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Toyoda S, Handa T, Yong H, Takahashi H, Shiwaku H. IMPDH2 forms spots at branching sites and distal ends of astrocyte stem processes. Genes Cells 2024; 29:150-158. [PMID: 38009721 DOI: 10.1111/gtc.13088] [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: 11/12/2023] [Accepted: 11/15/2023] [Indexed: 11/29/2023]
Abstract
Inosine monophosphate dehydrogenase (IMPDH) is a rate-limiting enzyme in the de novo GTP biosynthesis pathway. Recent studies suggest that IMPDH2, an isoform of IMPDH, can localize to specific subcellular compartments under certain conditions and regulate site-specific GTP availability and small GTPase activity in invasive cancer cells. However, it is unclear whether IMPDH2 plays a site-specific regulatory role in subcellular functions in healthy cells. In this study, we focused on brain cells and examined the localization pattern of IMPDH2. We discovered that IMPDH2 forms localized spots in the astrocytes of the adult mouse hippocampus. Further analysis of spot distribution in primary astrocyte cultures revealed that IMPDH2 spots are predominantly localized on branching sites and distal ends of astrocyte stem processes. Our findings suggest a potential unidentified role for IMPDH2 and GTP synthesis specifically at specialized nodes of astrocyte branches.
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Affiliation(s)
- Saori Toyoda
- Department of Psychiatry and Behavioral Sciences, Tokyo Medical and Dental University Graduate School, Tokyo, Japan
| | - Takehisa Handa
- Department of Psychiatry and Behavioral Sciences, Tokyo Medical and Dental University Graduate School, Tokyo, Japan
| | - Huang Yong
- Department of Neuropathology, Medical Research Institute and Center for Brain Integration Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hidehiko Takahashi
- Department of Psychiatry and Behavioral Sciences, Tokyo Medical and Dental University Graduate School, Tokyo, Japan
| | - Hiroki Shiwaku
- Department of Psychiatry and Behavioral Sciences, Tokyo Medical and Dental University Graduate School, Tokyo, Japan
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Ma S, Qiu Y, Zhang C. Cytoskeleton Rearrangement in Podocytopathies: An Update. Int J Mol Sci 2024; 25:647. [PMID: 38203817 PMCID: PMC10779434 DOI: 10.3390/ijms25010647] [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: 11/22/2023] [Revised: 12/14/2023] [Accepted: 01/01/2024] [Indexed: 01/12/2024] Open
Abstract
Podocyte injury can disrupt the glomerular filtration barrier (GFB), leading to podocytopathies that emphasize podocytes as the glomerulus's key organizer. The coordinated cytoskeleton is essential for supporting the elegant structure and complete functions of podocytes. Therefore, cytoskeleton rearrangement is closely related to the pathogenesis of podocytopathies. In podocytopathies, the rearrangement of the cytoskeleton refers to significant alterations in a string of slit diaphragm (SD) and focal adhesion proteins such as the signaling node nephrin, calcium influx via transient receptor potential channel 6 (TRPC6), and regulation of the Rho family, eventually leading to the disorganization of the original cytoskeletal architecture. Thus, it is imperative to focus on these proteins and signaling pathways to probe the cytoskeleton rearrangement in podocytopathies. In this review, we describe podocytopathies and the podocyte cytoskeleton, then discuss the molecular mechanisms involved in cytoskeleton rearrangement in podocytopathies and summarize the effects of currently existing drugs on regulating the podocyte cytoskeleton.
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Affiliation(s)
| | | | - Chun Zhang
- Department of Nephrology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430022, China; (S.M.); (Y.Q.)
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Wenkang H, Jingui L, Wei Z, Jiangli W, Zhengbin Y, Furong Z, Xuefeng Z. Multi-omics analysis reveals the microbial interactions of S. cerevisiae and L. plantarum on Suanyu, Chinese traditional fermented fish. Food Res Int 2023; 174:113525. [PMID: 37986426 DOI: 10.1016/j.foodres.2023.113525] [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: 07/16/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 11/22/2023]
Abstract
S. cerevisiae and L. plantarum play important roles in Suanyu fermentation. This study investigated the interaction between S. cerevisiae and L. plantarum during fermentation and its impact on metabolic pathways. Co-culturing S. cerevisiae and L. plantarum increased pH to 5.72, reduced TVB-N to 9.47 mg/mL, and achieved high utilization rates of sugars (98.9%) and proteins (73.7%). During microbial interactions, S. cerevisiae and L. plantarum produced antibiotics, including phenyllactate and Gentamicin C1a, inhibiting the growth of each other. S. cerevisiae used S-adenosyl-l-methionine to counteract acid production of L. plantarum, establishing dominance in Suanyu fermentation. Microbial interactions influenced carbohydrate and energy metabolism pathways, such as nicotinate and nicotinamide metabolism and purine metabolism. S. cerevisiae significantly impacted gene expression in protein synthesis and cell growth pathways, including ribosome, SNARE interactions, basal transcription factors, and MAPK signaling. These findings offer insights into microbial interactions and metabolic processes during Suanyu fermentation.
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Affiliation(s)
- Hu Wenkang
- College of Life Sciences, Guizhou University, Guiyang, China; Guizhou Provincial Key Laboratory of Agricultural and Animal Products Storage and Processing, Guiyang, China
| | - Liu Jingui
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China; Guizhou Provincial Key Laboratory of Agricultural and Animal Products Storage and Processing, Guiyang, China
| | - Zhang Wei
- College of Food Science and Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Wu Jiangli
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China; Guizhou Provincial Key Laboratory of Agricultural and Animal Products Storage and Processing, Guiyang, China
| | - Yang Zhengbin
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China; Guizhou Provincial Key Laboratory of Agricultural and Animal Products Storage and Processing, Guiyang, China
| | - Zhang Furong
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China; Guizhou Provincial Key Laboratory of Agricultural and Animal Products Storage and Processing, Guiyang, China
| | - Zeng Xuefeng
- School of Liquor and Food Engineering, Guizhou University, Guiyang, China; Guizhou Provincial Key Laboratory of Agricultural and Animal Products Storage and Processing, Guiyang, China.
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Li K, Xia J, Liu CG, Zhao XQ, Bai FW. Intracellular accumulation of c-di-GMP and its regulation on self-flocculation of the bacterial cells of Zymomonas mobilis. Biotechnol Bioeng 2023; 120:3234-3243. [PMID: 37526330 DOI: 10.1002/bit.28513] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/26/2023] [Accepted: 07/17/2023] [Indexed: 08/02/2023]
Abstract
Zymomonas mobilis is an emerging chassis for being engineered to produce bulk products due to its unique glycolysis through the Entner-Doudoroff pathway with less ATP produced for lower biomass accumulation and higher product yield. When self-flocculated, the bacterial cells are more productive, since they can self-immobilize within bioreactors for high density, and are more tolerant to stresses for higher product titers, but this morphology needs to be controlled properly to avoid internal mass transfer limitation associated with their strong self-flocculation. Herewith we explored the regulation of cyclic diguanosine monophosphate (c-di-GMP) on self-flocculation of the bacterial cells through activating cellulose biosynthesis. While ZMO1365 and ZMO0919 with GGDEF domains for diguanylate cyclase activity catalyze c-di-GMP biosynthesis, ZMO1487 with an EAL domain for phosphodiesterase activity catalyzes c-di-GMP degradation, but ZMO1055 and ZMO0401 contain the dual domains with phosphodiesterase activity predominated. Since c-di-GMP is synthesized from GTP, the intracellular accumulation of this signal molecule through deactivating phosphodiesterase activity is preferred for activating cellulose biosynthesis to flocculate the bacterial cells, because such a strategy exerts less perturbance on intracellular processes regulated by GTP. These discoveries are significant for not only engineering unicellular Z. mobilis strains with the self-flocculating morphology to boost production but also understanding mechanism underlying c-di-GMP biosynthesis and degradation in the bacterium.
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Affiliation(s)
- Kai Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Science, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Juan Xia
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Science, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Science, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Science, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Feng-Wu Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Science, School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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de Sousa DMB, Poupardin R, Villeda SA, Schroer AB, Fröhlich T, Frey V, Staffen W, Mrowetz H, Altendorfer B, Unger MS, Iglseder B, Paulweber B, Trinka E, Cadamuro J, Drerup M, Schallmoser K, Aigner L, Kniewallner KM. The platelet transcriptome and proteome in Alzheimer's disease and aging: an exploratory cross-sectional study. Front Mol Biosci 2023; 10:1196083. [PMID: 37457829 PMCID: PMC10348715 DOI: 10.3389/fmolb.2023.1196083] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/05/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction: Alzheimer's disease (AD) and aging are associated with platelet hyperactivity. However, the mechanisms underlying abnormal platelet function in AD and aging are yet poorly understood. Methods: To explore the molecular profile of AD and aged platelets, we investigated platelet activation (i.e., CD62P expression), proteome and transcriptome in AD patients, non-demented elderly, and young individuals as controls. Results: AD, aged and young individuals showed similar levels of platelet activation based on CD62P expression. However, AD and aged individuals had a proteomic signature suggestive of increased platelet activation compared with young controls. Transcriptomic profiling suggested the dysregulation of proteolytic machinery involved in regulating platelet function, particularly the ubiquitin-proteasome system in AD and autophagy in aging. The functional implication of these transcriptomic alterations remains unclear and requires further investigation. Discussion: Our data strengthen the evidence of enhanced platelet activation in aging and provide a first glimpse of the platelet transcriptomic changes occurring in AD.
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Affiliation(s)
- Diana M. Bessa de Sousa
- Institute of Molecular Regenerative Medicine, Paracelsus Medical University, Salzburg, Austria
- Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Salzburg, Austria
| | - Rodolphe Poupardin
- Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Salzburg, Austria
- Experimental and Clinical Cell Therapy Institute, Paracelsus Medical University, Salzburg, Austria
| | - Saul A. Villeda
- Department of Anatomy, University of California San Francisco, San Francisco, CA, United States
| | - Adam B. Schroer
- Department of Anatomy, University of California San Francisco, San Francisco, CA, United States
| | - Thomas Fröhlich
- Laboratory of Functional Genome Analysis (LAFUGA), Gene Center, Ludwig Maximilian University of Munich, Munich, Germany
| | - Vanessa Frey
- Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Salzburg, Austria
- Department of Neurology, Christian Doppler Clinic, Paracelsus Medical University, Salzburg, Austria
| | - Wolfgang Staffen
- Department of Neurology, Christian Doppler Clinic, Paracelsus Medical University, Salzburg, Austria
| | - Heike Mrowetz
- Institute of Molecular Regenerative Medicine, Paracelsus Medical University, Salzburg, Austria
- Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Salzburg, Austria
| | - Barbara Altendorfer
- Institute of Molecular Regenerative Medicine, Paracelsus Medical University, Salzburg, Austria
- Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Salzburg, Austria
| | - Michael S. Unger
- Institute of Molecular Regenerative Medicine, Paracelsus Medical University, Salzburg, Austria
- Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Salzburg, Austria
| | - Bernhard Iglseder
- Department of Neurology, Christian Doppler Clinic, Paracelsus Medical University, Salzburg, Austria
| | - Bernhard Paulweber
- Department of Internal Medicine, St. Johanns University Hospital, Paracelsus Medical University, Salzburg, Austria
| | - Eugen Trinka
- Department of Neurology, Christian Doppler Clinic, Paracelsus Medical University, Salzburg, Austria
- Department of Public Health, Health Services Research and Health Technology Assessment, UMIT-University for Health Sciences, Medical Informatics and Technology, Hall in Tirol, Austria
- Neuroscience Institute, Christian Doppler University Hospital, Paracelsus Medical University and Centre for Cognitive Neuroscience Salzburg, Salzburg, Austria
| | - Janne Cadamuro
- Department of Laboratory Medicine, University Hospital SALK, Salzburg, Austria
| | - Martin Drerup
- Department of Urology, Paracelsus Medical University, Salzburg, Austria
| | - Katharina Schallmoser
- Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Salzburg, Austria
- Department of Transfusion Medicine, Paracelsus Medical University, Salzburg, Austria
| | - Ludwig Aigner
- Institute of Molecular Regenerative Medicine, Paracelsus Medical University, Salzburg, Austria
- Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Salzburg, Austria
- Austrian Cluster for Tissue Regeneration, Vienna, Austria
| | - Kathrin M. Kniewallner
- Institute of Molecular Regenerative Medicine, Paracelsus Medical University, Salzburg, Austria
- Spinal Cord Injury and Tissue Regeneration Center Salzburg (SCI-TReCS), Paracelsus Medical University, Salzburg, Austria
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Bartas M, Slychko K, Červeň J, Pečinka P, Arndt-Jovin DJ, Jovin TM. Extensive Bioinformatics Analyses Reveal a Phylogenetically Conserved Winged Helix (WH) Domain (Zτ) of Topoisomerase IIα, Elucidating Its Very High Affinity for Left-Handed Z-DNA and Suggesting Novel Putative Functions. Int J Mol Sci 2023; 24:10740. [PMID: 37445918 DOI: 10.3390/ijms241310740] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 06/13/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
The dynamic processes operating on genomic DNA, such as gene expression and cellular division, lead inexorably to topological challenges in the form of entanglements, catenanes, knots, "bubbles", R-loops, and other outcomes of supercoiling and helical disruption. The resolution of toxic topological stress is the function attributed to DNA topoisomerases. A prominent example is the negative supercoiling (nsc) trailing processive enzymes such as DNA and RNA polymerases. The multiple equilibrium states that nscDNA can adopt by redistribution of helical twist and writhe include the left-handed double-helical conformation known as Z-DNA. Thirty years ago, one of our labs isolated a protein from Drosophila cells and embryos with a 100-fold greater affinity for Z-DNA than for B-DNA, and identified it as topoisomerase II (gene Top2, orthologous to the human UniProt proteins TOP2A and TOP2B). GTP increased the affinity and selectivity for Z-DNA even further and also led to inhibition of the isomerase enzymatic activity. An allosteric mechanism was proposed, in which topoII acts as a Z-DNA-binding protein (ZBP) to stabilize given states of topological (sub)domains and associated multiprotein complexes. We have now explored this possibility by comprehensive bioinformatic analyses of the available protein sequences of topoII representing organisms covering the whole tree of life. Multiple alignment of these sequences revealed an extremely high level of evolutionary conservation, including a winged-helix protein segment, here denoted as Zτ, constituting the putative structural homolog of Zα, the canonical Z-DNA/Z-RNA binding domain previously identified in the interferon-inducible RNA Adenosine-to-Inosine-editing deaminase, ADAR1p150. In contrast to Zα, which is separate from the protein segment responsible for catalysis, Zτ encompasses the active site tyrosine of topoII; a GTP-binding site and a GxxG sequence motif are in close proximity. Quantitative Zτ-Zα similarity comparisons and molecular docking with interaction scoring further supported the "B-Z-topoII hypothesis" and has led to an expanded mechanism for topoII function incorporating the recognition of Z-DNA segments ("Z-flipons") as an inherent and essential element. We further propose that the two Zτ domains of the topoII homodimer exhibit a single-turnover "conformase" activity on given G(ate) B-DNA segments ("Z-flipins"), inducing their transition to the left-handed Z-conformation. Inasmuch as the topoII-Z-DNA complexes are isomerase inactive, we infer that they fulfill important structural roles in key processes such as mitosis. Topoisomerases are preeminent targets of anti-cancer drug discovery, and we anticipate that detailed elucidation of their structural-functional interactions with Z-DNA and GTP will facilitate the design of novel, more potent and selective anti-cancer chemotherapeutic agents.
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Affiliation(s)
- Martin Bartas
- Department of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Kristyna Slychko
- Department of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Jiří Červeň
- Department of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Petr Pečinka
- Department of Biology and Ecology, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Donna J Arndt-Jovin
- Emeritus Laboratory of Cellular Dynamics, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Thomas M Jovin
- Emeritus Laboratory of Cellular Dynamics, Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
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Ding L, Sheriff S, Sontz RA, Merchant JL. Schlafen4 +-MDSC in Helicobacter-induced gastric metaplasia reveals role for GTPases. Front Immunol 2023; 14:1139391. [PMID: 37334372 PMCID: PMC10272601 DOI: 10.3389/fimmu.2023.1139391] [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: 01/06/2023] [Accepted: 05/22/2023] [Indexed: 06/20/2023] Open
Abstract
Introduction MDSCs express SCHLAFEN 4 (SLFN4) in Helicobacter-infected stomachs coincident with spasmolytic polypeptide-expressing metaplasia (SPEM), a precursor of gastric cancer. We aimed to characterize SLFN4+ cell identity and the role of Slfn4 in these cells. Methods Single-cell RNA sequencing was performed on immune cells sorted from PBMCs and stomachs prepared from uninfected and 6-month H. felis-infected mice. Knockdown of Slfn4 by siRNA or PDE5/6 inhibition by sildenafil were performed in vitro. Intracellular ATP/GTP levels and GTPase activity of immunoprecipitated Slfn4 complexes were measured using the GTPase-Glo assay kit. The intracellular level of ROS was quantified by the DCF-DA fluorescent staining, and apoptosis was determined by cleaved Caspase-3 and Annexin V expression. Gli1CreERT2 x Slfn4 fl/fl mice were generated and infected with H. felis. Sildenafil was administered twice over 2 weeks by gavaging H. felis infected mice ~4 months after inoculation once SPEM had developed. Results Slfn4 was highly induced in both monocytic and granulocytic MDSCs from infected stomachs. Both Slfn4 +-MDSC populations exhibited strong transcriptional signatures for type-I interferon responsive GTPases and exhibited T cell suppressor function. SLFN4-containing protein complexes immunoprecipitated from myeloid cell cultures treated with IFNa exhibited GTPase activity. Knocking down Slfn4 or PDE5/6 inhibition with sildenafil blocked IFNa induction of GTP, SLFN4 and NOS2. Moreover, IFNa induction of Slfn +-MDSC function was inhibited by inducing their reactive oxygen species (ROS) production and apoptosis through protein kinase G activation. Accordingly, in vivo disruption of Slfn4 in Gli1CreERT2 x Slfn4 fl/fl mice or pharmacologic inhibition by sildenafil after Helicobacter infection also suppressed SLFN4 and NOS2, reversed T cell suppression and mitigated SPEM development. Conclusion Taken together, SLFN4 regulates the activity of the GTPase pathway in MDSCs and precludes these cells from succumbing to the massive ROS generation when they acquire MDSC function.
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Affiliation(s)
| | | | | | - Juanita L. Merchant
- Department of Medicine-Gastroenterology, University of Arizona, Tucson, AZ, United States
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