (Rpd3L) complex is a Sin3 histone deacetylase complex (HDAC) that dynamically adapt to chromatin states to reinforce transcriptional silencing, yet the mechanisms governing the catalytic activation in chromatin context-dependent manner remain unclear. Here we present the cryo-electron microscopy structure of Rpd3L bound to both mono- and di-nucleosome substrate at near-atomic resolution, uncovering a substrate-guided allosteric activation mechanism. Rpd3L adopts an asymmetric architecture, in which the proximal catalytic module anchors the first nucleosome, while the Sin3 PAH domains engage linker DNA to reposition a second nucleosome. This spatial configuration brings the distal catalytic module into proximity with chromatin and unlocks its latent deacetylase activity. Biochemical and mass spectrometry analyses confirm that dual nucleosome engagement selectively enhances Rpd3L activity and broadens substrate specificity. Together, these findings establish a hierarchical mechanism by which Rpd3L interprets histone modifications and nucleosome organization to modulate its enzymatic output at promoter regions. Our study provides a framework for understanding higher-order chromatin repression mechanisms by chromatin-regulation complexes and co-repressors.
    DOI:  https://doi.org/10.1093/nar/gkag443
  9. Cell Chem Biol. 2026 May 21. pii: S2451-9456(26)00147-9. [Epub ahead of print]33(5): 591-593
    "SelO"ective NAD+ hydrolysis regulates mitochondrial NAD+ and homeostasis.
    Qing Zhang, Trina Chia Min Tan, Vincenzo Sorrentino.
      Nicotinamide adenine dinucleotide (NAD+) is a metabolic redox cofactor whose compartmentalization in mitochondria is crucial for cellular function; however, its regulation mechanisms are largely unknown. In a recent Cell publication, Jia et al.1 uncover that the enzyme SelO catalyzes mitochondrial NAD+ hydrolysis to regulate β-oxidation and maintain mitochondrial and liver homeostasis.
    DOI:  https://doi.org/10.1016/j.chembiol.2026.04.012
  10. Expert Opin Ther Pat. 2026 May 20. 1-22
    An updated patent review of histone deacetylase 6 inhibitors in neurodegenerative diseases (2020-2025).
    Sida Shen.
       INTRODUCTION: Histone deacetylase 6 (HDAC6) inhibitors have been widely explored as potential therapeutic approaches for oncological, autoimmune, cardiovascular, and neurodegenerative disorders. Recent clinical advancements in non-hydroxamate-based HDAC6 inhibitors highlight favorable drug-like properties and improved safety margins, enhancing suitability for long-term treatment.
    AREA COVERED: This review updates the clinical status of HDAC6 inhibitors, the evolution of HDAC6 inhibitor pharmacophores, and patent disclosures from 2020 to 2025 identified by SciFinder search and manual confirmation. It also describes pharmacological assessment of new selective HDAC6 inhibitors in in vitro and in vivo models of neurodegenerative diseases.
    EXPERT OPINION: Expanding interest in the development of 2-(difluoromethyl)-1,3,4-oxadiazole (1,3,4-DFMO) derivatives has yielded a diverse set of HDAC6 inhibitors with superior HDAC6 potency and selectivity and enhanced oral pharmacokinetic profiles. These characteristics have facilitated the identification of optimized drug candidates for treating both peripheral and central nervous neurodegenerative diseases. Among the emerging therapeutic applications, Charcot-Marie-Tooth (CMT) disease has become the leading focus in preclinical and early clinical development using HDAC6 inhibitors.
    Keywords:  HDAC6 inhibitor; hydrazide; hydroxamate; mutagenicity; neurodegenerative disorder; oxadiazole; α-tubulin acetylation
    DOI:  https://doi.org/10.1080/13543776.2026.2676080
  11. Int J Biol Sci. 2026 ;22(9): 4956-4975
    HDAC7-Induced Epigenetic Repression Modulates ATF3 Functional Plasticity in Colorectal Cancer Pathogenesis.
    Qi Wang, Donglei Ji, Yanjie Jia, Shuang Li, Wenjing Gao, Tingting Liang, Yingying Liang, Caroline Zeng, Chunyu Wang, Ka Lung Cheung, Quan Wang, Ming-Ming Zhou, Lei Zeng.
      Class IIa histone deacetylase 7 (HDAC7) regulates transcription primarily through scaffolding functions, but its molecular mechanisms in cancer pathogenesis remain incompletely understood. Here, we establish HDAC7 as a key epigenetic regulator in colorectal cancer (CRC). HDAC7 is overexpressed in CRC tumors and correlates with advanced disease stages, lymph node metastasis, and poor patient survival. Mechanistically, HDAC7 scaffolds a repressive complex with HDAC3 and the stress-responsive transcription factor ATF3. This reduces H3K27ac/H3K18ac occupancy and blocks BRD4/RNA polymerase II (Pol II) recruitment at ATF3 regulatory regions to epigenetically silence its transcription. Consequently, this repression inactivates ATF3's tumor-suppressive functions, activating oncogenic PI3K-Akt signaling while suppressing the Hippo pathway. Genetic depletion or pharmacological inhibition of HDAC7 disrupts this repressive complex, triggering a functional switch in ATF3. This promotes BRD4/Pol II recruitment and H3K27ac enrichment at the ATF3 locus, enabling ATF3 to undergo transcriptional self-activation. Reactivated ATF3 suppresses CRC proliferation and survival by downregulating Bcl-2, upregulating p21 (CDKN1A) to induce cell cycle arrest, promoting caspase-3-mediated apoptosis, and inhibiting PI3K-Akt signaling. Xenograft studies confirm that HDAC7 depletion suppresses tumorigenicity in vivo. Our work identifies HDAC7 as a molecular mediator that governs ATF3's functional plasticity through competitive cofactor recruitment, positioning HDAC7 inhibition as a therapeutic strategy to reactivate ATF3-mediated tumor suppression in CRC.
    Keywords:  ATF3; HDAC7; class IIa HDAC; colorectal cancer; epigenetic repression; scaffold protein
    DOI:  https://doi.org/10.7150/ijbs.121348
  12. Anticancer Agents Med Chem. 2026 May 11.
    Computational Design, Synthesis, and In Vitro Evaluation of Novel Piperazine-Based HDAC Inhibitors as Potential Breast Cancer Therapeutics.
    Sehija Dizdarevic, Dusan Ruzic, Tatjana Srdic-Radic, Zorica Vujić.
       INTRODUCTION: Limited treatment options and poor prognosis create a need for new therapies for triplenegative breast cancer. Modulating lysine acetylation of histone and non-histone proteins via histone deacetylase inhibitors is a promising strategy in cancer therapy. This study aimed to design, synthesize, and test novel panHDAC inhibitors in vitro, building on our previous research.
    METHODS: Compound design was based on a previously validated diphenylmethyl piperazine scaffold, used as a template for further modifications. In silico studies included molecular docking and pharmacokinetic profiling for absorption, distribution, metabolism, excretion, and toxicity. Compounds identified from these analyses were synthesized, tested for in vitro enzymatic inhibition, and evaluated for cytotoxicity on cancer cell lines using the MTT assay.
    RESULTS: Compound 8o had the strongest HDAC inhibitory profile. It was highly potent against HDAC6 (IC50 = 18.5 nM) and active against HDAC1 and HDAC8 (IC50 = 430 nM and 1620 nM, respectively). Compound 8p also inhibited HDAC6 (IC50 = 54 nM) but was less potent against the nuclear isoforms. Both compounds were less active than trichostatin A. In the cytotoxicity assay, 8o and 8p reduced the viability of triple-negative breast cancer cells in a dosedependent manner. Compound 8o was the most active (IC50 = 6.74 μM on MDA-MB-231), exceeding the effect of tubastatin A. Moderate activity was seen on MDA-MB-468 cells.
    DISCUSSION: In vitro enzymatic assays showed that compound 8o strongly inhibited HDAC6, similar to the reference compound 8b. However, its cellular activity did not exceed 8b, suggesting that factors other than target engagement may limit its cell efficacy. These findings show the need to combine biochemical and physicochemical data when optimising HDAC inhibitors for triple-negative breast cancer.
    CONCLUSION: Compounds 8o and 8p were identified as potent panHDAC inhibitors. They demonstrated cytotoxicity against triple-negative breast cancer cells. This provides a promising foundation for future structural optimization and preclinical development.
    Keywords:  Triple-negative breast cancer; cytotoxicity; drug design.; histone deacetylase inhibitors; molecular docking; panHDAC inhibition
    DOI:  https://doi.org/10.2174/0118715206448039260114072721
  13. Amino Acids. 2026 May 19.
    Methionine concentration regulates LSD1 acetylation in glioma cells.
    Jie Chang, Lude Wang, Yi Pan, Qiuwen Lou, Wenxia Xu.
      Glioma is a highly aggressive brain cancer with poor prognosis, characterized by vigorous methionine metabolism. While methionine restriction demonstrates broad anticancer effects, its mechanistic relationship with epigenetic regulators in glioma remains inadequately understood. This study reveals the molecular mechanism by which methionine restriction (0.1 mM) modulates the epigenetic regulator LSD1. Restricting methionine to 0.1 mM induced site-specific acetylation at LSD1 lysine residues K6 and K359, promoting its ubiquitin-proteasome-dependent degradation independently of transcriptional alterations. Multi-omics analysis revealed that LSD1 inhibition induced dual reprogramming: transcriptomic activation of the p38MAPK and ubiquitin-proteasome pathways, coupled with metabolomic suppression of the TCA cycle with accumulation of L-proline and other amino acid metabolites. The HDAC inhibitor TSA synergized with methionine restriction to enhance LSD1 acetylation and degradation, whereas K6R/K359R mutations stabilized LSD1, confirming the role of acetylation in proteasomal targeting. Functional validation via colony formation identified LSD1 as a key mediator of methionine restriction; LSD1 knockdown mimicked the growth inhibition of methionine starvation, while its overexpression partially restored proliferation. Collectively, these results establish the methionine-LSD1 axis as a crucial nutrient-sensing mechanism that drives glioma adaptation via epigenetic-metabolic crosstalk. This highlights potential combinatorial therapeutic strategies involving dietary methionine limitation and LSD1 acetylation-targeted therapy to disrupt tumor survival pathways.
    Keywords:  Acetylation; Glioma; LSD1; Metabolic reprogramming; Methionine metabolism; Ubiquitination
    DOI:  https://doi.org/10.1007/s00726-026-03527-z
  14. Appl Environ Microbiol. 2026 May 18. e0249825
    Global impact on metabolic capacity of yeast cell factories by optogenetic control of the cAMP-PKA axis.
    Mohamed Watad, Jonathan Trauth, Filipp Bezold, Ammar Baker, Bastian Pook, Johannes Scheffer, Hagen Nusshär, Sophia Hasenjäger, Nicole Paczia, Lars-Oliver Essen, Christof Taxis.
      Dynamic metabolic engineering enables temporal redirection of microbial metabolism from biomass production to product synthesis. Here, we show that optogenetic control of protein kinase A (PKA) activity via light-regulated modulation of intracellular cyclic AMP (cAMP) levels can enhance heterologous production of β-carotene and cordycepin in Saccharomyces cerevisiae. To enable exclusive, glucose-independent control of cAMP synthesis, the photoactivatable adenylyl cyclase bPAC from Beggiatoa sp. was introduced into cells lacking the endogenous adenylyl cyclase Cyr1 or with lowered Cyr1 levels using an optogenetically controlled degron. Despite being growth-competent under illumination, the bPAC-containing yeast strain showed alterations in energy metabolism under all conditions. Quantitative proteome analysis using timsTOF mass spectrometry revealed profound changes in central carbon metabolism, sulfur homeostasis, energy charge, and ribosome biogenesis upon uncoupling cAMP from nutrient-dependent regulation, particularly under sustained light activation. These results highlight the critical role of dynamic Cyr1-dependent regulation for central metabolism, and underscore the biotechnological promise of refined PKA-targeted strategies for eukaryotic cell factories.IMPORTANCECarbon-footprint-minimized production of fine chemicals, pharmaceuticals, and biofuels requires optimized microbial cell factories with tailored metabolic performance. We employed optogenetic dynamic metabolic engineering in baker's yeast by uncoupling nutrient sensing from cAMP signaling using a light-controlled adenylate cyclase. Precise light regulation of intracellular cAMP levels and PKA activity enabled acute control of the metabolism, redirecting resources toward product synthesis, and boosting the production of valuable compounds such as β-carotene and cordycepin. Quantitative proteomics revealed that uncoupling of the cAMP-PKA axis from glucose sensing profoundly reprograms the central carbon metabolism and other key cellular processes. This approach provides a blueprint for refined, light-tunable strategies targeting the cAMP-PKA axis directly with light, e.g., for enhanced bioethanol production. Moreover, our data provide evidence for the profound influence of the cAMP-PKA axis on metabolism and balanced energy production that are fundamental for efficient production in microbial cell factories.
    Keywords:  Ras/cAMP/PKA pathway; adenylate cyclase; energy metabolism; optogenetics; proteomics
    DOI:  https://doi.org/10.1128/aem.02498-25
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