bims-toxgon 2023-10-01 papers

bims-toxgon

Biomed News

on Toxoplasma gondii metabolism

Issue of 2023‒10‒01
eighteen papers selected by
Lakesh Kumar, BITS Pilani

The Toxoplasma gondii effector GRA83 modulates the host's innate immune response to regulate parasite infection.
Human neutrophil-like cells demonstrate antimicrobial responses to the chronic cyst form of Toxoplasma gondii.
AP2XII-1 is a negative regulator of merogony and presexual commitment in Toxoplasma gondii.
A transcriptional network required for bradyzoite development in Toxoplasma gondii is dispensable for recrudescent disease.
Visualization of parasite dynamics in the host tissues: application of tissue transparency technology to parasite research.
Toxoplasma gondii induces pyroptosis in human placental trophoblast and amniotic cells by inducing ROS production and activation of cathepsin B and NLRP1/NLRP3/NLRC4/AIM2 inflammasome.
Starving the Beast: Limiting Coenzyme A Biosynthesis to Prevent Disease and Transmission in Malaria.
Global profiling of ribosomal protein acetylation reveals essentiality of acetylation homeostasis in maintaining ribosome assembly and function.
Sirtuins and autophagy in lipid metabolism.
Nutrient-dependent signaling pathways that control autophagy in yeast.
Pf MORC protein regulates chromatin accessibility and transcriptional repression in the human malaria parasite, P. falciparum.
Time-resolved proximity biotinylation implicates a porin protein in export of transmembrane malaria parasite effectors.
TurboID-based proximity labelling reveals a connection between VPS34 and cellular homeostasis.
ULK1 forms distinct oligomeric states and nanoscopic structures during autophagy initiation.
Insights into the regulation of mitochondrial functions by PKA-mediated phosphorylation.
Molecular Mechanisms of Persistence in Protozoan Parasites.
Structural view on autophagosome formation.
First application of a droplet digital PCR to detect Toxoplasma gondii in mussels.

mSphere. 2023 Sep 28. e0026323

The Toxoplasma gondii effector GRA83 modulates the host's innate immune response to regulate parasite infection.

Amara C Thind, Caroline M Mota, Ana Paula N Gonçalves, Jihui Sha, James A Wohlschlegel, Tiago W P Mineo, Peter J Bradley.

  Toxoplasma gondii's propensity to infect its host and cause disease is highly dependent on its ability to modulate host cell functions. One of the strategies the parasite uses to accomplish this is via the export of effector proteins from the secretory dense granules. Dense granule (GRA) proteins are known to play roles in nutrient acquisition, host cell cycle manipulation, and immune regulation. Here, we characterize a novel dense granule protein named GRA83, which localizes to the parasitophorous vacuole (PV) in tachyzoites and bradyzoites. Disruption of GRA83 results in increased virulence, weight loss, and parasitemia during the acute infection, as well as a marked increase in the cyst burden during the chronic infection. This increased parasitemia was associated with an accumulation of inflammatory infiltrates in tissues in both acute and chronic infections. Murine macrophages infected with ∆gra83 tachyzoites produced less interleukin-12 (IL-12) in vitro, which was confirmed with reduced IL-12 and interferon-gamma in vivo. This dysregulation of cytokines correlates with reduced nuclear translocation of the p65 subunit of the nuclear factor-κB (NF-κB) complex. While GRA15 similarly regulates NF-κB, infection with ∆gra83/∆gra15 parasites did not further reduce p65 translocation to the host cell nucleus, suggesting these GRAs function in converging pathways. We also used proximity labeling experiments to reveal candidate GRA83 interacting T. gondii-derived partners. Taken together, this work reveals a novel effector that stimulates the innate immune response, enabling the host to limit the parasite burden. IMPORTANCE Toxoplasma gondii poses a significant public health concern as it is recognized as one of the leading foodborne pathogens in the United States. Infection with the parasite can cause congenital defects in neonates, life-threatening complications in immunosuppressed patients, and ocular disease. Specialized secretory organelles, including the dense granules, play an important role in the parasite's ability to efficiently invade and regulate components of the host's infection response machinery to limit parasite clearance and establish an acute infection. Toxoplasma's ability to avoid early clearance, while also successfully infecting the host long enough to establish a persistent chronic infection, is crucial in allowing for its transmission to a new host. While multiple GRAs directly modulate host signaling pathways, they do so in various ways highlighting the parasite's diverse arsenal of effectors that govern infection. Understanding how parasite-derived effectors harness host functions to evade defenses yet ensure a robust infection is important for understanding the complexity of the pathogen's tightly regulated infection. In this study, we characterize a novel secreted protein named GRA83 that stimulates the host cell's response to limit infection.

Keywords:  GRA15; GRA83; NF-κB; Toxoplasma gondii; dense granules; innate immunity

DOI:  https://doi.org/10.1128/msphere.00263-23
Parasite Immunol. 2023 Sep 30. e13011

Human neutrophil-like cells demonstrate antimicrobial responses to the chronic cyst form of Toxoplasma gondii.

Kristina V Bergersen, Ashley D Ramirez, Bill Kavvathas, Frances Mercer, Emma H Wilson.

  The protozoan parasite Toxoplasma gondii infects approximately 2.5 billion people worldwide. Infection induces a rapid dissemination of parasites throughout the body followed by the formation of lifelong cysts within neurons of the host brain. Both stages require a dynamic immune response comprised of both innate and adaptive cells. Neutrophils are a primary responding cell to acute infection and have been observed in the brain during murine chronic infection. Previous studies investigating human neutrophils found that invasion by Toxoplasma tachyzoites inhibits apoptosis of neutrophils, prolonging their survival under inflammatory conditions. Here, we demonstrate the differentiation of two distinct subsets following exposure of human neutrophil-like-cells (HNLC) to Toxoplasma cysts. In vitro stimulation and imaging studies show cyst-specific induction of cytokines and cyst clearance by HNLCs. Further testing demonstrates that aged HNLCs perform less phagocytosis of cysts compared to non-aged HNLCs. In conclusion, this study identifies a novel response of HNLCs to Toxoplasma cysts and may indicate a role for neutrophils in the clearance of cysts during human infection with Toxoplasma.

Keywords:  Toxoplasma gondii; chronic cysts; human; immune response; neutrophils

DOI:  https://doi.org/10.1111/pim.13011
mBio. 2023 Sep 26. e0178523

AP2XII-1 is a negative regulator of merogony and presexual commitment in Toxoplasma gondii.

Fuqiang Fan, Lilan Xue, Xiaoyan Yin, Nishith Gupta, Bang Shen.

  A transition from the asexual to sexual development in the widespread intracellular pathogen Toxoplasma gondii requires stage switching in its feline (definitive) host, but the mechanisms governing this process remain elusive. Here, we demonstrate a novel apicomplexan-specific transcription factor, TgAP2XII-1, that controls the transition of the acutely infectious tachyzoite stage to a presexual merozoite stage. The AP2XII-1 deletion mutants are elongated and replicate as merozoites by endopolygeny instead of endodyogeny, by which tachyzoites proliferate. Besides, the parasites lacking AP2XII-1 show a merozoite-type transcriptional profile. Indeed, AP2XII-1 directly targets many stage-specific genes via its interaction with the MORC complex, eventually repressing a repertoire of sex-related transcripts in tachyzoites. In conclusion, our work identifies AP2XII-1 as a merogony repressor, provides insight into the sexual commitment of T. gondii, and opens a gateway to culture the presexual stages of a model parasitic protist. IMPORTANCE Sexual development is vital for the transmission, genetic hybridization, and population evolution of apicomplexan pathogens, which include several clinically relevant parasites, such as Plasmodium, Eimeria, and Toxoplasma gondii. Previous studies have demonstrated different morphological characteristics and division patterns between asexual and sexual stages of the parasites. However, the primary regulation is poorly understood. A transition from the asexual to the sexual stage is supposedly triggered/accompanied by rewiring of gene expression and controlled by transcription factors and chromatin modulators. Herein, we discovered a tachyzoite-specific transcriptional factor AP2XII-1, which represses the presexual development in the asexual tachyzoite stage of T. gondii. Conditional knockdown of AP2XII-1 perturbs tachyzoite proliferation by endodyogeny and drives a transition to a morphologically and transcriptionally distinct merozoite stage. The results also suggest a hierarchical transcriptional regulation of sexual development by AP2 factors and provide a path to culturing merozoites and controlling inter-host transmission of T. gondii.

Keywords:  AP2 transcription factors; MORC; merogony; merozoite; sexual development

DOI:  https://doi.org/10.1128/mbio.01785-23
Nat Commun. 2023 Sep 28. 14(1): 6078

A transcriptional network required for bradyzoite development in Toxoplasma gondii is dispensable for recrudescent disease.

Sarah L Sokol-Borrelli, Sarah M Reilly, Michael J Holmes, Stephanie B Orchanian, Mackenzie D Massmann, Katherine G Sharp, Leah F Cabo, Hisham S Alrubaye, Bruno Martorelli Di Genova, Melissa B Lodoen, William J Sullivan, Jon P Boyle.

Identification of regulators of Toxoplasma gondii bradyzoite development and cyst formation is the most direct way to address the importance of parasite development in long-term persistence and reactivation of this parasite. Here we show that a T. gondii gene (named Regulator of Cystogenesis 1; ROCY1) is sufficient for T. gondii bradyzoite formation in vitro and in vivo. ROCY1 encodes an RNA binding protein that has a preference for 3' regulatory regions of hundreds of T. gondii transcripts, and its RNA-binding domains are required to mediate bradyzoite development. Female mice infected with ΔROCY1 parasites have reduced (>90%) cyst burden. While viable parasites can be cultivated from brain tissue for up to 6 months post-infection, chronic brain-resident ΔROCY1 parasites have reduced oral infectivity compared to wild type. Despite clear defects in bradyzoite formation and oral infectivity, ΔROCY1 parasites were able to reactivate with similar timing and magnitude as wild type parasites for up to 5 months post-infection. Therefore while ROCY1 is a critical regulator of the bradyzoite developmental pathway, it is not required for parasite reactivation, raising new questions about the persisting life stage responsible for causing recrudescent disease.

DOI: https://doi.org/10.1038/s41467-023-40948-w
J Vet Med Sci. 2023 Sep 28.

Visualization of parasite dynamics in the host tissues: application of tissue transparency technology to parasite research.

Yasuhiro Takashima.

  Many parasite species migrate to another site of infection after entering the host body. Such parasite dynamics are closely related to pathogenicity, but it is not easy to observe such parasite behavior deep within the organs. In recent years, technology that can make organs transparent has been developed that enables us to observe deep within organs ex vivo while maintaining their three-dimensional structure. This review describes a series of attempts to apply this technology to understand the behavior of Toxoplasma gondii in the host body. A series of studies has shown that T. gondii tachyzoites that infect leukocytes can reach target organs far from the site of invasion via the circulatory system. In addition, infected leukocytes in the bloodstream adhere more readily to vascular endothelial cells than uninfected leukocytes and are more likely to remain inside the target organs. When infected leukocytes adhere to the vascular endothelial cells of the target organ, the tachyzoites inside the cells immediately escape and infect the parenchyma of the organs. As described above, organ transparency technology is a powerful tool for understanding the internal dynamics of parasites.

Keywords:  Toxoplasma gondii; parasite dynamics; transparency; visualization

DOI:  https://doi.org/10.1292/jvms.23-0272
Am J Pathol. 2023 Sep 21. pii: S0002-9440(23)00362-0. [Epub ahead of print]

Toxoplasma gondii induces pyroptosis in human placental trophoblast and amniotic cells by inducing ROS production and activation of cathepsin B and NLRP1/NLRP3/NLRC4/AIM2 inflammasome.

Juan-Hua Quan, Fei Fei Gao, Tian-Zhong Ma, Wei Ye, Xiang Gao, Ming-Zhu Deng, Lan-Lan Yin, In-Wook Choi, Jae-Min Yuk, Guang-Ho Cha, Young-Ha Lee, Jia-Qi Chu.

  Toxoplasma gondii infection in pregnant women may cause fetal anomaly; however, the underlying mechanisms remain unclear. Here, we investigated whether T. gondii induces pyroptosis in human placental cells and the underlying mechanisms. Human placental trophoblast (BeWo and HTR-8/SVneo) and amniotic (WISH) cells were infected with T. gondii, and then ROS production, cathepsin B (CatB) release, inflammasome activation, and pyroptosis induction were evaluated. Moreover, the molecular mechanisms of these effects were investigated by treating the cells with ROS scavengers, a CatB inhibitor, or inflammasome-specific siRNA. We found that T. gondii infection induced ROS generation and CatB release into the cytosol in placental cells but decreased mitochondrial membrane potential. T. gondii-infected human placental cells and villi showed NLRP1, NLRP3, NLRC4, and AIM2 inflammasome activation and subsequent pyroptosis induction, as evidenced by increased expression of ASC, cleaved caspase-1, and mature IL-1β and gasdermin D cleavage. In addition to inflammasome activation and pyroptosis induction, adverse pregnancy outcome was revealed in a T. gondii-infected pregnant mouse model. Administration of ROS scavengers, CatB inhibitor, or inflammasome-specific siRNA into T. gondii-infected cells reversed these effects. Collectively, these findings show that T. gondii induces NLRP1/NLRP3/NLRC4/AIM2 inflammasome-dependent caspase-1-mediated pyroptosis via induction of ROS production and CatB activation in placental cells, and this mechanism may play an important role in inducing cell injury in congenital toxoplasmosis.

Keywords:  Congenital toxoplasmosis; Human placental cells; Inflammasomes; Pregnant mouse model; Pyroptosis; Toxoplasma gondii

DOI:  https://doi.org/10.1016/j.ajpath.2023.08.016
Int J Mol Sci. 2023 Sep 10. pii: 13915. [Epub ahead of print]24(18):

Starving the Beast: Limiting Coenzyme A Biosynthesis to Prevent Disease and Transmission in Malaria.

Brendan F Riske, Shirley Luckhart, Michael A Riehle.

  Malaria parasites must acquire all necessary nutrients from the vertebrate and mosquito hosts to successfully complete their life cycle. Failure to acquire these nutrients can limit or even block parasite development and presents a novel target for malaria control. One such essential nutrient is pantothenate, also known as vitamin B5, which the parasite cannot synthesize de novo and is required for the synthesis of coenzyme A (CoA) in the parasite. This review examines pantothenate and the CoA biosynthesis pathway in the human-mosquito-malaria parasite triad and explores possible approaches to leverage the CoA biosynthesis pathway to limit malaria parasite development in both human and mosquito hosts. This includes a discussion of sources for pantothenate for the mosquito, human, and parasite, examining the diverse strategies used by the parasite to acquire substrates for CoA synthesis across life stages and host resource pools and a discussion of drugs and alternative approaches being studied to disrupt CoA biosynthesis in the parasite. The latter includes antimalarial pantothenate analogs, known as pantothenamides, that have been developed to target this pathway during the human erythrocytic stages. In addition to these parasite-targeted drugs, we review studies of mosquito-targeted allosteric enzymatic regulators known as pantazines as an approach to limit pantothenate availability in the mosquito and subsequently deprive the parasite of this essential nutrient.

Keywords:  Anopheles; Plasmodium; malaria control; pantazine; pantothenamide; pantothenate; pantothenate kinase; phosphopantetheine; vitamin B5

DOI:  https://doi.org/10.3390/ijms241813915
Nucleic Acids Res. 2023 Sep 23. pii: gkad768. [Epub ahead of print]

Global profiling of ribosomal protein acetylation reveals essentiality of acetylation homeostasis in maintaining ribosome assembly and function.

Jinjing Ni, Shuxian Li, Yanan Lai, Zuoqiang Wang, Danni Wang, Yongcong Tan, Yongqiang Fan, Jie Lu, Yu-Feng Yao.

Acetylation is a global post-translational modification that regulates various cellular processes. Bacterial acetylomic studies have revealed extensive acetylation of ribosomal proteins. However, the role of acetylation in regulating ribosome function remains poorly understood. In this study, we systematically profiled ribosomal protein acetylation and identified a total of 289 acetylated lysine residues in 52 ribosomal proteins (r-proteins) from Salmonella Typhimurium. The majority of acetylated lysine residues of r-proteins were found to be regulated by both acetyltransferase Pat and metabolic intermediate acetyl phosphate. Our results show that acetylation plays a critical role in the assembly of the mature 70S ribosome complex by modulating r-proteins binding to rRNA. Moreover, appropriate acetylation is important for the interactions between elongation factors and polysomes, as well as regulating ribosome translation efficiency and fidelity. Dysregulation of acetylation could alter bacterial sensitivity to ribosome-targeting antibiotics. Collectively, our data suggest that the acetylation homeostasis of ribosomes is crucial for their assembly and function. Furthermore, this mechanism may represent a universal response to environmental signals across different cell types.

DOI: https://doi.org/10.1093/nar/gkad768
Cell Biochem Funct. 2023 Sep 27.

Sirtuins and autophagy in lipid metabolism.

Xuan Sun, Xiaoting Yang, Wanfei Gui, Songling Liu, Qingjun Gui.

  Sirtuins are a family of NAD+ -dependent deacetylases that regulate some important biological processes, including lipid metabolism and autophagy, through their deacetylase function. Autophagy is a new discovery in the field of lipid metabolism, which may provide a new idea for the regulation of lipid metabolism. There are many tandem parts in the regulation process of lipid metabolism and autophagy of sirtuins protein family. This paper summarized these tandem parts and proposed the possibility of sirtuins regulating lipid autophagy, as well as the interaction and synergy between sirtuins protein family. Currently, some natural drugs have been reported to affect metabolism by regulating sirtuins, some of which regulate autophagy by targeting sirtuins.

Keywords:  Sirtuins; autophagy; lipid metabolism; metabolic disease; natural drugs

DOI:  https://doi.org/10.1002/cbf.3860
FEBS Lett. 2023 Sep 27.

Nutrient-dependent signaling pathways that control autophagy in yeast.

Shree Padma Metur, Daniel J Klionsky.

  Macroautophagy/autophagy is a highly conserved catabolic process vital for cellular stress responses and maintaining equilibrium within the cell. Malfunctioning autophagy has been implicated in the pathogenesis of various diseases, including certain neurodegenerative disorders, diabetes, metabolic diseases and cancer. Cells face diverse metabolic challenges, such as limitations in nitrogen, carbon, and minerals such as phosphate and iron, necessitating the integration of complex metabolic information. Cells utilize a signal transduction network of sensors, transducers, and effectors to coordinate the execution of the autophagic response, concomitant with the severity of the nutrient-starvation condition. This review presents the current mechanistic understanding of how cells regulate the initiation of autophagy through various nutrient-dependent signaling pathways. Emphasizing findings from studies in yeast, we explore the emerging principles that underlie the nutrient-dependent regulation of autophagy, significantly shaping stress-induced autophagy responses under various metabolic stress conditions.

Keywords:  AMPK; PKA; TOR; autophagy regulation; nutrient homeostasis; signaling

DOI:  https://doi.org/10.1002/1873-3468.14741
bioRxiv. 2023 Sep 11. pii: 2023.09.11.557253. [Epub ahead of print]

Pf MORC protein regulates chromatin accessibility and transcriptional repression in the human malaria parasite, P. falciparum.

Z Chahine, M Gupta, T Lenz, T Hollin, S Abel, Cas Banks, A Saraf, J Prudhomme, L Florens, K G Le Roch.

The environmental challenges the human malaria parasite, Plasmodium falciparum , faces during its progression into its various lifecycle stages warrant the use of effective and highly regulated access to chromatin for transcriptional regulation. Microrchidia (MORC) proteins have been implicated in DNA compaction and gene silencing across plant and animal kingdoms. Accumulating evidence has shed light into the role MORC protein plays as a transcriptional switch in apicomplexan parasites. In this study, using CRISPR/Cas9 genome editing tool along with complementary molecular and genomics approaches, we demonstrate that Pf MORC not only modulates chromatin structure and heterochromatin formation throughout the parasite erythrocytic cycle, but is also essential to the parasite survival. Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) experiments suggest that Pf MORC binds to not only sub-telomeric regions and genes involved in antigenic variation but is also most likely a key modulator of stage transition. Protein knockdown experiments followed by chromatin conformation capture (Hi-C) studies indicate that downregulation of Pf MORC induces the collapse of the parasite heterochromatin structure leading to its death. All together these findings confirm that Pf MORC plays a crucial role in chromatin structure and gene regulation, validating this factor as a strong candidate for novel antimalarial strategies.

DOI: https://doi.org/10.1101/2023.09.11.557253
J Cell Sci. 2023 Sep 29. pii: jcs.260506. [Epub ahead of print]

Time-resolved proximity biotinylation implicates a porin protein in export of transmembrane malaria parasite effectors.

David Anaguano, Watcharatip Dedkhad, Carrie F Brooks, David W Cobb, Vasant Muralidharan.

  The malaria-causing parasite, Plasmodium falciparum completely remodels its host red blood cell (RBC) through the export of several hundred parasite proteins, including transmembrane proteins, across multiple membranes to the RBC. However, the process by which these exported membrane proteins are extracted from the parasite plasma membrane for export remains unknown. To address this question, we fused the exported membrane protein, skeleton binding protein 1 (SBP1), with TurboID, a rapid, efficient, and promiscuous biotin ligase (SBP1TbID). Using time-resolved, proximity biotinylation, and label-free quantitative proteomics, we identified two groups of SBP1TbID interactors: early interactors (pre-export) and late interactors (post-export). Notably, two promising membrane-associated proteins were identified as pre-export interactors, one of which possesses a predicted translocon domain, that could facilitate the export of membrane proteins. Further investigation using conditional mutants of these candidate proteins showed that these proteins were essential for asexual growth and localize to the host-parasite interface during early stages of the intraerythrocytic cycle. These data suggest that they may play a role in ushering membrane proteins from the PPM for export to the host RBC.

Keywords:  Host-parasite interactions; Malaria; Plasmodium falciparum; Protein export; Translocons

DOI:  https://doi.org/10.1242/jcs.260506
J Plant Physiol. 2023 Sep 20. pii: S0176-1617(23)00194-3. [Epub ahead of print]289 154100

TurboID-based proximity labelling reveals a connection between VPS34 and cellular homeostasis.

Taotao Wang, Xinjing Li, Ningjing Liu, Yi Yang, Qingqiu Gong.

  Unlike animals, plants and yeasts only have a class III phosphatidylinositol 3-kinase (PI3KC3). Its lipid product, phosphatidylinositol 3-phosphate (PtdIns-3-P, PI3P), organizes intracellular trafficking routes such as autophagosome formation, multivesicular body (MVB) formation, retro-transport from trans-Golgi network (TGN) to late Golgi, and the fusion events between autophagosomes and MVBs and the vacuole. The catalytic subunit of plant PI3KC3 is encoded by the essential gene Vacuolar Protein Sorting 34 (VPS34). Despite the importance of VPS34 in cellular homeostasis and plant development, a VPS34 interactome is lacking. Here we employed TurboID, an enzyme-catalyzed proximity labelling (PL) method, to describe a proximal interactome of Arabidopsis VPS34. TurboID catalyzed spatially restricted biotinylation and enabled VPS34-specific enrichment of 273 proteins from affinity purification coupled with mass spectrometry. The interactome confirmed known functions of VPS34 in endo-lysosomal trafficking. Intriguingly, carbohydrate metabolism was the most enriched Gene Ontology (GO) term, including glycolytic enzymes in the triose portion and enzymes functioning in chloroplast triose export and sucrose biosynthesis. The interaction between VPS34 and the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH, GAPC1/2) was validated in planta. Also verified was the interaction between VPS34 and the plasma membrane H+-ATPase AHA2, a primary determinant of membrane potential. Our study links PI3KC3 to carbohydrate metabolism and membrane potential, two key processes that maintain cellular homeostasis.

Keywords:  Glycolysis; Membrane trafficking; Phosphoinositide; Protein-protein interaction; TurboID; VPS34; Vacuole

DOI:  https://doi.org/10.1016/j.jplph.2023.154100
Sci Adv. 2023 Sep 29. 9(39): eadh4094

ULK1 forms distinct oligomeric states and nanoscopic structures during autophagy initiation.

Chiranjib Banerjee, Dushyant Mehra, Daihyun Song, Angel Mancebo, Ji-Man Park, Do-Hyung Kim, Elias M Puchner.

Autophagy induction involves extensive molecular and membrane reorganization. Despite substantial progress, the mechanism underlying autophagy initiation remains poorly understood. Here, we used quantitative photoactivated localization microscopy with single-molecule sensitivity to analyze the nanoscopic distribution of endogenous ULK1, the kinase that triggers autophagy. Under amino acid starvation, ULK1 formed large clusters containing up to 161 molecules at the endoplasmic reticulum. Cross-correlation analysis revealed that ULK1 clusters engaging in autophagosome formation require 30 or more molecules. The ULK1 structures with more than the threshold number contained varying levels of Atg13, Atg14, Atg16, LC3B, GEC1, and WIPI2. We found that ULK1 activity is dispensable for the initial clustering of ULK1, but necessary for the subsequent expansion of the clusters, which involves interaction with Atg14, Atg16, and LC3B and relies on Vps34 activity. This quantitative analysis at the single-molecule level has provided unprecedented insights into the behavior of ULK1 during autophagy initiation.

DOI: https://doi.org/10.1126/sciadv.adh4094
J Biochem. 2023 Sep 29. pii: mvad075. [Epub ahead of print]

Insights into the regulation of mitochondrial functions by PKA-mediated phosphorylation.

Shiori Akabane, Toshihiko Oka.

  Cyclic AMP (cAMP) - protein kinase A (PKA) signaling is a highly conserved pathway in eukaryotes and plays a central role in cell signaling cascades in response to environmental changes. Elevated cAMP levels promote the activation of PKA, which phosphorylates various downstream proteins. Many cytosolic and nuclear proteins, such as metabolic enzymes and transcriptional factors, have been identified as substrates for PKA, suggesting that PKA-mediated regulation occurs predominantly in the cytosol. Mitochondrial proteins are also phosphorylated by PKA, and PKA-mediated phosphorylation of mitochondrial proteins is considered to control a variety of mitochondrial functions, including oxidative phosphorylation, protein import, morphology, and quality control. In this review, we outline PKA mitochondrial substrates and summarize the regulation of mitochondrial functions through PKA-mediated phosphorylation.

Keywords:  PKA; cAMP; mitochondria; phosphorylation

DOI:  https://doi.org/10.1093/jb/mvad075
Microorganisms. 2023 Sep 07. pii: 2248. [Epub ahead of print]11(9):

Molecular Mechanisms of Persistence in Protozoan Parasites.

Asfiha Tarannum, Cristian Camilo Rodríguez-Almonacid, Jorge Salazar-Bravo, Zemfira N Karamysheva.

  Protozoan parasites are known for their remarkable capacity to persist within the bodies of vertebrate hosts, which frequently results in prolonged infections and the recurrence of diseases. Understanding the molecular mechanisms that underlie the event of persistence is of paramount significance to develop innovative therapeutic approaches, given that these pathways still need to be thoroughly elucidated. The present article provides a comprehensive overview of the latest developments in the investigation of protozoan persistence in vertebrate hosts. The focus is primarily on the function of persisters, their formation within the host, and the specific molecular interactions between host and parasite while they persist. Additionally, we examine the metabolomic, transcriptional, and translational changes that protozoan parasites undergo during persistence within vertebrate hosts, focusing on major parasites such as Plasmodium spp., Trypanosoma spp., Leishmania spp., and Toxoplasma spp. Key findings of our study suggest that protozoan parasites deploy several molecular and physiological strategies to evade the host immune surveillance and sustain their persistence. Furthermore, some parasites undergo stage differentiation, enabling them to acclimate to varying host environments and immune challenges. More often, stressors such as drug exposure were demonstrated to impact the formation of protozoan persisters significantly. Understanding the molecular mechanisms regulating the persistence of protozoan parasites in vertebrate hosts can reinvigorate our current insights into host-parasite interactions and facilitate the development of more efficacious disease therapeutics.

Keywords:  Apicomplexa; metabolome; protozoa persisters; translatome

DOI:  https://doi.org/10.3390/microorganisms11092248
FEBS Lett. 2023 Sep 27.

Structural view on autophagosome formation.

Nobuo N Noda.

  Autophagy is a conserved intracellular degradation system in eukaryotes, involving the sequestration of degradation targets into autophagosomes, which are subsequently delivered to lysosomes (or vacuoles in yeasts and plants) for degradation. In budding yeast, starvation-induced autophagosome formation relies on approximately 20 core Atg proteins, grouped into six functional categories: the Atg1/ULK complex, the phosphatidylinositol-3 kinase complex, the Atg9 transmembrane protein, the Atg2-Atg18/WIPI complex, the Atg8 lipidation system, and the Atg12-Atg5 conjugation system. Additionally, selective autophagy requires cargo receptors and other factors, including a fission factor, for specific sequestration. This review covers the 30-year history of structural studies on core Atg proteins and factors involved in selective autophagy, examining X-ray crystallography, NMR, and cryo-EM techniques. The molecular mechanisms of autophagy are explored based on protein structures, and future directions in the structural biology of autophagy are discussed, considering the advancements in the era of AlphaFold.

Keywords:  AlphaFold; autophagy; core Atg proteins; selective autophagy; structural studies

DOI:  https://doi.org/10.1002/1873-3468.14742
Front Microbiol. 2023 ;14 1238689

First application of a droplet digital PCR to detect Toxoplasma gondii in mussels.

Andrea Mancusi, Yolande T R Proroga, Angela Giordano, Santa Girardi, Francescantonio D'Orilia, Renato Pinto, Paolo Sarnelli, Laura Rinaldi, Federico Capuano, Maria Paola Maurelli.

  Toxoplasmosis, caused by the protozoan Toxoplasma gondii, is one of the main food-, water- and soil-borne zoonotic disease worldwide. Over the past 20 years many papers were published on the transmission of T. gondii by marine animals, including mollusks, which can concentrate the oocysts and release them. Sporulated oocysts may remain viable and infective for 18 months in seawater. Therefore, raw or undercooked bivalve mollusks pose a risk to humans. This study aimed to apply and validate for the first time a very sensitive digital droplet polymerase chain reaction (ddPCR) protocol to detect and quantify T. gondii DNA in mussels. Four concentration levels: 8000 genomic copies (gc)/μL, 800 gc/μL, 80 gc/μL, 8 gc/μL of a T. gondii reference DNA were tested. DNA was extracted from 80 pools of mussels (Mytilus galloprovincialis). Forty pools were contaminated with T. gondii reference DNA and used as positive controls, while 40 pools were used as negative controls. DdPCR reaction was prepared using a protocol, previously developed by the authors, for detection of T. gondii in meat. Amplification was obtained up 8 gc/μL. All infected replicates resulted positive, as well as no droplets were detected in negative controls. The droplets produced in the reaction ranged from 8,828 to 14,075 (average 12,627 droplets). The sensitivity and specificity of ddPCR were 100% (95%CI = 94.3-99.9). In addition, 100 pools of mussels collected in the Gulf of Naples were used to validate the protocol. Of these 16% were positive (95% CI = 9.7-25.0) for T. gondii. Samples were also tested by real-time PCR and no positive samples were found. Data obtained from ddPCR showed good identification of negative and positive samples with higher specificity and efficiency than real-time PCR. This tool could be very useful for a rapid sensitive detection of low DNA concentrations of T. gondii in mussels, reducing the risk of toxoplasmosis in humans.

Keywords:  Toxoplasma gondii; droplet digital polymerase chain reaction; mollusks; mussels; toxoplasmosis

DOI:  https://doi.org/10.3389/fmicb.2023.1238689