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Ji Y, Li J, Liang Y, Li L, Wang Y, Pi L, Xing P, Nomura CT, Chen S, Zhu C, Wang Q. Engineering the Tat-secretion pathway of Bacillus licheniformis for the secretion of cytoplasmic enzyme arginase. Appl Microbiol Biotechnol 2024; 108:89. [PMID: 38194145 DOI: 10.1007/s00253-023-12917-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/06/2023] [Accepted: 10/16/2023] [Indexed: 01/10/2024]
Abstract
The industrial bacterium Bacillus licheniformis has long been used as a microbial factory for the production of enzymes due to its ability to secrete copious amounts of native extracellular proteins and its generally regarded as safe (GRAS) status. However, most attempts to use B. licheniformis to produce heterologous and cytoplasmic enzymes primarily via the general secretory (Sec) pathway have had limited success. The twin-arginine transport (Tat) pathway offers a promising alternative for the extracellular export of Sec-incompatible proteins because it transports full, correctly folded proteins. However, compared to the Sec pathway, the yields of the Tat pathway have historically been too low for commercial use. To improve the export efficiency of the Tat pathway, we identified the optimal Tat-dependent signal peptides and increased the abundance of the Tat translocases, the signal peptidase (SPase), and the intracellular chaperones. These strategic modifications significantly improved the Tat-dependent secretion of the cytoplasmic enzyme arginase into the culture medium using B. licheniformis. The extracellular enzymatic activity of arginase showed a 5.2-fold increase after these modifications. Moreover, compared to the start strain B. licheniformis 0F3, the production of extracellular GFP was improved by 3.8 times using the strategic modified strain B. licheniformis 0F13, and the extracellular enzymatic activity of SOX had a 1.3-fold increase using the strain B. licheniformis 0F14. This Tat-based production chassis has the potential for enhanced production of Sec-incompatible enzymes, therefore expanding the capability of B. licheniformis as an efficient cellular factory for the production of high-value proteins. KEY POINTS: • Systematic genetic modification of Tat-pathway in B. licheniformis. • Significant enhancement of the secretion capacity of Tat pathway for delivery the cytoplasmic enzyme arginase. • A new platform for efficient extracellular production of Sec-incompatible enzymes.
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Affiliation(s)
- Yi Ji
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Science, Hubei University, Wuhan, 430062, People's Republic of China
| | - Junliang Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Science, Hubei University, Wuhan, 430062, People's Republic of China
| | - Yonglin Liang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Science, Hubei University, Wuhan, 430062, People's Republic of China
| | - Liang Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Science, Hubei University, Wuhan, 430062, People's Republic of China
| | - Yajun Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Science, Hubei University, Wuhan, 430062, People's Republic of China
| | - Li Pi
- Wuhan Grand Hoyo Co., Ltd, Wuhan, 430075, People's Republic of China
| | - Panpan Xing
- Wuhan Grand Hoyo Co., Ltd, Wuhan, 430075, People's Republic of China
| | - Christopher T Nomura
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844, USA
| | - Shouwen Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Science, Hubei University, Wuhan, 430062, People's Republic of China
| | - Chengjun Zhu
- Wuhan Grand Hoyo Co., Ltd, Wuhan, 430075, People's Republic of China.
| | - Qin Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, College of Life Science, Hubei University, Wuhan, 430062, People's Republic of China.
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2
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Zens B, Fäßler F, Hansen JM, Hauschild R, Datler J, Hodirnau VV, Zheden V, Alanko J, Sixt M, Schur FK. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. J Cell Biol 2024; 223:e202309125. [PMID: 38506714 PMCID: PMC10955043 DOI: 10.1083/jcb.202309125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/19/2024] [Accepted: 03/01/2024] [Indexed: 03/21/2024] Open
Abstract
The extracellular matrix (ECM) serves as a scaffold for cells and plays an essential role in regulating numerous cellular processes, including cell migration and proliferation. Due to limitations in specimen preparation for conventional room-temperature electron microscopy, we lack structural knowledge on how ECM components are secreted, remodeled, and interact with surrounding cells. We have developed a 3D-ECM platform compatible with sample thinning by cryo-focused ion beam milling, the lift-out extraction procedure, and cryo-electron tomography. Our workflow implements cell-derived matrices (CDMs) grown on EM grids, resulting in a versatile tool closely mimicking ECM environments. This allows us to visualize ECM for the first time in its hydrated, native context. Our data reveal an intricate network of extracellular fibers, their positioning relative to matrix-secreting cells, and previously unresolved structural entities. Our workflow and results add to the structural atlas of the ECM, providing novel insights into its secretion and assembly.
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Affiliation(s)
- Bettina Zens
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Florian Fäßler
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Jesse M. Hansen
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Robert Hauschild
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Julia Datler
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | | | - Vanessa Zheden
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Jonna Alanko
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Michael Sixt
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
| | - Florian K.M. Schur
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria
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Vitali DG, Fonseca D, Carvalho P. The derlin Dfm1 couples retrotranslocation of a folded protein domain to its proteasomal degradation. J Cell Biol 2024; 223:e202308074. [PMID: 38448163 DOI: 10.1083/jcb.202308074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/05/2023] [Accepted: 02/14/2024] [Indexed: 03/08/2024] Open
Abstract
Endoplasmic reticulum (ER) proteins are degraded by proteasomes in the cytosol through ER-associated degradation (ERAD). This process involves the retrotranslocation of substrates across the ER membrane, their ubiquitination, and membrane extraction by the Cdc48/Npl4/Ufd1 ATPase complex prior to delivery to proteasomes for degradation. How the presence of a folded luminal domain affects substrate retrotranslocation and this event is coordinated with subsequent ERAD steps remains unknown. Here, using a model substrate with a folded luminal domain, we showed that Cdc48 ATPase activity is sufficient to drive substrate retrotranslocation independently of ERAD membrane components. However, the complete degradation of the folded luminal domain required substrate-tight coupling of retrotranslocation and proteasomal degradation, which was ensured by the derlin Dfm1. Mutations in Dfm1 intramembrane rhomboid-like or cytosolic Cdc48-binding regions resulted in partial degradation of the substrate with accumulation of its folded domain. Our study revealed Dfm1 as a critical regulator of Cdc48-driven retrotranslocation and highlights the importance of coordinating substrate retrotranslocation and degradation during ERAD.
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Affiliation(s)
- Daniela G Vitali
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Daniel Fonseca
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Pedro Carvalho
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
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Yadav M, Sathe J, Teronpi V, Kumar A. Navigating the signaling landscape of Ralstonia solanacearum: a study of bacterial two-component systems. World J Microbiol Biotechnol 2024; 40:153. [PMID: 38564115 DOI: 10.1007/s11274-024-03950-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/10/2024] [Indexed: 04/04/2024]
Abstract
Ralstonia solanacearum, the bacterium that causes bacterial wilt, is a destructive phytopathogen that can infect over 450 different plant species. Several agriculturally significant crop plants, including eggplant, tomato, pepper, potato, and ginger, are highly susceptible to this plant disease, which has a global impact on crop quality and yield. There is currently no known preventive method that works well for bacterial wilt. Bacteria use two-component systems (TCSs) to sense their environment constantly and react appropriately. This is achieved by an extracellular sensor kinase (SK) capable of sensing a suitable signal and a cytoplasmic response regulator (RR) which gives a downstream response. Moreover, our investigation revealed that R. solanacearum GMI1000 possesses a substantial count of TCSs, specifically comprising 36 RRs and 27 SKs. While TCSs are known targets for various human pathogenic bacteria, such as Salmonella, the role of TCSs in R. solanacearum remains largely unexplored in this context. Notably, numerous inhibitors targeting TCSs have been identified, including GHL (Gyrase, Hsp, and MutL) compounds, Walk inhibitors, and anti-TCS medications like Radicicol. Consequently, the investigation into the involvement of TCSs in virulence and pathogenesis has gained traction; however, further research is imperative to ascertain whether TCSs could potentially supplant conventional anti-wilt therapies. This review delves into the prospective utilization of TCSs as an alternative anti-wilt therapy, focusing on the lethal phytopathogen R. solanacearum.
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Affiliation(s)
- Mohit Yadav
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India
| | - Janhavi Sathe
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India
- Institute for Stem Cell Science and Regenerative Medicine, Bangalore, Karnataka, 560065, India
| | - Valentina Teronpi
- Department of Zoology, Pandit Deendayal Upadhyaya Adarsha Mahavidyalaya, Behali, Biswanath, Assam, 784184, India
| | - Aditya Kumar
- Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, 784028, India.
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Ferrero-Bordera B, Bartel J, van Dijl JM, Becher D, Maaß S. From the outer space to the inner cell: deconvoluting the complexity of Bacillus subtilis disulfide stress responses by redox state and absolute abundance quantification of extracellular, membrane, and cytosolic proteins. Microbiol Spectr 2024; 12:e0261623. [PMID: 38358275 DOI: 10.1128/spectrum.02616-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
Understanding cellular mechanisms of stress management relies on omics data as a valuable resource. However, the lack of absolute quantitative data on protein abundances remains a significant limitation, particularly when comparing protein abundances across different cell compartments. In this study, we aimed to gain deeper insights into the proteomic responses of the Gram-positive model bacterium Bacillus subtilis to disulfide stress. We determined proteome-wide absolute abundances, focusing on different sub-cellular locations (cytosol and membrane) as well as the extracellular medium, and combined these data with redox state determination. To quantify secreted proteins in the culture medium, we developed a simple and straightforward protocol for the absolute quantification of extracellular proteins in bacteria. We concentrated extracellular proteins, which are highly diluted in the medium, using StrataClean beads along with a set of standard proteins to determine the extent of the concentration step. The resulting data set provides new insights into protein abundances in different sub-cellular compartments and the extracellular medium, along with a comprehensive proteome-wide redox state determination. Our study offers a quantitative understanding of disulfide stress management, protein production, and secretion in B. subtilis. IMPORTANCE Stress responses play a crucial role in bacterial survival and adaptation. The ability to quantitatively measure protein abundances and redox states in different cellular compartments and the extracellular environment is essential for understanding stress management mechanisms. In this study, we addressed the knowledge gap regarding absolute quantification of extracellular proteins and compared protein concentrations in various sub-cellular locations and in the extracellular medium under disulfide stress conditions. Our findings provide valuable insights into the protein production and secretion dynamics of B. subtilis, shedding light on its stress response strategies. Furthermore, the developed protocol for absolute quantification of extracellular proteins in bacteria presents a practical and efficient approach for future studies in the field. Overall, this research contributes to the quantitative understanding of stress management mechanisms and protein dynamics in B. subtilis, which can be used to enhance bacterial stress tolerance and protein-based biotechnological applications.
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Affiliation(s)
- Borja Ferrero-Bordera
- Department of Microbial Proteomics, University of Greifswald, Centre of Functional Genomics of Microbes, Institute of Microbiology, Greifswald, Germany
| | - Jürgen Bartel
- Department of Microbial Proteomics, University of Greifswald, Centre of Functional Genomics of Microbes, Institute of Microbiology, Greifswald, Germany
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Dörte Becher
- Department of Microbial Proteomics, University of Greifswald, Centre of Functional Genomics of Microbes, Institute of Microbiology, Greifswald, Germany
| | - Sandra Maaß
- Department of Microbial Proteomics, University of Greifswald, Centre of Functional Genomics of Microbes, Institute of Microbiology, Greifswald, Germany
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Chen JY, Lin PY, Hong WZ, Yang PC, Chiang SF, Chang HY, Ke TW, Liang JA, Chen WTL, Chao KSC, Huang KCY. Activation of STING by the novel liposomal TLC388 enhances the therapeutic response to anti-PD-1 antibodies in combination with radiotherapy. Cancer Immunol Immunother 2024; 73:92. [PMID: 38564022 PMCID: PMC10987363 DOI: 10.1007/s00262-024-03692-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 03/25/2024] [Indexed: 04/04/2024]
Abstract
Current immune checkpoint inhibiters (ICIs) have contrasting clinical results in poorly immunogenic cancers such as microsatellite-stable colorectal cancer (MSS-CRC). Therefore, understanding and developing the combinational therapeutics for ICI-unresponsive cancers is critical. Here, we demonstrated that the novel topoisomerase I inhibitor TLC388 can reshape the tumor immune landscape, corroborating their antitumor effects combined with radiotherapy as well as immunotherapy. We found that TLC388 significantly triggered cytosolic single-stranded DNA (ssDNA) accumulation for STING activation, leading to type I interferons (IFN-Is) production for increased cancer immunogenicity to enhance antitumor immunity. TLC388-treated tumors were infiltrated by a vast number of dendritic cells, immune cells, and costimulatory molecules, contributing to the favorable antitumor immune response within the tumor microenvironment. The infiltration of cytotoxic T and NK cells were more profoundly existed within tumors in combination with radiotherapy and ICIs, leading to superior therapeutic efficacy in poorly immunogenic MSS-CRC. Taken together, these results showed that the novel topoisomerase I inhibitor TLC388 increased cancer immunogenicity by ssDNA/STING-mediated IFN-I production, enhancing antitumor immunity for better therapeutic efficacy in combination with radiotherapy and ICIs for poorly immunogenic cancer.
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Affiliation(s)
- Jhen-Yu Chen
- Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung, 40402, Taiwan
- Translation Research Core, China Medical University Hospital, China Medical University, Taichung, 40402, Taiwan
| | - Po-Yu Lin
- Proton Therapy and Science Center, China Medical University Hospital, China Medical University, Taichung, 40402, Taiwan R.O.C
| | - Wei-Ze Hong
- Proton Therapy and Science Center, China Medical University Hospital, China Medical University, Taichung, 40402, Taiwan R.O.C
| | - Pei-Chen Yang
- Proton Therapy and Science Center, China Medical University Hospital, China Medical University, Taichung, 40402, Taiwan R.O.C
| | - Shu-Fen Chiang
- Lab of Precision Medicine, Feng-Yuan Hospital, Ministry of Health and Welfare, Taichung, 42055, Taiwan
| | - Hsin-Yu Chang
- Proton Therapy and Science Center, China Medical University Hospital, China Medical University, Taichung, 40402, Taiwan R.O.C
| | - Tao-Wei Ke
- Department of Colorectal Surgery, China Medical University Hospital, China Medical University, Taichung, 40402, Taiwan
- School of Chinese Medicine, China Medical University, Taichung, 40402, Taiwan
| | - Ji-An Liang
- Department of Radiation Oncology, China Medical University Hospital, China Medical University, Taichung, Taiwan
- Department of Radiation Oncology, School of Medicine, China Medical University, Taichung, 40402, Taiwan
| | - William Tzu-Liang Chen
- Department of Colorectal Surgery, China Medical University Hospital, China Medical University, Taichung, 40402, Taiwan
- Department of Colorectal Surgery, China Medical University HsinChu Hospital, China Medical University, HsinChu, 302, Taiwan
- School of Medicine, China Medical University, Taichung, 40402, Taiwan
| | - K S Clifford Chao
- Proton Therapy and Science Center, China Medical University Hospital, China Medical University, Taichung, 40402, Taiwan R.O.C..
- Department of Radiation Oncology, China Medical University Hospital, China Medical University, Taichung, Taiwan.
- Department of Radiation Oncology, School of Medicine, China Medical University, Taichung, 40402, Taiwan.
| | - Kevin Chih-Yang Huang
- Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung, 40402, Taiwan.
- Translation Research Core, China Medical University Hospital, China Medical University, Taichung, 40402, Taiwan.
- Cancer Biology and Precision Therapeutics Center, China Medical University, Taichung, 40402, Taiwan.
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7
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Zhu G, Zhang H, Xia M, Liu Y, Li M. EH domain-containing protein 2 (EHD2): Overview, biological function, and therapeutic potential. Cell Biochem Funct 2024; 42:e4016. [PMID: 38613224 DOI: 10.1002/cbf.4016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 04/14/2024]
Abstract
EH domain-containing protein 2 (EHD2) is a member of the EHD protein family and is mainly located in the plasma membrane, but can also be found in the cytoplasm and endosomes. EHD2 is also a nuclear-cytoplasmic shuttle protein. After entering the cell nuclear, EHD2 acts as a corepressor of transcription to inhibit gene transcription. EHD2 regulates a series of biological processes. As a key regulator of endocytic transport, EHD2 is involved in the formation and maintenance of endosomal tubules and vesicles, which are critical for the intracellular transport of proteins and other substances. The N-terminal of EHD2 is attached to the cell membrane, while its C-terminal binds to the actin-binding protein. After binding, EHD2 connects with the actin cytoskeleton, forming the curvature of the membrane and promoting cell endocytosis. EHD2 is also associated with membrane protein trafficking and receptor signaling, as well as in glucose metabolism and lipid metabolism. In this review, we highlight the recent advances in the function of EHD2 in various cellular processes and its potential implications in human diseases such as cancer and metabolic disease. We also discussed the prospects for the future of EHD2. EHD2 has a broad prospect as a therapeutic target for a variety of diseases. Further research is needed to explore its mechanism, which could pave the way for the development of targeted treatments.
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Affiliation(s)
- Guoqiang Zhu
- Department of Urology, Hengyang Medical School, The First Affiliated Hospital, University of South China, Hengyang, Hunan, China
| | - Hu Zhang
- Department of Urology, Hengyang Medical School, The First Affiliated Hospital, University of South China, Hengyang, Hunan, China
| | - Min Xia
- Hengyang Medical School, Institute of Clinical Medicine, The First Affiliated Hospital, University of South China, Hengyang, Hunan, China
- Hengyang Medical School, Cancer Research Institute, The First Affiliated Hospital, University of South China, Hengyang, Hunan, China
| | - Yiqi Liu
- Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Mingyong Li
- Department of Urology, Hengyang Medical School, The First Affiliated Hospital, University of South China, Hengyang, Hunan, China
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Olmo-Fontánez AM, Scordo JM, Schami A, Garcia-Vilanova A, Pino PA, Hicks A, Mishra R, Jose Maselli D, Peters JI, Restrepo BI, Nargan K, Naidoo T, Clemens DL, Steyn AJC, Thacker VV, Turner J, Schlesinger LS, Torrelles JB. Human alveolar lining fluid from the elderly promotes Mycobacterium tuberculosis intracellular growth and translocation into the cytosol of alveolar epithelial cells. Mucosal Immunol 2024; 17:155-168. [PMID: 38185331 DOI: 10.1016/j.mucimm.2024.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/15/2023] [Accepted: 01/03/2024] [Indexed: 01/09/2024]
Abstract
The elderly population is highly susceptible to developing respiratory diseases, including tuberculosis, a devastating disease caused by the airborne pathogen Mycobacterium tuberculosis (M.tb) that kills one person every 18 seconds. Once M.tb reaches the alveolar space, it contacts alveolar lining fluid (ALF), which dictates host-cell interactions. We previously determined that age-associated dysfunction of soluble innate components in human ALF leads to accelerated M.tb growth within human alveolar macrophages. Here we determined the impact of human ALF on M.tb infection of alveolar epithelial type cells (ATs), another critical lung cellular determinant of infection. We observed that elderly ALF (E-ALF)-exposed M.tb had significantly increased intracellular growth with rapid replication in ATs compared to adult ALF (A-ALF)-exposed bacteria, as well as a dampened inflammatory response. A potential mechanism underlying this accelerated growth in ATs was our observation of increased bacterial translocation into the cytosol, a compartment that favors bacterial replication. These findings in the context of our previous studies highlight how the oxidative and dysfunctional status of the elderly lung mucosa determines susceptibility to M.tb infection, including dampening immune responses and favoring bacterial replication within alveolar resident cell populations, including ATs, the most abundant resident cell type within the alveoli.
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Affiliation(s)
- Angélica M Olmo-Fontánez
- Population Health and Host-Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA; Integrated Biomedical Sciences Program, University of Texas Health Science Center at San Antonio, Texas, USA.
| | - Julia M Scordo
- Population Health and Host-Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA; Sam and Ann Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, Texas, USA
| | - Alyssa Schami
- Population Health and Host-Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA; Integrated Biomedical Sciences Program, University of Texas Health Science Center at San Antonio, Texas, USA
| | - Andreu Garcia-Vilanova
- Population Health and Host-Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Paula A Pino
- Population Health and Host-Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Amberlee Hicks
- Population Health and Host-Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Richa Mishra
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Diego Jose Maselli
- Division of Pulmonary and Critical Care Medicine, School of Medicine, University of Texas Health Science Center at San Antonio, Texas, USA
| | - Jay I Peters
- Division of Pulmonary and Critical Care Medicine, School of Medicine, University of Texas Health Science Center at San Antonio, Texas, USA
| | - Blanca I Restrepo
- Population Health and Host-Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA; University of Texas Health Science Center at Houston, School of Public Health, Brownsville campus, Brownsville, Texas, USA; South Texas Diabetes and Obesity Institute, University of Texas Rio Grande Valley, Edinburg, Texas, USA
| | - Kievershen Nargan
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa
| | - Threnesan Naidoo
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa; Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha, South Africa
| | - Daniel L Clemens
- University of California, Los Angeles Health Sciences, Los Angeles, California, USA
| | - Adrie J C Steyn
- Africa Health Research Institute, University of KwaZulu-Natal, Durban, South Africa; Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, USA; Centers for AIDS Research and Free Radical Biology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Vivek V Thacker
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Department of Infectious Diseases, Medical Microbiology and Hygiene, Medical Faculty Heidelberg, Heidelberg University, 69120 Heidelberg, Germany
| | - Joanne Turner
- Population Health and Host-Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Larry S Schlesinger
- Population Health and Host-Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Jordi B Torrelles
- Population Health and Host-Pathogen Interactions Programs, Texas Biomedical Research Institute, San Antonio, Texas, USA; International Center for the Advancement of Research and Education (I●CARE), Texas Biomedical Research Institute, San Antonio, TX, US.
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9
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Kalhor K, Chen CJ, Lee HS, Cai M, Nafisi M, Que R, Palmer CR, Yuan Y, Zhang Y, Li X, Song J, Knoten A, Lake BB, Gaut JP, Keene CD, Lein E, Kharchenko PV, Chun J, Jain S, Fan JB, Zhang K. Mapping human tissues with highly multiplexed RNA in situ hybridization. Nat Commun 2024; 15:2511. [PMID: 38509069 PMCID: PMC10954689 DOI: 10.1038/s41467-024-46437-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 02/23/2024] [Indexed: 03/22/2024] Open
Abstract
In situ transcriptomic techniques promise a holistic view of tissue organization and cell-cell interactions. There has been a surge of multiplexed RNA in situ mapping techniques but their application to human tissues has been limited due to their large size, general lower tissue quality and high autofluorescence. Here we report DART-FISH, a padlock probe-based technology capable of profiling hundreds to thousands of genes in centimeter-sized human tissue sections. We introduce an omni-cell type cytoplasmic stain that substantially improves the segmentation of cell bodies. Our enzyme-free isothermal decoding procedure allows us to image 121 genes in large sections from the human neocortex in <10 h. We successfully recapitulated the cytoarchitecture of 20 neuronal and non-neuronal subclasses. We further performed in situ mapping of 300 genes on a diseased human kidney, profiled >20 healthy and pathological cell states, and identified diseased niches enriched in transcriptionally altered epithelial cells and myofibroblasts.
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Affiliation(s)
- Kian Kalhor
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Chien-Ju Chen
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA, USA
| | - Ho Suk Lee
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Department of Electrical Engineering, University of California San Diego, La Jolla, CA, USA
| | - Matthew Cai
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Mahsa Nafisi
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Richard Que
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Carter R Palmer
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
- Program in Biomedical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Yixu Yuan
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Yida Zhang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | | | - Jinghui Song
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Amanda Knoten
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Blue B Lake
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Joseph P Gaut
- Department of Pathology and Immunology, Washington University School of Medicine, St.Louis, MO, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA
| | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA, 98103, USA
| | - Peter V Kharchenko
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Altos Labs, San Diego, CA, USA
| | - Jerold Chun
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Sanjay Jain
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pathology and Immunology, Washington University School of Medicine, St.Louis, MO, USA
| | | | - Kun Zhang
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Altos Labs, San Diego, CA, USA.
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10
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Jahun AS, Sorgeloos F, Goodfellow IG. An optimized protocol for the extraction and quantification of cytosolic DNA in mammalian cells. STAR Protoc 2024; 5:102913. [PMID: 38393950 PMCID: PMC10901131 DOI: 10.1016/j.xpro.2024.102913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/17/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Leakage of mitochondrial or nuclear DNA into the cytosol can occur following viral infections, radiation damage, and some cancers. Here, we present an optimized protocol for isolating and quantifying cytosolic DNA from mammalian cells. We describe steps for collecting cytosolic fractions from cells, extracting DNA using columns, and quantifying extracted DNA using qPCR. This straightforward protocol can be completed in as little as 5 hours, and allows for the identification of the source of DNA. For complete details on the use and execution of this protocol, please refer to Jahun et al.1.
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Affiliation(s)
- Aminu S Jahun
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital Level 5, Hills Road, CB2 0QQ Cambridge, UK.
| | - Frederic Sorgeloos
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital Level 5, Hills Road, CB2 0QQ Cambridge, UK; Université catholique de Louvain, de Duve Institute, MIPA-VIRO 74-49, 74 Avenue Hippocrate, 1200 Brussels, Belgium
| | - Ian G Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital Level 5, Hills Road, CB2 0QQ Cambridge, UK.
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11
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Zhang H, Yang Z, Yuan W, Liu J, Luo X, Zhang Q, Li Y, Chen J, Zhou Y, Lv J, Zhou N, Ma J, Tang K, Huang B. Sustained AhR activity programs memory fate of early effector CD8 + T cells. Proc Natl Acad Sci U S A 2024; 121:e2317658121. [PMID: 38437537 PMCID: PMC10945852 DOI: 10.1073/pnas.2317658121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 02/12/2024] [Indexed: 03/06/2024] Open
Abstract
Identification of mechanisms that program early effector T cells to either terminal effector T (Teff) or memory T (Tm) cells has important implications for protective immunity against infections and cancers. Here, we show that the cytosolic transcription factor aryl hydrocarbon receptor (AhR) is used by early Teff cells to program memory fate. Upon antigen engagement, AhR is rapidly up-regulated via reactive oxygen species signaling in early CD8+ Teff cells, which does not affect the effector response, but is required for memory formation. Mechanistically, activated CD8+ T cells up-regulate HIF-1α to compete with AhR for HIF-1β, leading to the loss of AhR activity in HIF-1αhigh short-lived effector cells, but sustained in HIF-1αlow memory precursor effector cells (MPECs) with the help of autocrine IL-2. AhR then licenses CD8+ MPECs in a quiescent state for memory formation. These findings partially resolve the long-standing issue of how Teff cells are regulated to differentiate into memory cells.
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Affiliation(s)
- Huafeng Zhang
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
| | - Zhuoshun Yang
- Institute of Biomedical Research, Department of Infectious Diseases, Regulatory Mechanism and Targeted Therapy for Liver Cancer Shiyan Key Laboratory, Hubei Provincial Clinical Research Center for Precise Diagnosis and Treatment of Liver Cancer, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei442000, China
- Department of Biochemistry and Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
| | - Wu Yuan
- Department of Biochemistry and Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
| | - Jincheng Liu
- Department of Biochemistry and Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
| | - Xiao Luo
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
| | - Qian Zhang
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
| | - Yonggang Li
- Hubei Provincial Key Laboratory for Applied Toxicology, Hubei Provincial Center for Disease Control and Prevention, Wuhan430079, China
| | - Jie Chen
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing100005, China
| | - Yabo Zhou
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing100005, China
| | - Jiadi Lv
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing100005, China
| | - Nannan Zhou
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing100005, China
| | - Jingwei Ma
- Department of Immunology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
| | - Ke Tang
- Department of Biochemistry and Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
| | - Bo Huang
- Department of Biochemistry and Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan430030, China
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing100005, China
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12
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Chatterjee S, Kon E, Sharma P, Peer D. Endosomal escape: A bottleneck for LNP-mediated therapeutics. Proc Natl Acad Sci U S A 2024; 121:e2307800120. [PMID: 38437552 PMCID: PMC10945858 DOI: 10.1073/pnas.2307800120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024] Open
Abstract
Lipid nanoparticles (LNPs) have recently emerged as a powerful and versatile clinically approved platform for nucleic acid delivery, specifically for mRNA vaccines. A major bottleneck in the field is the release of mRNA-LNPs from the endosomal pathways into the cytosol of cells where they can execute their encoded functions. The data regarding the mechanism of these endosomal escape processes are limited and contradicting. Despite extensive research, there is no consensus regarding the compartment of escape, the cause of the inefficient escape and are currently lacking a robust method to detect the escape. Here, we review the currently known mechanisms of endosomal escape and the available methods to study this process. We critically discuss the limitations and challenges of these methods and the possibilities to overcome these challenges. We propose that the development of currently lacking robust, quantitative high-throughput techniques to study endosomal escape is timely and essential. A better understanding of this process will enable better RNA-LNP designs with improved efficiency to unlock new therapeutic modalities.
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Affiliation(s)
- Sushmita Chatterjee
- Laboratory of Precision Nanomedicine, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel
- Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 69978, Israel
- Cancer Biology Research Center, Tel Aviv University, Tel Aviv 69978, Israel
| | - Edo Kon
- Laboratory of Precision Nanomedicine, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel
- Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 69978, Israel
- Cancer Biology Research Center, Tel Aviv University, Tel Aviv 69978, Israel
| | - Preeti Sharma
- Laboratory of Precision Nanomedicine, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel
- Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 69978, Israel
- Cancer Biology Research Center, Tel Aviv University, Tel Aviv 69978, Israel
| | - Dan Peer
- Laboratory of Precision Nanomedicine, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
- Department of Materials Sciences and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv 69978, Israel
- Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv 69978, Israel
- Cancer Biology Research Center, Tel Aviv University, Tel Aviv 69978, Israel
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13
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Marcuccio F, Chau CC, Tanner G, Elpidorou M, Finetti MA, Ajaib S, Taylor M, Lascelles C, Carr I, Macaulay I, Stead LF, Actis P. Single-cell nanobiopsy enables multigenerational longitudinal transcriptomics of cancer cells. Sci Adv 2024; 10:eadl0515. [PMID: 38446884 PMCID: PMC10917339 DOI: 10.1126/sciadv.adl0515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/31/2024] [Indexed: 03/08/2024]
Abstract
Single-cell RNA sequencing has revolutionized our understanding of cellular heterogeneity, but routine methods require cell lysis and fail to probe the dynamic trajectories responsible for cellular state transitions, which can only be inferred. Here, we present a nanobiopsy platform that enables the injection of exogenous molecules and multigenerational longitudinal cytoplasmic sampling from a single cell and its progeny. The technique is based on scanning ion conductance microscopy (SICM) and, as a proof of concept, was applied to longitudinally profile the transcriptome of single glioblastoma (GBM) brain tumor cells in vitro over 72 hours. The GBM cells were biopsied before and after exposure to chemotherapy and radiotherapy, and our results suggest that treatment either induces or selects for more transcriptionally stable cells. We envision the nanobiopsy will contribute to transforming standard single-cell transcriptomics from a static analysis into a dynamic assay.
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Affiliation(s)
- Fabio Marcuccio
- Faculty of Medicine, Imperial College London, London, UK
- Bragg Centre for Materials Research, University of Leeds, Leeds, UK
- School of Electronic and Electrical Engineering, University of Leeds, Leeds, UK
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Chalmers C. Chau
- Bragg Centre for Materials Research, University of Leeds, Leeds, UK
- School of Electronic and Electrical Engineering, University of Leeds, Leeds, UK
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Georgette Tanner
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Marilena Elpidorou
- School of Electronic and Electrical Engineering, University of Leeds, Leeds, UK
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Martina A. Finetti
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Shoaib Ajaib
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Morag Taylor
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Carolina Lascelles
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Ian Carr
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Iain Macaulay
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Lucy F. Stead
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Paolo Actis
- Bragg Centre for Materials Research, University of Leeds, Leeds, UK
- School of Electronic and Electrical Engineering, University of Leeds, Leeds, UK
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14
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Lu Y, Zhao M, Chen L, Wang Y, Liu T, Liu H. cGAS: action in the nucleus. Front Immunol 2024; 15:1380517. [PMID: 38515746 PMCID: PMC10954897 DOI: 10.3389/fimmu.2024.1380517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 02/23/2024] [Indexed: 03/23/2024] Open
Abstract
As a canonical cytoplasmic DNA sensor, cyclic GMP-AMP synthase (cGAS) plays a key role in innate immunity. In recent years, a growing number of studies have shown that cGAS can also be located in the nucleus and plays new functions such as regulating DNA damage repair, nuclear membrane repair, chromosome fusion, DNA replication, angiogenesis and other non-canonical functions. Meanwhile, the mechanisms underlying the nucleo-cytoplasmic transport and the regulation of cGAS activation have been revealed in recent years. Based on the current understanding of the structure, subcellular localization and canonical functions of cGAS, this review focuses on summarizing the mechanisms underlying nucleo-cytoplasmic transport, activity regulation and non-canonical functions of cGAS in the nucleus. We aim to provide insights into exploring the new functions of cGAS in the nucleus and advance its clinical translation.
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Affiliation(s)
- Yikai Lu
- Central Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Mengmeng Zhao
- Research Center of Translational Medicine, Jinan Central Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Li Chen
- Central Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Yan Wang
- Central Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Tianhao Liu
- Central Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Haipeng Liu
- Central Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, China
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15
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Nice JB, Collins SM, Agro SMJ, Sinani A, Moros SD, Pasch LM, Brown AC. Heterogeneity of Size and Toxin Distribution in Aggregatibacter actinomycetemcomitans Outer Membrane Vesicles. Toxins (Basel) 2024; 16:138. [PMID: 38535804 PMCID: PMC10974469 DOI: 10.3390/toxins16030138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/21/2024] [Accepted: 02/29/2024] [Indexed: 04/01/2024] Open
Abstract
Aggregatibacter actinomycetemcomitans is a Gram-negative bacterium associated with localized aggressive periodontitis as well as some systemic diseases. The strains of A. actinomycetemcomitans most closely associated with disease produce more of a secreted leukotoxin (LtxA) than isolates from healthy carriers, suggesting a key role for this toxin in disease progression. LtxA is released into the bacterial cytosol in a free form as well as in association with the surface of outer membrane vesicles (OMVs). We previously observed that the highly leukotoxic A. actinomycetemcomitans strain JP2 produces two populations of OMVs: a highly abundant population of small (<100 nm) OMVs and a less abundant population of large (>300 nm) OMVs. Here, we have developed a protocol to isolate the OMVs produced during each specific phase of growth and used this to demonstrate that small OMVs are produced throughout growth and lack LtxA, while large OMVs are produced only during the exponential phase and are enriched with LtxA. Our results indicate that surface-associated DNA drives the selective sorting of LtxA into large OMVs. This study provides valuable insights into the observed heterogeneity of A. actinomycetemcomitans vesicles and emphasizes the importance of understanding these variations in the context of bacterial pathogenesis.
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Affiliation(s)
- Justin B Nice
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Shannon M. Collins
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Samuel M. J. Agro
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Anxhela Sinani
- Department of Bioengineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Spencer D. Moros
- Department of Bioengineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Leah M. Pasch
- Department of Bioengineering, Lehigh University, Bethlehem, PA 18015, USA
| | - Angela C. Brown
- Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015, USA
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16
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Dye D, Cain JW. Efficacy of Wolbachia-based mosquito control: Predictions of a spatially discrete mathematical model. PLoS One 2024; 19:e0297964. [PMID: 38437189 PMCID: PMC10911593 DOI: 10.1371/journal.pone.0297964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 01/14/2024] [Indexed: 03/06/2024] Open
Abstract
Wolbachia is an endosymbiont bacterium present in many insect species. When Wolbachia-carrying male Aedes aegypti mosquitoes mate with non-carrier females, their embryos are not viable due to cytoplasmic incompatibility. This phenomenon has been exploited successfully for the purpose of controlling mosquito populations and the spread of mosquito-borne illnesses: Wolbachia carriers are bred and released into the environment. Because Wolbachia is not harmful to humans, this method of mosquito control is regarded as a safer alternative to pesticide spraying. In this article, we introduce a mathematical framework for exploring (i) whether a one-time release of Wolbachia carriers can elicit a sustained presence of carriers near the release site, and (ii) the extent to which spatial propagation of carriers may allow them to establish fixation in other territories. While some prior studies have formulated mosquito dispersal models using advection-reaction-diffusion PDEs, the predictive power of such models requires careful ecological mapping: advection and diffusion coefficients exhibit significant spatial dependence due to heterogeneity of resources and topography. Here, we adopt a courser-grained view, regarding the environment as a network of discrete, diffusively-coupled "habitats"-distinct zones of high mosquito density such as stagnant ponds. We extend two previously published single-habitat mosquito models to multiple habitats, and calculate rates of migration between pairs of habitats using dispersal kernels. Our primary results are quantitative estimates regarding how the success of carrier fixation in one or more habitats is determined by: the number of carriers released, sizes of habitats, distances between habitats, and the rate of migration between habitats. Besides yielding sensible and potentially useful predictions regarding the success of Wolbachia-based control, our framework applies to other approaches (e.g., gene drives) and contexts beyond the realm of insect pest control.
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Affiliation(s)
- David Dye
- Department of Mathematics, Harvard University, Cambridge, MA, United States of America
| | - John W. Cain
- Department of Mathematics, Harvard University, Cambridge, MA, United States of America
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17
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Li J, Canham SM, Wu H, Henault M, Chen L, Liu G, Chen Y, Yu G, Miller HR, Hornak V, Brittain SM, Michaud GA, Tutter A, Broom W, Digan ME, McWhirter SM, Sivick KE, Pham HT, Chen CH, Tria GS, McKenna JM, Schirle M, Mao X, Nicholson TB, Wang Y, Jenkins JL, Jain RK, Tallarico JA, Patel SJ, Zheng L, Ross NT, Cho CY, Zhang X, Bai XC, Feng Y. Activation of human STING by a molecular glue-like compound. Nat Chem Biol 2024; 20:365-372. [PMID: 37828400 PMCID: PMC10907298 DOI: 10.1038/s41589-023-01434-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 09/02/2023] [Indexed: 10/14/2023]
Abstract
Stimulator of interferon genes (STING) is a dimeric transmembrane adapter protein that plays a key role in the human innate immune response to infection and has been therapeutically exploited for its antitumor activity. The activation of STING requires its high-order oligomerization, which could be induced by binding of the endogenous ligand, cGAMP, to the cytosolic ligand-binding domain. Here we report the discovery through functional screens of a class of compounds, named NVS-STGs, that activate human STING. Our cryo-EM structures show that NVS-STG2 induces the high-order oligomerization of human STING by binding to a pocket between the transmembrane domains of the neighboring STING dimers, effectively acting as a molecular glue. Our functional assays showed that NVS-STG2 could elicit potent STING-mediated immune responses in cells and antitumor activities in animal models.
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Affiliation(s)
- Jie Li
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Stephen M Canham
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA.
| | - Hua Wu
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Martin Henault
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Lihao Chen
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Guoxun Liu
- Novartis Institutes for BioMedical Research, San Diego, CA, USA
| | - Yu Chen
- Novartis Institutes for BioMedical Research, San Diego, CA, USA
| | - Gary Yu
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Howard R Miller
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Viktor Hornak
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | | | - Antonin Tutter
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Wendy Broom
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | | | | | - Helen T Pham
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - George S Tria
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Markus Schirle
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Xiaohong Mao
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Yuan Wang
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Rishi K Jain
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | | | - Sejal J Patel
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Lianxing Zheng
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Nathan T Ross
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA
| | - Charles Y Cho
- Novartis Institutes for BioMedical Research, San Diego, CA, USA
| | - Xuewu Zhang
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Xiao-Chen Bai
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - Yan Feng
- Novartis Institutes for BioMedical Research, Cambridge, MA, USA.
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18
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Park JM, Park S, Seo YS, Kim JH, Lee MY. Cytosolic zinc mediates the cytotoxicity of thiol-reactive electrophiles in rat vascular smooth muscle cells. Food Chem Toxicol 2024; 185:114446. [PMID: 38244666 DOI: 10.1016/j.fct.2024.114446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/07/2023] [Accepted: 01/08/2024] [Indexed: 01/22/2024]
Abstract
The aberrant increase or dysregulation of cytosolic Zn2+ concentration ([Zn2+]cyt) has been associated with cellular dysfunction and cytotoxicity. In this study, we postulated that Zn2+ mediates the cytotoxicity of thiol-reactive electrophiles. This notion was grounded on earlier research, which revealed that thiol-reactive electrophiles may disrupt Zn2+-binding motifs, consequently causing Zn2+ to be released from Zn2+-binding proteins, and leading to a surge in [Zn2+]cyt. The thiol-reactive electrophiles N-ethylmaleimide (NEM) and diamide were observed to induce an increase in [Zn2+]cyt, possibly through the impairment of Zn2+-binding motifs, and subsequent stimulation of reactive oxygen species (ROS) formation, resulting in cytotoxicity in primary cultured rat vascular smooth muscle cells. These processes were negated by the thiol donor N-acetyl-L-cysteine and the Zn2+ chelator TPEN. Similar outcomes were detected with co-treatment involving Zn2+ and Zn2+ ionophores such as pyrithione or disulfiram. Moreover, TPEN was found to inhibit cytotoxicity triggered by short-term exposure to various thiol-reactive electrophiles including hydrogen peroxide, acrylamide, acrylonitrile, diethyl maleate, iodoacetic acid, and iodoacetamide. In conclusion, our findings suggest that cytosolic Zn2+ acts as a universal mediator in the cytotoxic effects produced by thiol-reactive electrophiles.
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Affiliation(s)
- Jung-Min Park
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Goyang-si, Gyeonggi-do, 10326, Republic of Korea
| | - Suin Park
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Goyang-si, Gyeonggi-do, 10326, Republic of Korea
| | - Yoon-Seok Seo
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Goyang-si, Gyeonggi-do, 10326, Republic of Korea
| | - Jae-Hyeong Kim
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Goyang-si, Gyeonggi-do, 10326, Republic of Korea
| | - Moo-Yeol Lee
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University, Goyang-si, Gyeonggi-do, 10326, Republic of Korea.
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19
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Scharte F, Franzkoch R, Hensel M. Flagella-mediated cytosolic motility of Salmonella enterica Paratyphi A aids in evasion of xenophagy but does not impact egress from host cells. Mol Microbiol 2024; 121:413-430. [PMID: 37278220 DOI: 10.1111/mmi.15104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/07/2023]
Abstract
Salmonella enterica is a common foodborne, facultative intracellular enteropathogen. Typhoidal serovars like Paratyphi A (SPA) are human restricted and cause severe systemic diseases, while many serovars like Typhimurium (STM) have a broad host range, and usually lead to self-limiting gastroenteritis. There are key differences between typhoidal and non-typhoidal Salmonella in pathogenesis, but underlying mechanisms remain largely unknown. Transcriptomes and phenotypes in epithelial cells revealed induction of motility, flagella and chemotaxis genes for SPA but not STM. SPA exhibited cytosolic motility mediated by flagella. In this study, we applied single-cell microscopy to analyze triggers and cellular consequences of cytosolic motility. Live-cell imaging (LCI) revealed that SPA invades host cells in a highly cooperative manner. Extensive membrane ruffling at invasion sites led to increased membrane damage in nascent Salmonella-containing vacuole, and subsequent cytosolic release. After release into the cytosol, motile bacteria showed the same velocity as under culture conditions in media. Reduced capture of SPA by autophagosomal membranes was observed by LCI and electron microscopy. Prior work showed that SPA does not use flagella-mediated motility for cell exit via the intercellular spread. However, cytosolic motile SPA was invasion-primed if released from host cells. Our results reveal flagella-mediated cytosolic motility as a possible xenophagy evasion mechanism that could drive disease progression and contributes to the dissemination of systemic infection.
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Affiliation(s)
- Felix Scharte
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
| | - Rico Franzkoch
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
- Universität Osnabrück, iBiOs-Integrated Bioimaging Facility, Osnabrück, Germany
| | - Michael Hensel
- Abteilung Mikrobiologie, Universität Osnabrück, Osnabrück, Germany
- Universität Osnabrück, CellNanOs-Center of Cellular Nanoanalytics, Osnabrück, Germany
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20
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Groh AC, Möller-Kerutt A, Gilhaus K, Höffken V, Nedvetsky P, Kleimann S, Behrens M, Ghosh S, Hansen U, Krahn MP, Ebnet K, Pavenstädt H, Ludwig A, Weide T. PALS1 is a key regulator of the lateral distribution of tight junction proteins in renal epithelial cells. J Cell Sci 2024; 137:jcs261303. [PMID: 38265145 DOI: 10.1242/jcs.261303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 12/04/2023] [Indexed: 01/25/2024] Open
Abstract
The evolutionarily conserved apical Crumbs (CRB) complex, consisting of the core components CRB3a (an isoform of CRB3), PALS1 and PATJ, plays a key role in epithelial cell-cell contact formation and cell polarization. Recently, we observed that deletion of one Pals1 allele in mice results in functional haploinsufficiency characterized by renal cysts. Here, to address the role of PALS1 at the cellular level, we generated CRISPR/Cas9-mediated PALS1-knockout MDCKII cell lines. The loss of PALS1 resulted in increased paracellular permeability, indicating an epithelial barrier defect. This defect was associated with a redistribution of several tight junction-associated proteins from bicellular to tricellular contacts. PALS1-dependent localization of tight junction proteins at bicellular junctions required its interaction with PATJ. Importantly, reestablishment of the tight junction belt upon transient F-actin depolymerization or upon Ca2+ removal was strongly delayed in PALS1-deficient cells. Additionally, the cytoskeleton regulator RhoA was redistributed from junctions into the cytosol under PALS1 knockout. Together, our data uncover a critical role of PALS1 in the coupling of tight junction proteins to the F-actin cytoskeleton, which ensures their correct distribution along bicellular junctions and the formation of tight epithelial barrier.
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Affiliation(s)
- Ann-Christin Groh
- University Hospital of Münster (UKM), Internal Medicine D (MedD), Department Molecular Nephrology, Albert-Schweitzer-Campus 1 Building A14, 48149 Münster, Germany
| | - Annika Möller-Kerutt
- University Hospital of Münster (UKM), Internal Medicine D (MedD), Department Molecular Nephrology, Albert-Schweitzer-Campus 1 Building A14, 48149 Münster, Germany
| | - Kevin Gilhaus
- University Hospital of Münster (UKM), Internal Medicine D (MedD), Department Molecular Nephrology, Albert-Schweitzer-Campus 1 Building A14, 48149 Münster, Germany
| | - Verena Höffken
- University Hospital of Münster (UKM), Internal Medicine D (MedD), Department Molecular Nephrology, Albert-Schweitzer-Campus 1 Building A14, 48149 Münster, Germany
| | - Pavel Nedvetsky
- University Hospital of Münster (UKM), Internal Medicine D (MedD), Medical Cell Biology, Albert-Schweitzer-Campus 1 Building A14, 48149 Münster, Germany
| | - Simon Kleimann
- University Hospital of Münster (UKM), Internal Medicine D (MedD), Department Molecular Nephrology, Albert-Schweitzer-Campus 1 Building A14, 48149 Münster, Germany
| | - Malina Behrens
- University Hospital of Münster (UKM), Internal Medicine D (MedD), Department Molecular Nephrology, Albert-Schweitzer-Campus 1 Building A14, 48149 Münster, Germany
| | - Sujasha Ghosh
- School of Biological Sciences and NTU Institute of Structural Biology (NISB), Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore City, Singapore
| | - Uwe Hansen
- University Hospital of Münster, Institute of Musculoskeletal Medicine (IMM), Head Core Facility Electron Microscopy, Domagkstraße 3, 48149 Münster, Germany
| | - Michael P Krahn
- University Hospital of Münster (UKM), Internal Medicine D (MedD), Medical Cell Biology, Albert-Schweitzer-Campus 1 Building A14, 48149 Münster, Germany
| | - Klaus Ebnet
- Institute-associated Research Group "Cell adhesion and cell polarity", Institute of Medical Biochemistry, Center for Molecular Biology of Inflammation (ZMBE), University of Münster, Von-Esmarch-Straße 56, 48149 Münster, Germany
| | - Hermann Pavenstädt
- University Hospital of Münster (UKM), Internal Medicine D (MedD), Department Molecular Nephrology, Albert-Schweitzer-Campus 1 Building A14, 48149 Münster, Germany
| | - Alexander Ludwig
- School of Biological Sciences and NTU Institute of Structural Biology (NISB), Nanyang Technological University, 60 Nanyang Drive, 637551 Singapore City, Singapore
| | - Thomas Weide
- University Hospital of Münster (UKM), Internal Medicine D (MedD), Department Molecular Nephrology, Albert-Schweitzer-Campus 1 Building A14, 48149 Münster, Germany
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21
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Hosseini A, Lindholm HT, Chen R, Mehdipour P, Marhon SA, Ishak CA, Moore PC, Classon M, Di Gioacchino A, Greenbaum B, De Carvalho DD. Retroelement decay by the exonuclease XRN1 is a viral mimicry dependency in cancer. Cell Rep 2024; 43:113684. [PMID: 38261511 DOI: 10.1016/j.celrep.2024.113684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 10/31/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024] Open
Abstract
Viral mimicry describes the immune response induced by endogenous stimuli such as double-stranded RNA (dsRNA) from endogenous retroelements. Activation of viral mimicry has the potential to kill cancer cells or augment anti-tumor immune responses. Here, we systematically identify mechanisms of viral mimicry adaptation associated with cancer cell dependencies. Among the top hits is the RNA decay protein XRN1 as an essential gene for the survival of a subset of cancer cell lines. XRN1 dependency is mediated by mitochondrial antiviral signaling protein and protein kinase R activation and is associated with higher levels of cytosolic dsRNA, higher levels of a subset of Alus capable of forming dsRNA, and higher interferon-stimulated gene expression, indicating that cells die due to induction of viral mimicry. Furthermore, dsRNA-inducing drugs such as 5-aza-2'-deoxycytidine and palbociclib can generate a synthetic dependency on XRN1 in cells initially resistant to XRN1 knockout. These results indicate that XRN1 is a promising target for future cancer therapeutics.
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Affiliation(s)
- Amir Hosseini
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Håvard T Lindholm
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Pathology, Oslo University Hospital-Rikshospitalet, 0372 Oslo, Norway
| | - Raymond Chen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Parinaz Mehdipour
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Ludwig Institute for Cancer Research, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Sajid A Marhon
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Charles A Ishak
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Paul C Moore
- Pfizer Centers for Therapeutic Innovation, South San Francisco, CA 94080, USA
| | - Marie Classon
- Pfizer Centers for Therapeutic Innovation, South San Francisco, CA 94080, USA
| | - Andrea Di Gioacchino
- Laboratoire de Physique de l'Ecole Normale Supérieure, PSL & CNRS UMR8063, Sorbonne Université, Université de Paris, Paris, France
| | - Benjamin Greenbaum
- Physiology, Biophysics & Systems Biology, Weill Cornell Medicine, Weill Cornell Medical College, New York, NY 10065, USA; Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Daniel D De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.
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22
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Gong X, Boyer JB, Gierlich S, Pożoga M, Weidenhausen J, Sinning I, Meinnel T, Giglione C, Wang Y, Hell R, Wirtz M. HYPK controls stability and catalytic activity of the N-terminal acetyltransferase A in Arabidopsis thaliana. Cell Rep 2024; 43:113768. [PMID: 38363676 DOI: 10.1016/j.celrep.2024.113768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 12/12/2023] [Accepted: 01/25/2024] [Indexed: 02/18/2024] Open
Abstract
The ribosome-tethered N-terminal acetyltransferase A (NatA) acetylates 52% of soluble proteins in Arabidopsis thaliana. This co-translational modification of the N terminus stabilizes diverse cytosolic plant proteins. The evolutionary conserved Huntingtin yeast partner K (HYPK) facilitates NatA activity in planta, but in vitro, its N-terminal helix α1 inhibits human NatA activity. To dissect the regulatory function of HYPK protein domains in vivo, we genetically engineer CRISPR-Cas9 mutants expressing a HYPK fragment lacking all functional domains (hypk-cr1) or an internally deleted HYPK variant truncating helix α1 but retaining the C-terminal ubiquitin-associated (UBA) domain (hypk-cr2). We find that the UBA domain of HYPK is vital for stabilizing the NatA complex in an organ-specific manner. The N terminus of HYPK, including helix α1, is critical for promoting NatA activity on substrates starting with various amino acids. Consequently, deleting only 42 amino acids inside the HYPK N terminus causes substantial destabilization of the plant proteome and higher tolerance toward drought stress.
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Affiliation(s)
- Xiaodi Gong
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Jean-Baptiste Boyer
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Simone Gierlich
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Marlena Pożoga
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | | | - Irmgard Sinning
- Heidelberg University Biochemistry Center, 69120 Heidelberg, Germany
| | - Thierry Meinnel
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Carmela Giglione
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Yonghong Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, 271018 Tai'an, China
| | - Rüdiger Hell
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany
| | - Markus Wirtz
- Centre for Organismal Studies, Heidelberg University, 69120 Heidelberg, Germany.
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23
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Kawaguchi K, Fujita N. Shaping transverse-tubules: central mechanisms that play a role in the cytosol zoning for muscle contraction. J Biochem 2024; 175:125-131. [PMID: 37848047 PMCID: PMC10873525 DOI: 10.1093/jb/mvad083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/19/2023] Open
Abstract
A transverse-tubule (T-tubule) is an invagination of the plasma membrane penetrating deep into muscle cells. An extensive membrane network of T-tubules is crucial for rapid and synchronized signal transmission from the cell surface to the entire sarcoplasmic reticulum for Ca2+ release, leading to muscle contraction. T-tubules are also indispensable for the formation and positioning of other muscle organelles. Their structure and physiological roles are relatively well established; however, the mechanisms shaping T-tubules require further elucidation. Centronuclear myopathy (CNM), an inherited muscular disorder, accompanies structural defects in T-tubules. Membrane traffic-related genes, including MTM1 (Myotubularin 1), DNM2 (Dynamin 2), and BIN1 (Bridging Integrator-1), were identified as causative genes of CNM. In addition, causative genes for other muscle diseases are also reported to be involved in the formation and maintenance of T-tubules. This review summarizes current knowledge on the mechanisms of how T-tubule formation and maintenance is regulated.
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Affiliation(s)
- Kohei Kawaguchi
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 S2-11 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
| | - Naonobu Fujita
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, 4259 S2-11 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
- Graduate School of Life Science and Technology, Tokyo Institute of Technology, 4259 S2-11 Nagatsuta-cho, Midori-ku, Yokohama 226-8503, Japan
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24
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Baz AA, Hao H, Lan S, Li Z, Liu S, Chen S, Chu Y. Neutrophil extracellular traps in bacterial infections and evasion strategies. Front Immunol 2024; 15:1357967. [PMID: 38433838 PMCID: PMC10906519 DOI: 10.3389/fimmu.2024.1357967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 01/26/2024] [Indexed: 03/05/2024] Open
Abstract
Neutrophils are innate immune cells that have a vital role in host defense systems. Neutrophil extracellular traps (NETs) are one of neutrophils' defense mechanisms against pathogens. NETs comprise an ejected lattice of chromatin associated with histones, granular proteins, and cytosolic proteins. They are thought to be an efficient strategy to capture and/or kill bacteria and received intensive research interest in the recent years. However, soon after NETs were identified, it was observed that certain bacteria were able to evade NET entrapment through many different mechanisms. Here, we outline the recent progress of NETs in bacterial infections and the strategies employed by bacteria to evade or withstand NETs. Identifying the molecules and mechanisms that modulate NET release will improve our understanding of the functions of NETs in infections and provide new avenues for the prevention and treatment of bacterial diseases.
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Affiliation(s)
- Ahmed Adel Baz
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
- Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agricultural and Rural Affairs, Lanzhou, China
- Key Laboratory of Veterinary Etiological Biology, Ministry of Agricultural and Rural Affairs, Lanzhou, China
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Assiut, Egypt
| | - Huafang Hao
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
- Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agricultural and Rural Affairs, Lanzhou, China
- Key Laboratory of Veterinary Etiological Biology, Ministry of Agricultural and Rural Affairs, Lanzhou, China
| | - Shimei Lan
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
- Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agricultural and Rural Affairs, Lanzhou, China
- Key Laboratory of Veterinary Etiological Biology, Ministry of Agricultural and Rural Affairs, Lanzhou, China
| | - Zhangcheng Li
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
- Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agricultural and Rural Affairs, Lanzhou, China
- Key Laboratory of Veterinary Etiological Biology, Ministry of Agricultural and Rural Affairs, Lanzhou, China
| | - Shuang Liu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
- Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agricultural and Rural Affairs, Lanzhou, China
- Key Laboratory of Veterinary Etiological Biology, Ministry of Agricultural and Rural Affairs, Lanzhou, China
| | - Shengli Chen
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
- Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agricultural and Rural Affairs, Lanzhou, China
- Key Laboratory of Veterinary Etiological Biology, Ministry of Agricultural and Rural Affairs, Lanzhou, China
| | - Yuefeng Chu
- State Key Laboratory for Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
- Gansu Province Research Center for Basic Disciplines of Pathogen Biology, Lanzhou, China
- Key Laboratory of Ruminant Disease Prevention and Control (West), Ministry of Agricultural and Rural Affairs, Lanzhou, China
- Key Laboratory of Veterinary Etiological Biology, Ministry of Agricultural and Rural Affairs, Lanzhou, China
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25
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Pennacchio FA, Poli A, Pramotton FM, Lavore S, Rancati I, Cinquanta M, Vorselen D, Prina E, Romano OM, Ferrari A, Piel M, Cosentino Lagomarsino M, Maiuri P. N2FXm, a method for joint nuclear and cytoplasmic volume measurements, unravels the osmo-mechanical regulation of nuclear volume in mammalian cells. Nat Commun 2024; 15:1070. [PMID: 38326317 PMCID: PMC10850064 DOI: 10.1038/s41467-024-45168-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 01/15/2024] [Indexed: 02/09/2024] Open
Abstract
In eukaryotes, cytoplasmic and nuclear volumes are tightly regulated to ensure proper cell homeostasis. However, current methods to measure cytoplasmic and nuclear volumes, including confocal 3D reconstruction, have limitations, such as relying on two-dimensional projections or poor vertical resolution. Here, to overcome these limitations, we describe a method, N2FXm, to jointly measure cytoplasmic and nuclear volumes in single cultured adhering human cells, in real time, and across cell cycles. We find that this method accurately provides joint size over dynamic measurements and at different time resolutions. Moreover, by combining several experimental perturbations and analyzing a mathematical model including osmotic effects and tension, we show that N2FXm can give relevant insights on how mechanical forces exerted by the cytoskeleton on the nuclear envelope can affect the growth of nucleus volume by biasing nuclear import. Our method, by allowing for accurate joint nuclear and cytoplasmic volume dynamic measurements at different time resolutions, highlights the non-constancy of the nucleus/cytoplasm ratio along the cell cycle.
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Affiliation(s)
- Fabrizio A Pennacchio
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
- Laboratory of Applied Mechanobiology, Department of Health Sciences and Technology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093, Zurich, Switzerland
| | - Alessandro Poli
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Francesca Michela Pramotton
- Laboratory of Thermodynamics in Emerging Technologies, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, Zurich, CH-8092, Switzerland
| | - Stefania Lavore
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Ilaria Rancati
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Mario Cinquanta
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Daan Vorselen
- Department of Biology and Howard Hughes Medical Institute, University of Washington, Seattle, WA, 98105, USA
| | - Elisabetta Prina
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Orso Maria Romano
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
| | - Aldo Ferrari
- Laboratory of Thermodynamics in Emerging Technologies, Department of Mechanical and Process Engineering, ETH Zurich, Sonneggstrasse 3, Zurich, CH-8092, Switzerland
| | - Matthieu Piel
- Institut Curie, PSL Research University, CNRS, UMR 144, F-75005, Paris, France
- Institut Pierre-Gilles de Gennes, PSL Research University, F-75005, Paris, France
| | - Marco Cosentino Lagomarsino
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy
- Dipartimento di Fisica, Università degli Studi di Milano, and I.N.F.N., Via Celoria 16, 20133, Milan, Italy
| | - Paolo Maiuri
- IFOM ETS-The AIRC Institute of Molecular Oncology, Via Adamello 16, 20139, Milan, Italy.
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, Via S. Pansini 5, 80131, Naples, Italy.
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26
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D'Urso B, Weil R, Génin P. [Optineurin and mitochondrial dysfunction in neurodegeneration]. Med Sci (Paris) 2024; 40:167-175. [PMID: 38411425 DOI: 10.1051/medsci/2023220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024] Open
Abstract
Optineurin (OPTN) is a multifunctional protein playing a crucial role as a receptor in selective autophagy. OPTN gene mutations are linked to diseases such as normal-tension glaucoma and amyotrophic lateral sclerosis. Recognized as a critical receptor for mitophagy, OPTN is pivotal in selectively degrading damaged mitochondria. This process is essential to prevent their accumulation, the generation of reactive oxygen species, and the release of pro-apoptotic factors. Mitophagy's quality control is governed by the PINK1 kinase and the cytosolic ubiquitin ligase Parkin, whose mutations are associated with Parkinson's disease. This review highlights recent insights emphasizing OPTN's role in mitophagy and its potential involvement in neurodegenerative diseases.
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Affiliation(s)
- Baptiste D'Urso
- CIMI-Paris, UPMC UMRS CR7 - Inserm U1135 - CNRS EMR8255, Faculté de médecine Sorbonne Université site Pitié-Salpêtrière, Paris, France - Sorbonne Université, Faculté des sciences et ingénierie, Paris, France
| | - Robert Weil
- CIMI-Paris, UPMC UMRS CR7 - Inserm U1135 - CNRS EMR8255, Faculté de médecine Sorbonne Université site Pitié-Salpêtrière, Paris, France
| | - Pierre Génin
- CIMI-Paris, UPMC UMRS CR7 - Inserm U1135 - CNRS EMR8255, Faculté de médecine Sorbonne Université site Pitié-Salpêtrière, Paris, France
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27
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Borst A. Connectivity Matrix Seriation via Relaxation. PLoS Comput Biol 2024; 20:e1011904. [PMID: 38377134 PMCID: PMC10906871 DOI: 10.1371/journal.pcbi.1011904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 03/01/2024] [Accepted: 02/09/2024] [Indexed: 02/22/2024] Open
Abstract
Volume electron microscopy together with computer-based image analysis are yielding neural circuit diagrams of ever larger regions of the brain. These datasets are usually represented in a cell-to-cell connectivity matrix and contain important information about prevalent circuit motifs allowing to directly test various theories on the computation in that brain structure. Of particular interest are the detection of cell assemblies and the quantification of feedback, which can profoundly change circuit properties. While the ordering of cells along the rows and columns doesn't change the connectivity, it can make special connectivity patterns recognizable. For example, ordering the cells along the flow of information, feedback and feedforward connections are segregated above and below the main matrix diagonal, respectively. Different algorithms are used to renumber matrices such as to minimize a given cost function, but either their performance becomes unsatisfying at a given size of the circuit or the CPU time needed to compute them scales in an unfavorable way with increasing number of neurons. Based on previous ideas, I describe an algorithm which is effective in matrix reordering with respect to both its performance as well as to its scaling in computing time. Rather than trying to reorder the matrix in discrete steps, the algorithm transiently relaxes the integer program by assigning a real-valued parameter to each cell describing its location on a continuous axis ('smooth-index') and finds the parameter set that minimizes the cost. I find that the smooth-index algorithm outperforms all algorithms I compared it to, including those based on topological sorting.
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Affiliation(s)
- Alexander Borst
- Max-Planck-Institute for Biological Intelligence, Martinsried, Germany
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28
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Mun SH, Hwang CS. Marchf6: A guardian against cytosol-spilled POMC-induced ferroptosis. Mol Cells 2024; 47:100008. [PMID: 38215826 PMCID: PMC10960111 DOI: 10.1016/j.mocell.2024.100008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/02/2024] [Indexed: 01/14/2024] Open
Affiliation(s)
- Sang-Hyeon Mun
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Cheol-Sang Hwang
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea.
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29
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Sneyers F, Speelman-Rooms F, Verhelst SHL, Bootman MD, Bultynck G. Cellular effects of BAPTA: Are they only about Ca 2+ chelation? Biochim Biophys Acta Mol Cell Res 2024; 1871:119589. [PMID: 37739271 DOI: 10.1016/j.bbamcr.2023.119589] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/06/2023] [Accepted: 09/10/2023] [Indexed: 09/24/2023]
Abstract
Intracellular Ca2+ signals play a vital role in a broad range of cell biological and physiological processes in all eukaryotic cell types. Dysregulation of Ca2+ signaling has been implicated in numerous human diseases. Over the past four decades, the understanding of how cells use Ca2+ as a messenger has flourished, largely because of the development of reporters that enable visualization of Ca2+ signals in different cellular compartments, and tools that can modulate cellular Ca2+ signaling. One such tool that is frequently used is BAPTA; a fast, high-affinity Ca2+-chelating molecule. By making use of a cell-permeable acetoxymethyl ester (AM) variant, BAPTA can be readily loaded into the cytosol of cells (referred to as BAPTAi), where it is trapped and able to buffer changes in cytosolic Ca2+. Due to the ease of loading of the AM version of BAPTA, this reagent has been used in hundreds of studies to probe the role of Ca2+ signaling in specific processes. As such, for decades, researchers have almost universally attributed changes in biological processes caused by BAPTAi to the involvement of Ca2+ signaling. However, BAPTAi has often been used without any form of control, and in many cases has neither been shown to be retained in cells for the duration of experiments nor to buffer any Ca2+ signals. Moreover, increasing evidence points to off-target cellular effects of BAPTA that are clearly not related to Ca2+ chelation. Here, we briefly introduce Ca2+ signaling and the history of Ca2+ chelators and fluorescent Ca2+ indicators. We highlight Ca2+-independent effects of BAPTAi on a broad range of molecular targets and describe some of BAPTAi's impacts on cell functions that occur independently of its Ca2+-chelating properties. Finally, we propose strategies for determining whether Ca2+ chelation, the binding of other metal ions, or off-target interactions with cell components are responsible for BAPTAi's effect on a particular process and suggest some future research directions.
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Affiliation(s)
- Flore Sneyers
- KU Leuven, Lab. Molecular & Cellular Signaling, Dep. Cellular & Molecular Medicine, Campus Gasthuisberg O/N-I bus 802, Herestraat 49, B-3000 Leuven, Belgium
| | - Femke Speelman-Rooms
- KU Leuven, Lab. Molecular & Cellular Signaling, Dep. Cellular & Molecular Medicine, Campus Gasthuisberg O/N-I bus 802, Herestraat 49, B-3000 Leuven, Belgium; KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestraat 49 box 901b, B-3000 Leuven, Belgium
| | - Steven H L Verhelst
- KU Leuven, Department of Cellular and Molecular Medicine, Laboratory of Chemical Biology, Herestraat 49 box 901b, B-3000 Leuven, Belgium
| | - Martin D Bootman
- The Open University, Cancer Research Group, School of Life, Health and Chemical Sciences, Milton Keynes, UK
| | - Geert Bultynck
- KU Leuven, Lab. Molecular & Cellular Signaling, Dep. Cellular & Molecular Medicine, Campus Gasthuisberg O/N-I bus 802, Herestraat 49, B-3000 Leuven, Belgium.
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30
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Coccarelli A, Pant S, Polydoros I, Harraz OF. A new model for evaluating pressure-induced vascular tone in small cerebral arteries. Biomech Model Mechanobiol 2024; 23:271-286. [PMID: 37925376 PMCID: PMC10901969 DOI: 10.1007/s10237-023-01774-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/17/2023] [Indexed: 11/06/2023]
Abstract
The capacity of small cerebral arteries (SCAs) to adapt to pressure fluctuations has a fundamental physiological role and appears to be relevant in different pathological conditions. Here, we present a new computational model for quantifying the link, and its contributors, between luminal pressure and vascular tone generation in SCAs. This is assembled by combining a chemical sub-model, representing pressure-induced smooth muscle cell (SMC) signalling, with a mechanical sub-model for the tone generation and its transduction at tissue level. The devised model can accurately reproduce the impact of luminal pressure on different cytoplasmic components involved in myogenic signalling, both in the control case and when combined with some specific pharmacological interventions. Furthermore, the model is also able to capture and predict experimentally recorded pressure-outer diameter relationships obtained for vessels under control conditions, both in a Ca2 + -free bath and under drug inhibition. The modularity of the proposed framework allows the integration of new components for the study of a broad range of processes involved in the vascular function.
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Affiliation(s)
- Alberto Coccarelli
- Zienkiewicz Institute for Modelling, Data and AI, Faculty of Science and Engineering, Swansea University, Swansea, UK.
| | - Sanjay Pant
- Zienkiewicz Institute for Modelling, Data and AI, Faculty of Science and Engineering, Swansea University, Swansea, UK
| | - Ioannis Polydoros
- Zienkiewicz Institute for Modelling, Data and AI, Faculty of Science and Engineering, Swansea University, Swansea, UK
| | - Osama F Harraz
- Department of Pharmacology, Larner College of Medicine, and Vermont Center for Cardiovascular and Brain Health, University of Vermont, Burlington, USA
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31
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Yoshikawa K, Saito S, Kadonosono T, Tanaka M, Okochi M. Osmotic stress induces the formation of migrasome-like vesicles. FEBS Lett 2024; 598:437-445. [PMID: 38339800 DOI: 10.1002/1873-3468.14816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/10/2024] [Accepted: 01/10/2024] [Indexed: 02/12/2024]
Abstract
Migrasomes are extracellular vesicles that form on the retraction fibers of migrating cells. In this study, we report the formation of migrasome-like vesicles enriched in tetraspanin 4 and containing cytoplasmic components in response to hypoosmotic stress. When migrating cells were subjected to hypoosmotic stress, vesicles with a size distribution of 0.5 to 2 μm formed on the retraction fibers, and vanished in a few minutes. The vesicles are rich in cholesterol, and their number was reduced when cells were pretreated with lipoprotein-deficient serum. The formation of migrasome-like vesicles upon hypoosmotic stress may provide biophysical cues regarding the cellular response to this external stimulus in cells and tissues.
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Grants
- 23K17843 Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and Technology of Japan
- 22K19913 Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and Technology of Japan
- 21H01726 Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and Technology of Japan
- 21H01725 Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science, and Technology of Japan
- JP21zf0127004 Moonshot Research and Development Program from the Japan Agency for Medical Research and Development (AMED)
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Affiliation(s)
- Koki Yoshikawa
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, Japan
| | - Shogo Saito
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, Japan
| | - Tetsuya Kadonosono
- Department of Life Science and Technology, Tokyo Institute of Technology, Yokohama-shi, Japan
| | - Masayoshi Tanaka
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, Yokohama-shi, Japan
| | - Mina Okochi
- Department of Chemical Science and Engineering, Tokyo Institute of Technology, Japan
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32
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Neary MT, Mulder LM, Kowalski PS, MacLoughlin R, Crean AM, Ryan KB. Nebulised delivery of RNA formulations to the lungs: From aerosol to cytosol. J Control Release 2024; 366:812-833. [PMID: 38101753 DOI: 10.1016/j.jconrel.2023.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023]
Abstract
In the past decade RNA-based therapies such as small interfering RNA (siRNA) and messenger RNA (mRNA) have emerged as new and ground-breaking therapeutic agents for the treatment and prevention of many conditions from viral infection to cancer. Most clinically approved RNA therapies are parenterally administered which impacts patient compliance and adds to healthcare costs. Pulmonary administration via inhalation is a non-invasive means to deliver RNA and offers an attractive alternative to injection. Nebulisation is a particularly appealing method due to the capacity to deliver large RNA doses during tidal breathing. In this review, we discuss the unique physiological barriers presented by the lung to efficient nebulised RNA delivery and approaches adopted to circumvent this problem. Additionally, the different types of nebulisers are evaluated from the perspective of their suitability for RNA delivery. Furthermore, we discuss recent preclinical studies involving nebulisation of RNA and analysis in in vitro and in vivo settings. Several studies have also demonstrated the importance of an effective delivery vector in RNA nebulisation therefore we assess the variety of lipid, polymeric and hybrid-based delivery systems utilised to date. We also consider the outlook for nebulised RNA medicinal products and the hurdles which must be overcome for successful clinical translation. In summary, nebulised RNA delivery has demonstrated promising potential for the treatment of several lung-related conditions such as asthma, COPD and cystic fibrosis, to which the mode of delivery is of crucial importance for clinical success.
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Affiliation(s)
- Michael T Neary
- SSPC, The SFI Research Centre for Pharmaceuticals, School of Pharmacy, University College Cork, Ireland; School of Pharmacy, University College Cork, Ireland
| | | | - Piotr S Kowalski
- School of Pharmacy, University College Cork, Ireland; APC Microbiome, University College Cork, Cork, Ireland
| | | | - Abina M Crean
- SSPC, The SFI Research Centre for Pharmaceuticals, School of Pharmacy, University College Cork, Ireland; School of Pharmacy, University College Cork, Ireland
| | - Katie B Ryan
- SSPC, The SFI Research Centre for Pharmaceuticals, School of Pharmacy, University College Cork, Ireland; School of Pharmacy, University College Cork, Ireland.
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33
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Ohtsu M, Jennings J, Johnston M, Breakspear A, Liu X, Stark K, Morris RJ, de Keijzer J, Faulkner C. Assaying Effector Cell-to-Cell Mobility in Plant Tissues Identifies Hypermobility and Indirect Manipulation of Plasmodesmata. Mol Plant Microbe Interact 2024; 37:84-92. [PMID: 37942798 DOI: 10.1094/mpmi-05-23-0052-ta] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2023]
Abstract
In plants, plasmodesmata establish cytoplasmic continuity between cells to allow for communication and resource exchange across the cell wall. While plant pathogens use plasmodesmata as a pathway for both molecular and physical invasion, the benefits of molecular invasion (cell-to-cell movement of pathogen effectors) are poorly understood. To establish a methodology for identification and characterization of the cell-to-cell mobility of effectors, we performed a quantitative live imaging-based screen of candidate effectors of the fungal pathogen Colletotrichum higginsianum. We predicted C. higginsianum effectors by their expression profiles, the presence of a secretion signal, and their predicted and in planta localization when fused to green fluorescent protein. We assayed for cell-to-cell mobility of nucleocytosolic effectors and identified 14 that are cell-to-cell mobile. We identified that three of these effectors are "hypermobile," showing cell-to-cell mobility greater than expected for a protein of that size. To explore the mechanism of hypermobility, we chose two hypermobile effectors and measured their impact on plasmodesmata function and found that even though they show no direct association with plasmodesmata, each increases the transport capacity of plasmodesmata. Thus, our methods for quantitative analysis of cell-to-cell mobility of candidate microbe-derived effectors, or any suite of host proteins, can identify cell-to-cell hypermobility and offer greater understanding of how proteins affect plasmodesmal function and intercellular connectivity. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Mina Ohtsu
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, U.K
| | - Joanna Jennings
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, U.K
| | - Matthew Johnston
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, U.K
| | - Andrew Breakspear
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, U.K
| | - Xiaokun Liu
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, U.K
| | - Kara Stark
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, U.K
| | - Richard J Morris
- Computational and Systems Biology, John Innes Centre, Norwich Research Park, U.K
| | - Jeroen de Keijzer
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, U.K
| | - Christine Faulkner
- Cell and Developmental Biology, John Innes Centre, Norwich Research Park, U.K
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34
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Suzuki T, Fujihira H. NGLY1: A fascinating, multifunctional molecule. Biochim Biophys Acta Gen Subj 2024; 1868:130379. [PMID: 37951368 DOI: 10.1016/j.bbagen.2023.130379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/04/2023] [Indexed: 11/14/2023]
Abstract
NGLY1, a cytoplasmic de-N-glycosylating enzyme is well conserved among eukaryotes. This enzyme has attracted considerable attention after mutations on the NGLY1 gene were found to cause a rare genetic disorder called NGLY1 deficiency. Recent explosive progress in NGLY1 research has revealed multi-functional aspects of this protein.
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Affiliation(s)
- Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), RIKEN, Saitama, Japan; Takeda-CiRA Joint Program (T-CiRA), Kanagawa, Japan.
| | - Haruhiko Fujihira
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), RIKEN, Saitama, Japan
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35
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Sakato-Antoku M, Patel-King RS, Balsbaugh JL, King SM. Methylation of ciliary dynein motors involves the essential cytosolic assembly factor DNAAF3/PF22. Proc Natl Acad Sci U S A 2024; 121:e2318522121. [PMID: 38261620 PMCID: PMC10835030 DOI: 10.1073/pnas.2318522121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 12/15/2023] [Indexed: 01/25/2024] Open
Abstract
Axonemal dynein motors drive ciliary motility and can consist of up to twenty distinct components with a combined mass of ~2 MDa. In mammals, failure of dyneins to assemble within the axonemal superstructure leads to primary ciliary dyskinesia. Syndromic phenotypes include infertility, rhinitis, severe bronchial conditions, and situs inversus. Nineteen specific cytosolic factors (Dynein Axonemal Assembly Factors; DNAAFs) are necessary for axonemal dynein assembly, although the detailed mechanisms involved remain very unclear. Here, we identify the essential assembly factor DNAAF3 as a structural ortholog of S-adenosylmethionine-dependent methyltransferases. We demonstrate that dynein heavy chains, especially those forming the ciliary outer arms, are methylated on key residues within various nucleotide-binding sites and on microtubule-binding domain helices directly involved in the transition to low binding affinity. These variable modifications, which are generally missing in a Chlamydomonas null mutant for the DNAAF3 ortholog PF22 (DAB1), likely impact on motor mechanochemistry fine-tuning the activities of individual dynein complexes.
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Affiliation(s)
- Miho Sakato-Antoku
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030-3305
| | - Ramila S Patel-King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030-3305
| | - Jeremy L Balsbaugh
- Proteomics and Metabolomics Facility, Center for Open Research Resources & Equipment, University of Connecticut, Storrs, CT 06269
| | - Stephen M King
- Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT 06030-3305
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36
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Manjunath KS, Singh S, Kalia P, Mangal M, Sharma BB, Singh N, Ray M, Rao M, Tomar BS. Commercial suitability and characterization of newly developed Erucastrum canariense (Can) sterile cytoplasm based cytoplasmic male sterile (CMS) lines in Indian cauliflower. Sci Rep 2024; 14:2346. [PMID: 38282114 PMCID: PMC10822850 DOI: 10.1038/s41598-024-52714-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 01/23/2024] [Indexed: 01/30/2024] Open
Abstract
The study presents the first to characterize novel Erucastrum canarianse Webb and Berthel (or Can) sterile cytoplasm-based CMS lines in Indian cauliflower (Brassica oleracea var. botrytis L.) and investigating their commercial suitability. Eleven Can-based CMS lines were examined for 12 agro-morphological and yield traits,18 floral traits, four seed yield traits together with three each of the Ogura (source: wild Japanese Radish) and Tour (Source: Brassica tournefortii) cytoplasms. All of the recorded floral and seed traits showed significant (P > 0.05) differences between the CMS lines of each group. Agro-morphological and yield traits in CMS lines and their maintainers, however, were non-significantly different. All the Can- and Ogura-based CMS lines showed flowering and appropriate seed formation by natural cross-pollination. Only two Tour cytoplasm-based CMS lines, Tour (DC-41-5) and Tour (DC-67), produced the smallest malformed flowers and stigma. The highest seed yield per plant in CMS lines was in Ogu (DC-98-4) and the lowest in Tour (DC-67). P14 and P15, two polymorphic mtDNA markers, were discovered for the Can CMS system for early detection. Five primers (ITS5a-ITS4, atpF-atpH, P16, rbeL and trnL), along with their maintainers, were sequenced and aligned to detect nucleotide changes including as additions and or deletions at different positions. The newly introduced E. canariense sterile cytoplasm-based CMS system in cauliflower is the subject of the first comprehensive report, which emphasises their potential as a further stable and reliable genetic mechanism for hybrid breeding.
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Affiliation(s)
- K S Manjunath
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Shrawan Singh
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Pritam Kalia
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Manisha Mangal
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Brij Bihari Sharma
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Naveen Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Mrinmoy Ray
- ICAR-Indian Agricultural Statistical Research Institute, New Delhi, 110012, India
| | - Mahesh Rao
- ICAR-National Institute of Plant Biotechnology, New Delhi, 110012, India
| | - Bhoopal Singh Tomar
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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37
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Chen T, Xie S, Cheng J, Zhao Q, Wu H, Jiang P, Du W. AKT1 phosphorylation of cytoplasmic ME2 induces a metabolic switch to glycolysis for tumorigenesis. Nat Commun 2024; 15:686. [PMID: 38263319 PMCID: PMC10805786 DOI: 10.1038/s41467-024-44772-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 01/04/2024] [Indexed: 01/25/2024] Open
Abstract
Many types of tumors feature aerobic glycolysis for meeting their increased energetic and biosynthetic demands. However, it remains still unclear how this glycolytic phenomenon is achieved and coordinated with other metabolic pathways in tumor cells in response to growth stimuli. Here we report that activation of AKT1 induces a metabolic switch to glycolysis from the mitochondrial metabolism via phosphorylation of cytoplasmic malic enzyme 2 (ME2), named ME2fl (fl means full length), favoring an enhanced glycolytic phenotype. Mechanistically, in the cytoplasm, AKT1 phosphorylates ME2fl at serine 9 in the mitochondrial localization signal peptide at the N-terminus, preventing its mitochondrial translocation. Unlike mitochondrial ME2, which accounts for adjusting the tricarboxylic acid (TCA) cycle, ME2fl functions as a scaffold that brings together the key glycolytic enzymes phosphofructokinase (PFKL), glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and pyruvate kinase M2 (PKM2), as well as Lactate dehydrogenase A (LDHA), to promote glycolysis in the cytosol. Thus, through phosphorylation of ME2fl, AKT1 enhances the glycolytic capacity of tumor cells in vitro and in vivo, revealing an unexpected role for subcellular translocation switching of ME2 mediated by AKT1 in the metabolic adaptation of tumor cells to growth stimuli.
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Affiliation(s)
- Taiqi Chen
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), South Medical University, Guangzhou, 510080, China
- State Key Laboratory of Molecular Oncology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Siyi Xie
- State Key Laboratory of Molecular Oncology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Jie Cheng
- State Key Laboratory of Molecular Oncology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China
| | - Qiao Zhao
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Hong Wu
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
- School of Life Sciences, Peking University, Beijing, 100084, China.
| | - Peng Jiang
- Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), South Medical University, Guangzhou, 510080, China.
- State Key Laboratory of Molecular Oncology, School of Life Sciences, Tsinghua University, Beijing, 100084, China.
- Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China.
| | - Wenjing Du
- State Key Laboratory of Common Mechanism Research for Major Diseases, Haihe Laboratory of Cell Ecosystem, Department of Cell Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, 100005, China.
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38
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Masuda D, Nakanishi I, Ohkubo K, Ito H, Matsumoto KI, Ichikawa H, Chatatikun M, Klangbud WK, Kotepui M, Imai M, Kawakami F, Kubo M, Matsui H, Tangpong J, Ichikawa T, Ozawa T, Yen HC, St Clair DK, Indo HP, Majima HJ. Mitochondria Play Essential Roles in Intracellular Protection against Oxidative Stress-Which Molecules among the ROS Generated in the Mitochondria Can Escape the Mitochondria and Contribute to Signal Activation in Cytosol? Biomolecules 2024; 14:128. [PMID: 38275757 PMCID: PMC10813015 DOI: 10.3390/biom14010128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/28/2023] [Accepted: 12/29/2023] [Indexed: 01/27/2024] Open
Abstract
Questions about which reactive oxygen species (ROS) or reactive nitrogen species (RNS) can escape from the mitochondria and activate signals must be addressed. In this study, two parameters, the calculated dipole moment (debye, D) and permeability coefficient (Pm) (cm s-1), are listed for hydrogen peroxide (H2O2), hydroxyl radical (•OH), superoxide (O2•-), hydroperoxyl radical (HO2•), nitric oxide (•NO), nitrogen dioxide (•NO2), peroxynitrite (ONOO-), and peroxynitrous acid (ONOOH) in comparison to those for water (H2O). O2•- is generated from the mitochondrial electron transport chain (ETC), and several other ROS and RNS can be generated subsequently. The candidates which pass through the mitochondrial membrane include ROS with a small number of dipoles, i.e., H2O2, HO2•, ONOOH, •OH, and •NO. The results show that the dipole moment of •NO2 is 0.35 D, indicating permeability; however, •NO2 can be eliminated quickly. The dipole moments of •OH (1.67 D) and ONOOH (1.77 D) indicate that they might be permeable. This study also suggests that the mitochondria play a central role in protecting against further oxidative stress in cells. The amounts, the long half-life, the diffusion distance, the Pm, the one-electron reduction potential, the pKa, and the rate constants for the reaction with ascorbate and glutathione are listed for various ROS/RNS, •OH, singlet oxygen (1O2), H2O2, O2•-, HO2•, •NO, •NO2, ONOO-, and ONOOH, and compared with those for H2O and oxygen (O2). Molecules with negative electrical charges cannot directly diffuse through the phospholipid bilayer of the mitochondrial membranes. Short-lived molecules, such as •OH, would be difficult to contribute to intracellular signaling. Finally, HO2• and ONOOH were selected as candidates for the ROS/RNS that pass through the mitochondrial membrane.
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Affiliation(s)
- Daisuke Masuda
- Department of Space Environmental Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima 890-8544, Kagoshima, Japan;
- Utilization & Engineering Department, Japan Manned Space Systems Corporation, 2-1-6 Tsukuba, Tsukuba 305-0047, Ibaraki, Japan
| | - Ikuo Nakanishi
- Quantum RedOx Chemistry Team, Institute for Quantum Life Science (iQLS), Quantum Life and Medical Science Directorate (QLMS), National Institutes for Quantum Science and Technology (QST), 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan;
| | - Kei Ohkubo
- Institute for Advanced Co-Creation Studies, Open and Transdisciplinary Research Initiatives, Osaka University, Suita 565-0871, Japan;
| | - Hiromu Ito
- Quantum RedOx Chemistry Team, Institute for Quantum Life Science (iQLS), Quantum Life and Medical Science Directorate (QLMS), National Institutes for Quantum Science and Technology (QST), 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan;
- Department of Maxillofacial Radiology, Field of Oncology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8544, Kagoshima, Japan
| | - Ken-ichiro Matsumoto
- Quantitative RedOx Sensing Group, Department of Radiation Regulatory Science Research, Institute for Radiological Science (NIRS), Quantum Life and Medical Science Directorate (QLMS), National Institutes for Quantum Science and Technology (QST), 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan;
| | - Hiroshi Ichikawa
- Department of Medical Life Systems, Graduate School of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Kyoto, Japan;
| | - Moragot Chatatikun
- School of Allied Health Sciences, Walailak University, Thasala, Nakhon Si Thammarat 80161, Thailand; (M.C.); (W.K.K.); (M.K.); (J.T.)
- Center of Excellence Research for Melioidosis and Microorganisms, Walailak University, Thasala, Nakhon Si Thammarat 80161, Thailand
| | - Wiyada Kwanhian Klangbud
- School of Allied Health Sciences, Walailak University, Thasala, Nakhon Si Thammarat 80161, Thailand; (M.C.); (W.K.K.); (M.K.); (J.T.)
- Center of Excellence Research for Melioidosis and Microorganisms, Walailak University, Thasala, Nakhon Si Thammarat 80161, Thailand
| | - Manas Kotepui
- School of Allied Health Sciences, Walailak University, Thasala, Nakhon Si Thammarat 80161, Thailand; (M.C.); (W.K.K.); (M.K.); (J.T.)
| | - Motoki Imai
- Regenerative Medicine and Cell Design Research Facility, School of Allied Health Sciences, Kitasato University, 1-15-1 Kitasato, Sagamihara 252-0373, Kanagawa, Japan; (M.I.); (F.K.); (M.K.); (T.I.)
- Department of Molecular Diagnostics, School of Allied Health Sciences, Kitasato University, 1-15-1 Kitasato, Sagamihara 252-0373, Kanagawa, Japan
| | - Fumitaka Kawakami
- Regenerative Medicine and Cell Design Research Facility, School of Allied Health Sciences, Kitasato University, 1-15-1 Kitasato, Sagamihara 252-0373, Kanagawa, Japan; (M.I.); (F.K.); (M.K.); (T.I.)
- Department of Regulation Biochemistry, Kitasato University Graduate School of Medical Sciences, 1-15-1 Kitasato, Sagamihara 252-0373, Kanagawa, Japan
- Department of Health Administration, School of Allied Health Sciences, Kitasato University, 1-15-1 Kitasato, Sagamihara 252-0373, Kanagawa, Japan
| | - Makoto Kubo
- Regenerative Medicine and Cell Design Research Facility, School of Allied Health Sciences, Kitasato University, 1-15-1 Kitasato, Sagamihara 252-0373, Kanagawa, Japan; (M.I.); (F.K.); (M.K.); (T.I.)
- Division of Microbiology, Kitasato University School of Allied Health Sciences, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0373, Kanagawa, Japan
- Department of Environmental Microbiology, Graduate School of Medical Sciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara 252-0373, Kanagawa, Japan
| | - Hirofumi Matsui
- Division of Gastroenterology, Graduate School of Comprehensive Human Science, University of Tsukuba, Tsukuba 305-8575, Ibaraki, Japan;
| | - Jitbanjong Tangpong
- School of Allied Health Sciences, Walailak University, Thasala, Nakhon Si Thammarat 80161, Thailand; (M.C.); (W.K.K.); (M.K.); (J.T.)
- Research Excellence Center for Innovation and Health Products (RECIHP), School of Allied Health Sciences, Walailak University, Thasala, Nakhon Si Thammarat 80160, Thailand
| | - Takafumi Ichikawa
- Regenerative Medicine and Cell Design Research Facility, School of Allied Health Sciences, Kitasato University, 1-15-1 Kitasato, Sagamihara 252-0373, Kanagawa, Japan; (M.I.); (F.K.); (M.K.); (T.I.)
- Department of Molecular Diagnostics, School of Allied Health Sciences, Kitasato University, 1-15-1 Kitasato, Sagamihara 252-0373, Kanagawa, Japan
| | - Toshihiko Ozawa
- Nihon Pharmaceutical University, 10281 Komuro, Ina-machi, Kitaadachi-gun, Saitama 362-0806, Saitama, Japan;
| | - Hsiu-Chuan Yen
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan;
- Department of Nephrology, Chang Gung Memorial Hospital at Linkou, Taoyuan 33305, Taiwan
| | - Daret K. St Clair
- Department of Toxicology and Cancer Biology, University of Kentucky College of Medicine, Lexington, KY 40536, USA;
| | - Hiroko P. Indo
- Department of Maxillofacial Radiology, Field of Oncology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8544, Kagoshima, Japan
| | - Hideyuki J. Majima
- Department of Space Environmental Medicine, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima 890-8544, Kagoshima, Japan;
- Department of Maxillofacial Radiology, Field of Oncology, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8544, Kagoshima, Japan
- School of Allied Health Sciences, Walailak University, Thasala, Nakhon Si Thammarat 80161, Thailand; (M.C.); (W.K.K.); (M.K.); (J.T.)
- Research Excellence Center for Innovation and Health Products (RECIHP), School of Allied Health Sciences, Walailak University, Thasala, Nakhon Si Thammarat 80160, Thailand
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39
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Jacobs-Wagner C. Through the looking glass: An adventure into the metastable world of the bacterial cytoplasm. Cell 2024; 187:228-234. [PMID: 38242080 DOI: 10.1016/j.cell.2023.11.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 11/12/2023] [Accepted: 11/28/2023] [Indexed: 01/21/2024]
Abstract
This personal story recounts the accidental observation, the struggles, the breakthroughs, and the collaborative spirit of a few individuals that led to the discovery that bacterial cells expend energy to effectively fluidize their otherwise "glass-like" cytoplasm and promote the dispersal of large cytoplasmic components. This adventure, which led us into an uncharted world at the intersection of cell biology and condensed matter physics about ten years ago, forever transformed the way I view cells and conduct research.
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Affiliation(s)
- Christine Jacobs-Wagner
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Sarafan Chemistry, Engineering, and Medicine for Human Health Institute, Stanford University, Stanford, CA 94305, USA; Department of Microbiology and Immunology, Stanford School of Medicine, Stanford, CA 94305, USA.
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40
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Akuma DC, Wodzanowski KA, Schwartz Wertman R, Exconde PM, Vázquez Marrero VR, Odunze CE, Grubaugh D, Shin S, Taabazuing C, Brodsky IE. Catalytic activity and autoprocessing of murine caspase-11 mediate noncanonical inflammasome assembly in response to cytosolic LPS. eLife 2024; 13:e83725. [PMID: 38231198 PMCID: PMC10794067 DOI: 10.7554/elife.83725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 12/06/2023] [Indexed: 01/18/2024] Open
Abstract
Inflammatory caspases are cysteine protease zymogens whose activation following infection or cellular damage occurs within supramolecular organizing centers (SMOCs) known as inflammasomes. Inflammasomes recruit caspases to undergo proximity-induced autoprocessing into an enzymatically active form that cleaves downstream targets. Binding of bacterial LPS to its cytosolic sensor, caspase-11 (Casp11), promotes Casp11 aggregation within a high-molecular-weight complex known as the noncanonical inflammasome, where it is activated to cleave gasdermin D and induce pyroptosis. However, the cellular correlates of Casp11 oligomerization and whether Casp11 forms an LPS-induced SMOC within cells remain unknown. Expression of fluorescently labeled Casp11 in macrophages revealed that cytosolic LPS induced Casp11 speck formation. Unexpectedly, catalytic activity and autoprocessing were required for Casp11 to form LPS-induced specks in macrophages. Furthermore, both catalytic activity and autoprocessing were required for Casp11 speck formation in an ectopic expression system, and processing of Casp11 via ectopically expressed TEV protease was sufficient to induce Casp11 speck formation. These data reveal a previously undescribed role for Casp11 catalytic activity and autoprocessing in noncanonical inflammasome assembly, and shed new light on the molecular requirements for noncanonical inflammasome assembly in response to cytosolic LPS.
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Affiliation(s)
- Daniel C Akuma
- Department of Pathobiology, University of Pennsylvania School of Veterinary MedicinePhiladelphiaUnited States
| | - Kimberly A Wodzanowski
- Department of Microbiology, University of Pennsylvania Perelman School of MedicinePhiladelphiaUnited States
| | - Ronit Schwartz Wertman
- Department of Pathobiology, University of Pennsylvania School of Veterinary MedicinePhiladelphiaUnited States
| | - Patrick M Exconde
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of MedicinePhiladelphiaUnited States
| | - Víctor R Vázquez Marrero
- Department of Microbiology, University of Pennsylvania Perelman School of MedicinePhiladelphiaUnited States
| | | | - Daniel Grubaugh
- Department of Pathobiology, University of Pennsylvania School of Veterinary MedicinePhiladelphiaUnited States
| | - Sunny Shin
- Department of Microbiology, University of Pennsylvania Perelman School of MedicinePhiladelphiaUnited States
| | - Cornelius Taabazuing
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of MedicinePhiladelphiaUnited States
| | - Igor E Brodsky
- Department of Pathobiology, University of Pennsylvania School of Veterinary MedicinePhiladelphiaUnited States
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41
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Wu J, Chen Y, Huang Y, Hao B, Dai S, Zhao L, Zhao Z, Zhao C, Zhang L, Li Y, Xu X, Li N, Huang AC, Zhou J, Tan M, Zhu W, Zhao Q. The cytosolic aminotransferase VAS1 coordinates aromatic amino acid biosynthesis and metabolism. Sci Adv 2024; 10:eadk0738. [PMID: 38198548 PMCID: PMC10780875 DOI: 10.1126/sciadv.adk0738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024]
Abstract
The aromatic amino acids (AAAs) phenylalanine, tyrosine, and tryptophan are basic protein units and precursors of diverse specialized metabolites that are essential for plant growth. Despite their significance, the mechanisms that regulate AAA homeostasis remain elusive. Here, we identified a cytosolic aromatic aminotransferase, REVERSAL OF SAV3 PHENOTYPE 1 (VAS1), as a suppressor of arogenate dehydrogenase 2 (adh2) in Arabidopsis (Arabidopsis thaliana). Genetic and biochemical analyses determined that VAS1 uses AAAs as amino donors, leading to the formation of 3-carboxyphenylalanine and 3-carboxytyrosine. These pathways represent distinct routes for AAA metabolism that are unique to specific plant species. Furthermore, we show that VAS1 is responsible for cytosolic AAA biosynthesis, and its enzymatic activity can be inhibited by 3-carboxyphenylalanine. These findings provide valuable insights into the crucial role of VAS1 in producing 3-carboxy AAAs, notably via recycling of AAAs in the cytosol, which maintains AAA homeostasis and allows plants to effectively coordinate the complex metabolic and biosynthetic pathways of AAAs.
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Affiliation(s)
- Jie Wu
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yanhong Chen
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yuxin Huang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bingbing Hao
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Shengkun Dai
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Lingling Zhao
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zhehui Zhao
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Beijing Key Laboratory of Active Substances Discovery and Druggability Evaluation, Department of Medicinal Chemistry, Institute of Materia Medica, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100050, China
| | - Cuihuan Zhao
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Limin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yunhai Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, CAS Centre for Excellence in Molecular Plant Biology, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xuexia Xu
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Nan Li
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ancheng C. Huang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, School of Life Sciences, SUSTech-PKU Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
| | - Jiahai Zhou
- CAS Key Laboratory for Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Wentao Zhu
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Qiao Zhao
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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42
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Peracchia C. Gap Junction Channel Regulation: A Tale of Two Gates-Voltage Sensitivity of the Chemical Gate and Chemical Sensitivity of the Fast Voltage Gate. Int J Mol Sci 2024; 25:982. [PMID: 38256055 PMCID: PMC10815820 DOI: 10.3390/ijms25020982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/08/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Gap junction channels are regulated by gates sensitive to cytosolic acidification and trans-junctional voltage (Vj). We propose that the chemical gate is a calmodulin (CaM) lobe. The fast-Vj gate is made primarily by the connexin's NH2-terminus domain (NT). The chemical gate closes the channel slowly and completely, while the fast-Vj gate closes the channel rapidly but incompletely. The chemical gate closes with increased cytosolic calcium concentration [Ca2+]i and with Vj gradients at Vj's negative side. In contrast, the fast-Vj gate closes at the positive or negative side of Vj depending on the connexin (Cx) type. Cxs with positively charged NT close at Vj's negative side, while those with negatively charged NT close at Vj's positive side. Cytosolic acidification alters in opposite ways the sensitivity of the fast-Vj gate: it increases the Vj sensitivity of negative gaters and decreases that of positive gaters. While the fast-Vj gate closes and opens instantaneously, the chemical gate often shows fluctuations, likely to reflect the shifting of the gate (CaM's N-lobe) in and out of the channel's pore.
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Affiliation(s)
- Camillo Peracchia
- Department of Pharmacology and Physiology, School of Medicine and Dentistry, University Rochester, Rochester, NY 14642-8711, USA
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43
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Hotton J, Gauchotte G, Mougel R, Migliorini M, Lacomme S, Battaglia-Hsu SF, Agopiantz M. Expressions of HuR, Methyl-HuR and Phospho-HuR in Endometrial Endometrioid Adenocarcinoma Are Associated with Clinical Features. Int J Mol Sci 2024; 25:954. [PMID: 38256026 PMCID: PMC10815350 DOI: 10.3390/ijms25020954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/03/2024] [Accepted: 01/09/2024] [Indexed: 01/24/2024] Open
Abstract
HuR regulates cytoplasmic mRNA stability and translatability, with its expression correlating with adverse outcomes in various cancers. This study aimed to assess the prognostic value and pro-oncogenic properties of HuR and its post-translational isoforms methyl-HuR and phospho-HuR in endometrial adenocarcinoma. Examining 89 endometrioid adenocarcinomas, we analyzed the relationship between HuR nuclear or cytoplasmic immunostaining, tumor-cell proliferation, and patient survival. HuR cytoplasmic expression was significantly increased in grade 3 vs. grade 1 adenocarcinomas (p < 0.001), correlating with worse overall survival (OS) (p = 0.02). Methyl-HuR cytoplasmic expression significantly decreased in grade 3 vs. grade 1 adenocarcinomas (p < 0.001) and correlated with better OS (p = 0.002). Phospho-HuR nuclear expression significantly decreased in grade 3 vs. grade 1 adenocarcinomas (p < 0.001) and non-significantly correlated with increased OS (p = 0.06). Cytoplasmic HuR expression strongly correlated with proliferation markers MCM6 (rho = 0.59 and p < 0.001) and Ki67 (rho = 0.49 and p < 0.001). Conversely, these latter inversely correlated with cytoplasmic methyl-HuR and nuclear phospho-HuR. Cytoplasmic HuR expression is a poor prognosis marker in endometrioid endometrial adenocarcinoma, while cytoplasmic methyl-HuR and nuclear phosphoHuR expressions are markers of better prognosis. This study highlights HuR as a promising potential therapeutic target, especially in treatment-resistant tumors, though further research is needed to understand the mechanisms regulating HuR subcellular localization and post-translational modifications.
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Affiliation(s)
- Judicaël Hotton
- Department of Gynecology and Obstetrics, CHRU de Nancy, Université de Lorraine, 54000 Nancy, France;
- INSERM U1256 NGERE, Université de Lorraine, 54500 Vandœuvre-lès-Nancy, France; (G.G.); (R.M.); (M.M.); (S.-F.B.-H.)
| | - Guillaume Gauchotte
- INSERM U1256 NGERE, Université de Lorraine, 54500 Vandœuvre-lès-Nancy, France; (G.G.); (R.M.); (M.M.); (S.-F.B.-H.)
- Department of Biopathology CHRU of Nancy, Institut de Cancérologie de Lorraine, BBB, CHRU de Nancy, Université de Lorraine, 54511 Vandœuvre-lès-Nancy, France
- Centre de Ressources Biologiques, BB-0033-00035, CHRU de Nancy, 54000 Nancy, France;
| | - Romane Mougel
- INSERM U1256 NGERE, Université de Lorraine, 54500 Vandœuvre-lès-Nancy, France; (G.G.); (R.M.); (M.M.); (S.-F.B.-H.)
- Department of Reproductive Medicine, CHRU de Nancy, Université de Lorraine, 54000 Nancy, France
| | - Mégane Migliorini
- INSERM U1256 NGERE, Université de Lorraine, 54500 Vandœuvre-lès-Nancy, France; (G.G.); (R.M.); (M.M.); (S.-F.B.-H.)
| | - Stéphanie Lacomme
- Centre de Ressources Biologiques, BB-0033-00035, CHRU de Nancy, 54000 Nancy, France;
| | - Shyue-Fang Battaglia-Hsu
- INSERM U1256 NGERE, Université de Lorraine, 54500 Vandœuvre-lès-Nancy, France; (G.G.); (R.M.); (M.M.); (S.-F.B.-H.)
| | - Mikaël Agopiantz
- INSERM U1256 NGERE, Université de Lorraine, 54500 Vandœuvre-lès-Nancy, France; (G.G.); (R.M.); (M.M.); (S.-F.B.-H.)
- Department of Reproductive Medicine, CHRU de Nancy, Université de Lorraine, 54000 Nancy, France
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Jia J, Zoeschg M, Barth H, Pulliainen AT, Ernst K. The Chaperonin TRiC/CCT Inhibitor HSF1A Protects Cells from Intoxication with Pertussis Toxin. Toxins (Basel) 2024; 16:36. [PMID: 38251252 PMCID: PMC10819386 DOI: 10.3390/toxins16010036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 01/03/2024] [Accepted: 01/07/2024] [Indexed: 01/23/2024] Open
Abstract
Pertussis toxin (PT) is a bacterial AB5-toxin produced by Bordetella pertussis and a major molecular determinant of pertussis, also known as whooping cough, a highly contagious respiratory disease. In this study, we investigate the protective effects of the chaperonin TRiC/CCT inhibitor, HSF1A, against PT-induced cell intoxication. TRiC/CCT is a chaperonin complex that facilitates the correct folding of proteins, preventing misfolding and aggregation, and maintaining cellular protein homeostasis. Previous research has demonstrated the significance of TRiC/CCT in the functionality of the Clostridioides difficile TcdB AB-toxin. Our findings reveal that HSF1A effectively reduces the levels of ADP-ribosylated Gαi, the specific substrate of PT, in PT-treated cells, without interfering with enzyme activity in vitro or the cellular binding of PT. Additionally, our study uncovers a novel interaction between PTS1 and the chaperonin complex subunit CCT5, which correlates with reduced PTS1 signaling in cells upon HSF1A treatment. Importantly, HSF1A mitigates the adverse effects of PT on cAMP signaling in cellular systems. These results provide valuable insights into the mechanisms of PT uptake and suggest a promising starting point for the development of innovative therapeutic strategies to counteract pertussis toxin-mediated pathogenicity.
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Affiliation(s)
- Jinfang Jia
- Institute of Experimental and Clinical Pharmacology, Toxicology and Pharmacology of Natural Products, Ulm University Medical Center, 89081 Ulm, Germany
| | - Manuel Zoeschg
- Institute of Experimental and Clinical Pharmacology, Toxicology and Pharmacology of Natural Products, Ulm University Medical Center, 89081 Ulm, Germany
| | - Holger Barth
- Institute of Experimental and Clinical Pharmacology, Toxicology and Pharmacology of Natural Products, Ulm University Medical Center, 89081 Ulm, Germany
| | | | - Katharina Ernst
- Institute of Experimental and Clinical Pharmacology, Toxicology and Pharmacology of Natural Products, Ulm University Medical Center, 89081 Ulm, Germany
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45
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Normoyle KP, Lillis KP, Staley KJ. Synthesis and Characterization of a Novel Concentration-Independent Fluorescent Chloride Indicator, ABP-Dextran, Optimized for Extracellular Chloride Measurement. Biomolecules 2024; 14:77. [PMID: 38254677 PMCID: PMC10813347 DOI: 10.3390/biom14010077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/24/2024] Open
Abstract
GABA, the primary inhibitory neurotransmitter, stimulates GABAA receptors (GABAARs) to increase the chloride conductance of the cytosolic membrane. The driving forces for membrane chloride currents are determined by the local differences between intracellular and extracellular chloride concentrations (Cli and Clo, respectively). While several strategies exist for the measurement of Cli, the field lacks tools for non-invasive measurement of Clo. We present the design and development of a fluorescent lifetime imaging (FLIM)-compatible small molecule, N(4-aminobutyl)phenanthridiunium (ABP) with the brightness, spectral features, sensitivity to chloride, and selectivity versus other anions to serve as a useful probe of Clo. ABP can be conjugated to dextran to ensure extracellular compartmentalization, and a second chloride-insensitive counter-label can be added for ratiometric imaging. We validate the utility of this novel sensor series in two sensor concentration-independent modes: FLIM or ratiometric intensity-based imaging.
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Affiliation(s)
- Kieran P. Normoyle
- Massachusetts General Hospital, Department of Neurology, 55 Fruit Street, Boston, MA 02114, USA; (K.P.N.); (K.P.L.)
- Harvard Medical School, Department of Neurology, 77 Louis Pasteur Avenue, Boston, MA 02115, USA
| | - Kyle P. Lillis
- Massachusetts General Hospital, Department of Neurology, 55 Fruit Street, Boston, MA 02114, USA; (K.P.N.); (K.P.L.)
- Harvard Medical School, Department of Neurology, 77 Louis Pasteur Avenue, Boston, MA 02115, USA
| | - Kevin J. Staley
- Massachusetts General Hospital, Department of Neurology, 55 Fruit Street, Boston, MA 02114, USA; (K.P.N.); (K.P.L.)
- Harvard Medical School, Department of Neurology, 77 Louis Pasteur Avenue, Boston, MA 02115, USA
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46
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Lin H, Suzuki K, Smith N, Li X, Nalbach L, Fuentes S, Spigelman AF, Dai XQ, Bautista A, Ferdaoussi M, Aggarwal S, Pepper AR, Roma LP, Ampofo E, Li WH, MacDonald PE. A role and mechanism for redox sensing by SENP1 in β-cell responses to high fat feeding. Nat Commun 2024; 15:334. [PMID: 38184650 PMCID: PMC10771529 DOI: 10.1038/s41467-023-44589-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 12/21/2023] [Indexed: 01/08/2024] Open
Abstract
Pancreatic β-cells respond to metabolic stress by upregulating insulin secretion, however the underlying mechanisms remain unclear. Here we show, in β-cells from overweight humans without diabetes and mice fed a high-fat diet for 2 days, insulin exocytosis and secretion are enhanced without increased Ca2+ influx. RNA-seq of sorted β-cells suggests altered metabolic pathways early following high fat diet, where we find increased basal oxygen consumption and proton leak, but a more reduced cytosolic redox state. Increased β-cell exocytosis after 2-day high fat diet is dependent on this reduced intracellular redox state and requires the sentrin-specific SUMO-protease-1. Mice with either pancreas- or β-cell-specific deletion of this fail to up-regulate exocytosis and become rapidly glucose intolerant after 2-day high fat diet. Mechanistically, redox-sensing by the SUMO-protease requires a thiol group at C535 which together with Zn+-binding suppresses basal protease activity and unrestrained β-cell exocytosis, and increases enzyme sensitivity to regulation by redox signals.
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Affiliation(s)
- Haopeng Lin
- Department of Pharmacology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- Guangzhou Laboratory, Guangzhou, 510005, Guangdong, China
| | - Kunimasa Suzuki
- Department of Pharmacology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Nancy Smith
- Department of Pharmacology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Xi Li
- Departments of Cell Biology and Biochemistry, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, 75390-9039, USA
| | - Lisa Nalbach
- Institute for Clinical & Experimental Surgery, Saarland University, Homburg/Saar, Germany
- Biophysics Department, Center for Human and Molecular Biology, Saarland University, Homburg/Saar, Germany
| | - Sonia Fuentes
- Departments of Cell Biology and Biochemistry, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, 75390-9039, USA
| | - Aliya F Spigelman
- Department of Pharmacology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Xiao-Qing Dai
- Department of Pharmacology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Austin Bautista
- Department of Pharmacology, University of Alberta, Edmonton, AB, T6G 2E1, Canada
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Mourad Ferdaoussi
- Faculty Saint-Jean, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Saloni Aggarwal
- Department of Surgery, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Andrew R Pepper
- Department of Surgery, University of Alberta, Edmonton, AB, T6G 2E1, Canada
| | - Leticia P Roma
- Biophysics Department, Center for Human and Molecular Biology, Saarland University, Homburg/Saar, Germany
| | - Emmanuel Ampofo
- Institute for Clinical & Experimental Surgery, Saarland University, Homburg/Saar, Germany
| | - Wen-Hong Li
- Departments of Cell Biology and Biochemistry, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd., Dallas, TX, 75390-9039, USA
| | - Patrick E MacDonald
- Department of Pharmacology, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
- Alberta Diabetes Institute, University of Alberta, Edmonton, AB, T6G 2E1, Canada.
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47
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Fukutani A, Westerblad H, Jardemark K, Bruton J. Ca 2+ and force during dynamic contractions in mouse intact skeletal muscle fibers. Sci Rep 2024; 14:689. [PMID: 38184730 PMCID: PMC10771458 DOI: 10.1038/s41598-023-51100-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/30/2023] [Indexed: 01/08/2024] Open
Abstract
Muscle fiber force production is determined by the excitation frequency of motor nerves, which induce transient increases in cytoplasmic free Ca2+ concentration ([Ca2+]i) and the force-generating capacity of the actomyosin cross-bridges. Previous studies suggest that, in addition to altered cross-bridge properties, force changes during dynamic (concentric or eccentric) contraction might be affected by Ca2+-dependent components. Here we investigated this by measuring [Ca2+]i and force in mouse muscle fibers undergoing isometric, concentric, and eccentric contractions. Intact single muscle fibers were dissected from the flexor digitorum brevis muscle of mice. Fibers were electrically activated isometrically at 30-100 Hz and after reaching the isometric force plateau, they were actively shortened or stretched. We calculated the ratio (relative changes) in force and [Ca2+]i attained in submaximal (30 Hz) and near-maximal (100 Hz) contractions under isometric or dynamic conditions. Tetanic [Ca2+]i was similar during isometric, concentric and eccentric phases of contraction at given stimulation frequencies while the forces were clearly different depending on the contraction types. The 30/100 Hz force ratio was significantly lower in the concentric (44.1 ± 20.3%) than in the isometric (50.3 ± 20.4%) condition (p = 0.005), whereas this ratio did not differ between eccentric and isometric conditions (p = 0.186). We conclude that the larger force decrease by decreasing the stimulation frequency during concentric than during isometric contraction is caused by decreased myofibrillar Ca2+ sensitivity, not by the decreased [Ca2+]i.
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Affiliation(s)
- Atsuki Fukutani
- Faculty of Sport and Health Science, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu, Shiga, 525-8577, Japan.
- Department of Physiology and Pharmacology, Karolinska Institute, Solna, Sweden.
| | - Håkan Westerblad
- Department of Physiology and Pharmacology, Karolinska Institute, Solna, Sweden
| | - Kent Jardemark
- Department of Physiology and Pharmacology, Karolinska Institute, Solna, Sweden
| | - Joseph Bruton
- Department of Physiology and Pharmacology, Karolinska Institute, Solna, Sweden
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48
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Kohler V, Kohler A, Berglund LL, Hao X, Gersing S, Imhof A, Nyström T, Höög JL, Ott M, Andréasson C, Büttner S. Nuclear Hsp104 safeguards the dormant translation machinery during quiescence. Nat Commun 2024; 15:315. [PMID: 38182580 PMCID: PMC10770042 DOI: 10.1038/s41467-023-44538-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 12/15/2023] [Indexed: 01/07/2024] Open
Abstract
The resilience of cellular proteostasis declines with age, which drives protein aggregation and compromises viability. The nucleus has emerged as a key quality control compartment that handles misfolded proteins produced by the cytosolic protein biosynthesis system. Here, we find that age-associated metabolic cues target the yeast protein disaggregase Hsp104 to the nucleus to maintain a functional nuclear proteome during quiescence. The switch to respiratory metabolism and the accompanying decrease in translation rates direct cytosolic Hsp104 to the nucleus to interact with latent translation initiation factor eIF2 and to suppress protein aggregation. Hindering Hsp104 from entering the nucleus in quiescent cells results in delayed re-entry into the cell cycle due to compromised resumption of protein synthesis. In sum, we report that cytosolic-nuclear partitioning of the Hsp104 disaggregase is a critical mechanism to protect the latent protein synthesis machinery during quiescence in yeast, ensuring the rapid restart of translation once nutrients are replenished.
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Affiliation(s)
- Verena Kohler
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden
- Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria
- Department of Molecular Biology, Umeå University, 90187, Umeå, Sweden
| | - Andreas Kohler
- Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria
- Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187, Umeå, Sweden
| | - Lisa Larsson Berglund
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Xinxin Hao
- Department of Microbiology and Immunology, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Sarah Gersing
- The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, 1165, Copenhagen, Denmark
| | - Axel Imhof
- Biomedical Center Munich, Faculty of Medicine, Ludwig Maximilian University of Munich, 82152, Planegg-Martinsried, Germany
| | - Thomas Nyström
- Department of Microbiology and Immunology, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Johanna L Höög
- Department of Chemistry and Molecular Biology, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Martin Ott
- Department of Biochemistry and Biophysics, Stockholm University, 10691, Stockholm, Sweden
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 40530, Gothenburg, Sweden
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden.
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, 10691, Stockholm, Sweden.
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49
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Humer C, Radiskovic T, Horváti K, Lindinger S, Groschner K, Romanin C, Höglinger C. Bidirectional Allosteric Coupling between PIP 2 Binding and the Pore of the Oncochannel TRPV6. Int J Mol Sci 2024; 25:618. [PMID: 38203789 PMCID: PMC10779433 DOI: 10.3390/ijms25010618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 12/31/2023] [Accepted: 01/01/2024] [Indexed: 01/12/2024] Open
Abstract
The epithelial ion channel TRPV6 plays a pivotal role in calcium homeostasis. Channel function is intricately regulated at different stages, involving the lipid phosphatidylinositol-4,5-bisphosphate (PIP2). Given that dysregulation of TRPV6 is associated with various diseases, including different types of cancer, there is a compelling need for its pharmacological targeting. Structural studies provide insights on how TRPV6 is affected by different inhibitors, with some binding to sites else occupied by lipids. These include the small molecule cis-22a, which, however, also binds to and thereby blocks the pore. By combining calcium imaging, electrophysiology and optogenetics, we identified residues within the pore and the lipid binding site that are relevant for regulation by cis-22a and PIP2 in a bidirectional manner. Yet, mutation of the cytosolic pore exit reduced inhibition by cis-22a but preserved sensitivity to PIP2 depletion. Our data underscore allosteric communication between the lipid binding site and the pore and vice versa for most sites along the pore.
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Affiliation(s)
- Christina Humer
- Institute of Biophysics, Johannes Kepler University Linz, 4020 Linz, Austria; (C.H.); (T.R.); (C.R.)
| | - Tamara Radiskovic
- Institute of Biophysics, Johannes Kepler University Linz, 4020 Linz, Austria; (C.H.); (T.R.); (C.R.)
| | - Kata Horváti
- Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, 1117 Budapest, Hungary;
| | - Sonja Lindinger
- Institute of Biophysics, Johannes Kepler University Linz, 4020 Linz, Austria; (C.H.); (T.R.); (C.R.)
| | - Klaus Groschner
- Gottfried Schatz Research Center, Division of Biophysics, Medical University of Graz, 8010 Graz, Austria;
| | - Christoph Romanin
- Institute of Biophysics, Johannes Kepler University Linz, 4020 Linz, Austria; (C.H.); (T.R.); (C.R.)
| | - Carmen Höglinger
- Institute of Biophysics, Johannes Kepler University Linz, 4020 Linz, Austria; (C.H.); (T.R.); (C.R.)
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50
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Mierke CT. Extracellular Matrix Cues Regulate Mechanosensing and Mechanotransduction of Cancer Cells. Cells 2024; 13:96. [PMID: 38201302 PMCID: PMC10777970 DOI: 10.3390/cells13010096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/29/2023] [Accepted: 01/01/2024] [Indexed: 01/12/2024] Open
Abstract
Extracellular biophysical properties have particular implications for a wide spectrum of cellular behaviors and functions, including growth, motility, differentiation, apoptosis, gene expression, cell-matrix and cell-cell adhesion, and signal transduction including mechanotransduction. Cells not only react to unambiguously mechanical cues from the extracellular matrix (ECM), but can occasionally manipulate the mechanical features of the matrix in parallel with biological characteristics, thus interfering with downstream matrix-based cues in both physiological and pathological processes. Bidirectional interactions between cells and (bio)materials in vitro can alter cell phenotype and mechanotransduction, as well as ECM structure, intentionally or unintentionally. Interactions between cell and matrix mechanics in vivo are of particular importance in a variety of diseases, including primarily cancer. Stiffness values between normal and cancerous tissue can range between 500 Pa (soft) and 48 kPa (stiff), respectively. Even the shear flow can increase from 0.1-1 dyn/cm2 (normal tissue) to 1-10 dyn/cm2 (cancerous tissue). There are currently many new areas of activity in tumor research on various biological length scales, which are highlighted in this review. Moreover, the complexity of interactions between ECM and cancer cells is reduced to common features of different tumors and the characteristics are highlighted to identify the main pathways of interaction. This all contributes to the standardization of mechanotransduction models and approaches, which, ultimately, increases the understanding of the complex interaction. Finally, both the in vitro and in vivo effects of this mechanics-biology pairing have key insights and implications for clinical practice in tumor treatment and, consequently, clinical translation.
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Affiliation(s)
- Claudia Tanja Mierke
- Biological Physics Division, Peter Debye Institute of Soft Matter Physics, Faculty of Physics and Earth Science, Leipzig University, Linnéstraße 5, 04103 Leipzig, Germany
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