1
|
Cabukusta B, Borst Pauwels S, Akkermans JJLL, Blomberg N, Mulder AA, Koning RI, Giera M, Neefjes J. The ORP9-ORP11 dimer promotes sphingomyelin synthesis. eLife 2024; 12:RP91345. [PMID: 39106189 PMCID: PMC11302984 DOI: 10.7554/elife.91345] [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: 08/09/2024] Open
Abstract
Numerous lipids are heterogeneously distributed among organelles. Most lipid trafficking between organelles is achieved by a group of lipid transfer proteins (LTPs) that carry lipids using their hydrophobic cavities. The human genome encodes many intracellular LTPs responsible for lipid trafficking and the function of many LTPs in defining cellular lipid levels and distributions is unclear. Here, we created a gene knockout library targeting 90 intracellular LTPs and performed whole-cell lipidomics analysis. This analysis confirmed known lipid disturbances and identified new ones caused by the loss of LTPs. Among these, we found major sphingolipid imbalances in ORP9 and ORP11 knockout cells, two proteins of previously unknown function in sphingolipid metabolism. ORP9 and ORP11 form a heterodimer to localize at the ER-trans-Golgi membrane contact sites, where the dimer exchanges phosphatidylserine (PS) for phosphatidylinositol-4-phosphate (PI(4)P) between the two organelles. Consequently, loss of either protein causes phospholipid imbalances in the Golgi apparatus that result in lowered sphingomyelin synthesis at this organelle. Overall, our LTP knockout library toolbox identifies various proteins in control of cellular lipid levels, including the ORP9-ORP11 heterodimer, which exchanges PS and PI(4)P at the ER-Golgi membrane contact site as a critical step in sphingomyelin synthesis in the Golgi apparatus.
Collapse
Affiliation(s)
- Birol Cabukusta
- Cell and Chemical Biology, Oncode Institute, Leiden University Medical CenterLeidenNetherlands
| | - Shalom Borst Pauwels
- Cell and Chemical Biology, Oncode Institute, Leiden University Medical CenterLeidenNetherlands
| | - Jimmy JLL Akkermans
- Cell and Chemical Biology, Oncode Institute, Leiden University Medical CenterLeidenNetherlands
| | - Niek Blomberg
- Centre for Proteomics and Metabolomics, Leiden University Medical CenterLeidenNetherlands
| | - Aat A Mulder
- Electron Microscopy Facility, Cell and Chemical Biology, Leiden University Medical CenterLeidenNetherlands
| | - Roman I Koning
- Electron Microscopy Facility, Cell and Chemical Biology, Leiden University Medical CenterLeidenNetherlands
| | - Martin Giera
- Centre for Proteomics and Metabolomics, Leiden University Medical CenterLeidenNetherlands
| | - Jacques Neefjes
- Cell and Chemical Biology, Oncode Institute, Leiden University Medical CenterLeidenNetherlands
| |
Collapse
|
2
|
Menary J, Fuller SS. New genomic techniques, old divides: Stakeholder attitudes towards new biotechnology regulation in the EU and UK. PLoS One 2024; 19:e0287276. [PMID: 38446826 PMCID: PMC10917245 DOI: 10.1371/journal.pone.0287276] [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: 06/01/2023] [Accepted: 11/21/2023] [Indexed: 03/08/2024] Open
Abstract
The European Union and United Kingdom are in the process of establishing new regulation regarding the use of new genomic techniques in crop and animal breeding. As part of this process, consultations have been launched to understand the views of stakeholders towards the use of new genomic techniques in plant and animal breeding. The responsible research and innovation framework emphasises the importance of dialogue between technology developers and stakeholders, including the public, but what are the opinions of stakeholders towards the regulation of NGTs in Europe and do they view these consultations as opportunities to engage with technology governance? We conducted semi-structured interviews with experts from a range of agri-food stakeholder groups in the European Union and United Kingdom to understand current attitudes towards new biotechnology regulation, how they viewed the process of consultation in both places and what influence they felt they had in shaping regulations. We found that the discussion is similar in both EU and UK, with predictable and fixed opinions determined by attitudes towards the perceived risks associated with direct mutagenesis. Both UK and EU consultations were considered to have the same weaknesses and stakeholders discussed a desire for more dialogic forms of engagement. We highlight several options for new forms of involvement in biotechnology regulation by exploring relevant responsible research and innovation literature.
Collapse
Affiliation(s)
- Jonathan Menary
- Health Systems Collaborative, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Sebastian S. Fuller
- Health Systems Collaborative, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
3
|
Akizawa H, Lopes EM, Fissore RA. Zn 2+ is essential for Ca 2+ oscillations in mouse eggs. eLife 2023; 12:RP88082. [PMID: 38099643 PMCID: PMC10723796 DOI: 10.7554/elife.88082] [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: 12/17/2023] Open
Abstract
Changes in the intracellular concentration of free calcium (Ca2+) underpin egg activation and initiation of development in animals and plants. In mammals, the Ca2+ release is periodical, known as Ca2+ oscillations, and mediated by the type 1 inositol 1,4,5-trisphosphate receptor (IP3R1). Another divalent cation, zinc (Zn2+), increases exponentially during oocyte maturation and is vital for meiotic transitions, arrests, and polyspermy prevention. It is unknown if these pivotal cations interplay during fertilization. Here, using mouse eggs, we showed that basal concentrations of labile Zn2+ are indispensable for sperm-initiated Ca2+ oscillations because Zn2+-deficient conditions induced by cell-permeable chelators abrogated Ca2+ responses evoked by fertilization and other physiological and pharmacological agonists. We also found that chemically or genetically generated eggs with lower levels of labile Zn2+ displayed reduced IP3R1 sensitivity and diminished ER Ca2+ leak despite the stable content of the stores and IP3R1 mass. Resupplying Zn2+ restarted Ca2+ oscillations, but excessive Zn2+ prevented and terminated them, hindering IP3R1 responsiveness. The findings suggest that a window of Zn2+ concentrations is required for Ca2+ responses and IP3R1 function in eggs, ensuring optimal response to fertilization and egg activation.
Collapse
Affiliation(s)
- Hiroki Akizawa
- Department of Veterinary and Animal Sciences, University of Massachusetts AmherstAmherstUnited States
| | - Emily M Lopes
- Department of Veterinary and Animal Sciences, University of Massachusetts AmherstAmherstUnited States
- Molecular and Cellular Biology Graduate Program, University of MassachusettsAmherstUnited States
| | - Rafael A Fissore
- Department of Veterinary and Animal Sciences, University of Massachusetts AmherstAmherstUnited States
| |
Collapse
|
4
|
Raza S, Wdowiak M, Grotek M, Adamkiewicz W, Nikiforow K, Mente P, Paczesny J. Enhancing the antimicrobial activity of silver nanoparticles against ESKAPE bacteria and emerging fungal pathogens by using tea extracts. NANOSCALE ADVANCES 2023; 5:5786-5798. [PMID: 37881701 PMCID: PMC10597549 DOI: 10.1039/d3na00220a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/12/2023] [Indexed: 10/27/2023]
Abstract
The sale of antibiotics and antifungals has skyrocketed since 2020. The increasing threat of pathogens like ESKAPE bacteria (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), which are effective in evading existing antibiotics, and yeasts like Candida auris or Cryptococcus neoformans is pressing to develop efficient antimicrobial alternatives. Nanoparticles, especially silver nanoparticles (AgNPs), are believed to be promising candidates to supplement or even replace antibiotics in some applications. Here, we propose a way to increase the antimicrobial efficiency of silver nanoparticles by using tea extracts (black, green, or red) for their synthesis. This allows for using lower concentrations of nanoparticles and obtaining the antimicrobial effect in a short time. We found that AgNPs synthesized using green tea extract (G-TeaNPs) are the most effective, causing approximately 80% bacterial cell death in Gram-negative bacteria within only 3 hours at a concentration of 0.1 mg mL-1, which is better than antibiotics. Ampicillin at the same concentration (0.1 mg mL-1) and within the same duration (3 h) causes only up to 40% decrease in the number of S. aureus and E. cloacae cells (non-resistant strains). The tested silver nanoparticles also have antifungal properties and are effective against C. auris and C. neoformans, which are difficult to eradicate using other means. We established that silver nanoparticles synthesized with tea extracts have higher antibacterial properties than silver nanoparticles alone. Such formulations using inexpensive tea extracts and lower concentrations of silver nanoparticles show a promising solution to fight various pathogens.
Collapse
Affiliation(s)
- Sada Raza
- Institute of Physical Chemistry, Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland +48 22 343 2071
| | - Mateusz Wdowiak
- Institute of Physical Chemistry, Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland +48 22 343 2071
| | - Mateusz Grotek
- Institute of Physical Chemistry, Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland +48 22 343 2071
- Military University of Technology gen. Sylwestra Kaliskiego 2 00-908 Warsaw Poland
| | - Witold Adamkiewicz
- Institute of Physical Chemistry, Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland +48 22 343 2071
| | - Kostiantyn Nikiforow
- Institute of Physical Chemistry, Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland +48 22 343 2071
| | - Pumza Mente
- Institute of Physical Chemistry, Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland +48 22 343 2071
| | - Jan Paczesny
- Institute of Physical Chemistry, Polish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland +48 22 343 2071
| |
Collapse
|
5
|
Abstract
Tumour growth and dissemination is largely dependent on nutrient availability. It has recently emerged that the tumour microenvironment is rich in a diverse array of lipids that increase in abundance with tumour progression and play a role in promoting tumour growth and metastasis. Here, we describe the pro-tumorigenic roles of lipid uptake, metabolism and synthesis and detail the therapeutic potential of targeting lipid metabolism in cancer. Additionally, we highlight new insights into the distinct immunosuppressive effects of lipids in the tumour microenvironment. Lipids threaten an anti-tumour environment whereby metabolic adaptation to lipid metabolism is linked to immune dysfunction. Finally, we describe the differential effects of commondietary lipids on cancer growth which may uncover a role for specific dietary regimens in association with traditional cancer therapies. Understanding the relationship between dietary lipids, tumour, and immune cells is important in the context of obesity which may reveal a possibility to harness the diet in the treatment of cancers.
Collapse
|
6
|
R-loop proximity proteomics identifies a role of DDX41 in transcription-associated genomic instability. Nat Commun 2021; 12:7314. [PMID: 34916496 PMCID: PMC8677849 DOI: 10.1038/s41467-021-27530-y] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 11/24/2021] [Indexed: 12/13/2022] Open
Abstract
Transcription poses a threat to genomic stability through the formation of R-loops that can obstruct progression of replication forks. R-loops are three-stranded nucleic acid structures formed by an RNA-DNA hybrid with a displaced non-template DNA strand. We developed RNA-DNA Proximity Proteomics to map the R-loop proximal proteome of human cells using quantitative mass spectrometry. We implicate different cellular proteins in R-loop regulation and identify a role of the tumor suppressor DDX41 in opposing R-loop and double strand DNA break accumulation in promoters. DDX41 is enriched in promoter regions in vivo, and can unwind RNA-DNA hybrids in vitro. R-loop accumulation upon loss of DDX41 is accompanied with replication stress, an increase in the formation of double strand DNA breaks and transcriptome changes associated with the inflammatory response. Germline loss-of-function mutations in DDX41 lead to predisposition to acute myeloid leukemia in adulthood. We propose that R-loop accumulation and genomic instability-associated inflammatory response may contribute to the development of familial AML with mutated DDX41.
Collapse
|
7
|
Kwiecien K, Brzoza P, Bak M, Majewski P, Skulimowska I, Bednarczyk K, Cichy J, Kwitniewski M. The methylation status of the chemerin promoter region located from - 252 to + 258 bp regulates constitutive but not acute-phase cytokine-inducible chemerin expression levels. Sci Rep 2020; 10:13702. [PMID: 32792625 PMCID: PMC7426834 DOI: 10.1038/s41598-020-70625-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 07/29/2020] [Indexed: 12/05/2022] Open
Abstract
Chemerin is a chemoattractant protein with adipokine properties encoded by the retinoic acid receptor responder 2 (RARRES2) gene. It has gained more attention in the past few years due to its multilevel impact on metabolism and immune responses. However, mechanisms controlling the constitutive and regulated expression of RARRES2 in a variety of cell types remain obscure. To our knowledge, this report is the first to show that DNA methylation plays an important role in the cell-specific expression of RARRES2 in adipocytes, hepatocytes, and B lymphocytes. Using luciferase reporter assays, we determined the proximal fragment of the RARRES2 gene promoter, located from - 252 to + 258 bp, to be a key regulator of transcription. Moreover, we showed that chemerin expression is regulated in murine adipocytes by acute-phase cytokines, interleukin 1β and oncostatin M. In contrast with adipocytes, these cytokines exerted a weak, if any, response in mouse hepatocytes, suggesting that the effects of IL-1β and OSM on chemerin expression is specific to fat tissue. Together, our findings highlight previously uncharacterized mediators and mechanisms that control chemerin expression.
Collapse
Affiliation(s)
- Kamila Kwiecien
- Department of Immunology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland
| | - Piotr Brzoza
- Department of Immunology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland
| | - Maciej Bak
- Swiss Institute of Bioinformatics, Biozentrum, University of Basel, 4056, Basel, Switzerland
| | - Pawel Majewski
- Department of Immunology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland
| | - Izabella Skulimowska
- Department of Immunology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland
| | - Kamil Bednarczyk
- Department of Immunology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland
| | - Joanna Cichy
- Department of Immunology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland
| | - Mateusz Kwitniewski
- Department of Immunology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, 30-387, Krakow, Poland.
| |
Collapse
|
8
|
Giese B, Frieß JL, Barton NH, Messer PW, Débarre F, Schetelig MF, Windbichler N, Meimberg H, Boëte C. Gene Drives: Dynamics and Regulatory Matters-A Report from the Workshop "Evaluation of Spatial and Temporal Control of Gene Drives," April 4-5, 2019, Vienna. Bioessays 2019; 41:e1900151. [PMID: 31589334 DOI: 10.1002/bies.201900151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Indexed: 01/19/2023]
Affiliation(s)
- Bernd Giese
- Institute of Safety/Security and Risk Sciences (ISR), University of Natural Resources and Life Sciences (BOKU), 1190, Vienna, Austria
| | - Johannes L Frieß
- Institute of Safety/Security and Risk Sciences (ISR), University of Natural Resources and Life Sciences (BOKU), 1190, Vienna, Austria
| | | | - Philipp W Messer
- Department of Computational Biology, Cornell University, Ithaca, NY, 14853, USA
| | - Florence Débarre
- CNRS, Sorbonne Université, Université Paris Est Créteil, Université Paris Diderot, INRA, IRD, Institute of Ecology and Environmental Sciences (IEES) - Paris, 75005, Paris, France
| | - Marc F Schetelig
- Institute for Insect Biotechnology, Justus-Liebig-University Gießen, 35390, Gießen, Germany
| | - Nikolai Windbichler
- Department of Life Sciences, Imperial College London, South Kensington Campus, SW7 2AZ, London, UK
| | - Harald Meimberg
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences (BOKU), 1180, Vienna, Austria
| | - Christophe Boëte
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France
| |
Collapse
|
9
|
Wang M, Yang D, Ma F, Zhu M, Shi Z, Miao X. OsHLH61-OsbHLH96 influences rice defense to brown planthopper through regulating the pathogen-related genes. RICE (NEW YORK, N.Y.) 2019; 12:9. [PMID: 30796564 PMCID: PMC6386760 DOI: 10.1186/s12284-019-0267-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 02/08/2019] [Indexed: 05/09/2023]
Abstract
BACKGROUND In plants, basic helix-loop-helix (bHLH) proteins form the largest transcription factor (TF) family. Among them, HLH proteins are a small group of atypical members that lack the basic domain, and form dimers with bHLH proteins. Although bHLH proteins have been proved to play important roles in plant development and physiology, the function of HLH proteins is rarely studied, not to mention in plant biotic resistance. Brown planthopper (BPH) is a kind of rice-specific insect that causes devastating yield losses each year. RESULTS In this study, we identified OsHLH61 gene that encodes HLH protein. OsHLH61 gene could be highly induced by BPH infestation. Furthermore, Methyl Jasmonic acid (Me-JA) and cis-12-oxo- phytodienoic acid (OPDA) induced expression of OsHLH61, while SA repressed it. We knocked down expression of OsHLH61 by RNA interference (RNAi), the transgenic plants were susceptible to BPH infestation. RNA-seq analysis revealed that some pathogen-related (PR) genes in the Salicylic acid (SA) signaling pathway that mediate plant immunity were obviously down-regulated in the OsHLH61 RNAi plants. Meanwhile, yeast two-hybrid assay and bimolecular luciferase complementation (BiLC) analysis identified bHLH096 to be an interacting factor of OsHLH61. Also, some PR genes were down-regulated in the OsbHLH96 over expressing lines. Expression of OsbHLH96 was inhibited. Besides, OsbHLH96 might interact with Jasmonate Zim-Domain3 (OsJAZ3). CONCLUSION Altogether, we identified an OsHLH61-OsbHLH96 complex that might mediate defense to BPH through regulating PR genes. And OsHLH61-OsbHLH96 might be important in mediating SA and JA signaling crosstalk.
Collapse
Affiliation(s)
- Meiling Wang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dongyong Yang
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Feilong Ma
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mulan Zhu
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences/Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Zhenying Shi
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xuexia Miao
- Key Laboratory of Insect Developmental and Evolutionary Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| |
Collapse
|
10
|
Technoscience and Biodiversity Conservation. Asian Bioeth Rev 2018; 10:245-259. [PMID: 33717291 DOI: 10.1007/s41649-018-0071-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 11/16/2018] [Accepted: 11/28/2018] [Indexed: 10/26/2022] Open
Abstract
The discovery of CRISPR/Cas9 has opened new avenues in gene editing. This system, usually considered as molecular scissors, permits the cutting of the DNA at a targeted site allowing the introduction of new genes or the removal or the modification of existing ones. The genome-editing, involving gene drive or not, is then considered with a strong interest in a variety of fields ranging from agriculture to public health and conservation biology. Given its controversial aspects, it is then no surprise that actors in biodiversity conservation do express conflicting views on this emerging and disruptive technology. The positions are ranging from a request for a moratorium to the will to test and deploy it in strategies aiming at eradicating invasive species of mammals on islands. Reviewing some of its recent developments brings light on the conflicts of interest, the financial support, and lobbying currently occurring in this growing field of biotechnology. While an optimistic view on the use of gene drive for ecosystem conservation was first promoted by several molecular biologists, the risks and uncertainties associated have now led to some reservations. Overall, the eventual use of this novel approach for conservation raises concerns related to the engagement of the public, the communication between scientists, and the public and the risk of a manufactured consent. There are also a series of essential ethical and philosophical questions on the relations we have with Nature that needs to be answered.
Collapse
|