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Nie X, Li Q, Chen X, Onyango S, Xie J, Nie S. Bacterial extracellular vesicles: Vital contributors to physiology from bacteria to host. Microbiol Res 2024; 284:127733. [PMID: 38678680 DOI: 10.1016/j.micres.2024.127733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 05/01/2024]
Abstract
Bacterial extracellular vesicles (bEVs) represent spherical particles with diameters ranging from 20 to 400 nm filled with multiple parental bacteria-derived components, including proteins, nucleic acids, lipids, and other biomolecules. The production of bEVs facilitates bacteria interacting with their environment and exerting biological functions. It is increasingly evident that the bEVs play integral roles in both bacterial and host physiology, contributing to environmental adaptations to functioning as health promoters for their hosts. This review highlights the current state of knowledge on the composition, biogenesis, and diversity of bEVs and the mechanisms by which different bEVs elicit effects on bacterial physiology and host health. We posit that an in-depth exploration of the mechanistic aspects of bEVs activity is essential to elucidate their health-promoting effects on the host and may facilitate the translation of bEVs into applications as novel natural biological nanomaterials.
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Affiliation(s)
- Xinke Nie
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Qiqiong Li
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | - Xinyang Chen
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China
| | | | - Junhua Xie
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China.
| | - Shaoping Nie
- State Key Laboratory of Food Science and Resources, Nanchang University, Nanchang 330047, China.
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2
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Adeleye SA, Yadavalli SS. Queuosine biosynthetic enzyme, QueE moonlights as a cell division regulator. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.31.565030. [PMID: 37961685 PMCID: PMC10635034 DOI: 10.1101/2023.10.31.565030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
In many organisms, stress responses to adverse environments can trigger secondary functions of certain proteins by altering protein levels, localization, activity, or interaction partners. Escherichia coli cells respond to the presence of specific cationic antimicrobial peptides by strongly activating the PhoQ/PhoP two-component signaling system, which regulates genes important for growth under this stress. As part of this pathway, a biosynthetic enzyme called QueE, which catalyzes a step in the formation of queuosine (Q) tRNA modification is upregulated. When cellular QueE levels are high, it co-localizes with the central cell division protein FtsZ at the septal site, blocking division and resulting in filamentous growth. Here we show that QueE affects cell size in a dose-dependent manner. Using alanine scanning mutagenesis of amino acids in the catalytic active site, we pinpoint particular residues in QueE that contribute distinctly to each of its functions - Q biosynthesis or regulation of cell division, establishing QueE as a moonlighting protein. We further show that QueE orthologs from enterobacteria like Salmonella typhimurium and Klebsiella pneumoniae also cause filamentation in these organisms, but the more distant counterparts from Pseudomonas aeruginosa and Bacillus subtilis lack this ability. By comparative analysis of E. coli QueE with distant orthologs, we elucidate a unique region in this protein that is responsible for QueEs secondary function as a cell division regulator. A dual-function protein like QueE is an exception to the conventional model of one gene, one enzyme, one function, which has divergent roles across a range of fundamental cellular processes including RNA modification and translation to cell division and stress response.
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3
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Adeleye SA, Yadavalli SS. Queuosine biosynthetic enzyme, QueE moonlights as a cell division regulator. PLoS Genet 2024; 20:e1011287. [PMID: 38768229 PMCID: PMC11142719 DOI: 10.1371/journal.pgen.1011287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/31/2024] [Accepted: 05/03/2024] [Indexed: 05/22/2024] Open
Abstract
In many organisms, stress responses to adverse environments can trigger secondary functions of certain proteins by altering protein levels, localization, activity, or interaction partners. Escherichia coli cells respond to the presence of specific cationic antimicrobial peptides by strongly activating the PhoQ/PhoP two-component signaling system, which regulates genes important for growth under this stress. As part of this pathway, a biosynthetic enzyme called QueE, which catalyzes a step in the formation of queuosine (Q) tRNA modification is upregulated. When cellular QueE levels are high, it co-localizes with the central cell division protein FtsZ at the septal site, blocking division and resulting in filamentous growth. Here we show that QueE affects cell size in a dose-dependent manner. Using alanine scanning mutagenesis of amino acids in the catalytic active site, we pinpoint residues in QueE that contribute distinctly to each of its functions-Q biosynthesis or regulation of cell division, establishing QueE as a moonlighting protein. We further show that QueE orthologs from enterobacteria like Salmonella typhimurium and Klebsiella pneumoniae also cause filamentation in these organisms, but the more distant counterparts from Pseudomonas aeruginosa and Bacillus subtilis lack this ability. By comparative analysis of E. coli QueE with distant orthologs, we elucidate a unique region in this protein that is responsible for QueE's secondary function as a cell division regulator. A dual-function protein like QueE is an exception to the conventional model of "one gene, one enzyme, one function", which has divergent roles across a range of fundamental cellular processes including RNA modification and translation to cell division and stress response.
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Affiliation(s)
- Samuel A. Adeleye
- Waksman Institute of Microbiology and Department of Genetics, Rutgers University, Piscataway New Jersey, United States of America
| | - Srujana S. Yadavalli
- Waksman Institute of Microbiology and Department of Genetics, Rutgers University, Piscataway New Jersey, United States of America
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4
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Hoskisson PA, Barona-Gómez F, Rozen DE. Phenotypic heterogeneity in Streptomyces colonies. Curr Opin Microbiol 2024; 78:102448. [PMID: 38447313 DOI: 10.1016/j.mib.2024.102448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/30/2024] [Accepted: 02/06/2024] [Indexed: 03/08/2024]
Abstract
Streptomyces are a large genus of multicellular bacteria best known for their prolific production of bioactive natural products. In addition, they play key roles in the mineralisation of insoluble resources, such as chitin and cellulose. Because of their multicellular mode of growth, colonies of interconnected hyphae extend over a large area that may experience different conditions in different parts of the colony. Here, we argue that within-colony phenotypic heterogeneity can allow colonies to simultaneously respond to divergent inputs from resources or competitors that are spatially and temporally dynamic. We discuss causal drivers of heterogeneity, including competitors, precursor availability, metabolic diversity and division of labour, that facilitate divergent phenotypes within Streptomyces colonies. We discuss the adaptive causes and consequences of within-colony heterogeneity, highlight current knowledge (gaps) and outline key questions for future studies.
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Affiliation(s)
- Paul A Hoskisson
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, 161 Cathedral Street, Glasgow G4 0RE, UK
| | | | - Daniel E Rozen
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, The Netherlands.
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5
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Lin C, Yu M, Wu X, Wang H, Wei M, Zhang L. Targeting Moonlighting Enzymes in Cancer. Molecules 2024; 29:1573. [PMID: 38611852 PMCID: PMC11013064 DOI: 10.3390/molecules29071573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 03/28/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Moonlighting enzymes are multifunctional proteins that perform multiple functions beyond their primary role as catalytic enzymes. Extensive research and clinical practice have demonstrated their pivotal roles in the development and progression of cancer, making them promising targets for drug development. This article delves into multiple notable moonlighting enzymes, including GSK-3, GAPDH, and ENO1, and with a particular emphasis on an enigmatic phosphatase, PTP4A3. We scrutinize their distinct roles in cancer and the mechanisms that dictate their ability to switch roles. Lastly, we discuss the potential of an innovative approach to develop drugs targeting these moonlighting enzymes: target protein degradation. This strategy holds promise for effectively tackling moonlighting enzymes in the context of cancer therapy.
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Affiliation(s)
- Chunxu Lin
- Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou 510006, China; (C.L.); (M.Y.); (X.W.); (H.W.)
| | - Mingyang Yu
- Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou 510006, China; (C.L.); (M.Y.); (X.W.); (H.W.)
| | - Ximei Wu
- Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou 510006, China; (C.L.); (M.Y.); (X.W.); (H.W.)
| | - Hui Wang
- Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou 510006, China; (C.L.); (M.Y.); (X.W.); (H.W.)
| | - Min Wei
- Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou 510006, China; (C.L.); (M.Y.); (X.W.); (H.W.)
| | - Luyong Zhang
- Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou 510006, China; (C.L.); (M.Y.); (X.W.); (H.W.)
- Jiangsu Key Laboratory of Drug Screening, China Pharmaceutical University, Nanjing 210009, China
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6
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Balint D, Brito IL. Human-gut bacterial protein-protein interactions: understudied but impactful to human health. Trends Microbiol 2024; 32:325-332. [PMID: 37805334 PMCID: PMC10990813 DOI: 10.1016/j.tim.2023.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 10/09/2023]
Abstract
The human gut microbiome is associated with a wide range of diseases; yet, the mechanisms these microbes use to influence human health are not fully understood. Protein-protein interactions (PPIs) are increasingly identified as a potential mechanism by which gut microbiota influence their human hosts. Similar to some PPIs observed in pathogens, many disease-relevant human-gut bacterial PPIs function by interacting with components of the immune system or the gut barrier. Here, we highlight recent advances in these two areas. It is our opinion that there is a vastly unexplored network of human-gut bacterial PPIs that contribute to the prevention or pathogenesis of various diseases and that future research is warranted to expand PPI discovery.
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Affiliation(s)
- Diana Balint
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA
| | - Ilana L Brito
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
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7
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Caron-Godon CA, Collington E, Wolf JL, Coletta G, Glerum DM. More than Just Bread and Wine: Using Yeast to Understand Inherited Cytochrome Oxidase Deficiencies in Humans. Int J Mol Sci 2024; 25:3814. [PMID: 38612624 PMCID: PMC11011759 DOI: 10.3390/ijms25073814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 03/26/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Inherited defects in cytochrome c oxidase (COX) are associated with a substantial subset of diseases adversely affecting the structure and function of the mitochondrial respiratory chain. This multi-subunit enzyme consists of 14 subunits and numerous cofactors, and it requires the function of some 30 proteins to assemble. COX assembly was first shown to be the primary defect in the majority of COX deficiencies 36 years ago. Over the last three decades, most COX assembly genes have been identified in the yeast Saccharomyces cerevisiae, and studies in yeast have proven instrumental in testing the impact of mutations identified in patients with a specific COX deficiency. The advent of accessible genome-wide sequencing capabilities has led to more patient mutations being identified, with the subsequent identification of several new COX assembly factors. However, the lack of genotype-phenotype correlations and the large number of genes involved in generating a functional COX mean that functional studies must be undertaken to assign a genetic variant as being causal. In this review, we provide a brief overview of the use of yeast as a model system and briefly compare the COX assembly process in yeast and humans. We focus primarily on the studies in yeast that have allowed us to both identify new COX assembly factors and to demonstrate the pathogenicity of a subset of the mutations that have been identified in patients with inherited defects in COX. We conclude with an overview of the areas in which studies in yeast are likely to continue to contribute to progress in understanding disease arising from inherited COX deficiencies.
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Affiliation(s)
- Chenelle A. Caron-Godon
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (C.A.C.-G.); (E.C.); (J.L.W.); (G.C.)
| | - Emma Collington
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (C.A.C.-G.); (E.C.); (J.L.W.); (G.C.)
| | - Jessica L. Wolf
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (C.A.C.-G.); (E.C.); (J.L.W.); (G.C.)
| | - Genna Coletta
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (C.A.C.-G.); (E.C.); (J.L.W.); (G.C.)
| | - D. Moira Glerum
- Department of Biology, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (C.A.C.-G.); (E.C.); (J.L.W.); (G.C.)
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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8
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Schieweck R, Götz M. Pan-cellular organelles and suborganelles-from common functions to cellular diversity? Genes Dev 2024; 38:98-114. [PMID: 38485267 PMCID: PMC10982711 DOI: 10.1101/gad.351337.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Cell diversification is at the base of increasing multicellular organism complexity in phylogeny achieved during ontogeny. However, there are also functions common to all cells, such as cell division, cell migration, translation, endocytosis, exocytosis, etc. Here we revisit the organelles involved in such common functions, reviewing recent evidence of unexpected differences of proteins at these organelles. For instance, centrosomes or mitochondria differ significantly in their protein composition in different, sometimes closely related, cell types. This has relevance for development and disease. Particularly striking is the high amount and diversity of RNA-binding proteins at these and other organelles, which brings us to review the evidence for RNA at different organelles and suborganelles. We include a discussion about (sub)organelles involved in translation, such as the nucleolus and ribosomes, for which unexpected cell type-specific diversity has also been reported. We propose here that the heterogeneity of these organelles and compartments represents a novel mechanism for regulating cell diversity. One reason is that protein functions can be multiplied by their different contributions in distinct organelles, as also exemplified by proteins with moonlighting function. The specialized organelles still perform pan-cellular functions but in a cell type-specific mode, as discussed here for centrosomes, mitochondria, vesicles, and other organelles. These can serve as regulatory hubs for the storage and transport of specific and functionally important regulators. In this way, they can control cell differentiation, plasticity, and survival. We further include examples highlighting the relevance for disease and propose to examine organelles in many more cell types for their possible differences with functional relevance.
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Affiliation(s)
- Rico Schieweck
- Institute of Biophysics, National Research Council (CNR) Unit at Trento, 38123 Povo, Italy;
- Biomedical Center (BMC), Department of Physiological Genomics, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
| | - Magdalena Götz
- Biomedical Center (BMC), Department of Physiological Genomics, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany;
- Institute of Stem Cell Research, Helmholtz Center Munich, German Research Center for Environmental Health, 82152 Planegg-Martinsried, Germany
- SYNERGY, Excellence Cluster of Systems Neurology, Biomedical Center, Ludwig-Maximilians-University, 82152 Planegg-Martinsried, Germany
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9
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Bernardini A, Tora L. Co-translational Assembly Pathways of Nuclear Multiprotein Complexes Involved in the Regulation of Gene Transcription. J Mol Biol 2024; 436:168382. [PMID: 38061625 DOI: 10.1016/j.jmb.2023.168382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/24/2023] [Accepted: 12/01/2023] [Indexed: 12/18/2023]
Abstract
Most factors that regulate gene transcription in eukaryotic cells are multimeric, often large, protein complexes. The understanding of the biogenesis pathways of such large and heterogeneous protein assemblies, as well as the dimerization partner choice among transcription factors, is crucial to interpret and control gene expression programs and consequent cell fate decisions. Co-translational assembly (Co-TA) is thought to play key roles in the biogenesis of protein complexes by directing complex formation during protein synthesis. In this review we discuss the principles of Co-TA with a special focus for the assembly of transcription regulatory complexes. We outline the expected molecular advantages of establishing co-translational interactions, pointing at the available, or missing, evidence for each of them. We hypothesize different molecular mechanisms based on Co-TA to explain the allocation "dilemma" of paralog proteins and subunits shared by different transcription complexes. By taking as a paradigm the different assembly pathways employed by three related transcription regulatory complexes (TFIID, SAGA and ATAC), we discuss alternative Co-TA strategies for nuclear multiprotein complexes and the widespread - yet specific - use of Co-TA for the formation of nuclear complexes involved in gene transcription. Ultimately, we outlined a series of open questions which demand well-defined lines of research to investigate the principles of gene regulation that rely on the coordinated assembly of protein complexes.
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Affiliation(s)
- Andrea Bernardini
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964 Illkirch, France; Université de Strasbourg, Illkirch, France.
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964 Illkirch, France; Université de Strasbourg, Illkirch, France.
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10
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Nawn D, Hassan SS, Sil M, Ghosh A, Goswami A, Basu P, Dayhoff GW, Lundstrom K, Uversky VN. The distal-proximal relationships among the human moonlighting proteins: Evolutionary hotspots and Darwinian checkpoints. Int J Biol Macromol 2024; 259:128998. [PMID: 38176503 DOI: 10.1016/j.ijbiomac.2023.128998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024]
Abstract
Moonlighting proteins, known for their ability to perform multiple, often unrelated functions within a single polypeptide chain, challenge the traditional "one gene, one protein, one function" paradigm. As organisms evolved, their genomes remained relatively stable in size, but the introduction of post-translational modifications and sub-strategies like protein promiscuity and intrinsic disorder enabled multifunctionality. Enzymes, in particular, exemplify this phenomenon, engaging in unrelated processes alongside their primary catalytic roles. This study employs a systematic, quantitative informatics approach to shed light on human moonlighting protein sequences. Phylogenetic analyses of human moonlighting proteins are presented, elucidating the distal-proximal relationships among these proteins based on sequence-derived quantitative features. The findings unveil the captivating world of human moonlighting proteins, urging further investigations in the emerging field of moonlighting proteomics, with the potential for significant contributions to our understanding of multifunctional proteins and their roles in diverse cellular processes and diseases.
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Affiliation(s)
- Debaleena Nawn
- Biological Science Division, Indian Statistical Institute, 203 B.T Road, Kolkata, 700108, West Bengal, India; Indian Research Institute for Integrated Medicine (IRIIM), Unsani, Howrah, 711302, West Bengal, India.
| | - Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, West Bengal, India.
| | - Moumita Sil
- Biological Science Division, Indian Statistical Institute, 203 B.T Road, Kolkata, 700108, West Bengal, India.
| | - Ankita Ghosh
- Biological Science Division, Indian Statistical Institute, 203 B.T Road, Kolkata, 700108, West Bengal, India.
| | - Arunava Goswami
- Biological Science Division, Indian Statistical Institute, 203 B.T Road, Kolkata, 700108, West Bengal, India.
| | - Pallab Basu
- School of Physics, University of the Witwatersrand, Johannesburg, Braamfontein 2000, South Africa; Woxsen School of Sciences, Woxsen University, Hyderabad 500 033, Telangana, India.
| | - Guy W Dayhoff
- Department of Chemistry, University of South Florida, Tampa, FL 33612, USA.
| | | | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
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Chelladurai M, Xu D, Izraely S, Ben-Menachem S, Bengaiev R, Sagi-Assif O, Yuan W, Pasmanik Chor M, Hoon DS, Lu W, Witz IP. A heterodimer of α and β hemoglobin chains functions as an innate anticancer agent. Int J Cancer 2024; 154:561-572. [PMID: 37675956 DOI: 10.1002/ijc.34702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 07/25/2023] [Accepted: 08/01/2023] [Indexed: 09/08/2023]
Abstract
Metastatic (as well as tumor) microenvironments contain both cancer-promoting and cancer-restraining factors. The balance between these opposing forces determines the fate of cancer cells that disseminate to secondary organ sites. In search for microenvironmental drivers or inhibitors of metastasis, we identified, in a previous study, the beta subunit of hemoglobin (HBB) as a lung-derived antimetastatic factor. In the present study, exploring mechanisms regulating melanoma brain metastasis, we discovered that brain-derived factors restrain proliferation and induce apoptosis and necrosis of brain-metastasizing melanoma cells. Employing various purification procedures, we identified a heterodimer composed of hemoglobin alpha and beta chains that perform these antimetastatic functions. Neither the alpha nor the beta subunit alone was inhibitory. An alpha/beta chain dimer chemically purified from human hemoglobin inhibited the cell viability of primary melanomas, melanoma brain metastasis (MBM), and breast cancer cell lines. The dimer-induced DNA damage, cell cycle arrest at the SubG1 phase, apoptosis, and significant necrosis in four MBM cell lines. Proteomic analysis of dimer-treated MBM cells revealed that the dimer downregulates the expression of BRD4, GAB2, and IRS2 proteins, playing crucial roles in cancer cell sustainability and progression. Thus, we hypothesize that the hemoglobin dimer functions as a resistance factor against brain-metastasizing cancer cells.
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Affiliation(s)
- Maharrish Chelladurai
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Dan Xu
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Sivan Izraely
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Shlomit Ben-Menachem
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Roman Bengaiev
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Orit Sagi-Assif
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Weirong Yuan
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Metsada Pasmanik Chor
- Bioinformatics Unit, The George S. Wise Faculty of Life Science, Tel Aviv University, Tel-Aviv, Israel
| | - Dave S Hoon
- Department of Translational Molecular Medicine and Sequencing Center, Saint John's Cancer Institute at Providence Saint John's Health Center, Santa Monica, California, USA
| | - Wuyuan Lu
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Isaac P Witz
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
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12
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Gao CW, Lin W, Riddle RC, Kushwaha P, Boukas L, Björnsson HT, Hansen KD, Fahrner JA. A mouse model of Weaver syndrome displays overgrowth and excess osteogenesis reversible with KDM6A/6B inhibition. JCI Insight 2024; 9:e173392. [PMID: 38015625 PMCID: PMC10906465 DOI: 10.1172/jci.insight.173392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/14/2023] [Indexed: 11/30/2023] Open
Abstract
Weaver syndrome is a Mendelian disorder of the epigenetic machinery (MDEM) caused by germline pathogenic variants in EZH2, which encodes the predominant H3K27 methyltransferase and key enzymatic component of Polycomb repressive complex 2 (PRC2). Weaver syndrome is characterized by striking overgrowth and advanced bone age, intellectual disability, and distinctive facies. We generated a mouse model for the most common Weaver syndrome missense variant, EZH2 p.R684C. Ezh2R684C/R684C mouse embryonic fibroblasts (MEFs) showed global depletion of H3K27me3. Ezh2R684C/+ mice had abnormal bone parameters, indicative of skeletal overgrowth, and Ezh2R684C/+ osteoblasts showed increased osteogenic activity. RNA-Seq comparing osteoblasts differentiated from Ezh2R684C/+, and Ezh2+/+ BM-mesenchymal stem cells (BM-MSCs) indicated collective dysregulation of the BMP pathway and osteoblast differentiation. Inhibition of the opposing H3K27 demethylases KDM6A and KDM6B substantially reversed the excessive osteogenesis in Ezh2R684C/+ cells both at the transcriptional and phenotypic levels. This supports both the ideas that writers and erasers of histone marks exist in a fine balance to maintain epigenome state and that epigenetic modulating agents have therapeutic potential for the treatment of MDEMs.
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Affiliation(s)
- Christine W. Gao
- Department of Genetic Medicine
- Department of Molecular Biology and Genetics, and
| | | | - Ryan C. Riddle
- Department of Orthopaedic Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Orthopaedics, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Research and Development Service, Baltimore Veterans Administration Medical Center, Baltimore, Maryland, USA
| | - Priyanka Kushwaha
- Department of Orthopaedic Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Leandros Boukas
- Department of Genetic Medicine
- Department of Biostatistics, Johns Hopkins University School of Public Health, Baltimore, Maryland, USA
| | - Hans T. Björnsson
- Department of Genetic Medicine
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland
- Landspítali University Hospital, Reykjavík, Iceland
| | - Kasper D. Hansen
- Department of Genetic Medicine
- Department of Biostatistics, Johns Hopkins University School of Public Health, Baltimore, Maryland, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jill A. Fahrner
- Department of Genetic Medicine
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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13
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Gismene C, González JEH, de Freitas Calmon M, Nascimento AFZ, Santisteban ARN, Calil FA, da Silva ADT, Rahal P, Góes RM, Arni RK, Mariutti RB. Necrotic activity of ExhC from Mammaliicoccus sciuri is mediated by specific amino acid residues. Int J Biol Macromol 2024; 254:127741. [PMID: 38287568 DOI: 10.1016/j.ijbiomac.2023.127741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 01/31/2024]
Abstract
Mammaliicoccus sciuri, a commensal and pathogenic bacterium of significant clinical and veterinary relevance, expresses exfoliative toxin C (ExhC), a specific glutamyl endopeptidase belonging to the chymotrypsin family as the principal virulence factor. However, unlike most members of this family, ETs are inactive against a wide range of substrates and possess exquisite specificity for desmoglein-1 (Dsg1), a cadherin-like adhesion molecule that is crucial to maintain tissue integrity, thereby preventing the separation of skin cells and the entry of pathogens. ExhC is of clinical importance since in addition to causing exfoliation in pigs and mice, it induces necrosis in multiple mammalian cell lines, a property not observed for other ETs. Previous experiments have implicated the ExhC79-128 fragment in causing necrosis. Site-directed mutagenesis of specific residues within this fragment were studied and led to the design of an ExhC variant containing four-point mutations (ExhCmut4) lacking necrotic potential but retaining nearly wild-type (wt) levels of enzymatic activity. Moreover, the determination of the ExhCwt and ExhCmut4 crystal structures identified the conformation in the necrosis-linked region. These results constitute an important step toward the understanding of the mechanisms underlying the necrotic and epidermolytic activity of ExhC.
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Affiliation(s)
- Carolina Gismene
- Multiuser Center for Biomolecular Innovation, São Paulo State University - UNESP, São José do Rio Preto, SP, Brazil
| | | | - Marília de Freitas Calmon
- Laboratory of Genomic Studies, São Paulo State University - UNESP, São José do Rio Preto, SP, Brazil
| | - Andrey Fabricio Ziem Nascimento
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil
| | | | - Felipe Antunes Calil
- Multiuser Center for Biomolecular Innovation, São Paulo State University - UNESP, São José do Rio Preto, SP, Brazil
| | - Alana Della Torre da Silva
- Department of Biological Sciences, São Paulo State University - UNESP, São José do Rio Preto, SP, Brazil
| | - Paula Rahal
- Laboratory of Genomic Studies, São Paulo State University - UNESP, São José do Rio Preto, SP, Brazil
| | - Rejane Maira Góes
- Department of Biological Sciences, São Paulo State University - UNESP, São José do Rio Preto, SP, Brazil
| | - Raghuvir Krishnaswamy Arni
- Multiuser Center for Biomolecular Innovation, São Paulo State University - UNESP, São José do Rio Preto, SP, Brazil
| | - Ricardo Barros Mariutti
- Multiuser Center for Biomolecular Innovation, São Paulo State University - UNESP, São José do Rio Preto, SP, Brazil.
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14
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Chae HB, Bae SB, Paeng SK, Wi SD, Thi Phan KA, Lee SY. S-nitrosylation switches the Arabidopsis redox sensor protein, QSOX1, from an oxidoreductase to a molecular chaperone under heat stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108219. [PMID: 38048703 DOI: 10.1016/j.plaphy.2023.108219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 11/20/2023] [Indexed: 12/06/2023]
Abstract
The Arabidopsis quiescin sulfhydryl oxidase 1 (QSOX1) thiol-based redox sensor has been identified as a negative regulator of plant immunity. Here, we have found that small molecular weight proteins of QSOX1 were converted to high molecular weight (HMW) complexes upon exposure to heat stress and that this was accompanied by a switch in QSOX1 function from a thiol-reductase to a molecular chaperone. Plant treatment with S-nitrosoglutathione (GSNO), which causes nitrosylation of cysteine residues (S-nitrosylation), but not with H2O2, induced HMW QSOX1 complexes. Thus, functional switching of QSOX1 is induced by GSNO treatment. Accordingly, simultaneous treatment of plants with heat shock and GSNO led to a significant increase in QSOX1 chaperone activity by increasing its oligomerization. Consequently, transgenic Arabidopsis overexpressing QSOX1 (QSOX1OE) showed strong resistance to heat shock, whereas qsox1 knockout plants exhibited high sensitivity to heat stress. Plant treatment with GSNO under heat stress conditions increased their resistance to heat shock. We conclude that S-nitrosylation allows the thiol-based redox sensor, QSOX1, to respond to various external stresses in multiple ways.
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Affiliation(s)
- Ho Byoung Chae
- Division of Applied Life Sciences (BK21), PMBBRC, and Plant Biological Rhythm Research Center, Gyeongsang National University, Jinju, 52828, South Korea
| | - Su Bin Bae
- Division of Applied Life Sciences (BK21), PMBBRC, and Plant Biological Rhythm Research Center, Gyeongsang National University, Jinju, 52828, South Korea
| | - Seol Ki Paeng
- Division of Applied Life Sciences (BK21), PMBBRC, and Plant Biological Rhythm Research Center, Gyeongsang National University, Jinju, 52828, South Korea
| | - Seong Dong Wi
- Division of Applied Life Sciences (BK21), PMBBRC, and Plant Biological Rhythm Research Center, Gyeongsang National University, Jinju, 52828, South Korea
| | - Kieu Anh Thi Phan
- Division of Applied Life Sciences (BK21), PMBBRC, and Plant Biological Rhythm Research Center, Gyeongsang National University, Jinju, 52828, South Korea
| | - Sang Yeol Lee
- Division of Applied Life Sciences (BK21), PMBBRC, and Plant Biological Rhythm Research Center, Gyeongsang National University, Jinju, 52828, South Korea.
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15
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Werelusz P, Galiniak S, Mołoń M. Molecular functions of moonlighting proteins in cell metabolic processes. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119598. [PMID: 37774631 DOI: 10.1016/j.bbamcr.2023.119598] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 09/10/2023] [Accepted: 09/17/2023] [Indexed: 10/01/2023]
Abstract
Moonlighting proteins have more than one physiologically significant role within one polypeptide chain. The multifunctionality of proteins was first described in 1987 by Joram Piatigorsky and Graeme Wistow. Cells can benefit from involvement of these proteins in biological processes in several ways, e.g. at the energy level. Furthermore, cells have developed a number of mechanisms to change these proteins' functions. Moonlighting proteins are found in all types of organisms, including prokaryotes, eukaryotes, and even viruses. These proteins include a variety of enzymes that serve as receptors, secreted cytokines, transcription factors, or proteasome components. Additionally, there are many combinations of functions, e.g. among receptors and transcription factors, chaperones and cytokines, as well as transcription factors within the ribosome. This work describes enzymes involved in several important metabolic processes in cells, namely cellular respiration, gluconeogenesis, the urea cycle, and pentose phosphate metabolism.
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Affiliation(s)
| | - Sabina Galiniak
- Institute of Medical Sciences, Rzeszów University, Rzeszów, Poland
| | - Mateusz Mołoń
- Institute of Biology, Rzeszów University, Rzeszów, Poland.
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16
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López-Pérez M, Aguirre-Garrido F, Herrera-Zúñiga L, Fernández FJ. Gene as a dynamical notion: An extensive and integrative vision. Redefining the gene concept, from traditional to genic-interaction, as a new dynamical version. Biosystems 2023; 234:105060. [PMID: 37844827 DOI: 10.1016/j.biosystems.2023.105060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/08/2023] [Accepted: 10/10/2023] [Indexed: 10/18/2023]
Abstract
The current concept of gene has been very useful during the 20th and 21st centuries. However, recent advances in molecular biology and bioinformatics, which have further diversified the functional and adaptive profile of genetic information and its integration with cell physiology and environmental response, have contributed to focusing on additional new gene properties besides the traditional definition. Considering the inherent complexity of gene expression, whose adaptive objective must be referred to the Tortoise-Hare model, in which two tendencies converge, one focused on rapid adaptation to achieve survival, and the other that prevents an over-adaptation effect. In this context, a revision of the gene concept must be made, which must include these new mechanisms and approaches. In this paper, we propose a new conception of the idea of a gene that moves from a static and defined version of hereditary information to a dynamic idea that preponderates gene interaction (circumscribed to that established between protein-protein, protein-nucleic acid, and nucleic acid-nucleic acid) and the selection it exerts, as the irreducible element that works in a coordinated way in a genomic regulatory network (GRN).
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Affiliation(s)
- Marcos López-Pérez
- Environmental Sciences Department, Universidad Autónoma Metropolitana (Lerma Unit) Av. de las Garzas N° 10, Col. El Panteón, Municipio de Lerma de Villada, Estado de México, C.P. 52005, Mexico.
| | - Félix Aguirre-Garrido
- Environmental Sciences Department, Universidad Autónoma Metropolitana (Lerma Unit) Av. de las Garzas N° 10, Col. El Panteón, Municipio de Lerma de Villada, Estado de México, C.P. 52005, Mexico
| | - Leonardo Herrera-Zúñiga
- Chemistry Department, Universidad Autónoma Metropolitana (Iztapalapa Unit), C.P. 09340, Mexico City, Mexico
| | - Francisco J Fernández
- Biotechnology Department, Universidad Autónoma Metropolitana (Iztapalapa Unit), C.P. 09340, Mexico City, Mexico.
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17
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Vande Zande P, Siddiq MA, Hodgins-Davis A, Kim L, Wittkopp PJ. Active compensation for changes in TDH3 expression mediated by direct regulators of TDH3 in Saccharomyces cerevisiae. PLoS Genet 2023; 19:e1011078. [PMID: 38091349 PMCID: PMC10752532 DOI: 10.1371/journal.pgen.1011078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/27/2023] [Accepted: 11/22/2023] [Indexed: 12/26/2023] Open
Abstract
Genetic networks are surprisingly robust to perturbations caused by new mutations. This robustness is conferred in part by compensation for loss of a gene's activity by genes with overlapping functions, such as paralogs. Compensation occurs passively when the normal activity of one paralog can compensate for the loss of the other, or actively when a change in one paralog's expression, localization, or activity is required to compensate for loss of the other. The mechanisms of active compensation remain poorly understood in most cases. Here we investigate active compensation for the loss or reduction in expression of the Saccharomyces cerevisiae gene TDH3 by its paralog TDH2. TDH2 is upregulated in a dose-dependent manner in response to reductions in TDH3 by a mechanism requiring the shared transcriptional regulators Gcr1p and Rap1p. TDH1, a second and more distantly related paralog of TDH3, has diverged in its regulation and is upregulated by another mechanism. Other glycolytic genes regulated by Rap1p and Gcr1p show changes in expression similar to TDH2, suggesting that the active compensation by TDH3 paralogs is part of a broader homeostatic response mediated by shared transcriptional regulators.
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Affiliation(s)
- Pétra Vande Zande
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Mohammad A. Siddiq
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Andrea Hodgins-Davis
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lisa Kim
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Patricia J. Wittkopp
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America
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18
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Lakhani AA, Thompson SL, Sheltzer JM. Aneuploidy in human cancer: new tools and perspectives. Trends Genet 2023; 39:968-980. [PMID: 37778926 PMCID: PMC10715718 DOI: 10.1016/j.tig.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/04/2023] [Accepted: 09/07/2023] [Indexed: 10/03/2023]
Abstract
Chromosome copy number imbalances, otherwise known as aneuploidies, are a common but poorly understood feature of cancer. Here, we describe recent advances in both detecting and manipulating aneuploidies that have greatly advanced our ability to study their role in tumorigenesis. In particular, new clustered regularly interspaced short palindromic repeats (CRISPR)-based techniques have been developed that allow the creation of isogenic cell lines with specific chromosomal changes, thereby facilitating experiments in genetically controlled backgrounds to uncover the consequences of aneuploidy. These approaches provide increasing evidence that aneuploidy is a key driver of cancer development and enable the identification of multiple dosage-sensitive genes encoded on aneuploid chromosomes. Consequently, measuring aneuploidy may inform clinical prognosis, while treatment strategies that target aneuploidy could represent a novel method to counter malignant growth.
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Affiliation(s)
- Asad A Lakhani
- Cold Spring Harbor Laboratory School of Biological Sciences, Cold Spring, Harbor, NY 11724, USA
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19
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Soto Perezchica MM, Guerrero Barrera AL, Avelar Gonzalez FJ, Quezada Tristan T, Macias Marin O. Actinobacillus pleuropneumoniae, surface proteins and virulence: a review. Front Vet Sci 2023; 10:1276712. [PMID: 38098987 PMCID: PMC10720984 DOI: 10.3389/fvets.2023.1276712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Accepted: 10/17/2023] [Indexed: 12/17/2023] Open
Abstract
Actinobacillus pleuropneumoniae (App) is a globally distributed Gram-negative bacterium that produces porcine pleuropneumonia. This highly contagious disease produces high morbidity and mortality in the swine industry. However, no effective vaccine exists to prevent it. The infection caused by App provokes characteristic lesions, such as edema, inflammation, hemorrhage, and necrosis, that involve different virulence factors. The colonization and invasion of host surfaces involved structures and proteins such as outer membrane vesicles (OMVs), pili, flagella, adhesins, outer membrane proteins (OMPs), also participates proteases, autotransporters, and lipoproteins. The recent findings on surface structures and proteins described in this review highlight them as potential immunogens for vaccine development.
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Affiliation(s)
- María M. Soto Perezchica
- Laboratorio de Biología Celular y Tisular, Departamento de Morfología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Mexico
| | - Alma L. Guerrero Barrera
- Laboratorio de Biología Celular y Tisular, Departamento de Morfología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Mexico
| | - Francisco J. Avelar Gonzalez
- Laboratorio de Estudios Ambientales, Departamento de Fisiología y Farmacología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Mexico
| | - Teodulo Quezada Tristan
- Departamento de Ciencias Veterinaria, Centro de Ciencias Agropecuarias, Universidad Autónoma de Aguascalientes, Aguascalientes, Mexico
| | - Osvaldo Macias Marin
- Laboratorio de Biología Celular y Tisular, Departamento de Morfología, Centro de Ciencias Básicas, Universidad Autónoma de Aguascalientes, Aguascalientes, Mexico
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20
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Ancarola ME, Maldonado LL, García LCA, Franchini GR, Mourglia-Ettlin G, Kamenetzky L, Cucher MA. A Comparative Analysis of the Protein Cargo of Extracellular Vesicles from Helminth Parasites. Life (Basel) 2023; 13:2286. [PMID: 38137887 PMCID: PMC10744797 DOI: 10.3390/life13122286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 11/15/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
Helminth parasites cause debilitating-sometimes fatal-diseases in humans and animals. Despite their impact on global health, mechanisms underlying host-parasite interactions are still poorly understood. One such mechanism involves the exchange of extracellular vesicles (EVs), which are membrane-enclosed subcellular nanoparticles. To date, EV secretion has been studied in helminth parasites, including EV protein content. However, information is highly heterogeneous, since it was generated in multiple species, using varied protocols for EV isolation and data analysis. Here, we compared the protein cargo of helminth EVs to identify common markers for each taxon. For this, we integrated published proteomic data and performed a comparative analysis through an orthology approach. Overall, only three proteins were common in the EVs of the seven analyzed species. Additionally, varied repertoires of proteins with moonlighting activity, vaccine antigens, canonical and non-canonical proteins related to EV biogenesis, taxon-specific proteins of unknown function and RNA-binding proteins were observed in platyhelminth and nematode EVs. Despite the lack of consensus on EV isolation protocols and protein annotation, several proteins were shown to be consistently detected in EV preparations from organisms at different taxa levels, providing a starting point for a selective biochemical characterization.
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Affiliation(s)
- María Eugenia Ancarola
- Department of Microbiology, School of Medicine, University of Buenos Aires, Buenos Aires C1121, Argentina; (M.E.A.); (L.L.M.)
- Institute of Research on Microbiology and Medical Parasitology (IMPaM, UBA-CONICET), University of Buenos Aires, Buenos Aires C1121, Argentina
| | - Lucas L. Maldonado
- Department of Microbiology, School of Medicine, University of Buenos Aires, Buenos Aires C1121, Argentina; (M.E.A.); (L.L.M.)
- Institute of Research on Microbiology and Medical Parasitology (IMPaM, UBA-CONICET), University of Buenos Aires, Buenos Aires C1121, Argentina
- Instituto de Tecnología (INTEC), Universidad Argentina de la Empresa (UADE), Buenos Aires C1073, Argentina
| | - Lucía C. A. García
- Department of Microbiology, School of Medicine, University of Buenos Aires, Buenos Aires C1121, Argentina; (M.E.A.); (L.L.M.)
- Institute of Research on Microbiology and Medical Parasitology (IMPaM, UBA-CONICET), University of Buenos Aires, Buenos Aires C1121, Argentina
| | - Gisela R. Franchini
- Instituto de Investigaciones Bioquímicas de La Plata (INIBIOLP), Facultad de Ciencias Médicas, Universidad Nacional de La Plata (UNLP)-Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), La Plata B1900, Argentina;
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata (UNLP), La Plata B1900, Argentina
| | - Gustavo Mourglia-Ettlin
- Área Inmunología, Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo 11800, Uruguay;
| | - Laura Kamenetzky
- Instituto de Biociencias, Biotecnología y Biología Traslacional, Departamento de Fisiología y Biología Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires C1428, Argentina;
| | - Marcela A. Cucher
- Department of Microbiology, School of Medicine, University of Buenos Aires, Buenos Aires C1121, Argentina; (M.E.A.); (L.L.M.)
- Institute of Research on Microbiology and Medical Parasitology (IMPaM, UBA-CONICET), University of Buenos Aires, Buenos Aires C1121, Argentina
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21
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Woodruff GC, Willis JH, Johnson E, Phillips PC. Widespread changes in gene expression accompany body size evolution in nematodes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.30.564729. [PMID: 37961435 PMCID: PMC10635002 DOI: 10.1101/2023.10.30.564729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Body size is a fundamental trait that drives multiple evolutionary and ecological patterns. Caenorhabditis inopinata is a fig-associated nematode that is exceptionally large relative to other members of the genus, including C. elegans. We previously showed that C. inopinata is large primarily due to postembryonic cell size expansion that occurs during the larval-to-adult transition. Here, we describe gene expression patterns in C. elegans and C. inopinata throughout this developmental period to understand the transcriptional basis of body size change. We performed RNA-seq in both species across the L3, L4, and adult stages. Most genes are differentially expressed across all developmental stages, consistent with C. inopinata's divergent ecology and morphology. We also used a model comparison approach to identify orthologs with divergent dynamics across this developmental period between the two species. This included genes connected to neurons, behavior, stress response, developmental timing, and small RNA/chromatin regulation. Multiple hypodermal collagens were also observed to harbor divergent developmental dynamics across this period, and genes important for molting and body morphology were also detected. Genes associated with TGF-β signaling revealed idiosyncratic and unexpected transcriptional patterns given their role in body size regulation in C. elegans. Widespread transcriptional divergence between these species is unexpected and may be a signature of the ecological and morphological divergence of C. inopinata. Alternatively, transcriptional turnover may be the rule in the Caenorhabditis genus, indicative of widespread developmental system drift among species. This work lays the foundation for future functional genetic studies interrogating the bases of body size evolution in this group.
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Affiliation(s)
- Gavin C Woodruff
- University of Oregon, Eugene, Oregon, USA
- Current institution: University of Oklahoma, Norman, Oklahoma, USA
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22
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Jühlen R, Fahrenkrog B. From the sideline: Tissue-specific nucleoporin function in health and disease, an update. FEBS Lett 2023; 597:2750-2768. [PMID: 37873737 DOI: 10.1002/1873-3468.14761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/26/2023] [Accepted: 10/04/2023] [Indexed: 10/25/2023]
Abstract
The subcellular compartmentalisation of eukaryotic cells requires selective exchange between the cytoplasm and the nucleus. Intact nucleocytoplasmic transport is vital for normal cell function and mutations in the executing machinery have been causally linked to human disease. Central players in nucleocytoplasmic exchange are nuclear pore complexes (NPCs), which are built from ~30 distinct proteins collectively termed nucleoporins. Aberrant nucleoporin expression was detected in human cancers and autoimmune diseases since quite some time, while it was through the increasing use of next generation sequencing that mutations in nucleoporin genes associated with mainly rare hereditary diseases were revealed. The number of newly identified mutations is steadily increasing, as is the number of diseases. Mutational hotspots have emerged: mutations in the scaffold nucleoporins seemingly affect primarily inner organs, such as heart, kidney, and ovaries, whereas genetic alterations in peripheral, cytoplasmic nucleoporins affect primarily the central nervous system and development. In this review, we summarise latest insights on altered nucleoporin function in the context of human hereditary disorders, with a focus on those where mechanistic insights are beginning to emerge.
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Affiliation(s)
- Ramona Jühlen
- Institute of Biochemistry and Molecular Cell Biology, Medical School, RWTH Aachen University, Aachen, Germany
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23
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Karpenko MN, Muruzheva ZM, Ilyechova EY, Babich PS, Puchkova LV. Abnormalities in Copper Status Associated with an Elevated Risk of Parkinson's Phenotype Development. Antioxidants (Basel) 2023; 12:1654. [PMID: 37759957 PMCID: PMC10525645 DOI: 10.3390/antiox12091654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 09/29/2023] Open
Abstract
In the last 15 years, among the many reasons given for the development of idiopathic forms of Parkinson's disease (PD), copper imbalance has been identified as a factor, and PD is often referred to as a copper-mediated disorder. More than 640 papers have been devoted to the relationship between PD and copper status in the blood, which include the following markers: total copper concentration, enzymatic ceruloplasmin (Cp) concentration, Cp protein level, and non-ceruloplasmin copper level. Most studies measure only one of these markers. Therefore, the existence of a correlation between copper status and the development of PD is still debated. Based on data from the published literature, meta-analysis, and our own research, it is clear that there is a connection between the development of PD symptoms and the number of copper atoms, which are weakly associated with the ceruloplasmin molecule. In this work, the link between the risk of developing PD and various inborn errors related to copper metabolism, leading to decreased levels of oxidase ceruloplasmin in the circulation and cerebrospinal fluid, is discussed.
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Affiliation(s)
- Marina N. Karpenko
- I.P. Pavlov Department of Physiology, Research Institute of Experimental Medicine, 197376 St. Petersburg, Russia; (M.N.K.); (Z.M.M.)
- Institute of Biomedical Systems and Biotechnology, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia;
| | - Zamira M. Muruzheva
- I.P. Pavlov Department of Physiology, Research Institute of Experimental Medicine, 197376 St. Petersburg, Russia; (M.N.K.); (Z.M.M.)
- State Budgetary Institution of Health Care “Leningrad Regional Clinical Hospital”, 194291 St. Petersburg, Russia
| | - Ekaterina Yu. Ilyechova
- Institute of Biomedical Systems and Biotechnology, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia;
- Research Center of Advanced Functional Materials and Laser Communication Systems, ADTS Institute, ITMO University, 197101 St. Petersburg, Russia
- Department of Molecular Genetics, Research Institute of Experimental Medicine, 197376 St. Petersburg, Russia
| | - Polina S. Babich
- Department of Zoology and Genetics, Faculty of Biology, Herzen State Pedagogical University of Russia, 191186 St. Petersburg, Russia;
| | - Ludmila V. Puchkova
- Institute of Biomedical Systems and Biotechnology, Peter the Great St. Petersburg Polytechnic University, 195251 St. Petersburg, Russia;
- Research Center of Advanced Functional Materials and Laser Communication Systems, ADTS Institute, ITMO University, 197101 St. Petersburg, Russia
- Department of Molecular Genetics, Research Institute of Experimental Medicine, 197376 St. Petersburg, Russia
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24
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Weiland-Bräuer N, Koutsouveli V, Langfeldt D, Schmitz RA. First insights into the Aurelia aurita transcriptome response upon manipulation of its microbiome. Front Microbiol 2023; 14:1183627. [PMID: 37637120 PMCID: PMC10448538 DOI: 10.3389/fmicb.2023.1183627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 07/18/2023] [Indexed: 08/29/2023] Open
Abstract
Introduction The associated diverse microbiome contributes to the overall fitness of Aurelia aurita, particularly to asexual reproduction. However, how A. aurita maintains this specific microbiome or reacts to manipulations is unknown. Methods In this report, the response of A. aurita to manipulations of its native microbiome was studied by a transcriptomics approach. Microbiome-manipulated polyps were generated by antibiotic treatment and challenging polyps with a non-native, native, and potentially pathogenic bacterium. Total RNA extraction followed by RNAseq resulted in over 155 million reads used for a de novo assembly. Results The transcriptome analysis showed that the antibiotic-induced change and resulting reduction of the microbiome significantly affected the host transcriptome, e.g., genes involved in processes related to immune response and defense mechanisms were highly upregulated. Similarly, manipulating the microbiome by challenging the polyp with a high load of bacteria (2 × 107 cells/polyp) resulted in induced transcription of apoptosis-, defense-, and immune response genes. A second focus was on host-derived quorum sensing interference as a potential defense strategy. Quorum Quenching (QQ) activities and the respective encoding QQ-ORFs of A. aurita were identified by functional screening a cDNA-based expression library generated in Escherichia coli. Corresponding sequences were identified in the transcriptome assembly. Moreover, gene expression analysis revealed differential expression of QQ genes depending on the treatment, strongly suggesting QQ as an additional defense strategy. Discussion Overall, this study allows first insights into A. aurita's response to manipulating its microbiome, thus paving the way for an in-depth analysis of the basal immune system and additional fundamental defense strategies.
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Affiliation(s)
| | - Vasiliki Koutsouveli
- GEOMAR Helmholtz Center for Ocean Research Kiel, Düsternbrooker Weg, Kiel, Germany
| | | | - Ruth A. Schmitz
- Institute of General Microbiology, Kiel University, Kiel, Germany
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25
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Gasparski AN, Moissoglu K, Pallikkuth S, Meydan S, Guydosh NR, Mili S. mRNA location and translation rate determine protein targeting to dual destinations. Mol Cell 2023; 83:2726-2738.e9. [PMID: 37506697 PMCID: PMC10530421 DOI: 10.1016/j.molcel.2023.06.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 04/25/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023]
Abstract
Numerous proteins are targeted to two or multiple subcellular destinations where they exert distinct functional consequences. The balance between such differential targeting is thought to be determined post-translationally, relying on protein sorting mechanisms. Here, we show that mRNA location and translation rate can also determine protein targeting by modulating protein binding to specific interacting partners. Peripheral localization of the NET1 mRNA and fast translation lead to higher cytosolic retention of the NET1 protein by promoting its binding to the membrane-associated scaffold protein CASK. By contrast, perinuclear mRNA location and/or slower translation rate favor nuclear targeting by promoting binding to importins. This mRNA location-dependent mechanism is modulated by physiological stimuli and profoundly impacts NET1 function in cell motility. These results reveal that the location of protein synthesis and the rate of translation elongation act in coordination as a "partner-selection" mechanism that robustly influences protein distribution and function.
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Affiliation(s)
- Alexander N Gasparski
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Konstadinos Moissoglu
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sandeep Pallikkuth
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Sezen Meydan
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA; National Institute of General Medical Sciences, NIH, Bethesda, MD 20892, USA
| | - Nicholas R Guydosh
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - Stavroula Mili
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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26
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Gupta S, Westacott MJ, Ayers DG, Weiss SJ, Whitley P, Mueller C, Weaver DC, Schneider DJ, Karimpour-Fard A, Hunter LE, Drolet DW, Janjic N. Plasma proteome of growing tumors. Sci Rep 2023; 13:12195. [PMID: 37500700 PMCID: PMC10374562 DOI: 10.1038/s41598-023-38079-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/03/2023] [Indexed: 07/29/2023] Open
Abstract
Early detection of cancer is vital for the best chance of successful treatment, but half of all cancers are diagnosed at an advanced stage. A simple and reliable blood screening test applied routinely would therefore address a major unmet medical need. To gain insight into the value of protein biomarkers in early detection and stratification of cancer we determined the time course of changes in the plasma proteome of mice carrying transplanted human lung, breast, colon, or ovarian tumors. For protein measurements we used an aptamer-based assay which simultaneously measures ~ 5000 proteins. Along with tumor lineage-specific biomarkers, we also found 15 markers shared among all cancer types that included the energy metabolism enzymes glyceraldehyde-3-phosphate dehydrogenase, glucose-6-phophate isomerase and dihydrolipoyl dehydrogenase as well as several important biomarkers for maintaining protein, lipid, nucleotide, or carbohydrate balance such as tryptophanyl t-RNA synthetase and nucleoside diphosphate kinase. Using significantly altered proteins in the tumor bearing mice, we developed models to stratify tumor types and to estimate the minimum detectable tumor volume. Finally, we identified significantly enriched common and unique biological pathways among the eight tumor cell lines tested.
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Affiliation(s)
- Shashi Gupta
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO, 80301, USA
| | | | - Deborah G Ayers
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO, 80301, USA
| | - Sophie J Weiss
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO, 80301, USA
| | - Penn Whitley
- Boulder BioConsulting, Inc., 325 S 68th St., Boulder, CO, 80303, USA
| | | | - Daniel C Weaver
- Boulder BioConsulting, Inc., 325 S 68th St., Boulder, CO, 80303, USA
| | | | - Anis Karimpour-Fard
- University of Colorado School of Medicine, Mailstop 8303, Aurora, CO, 80045, USA
| | - Lawrence E Hunter
- University of Colorado School of Medicine, Mailstop 8303, Aurora, CO, 80045, USA
| | - Daniel W Drolet
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO, 80301, USA
| | - Nebojsa Janjic
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO, 80301, USA.
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Gao CW, Lin W, Riddle RC, Kushwaha P, Boukas L, Björnsson HT, Hansen KD, Fahrner JA. Novel mouse model of Weaver syndrome displays overgrowth and excess osteogenesis reversible with KDM6A/6B inhibition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.23.546270. [PMID: 37425751 PMCID: PMC10327066 DOI: 10.1101/2023.06.23.546270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Weaver syndrome is a Mendelian disorder of the epigenetic machinery (MDEM) caused by germline pathogenic variants in EZH2, which encodes the predominant H3K27 methyltransferase and key enzymatic component of Polycomb repressive complex 2 (PRC2). Weaver syndrome is characterized by striking overgrowth and advanced bone age, intellectual disability, and distinctive facies. We generated a mouse model for the most common Weaver syndrome missense variant, EZH2 p.R684C. Ezh2R684C/R684C mouse embryonic fibroblasts (MEFs) showed global depletion of H3K27me3. Ezh2R684C/+ mice had abnormal bone parameters indicative of skeletal overgrowth, and Ezh2R684C/+ osteoblasts showed increased osteogenic activity. RNA-seq comparing osteoblasts differentiated from Ezh2R684C/+ and Ezh2+/+ bone marrow mesenchymal stem cells (BM-MSCs) indicated collective dysregulation of the BMP pathway and osteoblast differentiation. Inhibition of the opposing H3K27 demethylases Kdm6a/6b substantially reversed the excessive osteogenesis in Ezh2R684C/+ cells both at the transcriptional and phenotypic levels. This supports both the ideas that writers and erasers of histone marks exist in a fine balance to maintain epigenome state, and that epigenetic modulating agents have therapeutic potential for the treatment of MDEMs.
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Affiliation(s)
- Christine W Gao
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD
| | - WanYing Lin
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Ryan C Riddle
- Department of Orthopaedic Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Orthopaedics, University of Maryland School of Medicine, Baltimore, MD
- Research and Development Service, Baltimore Veterans Administration Medical Center, Baltimore, MD
| | - Priyanka Kushwaha
- Department of Orthopaedic Surgery, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Leandros Boukas
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Biostatistics, Johns Hopkins University School of Public Health, Baltimore, MD
| | - Hans T Björnsson
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland
- Landspítali University Hospital, Reykjavík, Iceland
| | - Kasper D Hansen
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Biostatistics, Johns Hopkins University School of Public Health, Baltimore, MD
| | - Jill A Fahrner
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD
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28
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Wagner S, Whiteley SL, Castelli M, Patel HR, Deveson IW, Blackburn J, Holleley CE, Marshall Graves JA, Georges A. Gene expression of male pathway genes sox9 and amh during early sex differentiation in a reptile departs from the classical amniote model. BMC Genomics 2023; 24:243. [PMID: 37147622 PMCID: PMC10163765 DOI: 10.1186/s12864-023-09334-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 04/25/2023] [Indexed: 05/07/2023] Open
Abstract
BACKGROUND Sex determination is the process whereby the bipotential embryonic gonads become committed to differentiate into testes or ovaries. In genetic sex determination (GSD), the sex determining trigger is encoded by a gene on the sex chromosomes, which activates a network of downstream genes; in mammals these include SOX9, AMH and DMRT1 in the male pathway, and FOXL2 in the female pathway. Although mammalian and avian GSD systems have been well studied, few data are available for reptilian GSD systems. RESULTS We conducted an unbiased transcriptome-wide analysis of gonad development throughout differentiation in central bearded dragon (Pogona vitticeps) embryos with GSD. We found that sex differentiation of transcriptomic profiles occurs at a very early stage, before the gonad consolidates as a body distinct from the gonad-kidney complex. The male pathway genes dmrt1 and amh and the female pathway gene foxl2 play a key role in early sex differentiation in P. vitticeps, but the central player of the mammalian male trajectory, sox9, is not differentially expressed in P. vitticeps at the bipotential stage. The most striking difference from GSD systems of other amniotes is the high expression of the male pathway genes amh and sox9 in female gonads during development. We propose that a default male trajectory progresses if not repressed by a W-linked dominant gene that tips the balance of gene expression towards the female trajectory. Further, weighted gene expression correlation network analysis revealed novel candidates for male and female sex differentiation. CONCLUSION Our data reveal that interpretation of putative mechanisms of GSD in reptiles cannot solely depend on lessons drawn from mammals.
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Affiliation(s)
- Susan Wagner
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
| | - Sarah L Whiteley
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
- Australian National Wildlife Collection CSIRO, National Research Collections Australia, Crace, ACT, Australia
| | - Meghan Castelli
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
- Australian National Wildlife Collection CSIRO, National Research Collections Australia, Crace, ACT, Australia
| | - Hardip R Patel
- Genome Sciences Department. John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Ira W Deveson
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - James Blackburn
- Kinghorn Centre for Clinical Genomics, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Faculty of Medicine, St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Clare E Holleley
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
- Australian National Wildlife Collection CSIRO, National Research Collections Australia, Crace, ACT, Australia
| | - Jennifer A Marshall Graves
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia
- School of Life Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Arthur Georges
- Institute for Applied Ecology, University of Canberra, Bruce, ACT, Australia.
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29
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Lesko MA, Chandrashekarappa DG, Jordahl EM, Oppenheimer KG, Bowman RW, Shang C, Durrant JD, Schmidt MC, O’Donnell AF. Changing course: Glucose starvation drives nuclear accumulation of Hexokinase 2 in S. cerevisiae. PLoS Genet 2023; 19:e1010745. [PMID: 37196001 PMCID: PMC10228819 DOI: 10.1371/journal.pgen.1010745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 05/30/2023] [Accepted: 04/14/2023] [Indexed: 05/19/2023] Open
Abstract
Glucose is the preferred carbon source for most eukaryotes, and the first step in its metabolism is phosphorylation to glucose-6-phosphate. This reaction is catalyzed by hexokinases or glucokinases. The yeast Saccharomyces cerevisiae encodes three such enzymes, Hxk1, Hxk2, and Glk1. In yeast and mammals, some isoforms of this enzyme are found in the nucleus, suggesting a possible moonlighting function beyond glucose phosphorylation. In contrast to mammalian hexokinases, yeast Hxk2 has been proposed to shuttle into the nucleus in glucose-replete conditions, where it reportedly moonlights as part of a glucose-repressive transcriptional complex. To achieve its role in glucose repression, Hxk2 reportedly binds the Mig1 transcriptional repressor, is dephosphorylated at serine 15 and requires an N-terminal nuclear localization sequence (NLS). We used high-resolution, quantitative, fluorescent microscopy of live cells to determine the conditions, residues, and regulatory proteins required for Hxk2 nuclear localization. Countering previous yeast studies, we find that Hxk2 is largely excluded from the nucleus under glucose-replete conditions but is retained in the nucleus under glucose-limiting conditions. We find that the Hxk2 N-terminus does not contain an NLS but instead is necessary for nuclear exclusion and regulating multimerization. Amino acid substitutions of the phosphorylated residue, serine 15, disrupt Hxk2 dimerization but have no effect on its glucose-regulated nuclear localization. Alanine substation at nearby lysine 13 affects dimerization and maintenance of nuclear exclusion in glucose-replete conditions. Modeling and simulation provide insight into the molecular mechanisms of this regulation. In contrast to earlier studies, we find that the transcriptional repressor Mig1 and the protein kinase Snf1 have little effect on Hxk2 localization. Instead, the protein kinase Tda1 regulates Hxk2 localization. RNAseq analyses of the yeast transcriptome dispels the idea that Hxk2 moonlights as a transcriptional regulator of glucose repression, demonstrating that Hxk2 has a negligible role in transcriptional regulation in both glucose-replete and limiting conditions. Our studies define a new model of cis- and trans-acting regulators of Hxk2 dimerization and nuclear localization. Based on our data, the nuclear translocation of Hxk2 in yeast occurs in glucose starvation conditions, which aligns well with the nuclear regulation of mammalian orthologs. Our results lay the foundation for future studies of Hxk2 nuclear activity.
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Affiliation(s)
- Mitchell A. Lesko
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Dakshayini G. Chandrashekarappa
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Eric M. Jordahl
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Katherine G. Oppenheimer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Ray W. Bowman
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Chaowei Shang
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Jacob D. Durrant
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Martin C. Schmidt
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Allyson F. O’Donnell
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
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30
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Gasparski AN, Moissoglu K, Pallikkuth S, Meydan S, Guydosh NR, Mili S. mRNA Location and Translation Rate Determine Protein Targeting to Dual Destinations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538105. [PMID: 37163129 PMCID: PMC10168211 DOI: 10.1101/2023.04.24.538105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Numerous proteins are targeted to two or multiple subcellular destinations where they exert distinct functional consequences. The balance between such differential targeting is thought to be determined post-translationally, relying on protein sorting mechanisms. Here, we show that protein targeting can additionally be determined by mRNA location and translation rate, through modulating protein binding to specific interacting partners. Peripheral localization of the NET1 mRNA and fast translation lead to higher cytosolic retention of the NET1 protein, through promoting its binding to the membrane-associated scaffold protein CASK. By contrast, perinuclear mRNA location and/or slower translation rate favor nuclear targeting, through promoting binding to importins. This mRNA location-dependent mechanism is modulated by physiological stimuli and profoundly impacts NET1 function in cell motility. These results reveal that the location of protein synthesis and the rate of translation elongation act in coordination as a 'partner-selection' mechanism that robustly influences protein distribution and function.
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Affiliation(s)
- Alexander N. Gasparski
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, 20892, MD, USA
| | - Konstadinos Moissoglu
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, 20892, MD, USA
| | - Sandeep Pallikkuth
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, 20892, MD, USA
| | - Sezen Meydan
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, 20892, MD, USA
- National Institute of General Medical Sciences, NIH, Bethesda, 20892, MD, USA
| | - Nicholas R. Guydosh
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, 20892, MD, USA
| | - Stavroula Mili
- Laboratory of Cellular and Molecular Biology, National Cancer Institute, NIH, Bethesda, 20892, MD, USA
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31
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Gupta MN, Uversky VN. Moonlighting enzymes: when cellular context defines specificity. Cell Mol Life Sci 2023; 80:130. [PMID: 37093283 PMCID: PMC11073002 DOI: 10.1007/s00018-023-04781-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/13/2023] [Accepted: 04/15/2023] [Indexed: 04/25/2023]
Abstract
It is not often realized that the absolute protein specificity is an exception rather than a rule. Two major kinds of protein multi-specificities are promiscuity and moonlighting. This review discusses the idea of enzyme specificity and then focusses on moonlighting. Some important examples of protein moonlighting, such as crystallins, ceruloplasmin, metallothioniens, macrophage migration inhibitory factor, and enzymes of carbohydrate metabolism are discussed. How protein plasticity and intrinsic disorder enable the removing the distinction between enzymes and other biologically active proteins are outlined. Finally, information on important roles of moonlighting in human diseases is updated.
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Affiliation(s)
- Munishwar Nath Gupta
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology, Hauz Khas, New Delhi, 110016, India
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Downs Blvd., MDC07, Tampa, FL, 33612-4799, USA.
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32
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Serrat J, Becerro-Recio D, Torres-Valle M, Simón F, Valero MA, Bargues MD, Mas-Coma S, Siles-Lucas M, González-Miguel J. Fasciola hepatica juveniles interact with the host fibrinolytic system as a potential early-stage invasion mechanism. PLoS Negl Trop Dis 2023; 17:e0010936. [PMID: 37083884 PMCID: PMC10155961 DOI: 10.1371/journal.pntd.0010936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 05/03/2023] [Accepted: 03/20/2023] [Indexed: 04/22/2023] Open
Abstract
BACKGROUND The trematode Fasciola hepatica is the most widespread causative agent of fasciolosis, a parasitic disease that mainly affects humans and ruminants worldwide. During F. hepatica infection, newly excysted juveniles (FhNEJ) emerge in the duodenum of the mammalian host and migrate towards their definitive location, the intra-hepatic biliary ducts. Understanding how F. hepatica traverses the intestinal wall and migrates towards the liver is pivotal for the development of more successful strategies against fasciolosis. The central enzyme of the mammalian fibrinolytic system is plasmin, a serine protease whose functions are exploited by a number of parasite species owing to its broad spectrum of substrates, including components of tissue extracellular matrices. The aim of the present work is to understand whether FhNEJ co-opt the functions of their host fibrinolytic system as a mechanism to facilitate trans-intestinal migration. METHODOLOGY/PRINCIPAL FINDINGS A tegument-enriched antigenic extract of FhNEJ (FhNEJ-Teg) was obtained in vitro, and its capability to bind the zymogen plasminogen (PLG) and enhance its conversion to the active protease, plasmin, were analyzed by a combination of enzyme-linked immunosorbent, chromogenic and immunofluorescence assays. Additionally, PLG-binding proteins in FhNEJ-Teg were identified by bidimensional electrophoresis coupled to mass spectrometry analysis, and the interactions were validated using FhNEJ recombinant proteins. CONCLUSIONS/SIGNIFICANCE Our results show that FhNEJ-Teg contains proteins that bind PLG and stimulate its activation to plasmin, which could facilitate the traversal of the intestinal wall by FhNEJ and contribute to the successful establishment of the parasite within its mammalian host. Altogether, our findings contribute to a better understanding of host-parasite relationships during early fasciolosis and may be exploited from a pharmacological and/or immunological perspective for the development of treatment and control strategies against this global disease.
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Affiliation(s)
- Judit Serrat
- Laboratory of Helminth Parasites of Zoonotic Importance (ATENEA), Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), Salamanca, Spain
| | - David Becerro-Recio
- Laboratory of Helminth Parasites of Zoonotic Importance (ATENEA), Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), Salamanca, Spain
| | - María Torres-Valle
- Laboratory of Helminth Parasites of Zoonotic Importance (ATENEA), Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), Salamanca, Spain
| | - Fernando Simón
- Laboratory of Parasitology, Faculty of Pharmacy, University of Salamanca, Salamanca, Spain
| | - María Adela Valero
- Departamento de Parasitología, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos IIII, Madrid, Spain
| | - María Dolores Bargues
- Departamento de Parasitología, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos IIII, Madrid, Spain
| | - Santiago Mas-Coma
- Departamento de Parasitología, Facultad de Farmacia, Universidad de Valencia, Valencia, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos IIII, Madrid, Spain
| | - Mar Siles-Lucas
- Laboratory of Helminth Parasites of Zoonotic Importance (ATENEA), Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), Salamanca, Spain
| | - Javier González-Miguel
- Laboratory of Helminth Parasites of Zoonotic Importance (ATENEA), Institute of Natural Resources and Agrobiology of Salamanca (IRNASA-CSIC), Salamanca, Spain
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Zwarycz AS, Page T, Nikolova G, Radford EJ, Whitworth DE. Predatory Strategies of Myxococcus xanthus: Prey Susceptibility to OMVs and Moonlighting Enzymes. Microorganisms 2023; 11:microorganisms11040874. [PMID: 37110297 PMCID: PMC10141889 DOI: 10.3390/microorganisms11040874] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/24/2023] [Accepted: 03/25/2023] [Indexed: 03/31/2023] Open
Abstract
Predatory outer membrane vesicles (OMVs) secreted by myxobacteria fuse readily with the outer membranes of Gram-negative bacteria, introducing toxic cargo into their prey. Here we used a strain of the myxobacterium Myxococcus xanthus that produces fluorescent OMVs to assay the uptake of OMVs by a panel of Gram-negative bacteria. M. xanthus strains took up significantly less OMV material than the tested prey strains, suggesting that re-fusion of OMVs with producing organisms is somehow inhibited. The OMV killing activity against different prey correlated strongly with the predatory activity of myxobacterial cells, however, there was no correlation between OMV killing activity and their propensity to fuse with different prey. It has previously been proposed that M. xanthus GAPDH stimulates the predatory activity of OMVs by enhancing OMV fusion with prey cells. Therefore, we expressed and purified active fusion proteins of M. xanthus glyceraldehyde-3-phosphate dehydrogenase and phosphoglycerate kinase (GAPDH and PGK; moonlighting enzymes with additional activities beyond their roles in glycolysis/gluconeogenesis) to investigate any involvement in OMV-mediated predation. Neither GAPDH nor PGK caused lysis of prey cells or enhanced OMV-mediated lysis of prey cells. However, both enzymes were found to inhibit the growth of Escherichia coli, even in the absence of OMVs. Our results suggest that fusion efficiency is not a determinant of prey killing, but instead resistance to the cargo of OMVs and co-secreted enzymes dictates whether organisms can be preyed upon by myxobacteria.
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34
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Li Y, Huang J, Bao L, Zhu J, Duan W, Zheng H, Wang H, Jiang Y, Liu W, Zhang M, Yu Y, Yi C, Ji X. RNA Pol II preferentially regulates ribosomal protein expression by trapping disassociated subunits. Mol Cell 2023; 83:1280-1297.e11. [PMID: 36924766 DOI: 10.1016/j.molcel.2023.02.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 12/12/2022] [Accepted: 02/23/2023] [Indexed: 03/17/2023]
Abstract
RNA polymerase II (RNA Pol II) has been recognized as a passively regulated multi-subunit holoenzyme. However, the extent to which RNA Pol II subunits might be important beyond the RNA Pol II complex remains unclear. Here, fractions containing disassociated RPB3 (dRPB3) were identified by size exclusion chromatography in various cells. Through a unique strategy, i.e., "specific degradation of disassociated subunits (SDDS)," we demonstrated that dRPB3 functions as a regulatory component of RNA Pol II to enable the preferential control of 3' end processing of ribosomal protein genes directly through its N-terminal domain. Machine learning analysis of large-scale genomic features revealed that the little elongation complex (LEC) helps to specialize the functions of dRPB3. Mechanistically, dRPB3 facilitates CBC-PCF11 axis activity to increase the efficiency of 3' end processing. Furthermore, RPB3 is dynamically regulated during development and diseases. These findings suggest that RNA Pol II gains specific regulatory functions by trapping disassociated subunits in mammalian cells.
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Affiliation(s)
- Yuanjun Li
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jie Huang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Lijun Bao
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Junyi Zhu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Wenjia Duan
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Haonan Zheng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yongpeng Jiang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Weiwei Liu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Meiling Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yang Yu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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Cell surface-bound La protein regulates the cell fusion stage of osteoclastogenesis. Nat Commun 2023; 14:616. [PMID: 36739273 PMCID: PMC9899215 DOI: 10.1038/s41467-023-36168-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/16/2023] [Indexed: 02/06/2023] Open
Abstract
Multinucleated osteoclasts, essential for skeletal remodeling in health and disease, are formed by the fusion of osteoclast precursors, where each fusion event raises their bone-resorbing activity. Here we show that the nuclear RNA chaperone, La protein has an additional function as an osteoclast fusion regulator. Monocyte-to-osteoclast differentiation starts with a drastic decrease in La levels. As fusion begins, La reappears as a low molecular weight species at the osteoclast surface, where it promotes fusion. La's role in promoting osteoclast fusion is independent of canonical La-RNA interactions and involves direct interactions between La and Annexin A5, which anchors La to transiently exposed phosphatidylserine at the surface of fusing osteoclasts. Disappearance of cell-surface La, and the return of full length La to the nuclei of mature, multinucleated osteoclasts, acts as an off switch of their fusion activity. Targeting surface La in a novel explant model of fibrous dysplasia inhibits excessive osteoclast formation characteristic of this disease, highlighting La's potential as a therapeutic target.
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36
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Yadav P, Singh R, Sur S, Bansal S, Chaudhry U, Tandon V. Moonlighting proteins: beacon of hope in era of drug resistance in bacteria. Crit Rev Microbiol 2023; 49:57-81. [PMID: 35220864 DOI: 10.1080/1040841x.2022.2036695] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Moonlighting proteins (MLPs) are ubiquitous and provide a unique advantage to bacteria performing multiple functions using the same genomic content. Targeting MLPs can be considered as a futuristic approach in fighting drug resistance problem. This review follows the MLP trail from its inception to the present-day state, describing a few bacterial MLPs, viz., glyceraldehyde 3'-phosphate dehydrogenase, phosphoglucose isomerase glutamate racemase (GR), and DNA gyrase. Here, we carve out that targeting MLPs are the beacon of hope in an era of increasing drug resistance in bacteria. Evolutionary stability, structure-functional relationships, protein diversity, possible drug targets, and identification of new drugs against bacterial MLP are given due consideration. Before the final curtain calls, we provide a comprehensive list of small molecules that inhibit the biochemical activity of MLPs, which can aid the development of novel molecules to target MLPs for therapeutic applications.
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Affiliation(s)
- Pramod Yadav
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India.,Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, New Delhi, India
| | - Raja Singh
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
| | - Souvik Sur
- Research and Development Center, Teerthanker Mahaveer University, Uttar Pradesh, India
| | - Sandhya Bansal
- Norton Thoracic Institute, St. Joseph's Hospital, and Medical Center, Phoenix, AZ, USA
| | - Uma Chaudhry
- Bhaskaracharya College of Applied Sciences, University of Delhi, New Delhi, India
| | - Vibha Tandon
- Special Center for Molecular Medicine, Jawaharlal Nehru University, New Delhi, India
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Rieu P, Turchi L, Thévenon E, Zarkadas E, Nanao M, Chahtane H, Tichtinsky G, Lucas J, Blanc-Mathieu R, Zubieta C, Schoehn G, Parcy F. The F-box protein UFO controls flower development by redirecting the master transcription factor LEAFY to new cis-elements. NATURE PLANTS 2023; 9:315-329. [PMID: 36732360 DOI: 10.1038/s41477-022-01336-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
In angiosperms, flower development requires the combined action of the transcription factor LEAFY (LFY) and the ubiquitin ligase adaptor F-box protein, UNUSUAL FLORAL ORGANS (UFO), but the molecular mechanism underlying this synergy has remained unknown. Here we show in transient assays and stable transgenic plants that the connection to ubiquitination pathways suggested by the UFO F-box domain is mostly dispensable. On the basis of biochemical and genome-wide studies, we establish that UFO instead acts by forming an active transcriptional complex with LFY at newly discovered regulatory elements. Structural characterization of the LFY-UFO-DNA complex by cryo-electron microscopy further demonstrates that UFO performs this function by directly interacting with both LFY and DNA. Finally, we propose that this complex might have a deep evolutionary origin, largely predating flowering plants. This work reveals a unique mechanism of an F-box protein directly modulating the DNA binding specificity of a master transcription factor.
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Affiliation(s)
- Philippe Rieu
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France
| | - Laura Turchi
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France
- Translational Innovation in Medicine and Complexity, Université Grenoble Alpes, CNRS, Grenoble, France
| | - Emmanuel Thévenon
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France
| | - Eleftherios Zarkadas
- IBS, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
- EMBL, ISBG, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
| | - Max Nanao
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble, France
| | - Hicham Chahtane
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France
- Green Mission Pierre Fabre, Conservatoire Botanique Pierre Fabre, Institut de Recherche Pierre Fabre, Soual, France
| | - Gabrielle Tichtinsky
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France
| | - Jérémy Lucas
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France
| | - Romain Blanc-Mathieu
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France
| | - Chloe Zubieta
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France
| | - Guy Schoehn
- IBS, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, IRIG-DBSCI-LPCV, Université Grenoble Alpes, CEA, CNRS, INRAE, Grenoble, France.
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Hendriks WJAJ, van Cruchten RTP, Pulido R. Hereditable variants of classical protein tyrosine phosphatase genes: Will they prove innocent or guilty? Front Cell Dev Biol 2023; 10:1051311. [PMID: 36755664 PMCID: PMC9900141 DOI: 10.3389/fcell.2022.1051311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/28/2022] [Indexed: 01/24/2023] Open
Abstract
Protein tyrosine phosphatases, together with protein tyrosine kinases, control many molecular signaling steps that control life at cellular and organismal levels. Impairing alterations in the genes encoding the involved proteins is expected to profoundly affect the quality of life-if compatible with life at all. Here, we review the current knowledge on the effects of germline variants that have been reported for genes encoding a subset of the protein tyrosine phosphatase superfamily; that of the thirty seven classical members. The conclusion must be that the newest genome research tools produced an avalanche of data that suggest 'guilt by association' for individual genes to specific disorders. Future research should face the challenge to investigate these accusations thoroughly and convincingly, to reach a mature genotype-phenotype map for this intriguing protein family.
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Affiliation(s)
- Wiljan J. A. J. Hendriks
- Department of Cell Biology, Radboud University Medical Centre, Nijmegen, The Netherlands,*Correspondence: Wiljan J. A. J. Hendriks,
| | | | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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Zande PV, Wittkopp PJ. Active compensation for changes in TDH3 expression mediated by direct regulators of TDH3 in Saccharomyces cerevisiae. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.13.523977. [PMID: 36711763 PMCID: PMC9882118 DOI: 10.1101/2023.01.13.523977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Genetic networks are surprisingly robust to perturbations caused by new mutations. This robustness is conferred in part by compensation for loss of a gene's activity by genes with overlapping functions, such as paralogs. Compensation occurs passively when the normal activity of one paralog can compensate for the loss of the other, or actively when a change in one paralog's expression, localization, or activity is required to compensate for loss of the other. The mechanisms of active compensation remain poorly understood in most cases. Here we investigate active compensation for the loss or reduction in expression of the Saccharomyces cerevisiae gene TDH3 by its paralogs TDH1 and TDH2. TDH1 and TDH2 are upregulated in a dose-dependent manner in response to reductions in TDH3 by a mechanism requiring the shared transcriptional regulators Gcr1p and Rap1p. Other glycolytic genes regulated by Rap1p and Gcr1p show changes in expression similar to TDH2, suggesting that the active compensation by TDH3 paralogs is part of a broader homeostatic response mediated by shared transcriptional regulators.
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Affiliation(s)
- Pétra Vande Zande
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Current address: Department of Microbiology and Immunology, University of Minnesota, Minneapolis, MN, USA
| | - Patricia J Wittkopp
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
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40
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Girish V, Lakhani AA, Scaduto CM, Thompson SL, Brown LM, Hagenson RA, Sausville EL, Mendelson BE, Lukow DA, Yuan ML, Kandikuppa PK, Stevens EC, Lee SN, Salovska B, Li W, Smith JC, Taylor AM, Martienssen RA, Liu Y, Sun R, Sheltzer JM. Oncogene-like addiction to aneuploidy in human cancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523344. [PMID: 36711674 PMCID: PMC9882055 DOI: 10.1101/2023.01.09.523344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Most cancers exhibit aneuploidy, but its functional significance in tumor development is controversial. Here, we describe ReDACT (Restoring Disomy in Aneuploid cells using CRISPR Targeting), a set of chromosome engineering tools that allow us to eliminate specific aneuploidies from cancer genomes. Using ReDACT, we created a panel of isogenic cells that have or lack common aneuploidies, and we demonstrate that trisomy of chromosome 1q is required for malignant growth in cancers harboring this alteration. Mechanistically, gaining chromosome 1q increases the expression of MDM4 and suppresses TP53 signaling, and we show that TP53 mutations are mutually-exclusive with 1q aneuploidy in human cancers. Thus, specific aneuploidies play essential roles in tumorigenesis, raising the possibility that targeting these "aneuploidy addictions" could represent a novel approach for cancer treatment.
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Affiliation(s)
- Vishruth Girish
- Yale University School of Medicine, New Haven, CT 06511
- Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | | | | | | | | | | | | | | | | | - Monet Lou Yuan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
| | | | | | - Sophia N. Lee
- Yale University School of Medicine, New Haven, CT 06511
| | | | - Wenxue Li
- Yale University School of Medicine, New Haven, CT 06511
| | - Joan C. Smith
- Yale University School of Medicine, New Haven, CT 06511
| | | | - Robert A. Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yansheng Liu
- Yale University School of Medicine, New Haven, CT 06511
| | - Ruping Sun
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455
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Ahandoust S, Li K, Sun X, Li BY, Yokota H, Na S. Intracellular and extracellular moesins differentially regulate Src activity and β-catenin translocation to the nucleus in breast cancer cells. Biochem Biophys Res Commun 2023; 639:62-69. [PMID: 36470073 DOI: 10.1016/j.bbrc.2022.11.075] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 11/24/2022] [Indexed: 11/30/2022]
Abstract
It is increasingly recognized that a single protein can have multiple, sometimes paradoxical, roles in cell functions as well as pathological conditions depending on its cellular locations. Here we report that moesins (MSNs) in the intracellular and extracellular domains present opposing roles in pro-tumorigenic signaling in breast cancer cells. Using live cell imaging with fluorescence resonance energy transfer (FRET)- and green fluorescent protein (GFP)-based biosensors, we investigated the molecular mechanism underlying the cellular location-dependent effect of MSN on Src and β-catenin signaling in MDA-MB-231 breast cancer cells. Inhibition of intracellular MSN decreased the activities of Src and FAK, whereas overexpression of intracellular MSN increased them. By contrast, extracellular MSN decreased the activities of Src, FAK, and RhoA, as well as β-catenin translocation to the nucleus. Consistently, Western blotting and MTT-based analysis showed that overexpression of intracellular MSN elevated the expression of oncogenic genes, such as p-Src, β-catenin, Lrp5, MMP9, Runx2, and Snail, as well as cell viability, whereas extracellular MSN suppressed them. Conditioned medium derived from MSN-overexpressing mesenchymal stem cells or osteocytes showed the anti-tumor effects by inhibiting the Src activity and β-catenin translocation to the nucleus as well as the activities of FAK and RhoA and MTT-based cell viability. Conditioned medium derived from MSN-inhibited cells increased the Src activity, but it did not affect the activities of FAK and RhoA. Silencing CD44 and/or FN1 in MDA-MB-231 cells blocked the suppression of Src activity and β-catenin accumulation in the nucleus by extracellular MSN. Collectively, the results suggest that cellular location-specific MSN is a strong regulator of Src and β-catenin signaling in breast cancer cells, and that extracellular MSN exerts tumor-suppressive effects via its interaction with CD44 and FN1.
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Affiliation(s)
- Sina Ahandoust
- Department of Biomedical Engineering, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Kexin Li
- Department of Biomedical Engineering, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA; Department of Pharmacology, School of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Xun Sun
- Department of Biomedical Engineering, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA; Department of Pharmacology, School of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Bai-Yan Li
- Department of Pharmacology, School of Pharmacy, Harbin Medical University, Harbin, 150081, China
| | - Hiroki Yokota
- Department of Biomedical Engineering, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Sungsoo Na
- Department of Biomedical Engineering, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202, USA.
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Huerta M, Franco-Serrano L, Amela I, Perez-Pons JA, Piñol J, Mozo-Villarías A, Querol E, Cedano J. Role of Moonlighting Proteins in Disease: Analyzing the Contribution of Canonical and Moonlighting Functions in Disease Progression. Cells 2023; 12:cells12020235. [PMID: 36672169 PMCID: PMC9857295 DOI: 10.3390/cells12020235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 01/09/2023] Open
Abstract
The term moonlighting proteins refers to those proteins that present alternative functions performed by a single polypeptide chain acquired throughout evolution (called canonical and moonlighting, respectively). Over 78% of moonlighting proteins are involved in human diseases, 48% are targeted by current drugs, and over 25% of them are involved in the virulence of pathogenic microorganisms. These facts encouraged us to study the link between the functions of moonlighting proteins and disease. We found a large number of moonlighting functions activated by pathological conditions that are highly involved in disease development and progression. The factors that activate some moonlighting functions take place only in pathological conditions, such as specific cellular translocations or changes in protein structure. Some moonlighting functions are involved in disease promotion while others are involved in curbing it. The disease-impairing moonlighting functions attempt to restore the homeostasis, or to reduce the damage linked to the imbalance caused by the disease. The disease-promoting moonlighting functions primarily involve the immune system, mesenchyme cross-talk, or excessive tissue proliferation. We often find moonlighting functions linked to the canonical function in a pathological context. Moonlighting functions are especially coordinated in inflammation and cancer. Wound healing and epithelial to mesenchymal transition are very representative. They involve multiple moonlighting proteins with a different role in each phase of the process, contributing to the current-phase phenotype or promoting a phase switch, mitigating the damage or intensifying the remodeling. All of this implies a new level of complexity in the study of pathology genesis, progression, and treatment. The specific protein function involved in a patient's progress or that is affected by a drug must be elucidated for the correct treatment of diseases.
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Comparative RNA-Sequencing Analysis Reveals High Complexity and Heterogeneity of Transcriptomic and Immune Profiles in Hepatocellular Carcinoma Tumors of Viral (HBV, HCV) and Non-Viral Etiology. MEDICINA (KAUNAS, LITHUANIA) 2022; 58:medicina58121803. [PMID: 36557005 PMCID: PMC9785216 DOI: 10.3390/medicina58121803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022]
Abstract
Background and Objectives: Hepatocellular carcinoma (HCC), the most common type of primary liver cancer, is the leading cause of cancer-related mortality. It arises and progresses against fibrotic or cirrhotic backgrounds mainly due to infection with hepatitis viruses B (HBV) or C (HCV) or non-viral causes that lead to chronic inflammation and genomic changes. A better understanding of molecular and immune mechanisms in HCC subtypes is needed. Materials and Methods: To identify transcriptional changes in primary HCC tumors with or without hepatitis viral etiology, we analyzed the transcriptomes of 24 patients by next-generation sequencing. Results: We identified common and unique differentially expressed genes for each etiological tumor group and analyzed the expression of SLC, ATP binding cassette, cytochrome 450, cancer testis, and heat shock protein genes. Metascape functional enrichment analysis showed mainly upregulated cell-cycle pathways in HBV and HCV and upregulated cell response to stress in non-viral infection. GeneWalk analysis identified regulator, hub, and moonlighting genes and highlighted CCNB1, ACTN2, BRCA1, IGF1, CDK1, AURKA, AURKB, and TOP2A in the HCV group and HSF1, HSPA1A, HSP90AA1, HSPB1, HSPA5, PTK2, and AURKB in the group without viral infection as hub genes. Immune infiltrate analysis showed that T cell, cytotoxic, and natural killer cell markers were significantly more highly expressed in HCV than in non-viral tumors. Genes associated with monocyte activation had the highest expression levels in HBV, while high expression of genes involved in primary adaptive immune response and complement receptor activity characterized tumors without viral infection. Conclusions: Our comprehensive study underlines the high degree of complexity of immune profiles in the analyzed groups, which adds to the heterogeneous HCC genomic landscape. The biomarkers identified in each HCC group might serve as therapeutic targets.
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Sales de Queiroz A, Sales Santa Cruz G, Jean-Marie A, Mazauric D, Roux J, Cazals F. Gene prioritization based on random walks with restarts and absorbing states, to define gene sets regulating drug pharmacodynamics from single-cell analyses. PLoS One 2022; 17:e0268956. [PMID: 36342924 PMCID: PMC9639845 DOI: 10.1371/journal.pone.0268956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 05/12/2022] [Indexed: 11/09/2022] Open
Abstract
Prioritizing genes for their role in drug sensitivity, is an important step in understanding drugs mechanisms of action and discovering new molecular targets for co-treatment. To formalize this problem, we consider two sets of genes X and P respectively composing the gene signature of cell sensitivity at the drug IC50 and the genes involved in its mechanism of action, as well as a protein interaction network (PPIN) containing the products of X and P as nodes. We introduce Genetrank, a method to prioritize the genes in X for their likelihood to regulate the genes in P. Genetrank uses asymmetric random walks with restarts, absorbing states, and a suitable renormalization scheme. Using novel so-called saturation indices, we show that the conjunction of absorbing states and renormalization yields an exploration of the PPIN which is much more progressive than that afforded by random walks with restarts only. Using MINT as underlying network, we apply Genetrank to a predictive gene signature of cancer cells sensitivity to tumor-necrosis-factor-related apoptosis-inducing ligand (TRAIL), performed in single-cells. Our ranking provides biological insights on drug sensitivity and a gene set considerably enriched in genes regulating TRAIL pharmacodynamics when compared to the most significant differentially expressed genes obtained from a statistical analysis framework alone. We also introduce gene expression radars, a visualization tool embedded in MA plots to assess all pairwise interactions at a glance on graphical representations of transcriptomics data. Genetrank is made available in the Structural Bioinformatics Library (https://sbl.inria.fr/doc/Genetrank-user-manual.html). It should prove useful for mining gene sets in conjunction with a signaling pathway, whenever other approaches yield relatively large sets of genes.
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Affiliation(s)
| | | | | | | | - Jérémie Roux
- CNRS UMR 7284, Inserm U 1081, Institut de Recherche sur le Cancer et le Vieillissement de Nice, Centre Antoine Lacassagne, Universite Côte d’Azur, Nice, France
- * E-mail: (FC); (JR)
| | - Frédéric Cazals
- Inria, Université Côte d’Azur, Nice, France
- * E-mail: (FC); (JR)
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Ranava D, Scheidler CM, Pfanzelt M, Fiedler M, Sieber SA, Schneider S, Yap MNF. Bidirectional sequestration between a bacterial hibernation factor and a glutamate metabolizing protein. Proc Natl Acad Sci U S A 2022; 119:e2207257119. [PMID: 36122228 PMCID: PMC9522360 DOI: 10.1073/pnas.2207257119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/29/2022] [Indexed: 11/18/2022] Open
Abstract
Bacterial hibernating 100S ribosomes (the 70S dimers) are excluded from translation and are protected from ribonucleolytic degradation, thereby promoting long-term viability and increased regrowth. No extraribosomal target of any hibernation factor has been reported. Here, we discovered a previously unrecognized binding partner (YwlG) of hibernation-promoting factor (HPF) in the human pathogen Staphylococcus aureus. YwlG is an uncharacterized virulence factor in S. aureus. We show that the HPF-YwlG interaction is direct, independent of ribosome binding, and functionally linked to cold adaptation and glucose metabolism. Consistent with the distant resemblance of YwlG to the hexameric structures of nicotinamide adenine dinucleotide (NAD)-specific glutamate dehydrogenases (GDHs), YwlG overexpression can compensate for a loss of cellular GDH activity. The reduced abundance of 100S complexes and the suppression of YwlG-dependent GDH activity provide evidence for a two-way sequestration between YwlG and HPF. These findings reveal an unexpected layer of regulation linking the biogenesis of 100S ribosomes to glutamate metabolism.
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Affiliation(s)
- David Ranava
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | | | - Martin Pfanzelt
- Department of Chemistry, Chair of Organic Chemistry III, Center for Functional Protein Assemblies (CPA), Technische Universität München, 80333 Garching, Germany
| | - Michaela Fiedler
- Department of Chemistry, Chair of Organic Chemistry III, Center for Functional Protein Assemblies (CPA), Technische Universität München, 80333 Garching, Germany
| | - Stephan A. Sieber
- Department of Chemistry, Chair of Organic Chemistry III, Center for Functional Protein Assemblies (CPA), Technische Universität München, 80333 Garching, Germany
| | - Sabine Schneider
- Department of Chemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Mee-Ngan F. Yap
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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Hurtado-Rios JJ, Carrasco-Navarro U, Almanza-Pérez JC, Ponce-Alquicira E. Ribosomes: The New Role of Ribosomal Proteins as Natural Antimicrobials. Int J Mol Sci 2022; 23:ijms23169123. [PMID: 36012387 PMCID: PMC9409020 DOI: 10.3390/ijms23169123] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/08/2022] [Accepted: 08/11/2022] [Indexed: 12/14/2022] Open
Abstract
Moonlighting proteins are those capable of performing more than one biochemical or biophysical function within the same polypeptide chain. They have been a recent focus of research due to their potential applications in the health, pharmacological, and nutritional sciences. Among them, some ribosomal proteins involved in assembly and protein translation have also shown other functionalities, including inhibiting infectious bacteria, viruses, parasites, fungi, and tumor cells. Therefore, they may be considered antimicrobial peptides (AMPs). However, information regarding the mechanism of action of ribosomal proteins as AMPs is not yet fully understood. Researchers have suggested that the antimicrobial activity of ribosomal proteins may be associated with an increase in intracellular reactive oxidative species (ROS) in target cells, which, in turn, could affect membrane integrity and cause their inactivation and death. Moreover, the global overuse of antibiotics has resulted in an increase in pathogenic bacteria resistant to common antibiotics. Therefore, AMPs such as ribosomal proteins may have potential applications in the pharmaceutical and food industries in the place of antibiotics. This article provides an overview of the potential roles of ribosomes and AMP ribosomal proteins in conjunction with their potential applications.
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Affiliation(s)
- Jessica J. Hurtado-Rios
- Departamento de Biotecnología, Universidad Autónoma Metropolitana Unidad Iztapalapa, Av. San Rafael Atlixco 186, Col. Vicentina, Ciudad de México 09340, Mexico
| | - Ulises Carrasco-Navarro
- Departamento de Biotecnología, Universidad Autónoma Metropolitana Unidad Iztapalapa, Av. San Rafael Atlixco 186, Col. Vicentina, Ciudad de México 09340, Mexico
| | - Julio Cesar Almanza-Pérez
- Departamento de Ciencias de la Salud, Universidad Autónoma Metropolitana Unidad Iztapalapa, Av. San Rafael Atlixco 186, Col. Vicentina, Ciudad de México 09340, Mexico
| | - Edith Ponce-Alquicira
- Departamento de Biotecnología, Universidad Autónoma Metropolitana Unidad Iztapalapa, Av. San Rafael Atlixco 186, Col. Vicentina, Ciudad de México 09340, Mexico
- Correspondence: ; Tel.: +52-55-58044600 (ext. 2676)
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Messina G, Prozzillo Y, Monache FD, Santopietro MV, Dimitri P. Evolutionary conserved relocation of chromatin remodeling complexes to the mitotic apparatus. BMC Biol 2022; 20:172. [PMID: 35922843 PMCID: PMC9351137 DOI: 10.1186/s12915-022-01365-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/29/2022] [Indexed: 01/02/2023] Open
Abstract
Background ATP-dependent chromatin remodeling complexes are multi-protein machines highly conserved across eukaryotic genomes. They control sliding and displacing of the nucleosomes, modulating histone-DNA interactions and making nucleosomal DNA more accessible to specific binding proteins during replication, transcription, and DNA repair, which are processes involved in cell division. The SRCAP and p400/Tip60 chromatin remodeling complexes in humans and the related Drosophila Tip60 complex belong to the evolutionary conserved INO80 family, whose main function is promoting the exchange of canonical histone H2A with the histone variant H2A in different eukaryotic species. Some subunits of these complexes were additionally shown to relocate to the mitotic apparatus and proposed to play direct roles in cell division in human cells. However, whether this phenomenon reflects a more general function of remodeling complex components and its evolutionary conservation remains unexplored. Results We have combined cell biology, reverse genetics, and biochemical approaches to study the subcellular distribution of a number of subunits belonging to the SRCAP and p400/Tip60 complexes and assess their involvement during cell division progression in HeLa cells. Interestingly, beyond their canonical chromatin localization, the subunits under investigation accumulate at different sites of the mitotic apparatus (centrosomes, spindle, and midbody), with their depletion yielding an array of aberrant outcomes of mitosis and cytokinesis, thus causing genomic instability. Importantly, this behavior was conserved by the Drosophila melanogaster orthologs tested, despite the evolutionary divergence between fly and humans has been estimated at approximately 780 million years ago. Conclusions Overall, our results support the existence of evolutionarily conserved diverse roles of chromatin remodeling complexes, whereby subunits of the SRCAP and p400/Tip60 complexes relocate from the interphase chromatin to the mitotic apparatus, playing moonlighting functions required for proper execution of cell division. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01365-5.
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Affiliation(s)
- Giovanni Messina
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy. .,Istituto Pasteur Italia, Fondazione Cenci Bolognetti, Rome, Italy.
| | - Yuri Prozzillo
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | - Francesca Delle Monache
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy
| | | | - Patrizio Dimitri
- Dipartimento di Biologia e Biotecnologie "Charles Darwin", Sapienza Università di Roma, Rome, Italy.
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Gantsova EA, Gavrilenkova AA, Serova OV, Deyev IE. Changes in the Expression of the gapdh Gene in the Organs of insrr Knockout Mice. DOKLADY BIOLOGICAL SCIENCES : PROCEEDINGS OF THE ACADEMY OF SCIENCES OF THE USSR, BIOLOGICAL SCIENCES SECTIONS 2022; 505:113-118. [PMID: 36038798 DOI: 10.1134/s0012496622040056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Revised: 05/10/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
The most important property of a living organism is the maintenance of optimal acid-base balance and the ionic composition of the internal environment. The kidneys are one of the main pH-regulating organs in the body. Receptor tyrosine kinase IRR (an insulin receptor-related receptor) is an alkaline pH-sensor. In mice (Mus Musculus) with a knockout of the insrr gene encoding the IRR receptor, bicarbonate secretion is impaired under the conditions of alkaline loading, which indicates the role of the receptor tyrosine kinase IRR in the regulation of acid-base balance in the body. In order to search for proteins functionally associated with the receptor tyrosine kinase IRR, we performed a large-scale sequencing of the mouse kidney transcriptome of wild type and insrr knockout mice kept under normal conditions and under alkaline conditions. As a result, we found a decrease in the gapdh gene expression in the kidneys of insrr knockout mice compared to wild type mice. RNA sequencing data were confirmed by TaqMan real-time PCR and Western blotting. Using the TaqMan real-time PCR method, we revealed a decrease in the level of gapdh expression not only in the kidneys, but also in the liver and brain of insrr knockout mice. Thus, the changes in the gapdh gene expression in the kidneys of insrr knockout mice may indicate a functional relationship between genes and a possible role of GAPDH in previously undescribed molecular mechanisms of regulation of acid-base balance in the body.
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Affiliation(s)
- E A Gantsova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, 117997, Moscow, Russia.
| | - A A Gavrilenkova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, 117997, Moscow, Russia
- Moscow Institute of Physics and Technology, 141701, Dolgoprudnyi, Moscov oblast, Russia
| | - O V Serova
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, 117997, Moscow, Russia
| | - I E Deyev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, 117997, Moscow, Russia
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Su L, Sun Z, Qi F, Su H, Qian L, Li J, Zuo L, Huang J, Yu Z, Li J, Chen Z, Zhang S. GRP75-driven, cell-cycle-dependent macropinocytosis of Tat/pDNA-Ca 2+ nanoparticles underlies distinct gene therapy effect in ovarian cancer. J Nanobiotechnology 2022; 20:340. [PMID: 35858873 PMCID: PMC9301890 DOI: 10.1186/s12951-022-01530-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/26/2022] [Indexed: 11/10/2022] Open
Abstract
Practice of tumor-targeted suicide gene therapy is hampered by unsafe and low efficient delivery of plasmid DNA (pDNA). Using HIV-Tat-derived peptide (Tat) to non-covalently form Tat/pDNA complexes advances the delivery performance. However, this innovative approach is still limited by intracellular delivery efficiency and cell-cycle status. In this study, Tat/pDNA complexes were further condensed into smaller, nontoxic nanoparticles by Ca2+ addition. Formulated Tat/pDNA-Ca2+ nanoparticles mainly use macropinocytosis for intercellular delivery, and their macropinocytic uptake was persisted in mitosis (M-) phase and highly activated in DNA synthesis (S-) phase of cell-cycle. Over-expression or phosphorylation of a mitochondrial chaperone, 75-kDa glucose-regulated protein (GRP75), promoted monopolar spindle kinase 1 (MPS1)-controlled centrosome duplication and cell-cycle progress, but also driven cell-cycle-dependent macropinocytosis of Tat/pDNA-Ca2+ nanoparticles. Further in vivo molecular imaging based on DF (Fluc-eGFP)-TF (RFP-Rluc-HSV-ttk) system showed that Tat/pDNA-Ca2+ nanoparticles exhibited highly suicide gene therapy efficiency in mouse model xenografted with human ovarian cancer. Furthermore, arresting cell-cycle at S-phase markedly enhanced delivery performance of Tat/pDNA-Ca2+ nanoparticles, whereas targeting GRP75 reduced their macropinocytic delivery. More importantly, in vivo targeting GRP75 combined with cell-cycle or macropinocytosis inhibitors exhibited distinct suicide gene therapy efficiency. In summary, our data highlight that mitochondrial chaperone GRP75 moonlights as a biphasic driver underlying cell-cycle-dependent macropinocytosis of Tat/pDNA-Ca2+ nanoparticles in ovarian cancer.
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Affiliation(s)
- Linjia Su
- Department of Cell Biology, School of Medicine, Nankai University, Nankai District, 94 Weijin Road, Tianjin, 300071, People's Republic of China
| | - Zhe Sun
- School of Life Sciences, Tianjin University, Weijin Road 92, Tianjin, 300072, China
| | - Fangzheng Qi
- Department of Cell Biology, School of Medicine, Nankai University, Nankai District, 94 Weijin Road, Tianjin, 300071, People's Republic of China
| | - Huishan Su
- Department of Cell Biology, School of Medicine, Nankai University, Nankai District, 94 Weijin Road, Tianjin, 300071, People's Republic of China
| | - Luomeng Qian
- Department of Cell Biology, School of Medicine, Nankai University, Nankai District, 94 Weijin Road, Tianjin, 300071, People's Republic of China
| | - Jing Li
- Department of Cell Biology, School of Medicine, Nankai University, Nankai District, 94 Weijin Road, Tianjin, 300071, People's Republic of China
| | - Liang Zuo
- Department of Cell Biology, School of Medicine, Nankai University, Nankai District, 94 Weijin Road, Tianjin, 300071, People's Republic of China
| | - Jinhai Huang
- School of Life Sciences, Tianjin University, Weijin Road 92, Tianjin, 300072, China
| | - Zhilin Yu
- State Key Laboratory of Medicinal Chemical Biology, College of Chemistry, Nankai University, Weijin Road 94, Tianjin, 300071, China
| | - Jinping Li
- Department of Medical Biochemistry and Microbiology, Uppsala University, 75123, Uppsala, Sweden
| | - Zhinan Chen
- National Translational Science Center for Molecular Medicine, Department of Cell Biology, State Key Laboratory of Cancer Biology, Fourth Military Medical University, Xi'an, 710032, China
| | - Sihe Zhang
- Department of Cell Biology, School of Medicine, Nankai University, Nankai District, 94 Weijin Road, Tianjin, 300071, People's Republic of China.
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50
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Manrubia S. The simple emergence of complex molecular function. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2022; 380:20200422. [PMID: 35599566 DOI: 10.1098/rsta.2020.0422] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
At odds with a traditional view of molecular evolution that seeks a descent-with-modification relationship between functional sequences, new functions can emerge de novo with relative ease. At early times of molecular evolution, random polymers could have sufficed for the appearance of incipient chemical activity, while the cellular environment harbours a myriad of proto-functional molecules. The emergence of function is facilitated by several mechanisms intrinsic to molecular organization, such as redundant mapping of sequences into structures, phenotypic plasticity, modularity or cooperative associations between genomic sequences. It is the availability of niches in the molecular ecology that filters new potentially functional proposals. New phenotypes and subsequent levels of molecular complexity could be attained through combinatorial explorations of currently available molecular variants. Natural selection does the rest. This article is part of the theme issue 'Emergent phenomena in complex physical and socio-technical systems: from cells to societies'.
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Affiliation(s)
- Susanna Manrubia
- Grupo Interdisciplinar de Sistemas Complejos (GISC), Madrid, Spain
- Systems Biology Department, National Biotechnology Centre (CSIC), c/Darwin 3, 28049 Madrid, Spain
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