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Tareb R, Rezé S, Harb M, Dubreil L, Monnet V, Björkroth J, Passerini D, Leroi F, Pilet MF. A bacteriolysin of Lactococcus carnosus is potentially involved in mediating contact-dependent antagonism against Listeria monocytogenes. Sci Rep 2025; 15:18595. [PMID: 40425677 PMCID: PMC12116727 DOI: 10.1038/s41598-025-03177-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2024] [Accepted: 05/19/2025] [Indexed: 05/29/2025] Open
Abstract
Lactococcus carnosus CNCM I-4031 is a psychrotrophic lactic acid bacterium used for the biopreservation of seafood. It effectively inhibits the growth of spoilage and pathogenic bacteria, such as Listeria monocytogenes, through an atypical mechanism that relies on direct cell-to-cell contact, without producing conventional antimicrobial compounds like diffusible bacteriocins, which are released into the environment to eliminate nearby cells during interbacterial competition. However, the precise molecular mechanism behind this bacterial interaction remains to be fully understood. In this study, Label-free LC-MS/MS shotgun proteomics and gene expression analysis were used to examine cell envelope protein expression in L. carnosus when cultivated alone and in co-culture with L. monocytogenes. The investigation identified a specific cell wall protein, named LYSO, which has a toxic C-terminal domain and demonstrates peptidoglycan hydrolysis activity against L. monocytogenes. Further analysis using knockout mutants provided additional evidence for the involvement of LYSO in the inhibition activity. These findings suggest the significant role of this bacteriolysin in the contact-dependent mechanism of L. carnosus against L. monocytogenes.
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Affiliation(s)
| | | | | | | | - Veronique Monnet
- PAPPSO, Micalis Institute, INRAE, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Johanna Björkroth
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
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Demeshkina NA, Ferré-D'Amaré AR. Large-scale purifications reveal yeast and human stress granule cores are heterogeneous particles with complex transcriptomes and proteomes. Cell Rep 2025; 44:115738. [PMID: 40413746 DOI: 10.1016/j.celrep.2025.115738] [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: 10/10/2024] [Revised: 03/14/2025] [Accepted: 05/02/2025] [Indexed: 05/27/2025] Open
Abstract
Stress granules are a conserved response of eukaryotic cells to environmental insults. These cytoplasmic ribonucleoprotein condensates have hitherto been primarily studied by microscopy, which showed previously that they comprise dense ∼200 nm cores embedded in a diffuse shell. We have developed large-scale purifications of budding yeast and mammalian (HEK293T cell) stress granule cores that do not rely on immunoprecipitation of candidate protein constituents. These unbiased preparations reveal that stress granule cores are discrete particles with variable size (average, 135 and 225 nm for yeast and human, respectively) and shape. Proteomics and transcriptomics demonstrate complex composition. The results of hybridization chain reaction fluorescence in situ hybridization (FISH) analyses in HEK293T cells are consistent with stress granule cores having heterogeneous composition, i.e., each stress granule core particle contains only a limited number of mRNA species. Biochemical purification now opens the way to mechanistic analysis of the heterogeneity and complexity of stress granules.
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Affiliation(s)
- Natalia A Demeshkina
- Laboratory of Nucleic Acids, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Adrian R Ferré-D'Amaré
- Laboratory of Nucleic Acids, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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3
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Tuieng RJ, Disney C, Cartmell SH, Kirwan CC, Eckersley A, Newham E, Gupta HS, Hoyland JA, Lee PD, Sherratt MJ. Impact of therapeutic X-ray exposure on collagen I and associated proteins. Acta Biomater 2025; 197:294-311. [PMID: 40058620 DOI: 10.1016/j.actbio.2025.03.004] [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: 05/18/2024] [Revised: 02/11/2025] [Accepted: 03/03/2025] [Indexed: 03/23/2025]
Abstract
Biological tissues are exposed to X-rays in medical applications (such as diagnosis and radiotherapy) and in research studies (for example microcomputed X-ray tomography: microCT). Radiotherapy may deliver doses up to 50Gy to both tumour and healthy tissues, resulting in undesirable clinical side effects which can compromise quality of life. Whilst cellular responses to X-rays are relatively well-characterised, X-ray-induced structural damage to the extracellular matrix (ECM) is poorly understood. This study tests the hypotheses that ECM proteins and ECM-rich tissues (purified collagen I and rat tail tendons respectively) are structurally compromised by exposure to X-ray doses used in breast radiotherapy. Protein gel electrophoresis demonstrated that breast radiotherapy equivalent doses can induce fragmentation of the constituent α chains in solubilised purified collagen I. However, assembly into fibrils, either in vitro or in vivo, prevented X-ray-induced fragmentation but not structural changes (as characterised by LC-MS/MS and peptide location fingerprinting: PLF). In subsequent experiments exposure to higher (synchrotron) X-ray doses induced substantial fragmentation of solubilised and fibrillar (chicken tendon) collagen I. LC-MS/MS and PLF analysis of synchrotron-irradiated tendon identified structure-associated changes in collagens I, VI, XII, proteoglycans including aggrecan, decorin, and fibromodulin, and the elastic fibre component fibulin-1. Thus, exposure to radiotherapy X-rays can affect the structure of key tissue ECM components, although additional studies will be required to understand dose dependent effects. STATEMENT OF SIGNIFICANCE: Biological systems are routinely exposed to X-rays during medical treatments (radiotherapy) and in imaging studies (microCT). Whilst the impact of ionising radiation on cells is well characterised, the interactions between X-rays and the extracellular matrix are not. Here, we show that relatively low dose breast radiotherapy X-rays are sufficient to affect the structure of collagen I in both its solubilised and fibrillar forms. Although the impact of intermediate X-ray doses on extracellular proteins was not determined, the high dose exposures which are achievable using a synchrotron source had an even greater effect on the structure of collagen I molecules and, in tendon, on the structures of many accessory extracellular matrix proteins, The unwanted side effects of radiotherapy may therefore be due to not only cellular damage but also damage to the surrounding matrix.
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Affiliation(s)
- Ren Jie Tuieng
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester M13 9PT, UK; Singapore Nuclear Research and Safety Initiative, National University of Singapore, Singapore 118415
| | - Catherine Disney
- Department of Mechanical Engineering, University College London, London WC1E 7JE, UK; Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
| | - Sarah H Cartmell
- Department of Materials, School of Natural Sciences, Faculty of Science and Engineering and The Henry Royce Institute, Royce Hub Building, The University of Manchester, M13 9PL, Manchester, UK
| | - Cliona C Kirwan
- Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oglesby Cancer Research Building, Manchester Cancer Research Centre, Wilmslow Road, Manchester M20 4BX, UK; The Nightingale Breast Cancer Unit, Wythenshawe Hospital, Manchester University NHS Foundation Trust, M23 9LT, Manchester, UK
| | - Alexander Eckersley
- Manchester Cell-Matrix Centre, Division of Musculoskeletal & Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester M13 9PT, UK
| | - Elis Newham
- School of Engineering and Materials Science & Institute of Bioengineering, Queen Mary University of London, London E1 4NS, UK; Section Palaeontology, Institute of Geosciences, Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Himadri S Gupta
- School of Engineering and Materials Science & Institute of Bioengineering, Queen Mary University of London, London E1 4NS, UK
| | - Judith A Hoyland
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester M13 9PT, UK
| | - Peter D Lee
- Department of Mechanical Engineering, University College London, London WC1E 7JE, UK
| | - Michael J Sherratt
- Division of Cell Matrix Biology & Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester M13 9PT, UK.
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Lama B, Park H, Saraf A, Hassebroek V, Keifenheim D, Saito-Fujita T, Saitoh N, Aksenova V, Arnaoutov A, Dasso M, Clarke DJ, Azuma Y. PICH impacts the spindle assembly checkpoint via its DNA translocase and SUMO-interaction activities. Life Sci Alliance 2025; 8:e202403140. [PMID: 39919802 PMCID: PMC11806350 DOI: 10.26508/lsa.202403140] [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: 11/19/2024] [Revised: 01/30/2025] [Accepted: 01/31/2025] [Indexed: 02/09/2025] Open
Abstract
Either inhibiting or stabilizing SUMOylation in mitosis causes defects in chromosome segregation, suggesting that dynamic mitotic SUMOylation of proteins is critical to maintain integrity of the genome. Polo-like kinase 1-interacting checkpoint helicase (PICH), a mitotic chromatin remodeling enzyme, interacts with SUMOylated chromosomal proteins via three SUMO-interacting motifs (SIMs) to control their association with chromosomes. Using cell lines with conditional PICH depletion/PICH replacement, we revealed mitotic defects associated with compromised PICH functions toward SUMOylated chromosomal proteins. Defects in either remodeling activity or SIMs of PICH delayed mitotic progression caused by activation of the spindle assembly checkpoint (SAC) indicated by extended duration of Mad1 foci at centromeres. Proteomics analysis of chromosomal SUMOylated proteins whose abundance is controlled by PICH activity identified candidate proteins to explain the SAC activation phenotype. Among the identified candidates, Bub1 kinetochore abundance is increased upon loss of PICH. Our results demonstrated a novel relationship between PICH and the SAC, where PICH directly or indirectly affects Bub1 association at the kinetochore and impacts SAC activity to control mitosis.
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Affiliation(s)
- Bunu Lama
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Hyewon Park
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Anita Saraf
- Mass Spectrometry and Analytical Proteomics Laboratory, University of Kansas, Lawrence, KS, USA
| | - Victoria Hassebroek
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
| | - Daniel Keifenheim
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Tomoko Saito-Fujita
- Division of Cancer Biology, The Cancer Institute of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Noriko Saitoh
- Division of Cancer Biology, The Cancer Institute of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Vasilisa Aksenova
- Division of Molecular and Cellular Biology, National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Alexei Arnaoutov
- Division of Molecular and Cellular Biology, National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Mary Dasso
- Division of Molecular and Cellular Biology, National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Duncan J Clarke
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Yoshiaki Azuma
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS, USA
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Dwyer K, Essak MA, Awada A, Dhoondia Z, Ansari A. Protein-interaction network analysis reveals a role of Prp19 splicing factor in transcription of both intron-containing and intron-lacking genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.31.646471. [PMID: 40236183 PMCID: PMC11996550 DOI: 10.1101/2025.03.31.646471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/17/2025]
Abstract
We have previously demonstrated that the transcription-dependent interaction of the promoter and terminator ends of a gene, which results in the formation of a gene loop, is facilitated by the interaction of the general transcription factor TFIIB with the CF1, CPF and Rat1 termination complexes. To further elucidate the protein-protein interactions that stabilize gene loop, we performed mass spectrometry of affinity purified termination complexes from chromatin fraction. Quantitative proteomic analysis revealed additional interactions of termination factors with TFIID and SAGA complex. Since gene looping of intron-containing genes involves additional contacts of the promoter and terminator with the intron, we examined if termination factors interact with the splicing factors as well. All three termination complexes displayed statistically significant interactions with Prp19, Prp43, Sub2, Snu114, Brr2 and Smb1 splicing factors. Since Prp43 and Prp19 consistently emerged as the interactor of both initiation and termination factors, we affinity-purified both and performed mass spectrometry. Prp19 exhibited interactions with subunits of TFIID, CPF complex, and the RSC chromatin remodeling complex. These interactions were observed exclusively in the chromatin context, thereby implicating the factor in transcription of protein coding genes. Since fewer than 4% of yeast genes contain introns, we hypothesized that Prp19 might have a broader role in RNAPII transcription cycle. Auxin-mediated depletion of Prp19 resulted in about two-fold decrease in transcription of a subset of both intron-containing and intron-lacking genes. Specifically, the promoter recruitment of TBP registered a significant decline in the absence of Prp19. Chromatin immunoprecipitation (ChIP) analysis revealed crosslinking of Prp19 to the promoter proximal as well as downstream regions of both intronic and non-intronic genes. These findings demonstrate that Prp19 has a novel role in the initiation step of transcription in yeast.
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Jain A, Heremans I, Rademaker G, Detomasi TC, Rohweder P, Anderson D, Zhang J, Hernandez GA, Gupta S, von Linde T, Lange M, Spacci M, Luo J, Citron YR, Olzmann JA, Dawson DW, Craik CS, Bommer G, Perera RM, Zoncu R. Leucine aminopeptidase LyLAP enables lysosomal degradation of membrane proteins. Science 2025; 387:eadq8331. [PMID: 40146846 DOI: 10.1126/science.adq8331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2024] [Revised: 11/25/2024] [Accepted: 01/13/2025] [Indexed: 03/29/2025]
Abstract
Breakdown of every transmembrane protein trafficked to lysosomes requires proteolysis of their hydrophobic helical transmembrane domains. Combining lysosomal proteomics with functional genomic datasets, we identified lysosomal leucine aminopeptidase (LyLAP; formerly phospholipase B domain-containing 1) as the hydrolase most tightly associated with elevated endocytosis. Untargeted metabolomics and biochemical reconstitution demonstrated that LyLAP is a processive monoaminopeptidase with preference for amino-terminal leucine. This activity was necessary and sufficient for the breakdown of hydrophobic transmembrane domains. LyLAP was up-regulated in pancreatic ductal adenocarcinoma (PDA), which relies on macropinocytosis for nutrient uptake. In PDA cells, LyLAP ablation led to the buildup of undigested hydrophobic peptides, lysosomal membrane damage, and growth inhibition. Thus, LyLAP enables lysosomal degradation of membrane proteins and protects lysosomal integrity in highly endocytic cancer cells.
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Affiliation(s)
- Aakriti Jain
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Isaac Heremans
- Metabolic Research Group, de Duve Institute and WELBIO, Universite Catholique de Louvain, Brussels, Belgium
| | - Gilles Rademaker
- Department of Anatomy and Helen Diller Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Tyler C Detomasi
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Peter Rohweder
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Dashiell Anderson
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Justin Zhang
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Grace A Hernandez
- Department of Anatomy and Helen Diller Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Suprit Gupta
- Department of Anatomy and Helen Diller Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Teresa von Linde
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Mike Lange
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, USA
| | - Martina Spacci
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Jiayi Luo
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Y Rose Citron
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - James A Olzmann
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA, USA
| | - David W Dawson
- Department of Pathology and Laboratory Medicine and Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA, USA
| | - Charles S Craik
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Guido Bommer
- Metabolic Research Group, de Duve Institute and WELBIO, Universite Catholique de Louvain, Brussels, Belgium
| | - Rushika M Perera
- Department of Anatomy and Helen Diller Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Roberto Zoncu
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
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Zagorščak M, Abdelhakim L, Rodriguez-Granados NY, Široká J, Ghatak A, Bleker C, Blejec A, Zrimec J, Novák O, Pěnčík A, Baebler Š, Perez Borroto L, Schuy C, Županič A, Afjehi-Sadat L, Wurzinger B, Weckwerth W, Pompe Novak M, Knight MR, Strnad M, Bachem C, Chaturvedi P, Sonnewald S, Sasidharan R, Panzarová K, Gruden K, Teige M. Integration of multi-omics data and deep phenotyping provides insights into responses to single and combined abiotic stress in potato. PLANT PHYSIOLOGY 2025; 197:kiaf126. [PMID: 40173380 PMCID: PMC12012603 DOI: 10.1093/plphys/kiaf126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2025] [Accepted: 02/21/2025] [Indexed: 04/04/2025]
Abstract
Potato (Solanum tuberosum) is highly water and space efficient but susceptible to abiotic stresses such as heat, drought, and flooding, which are severely exacerbated by climate change. Our understanding of crop acclimation to abiotic stress, however, remains limited. Here, we present a comprehensive molecular and physiological high-throughput profiling of potato (Solanum tuberosum, cv. Désirée) under heat, drought, and waterlogging applied as single stresses or in combinations designed to mimic realistic future scenarios. Stress responses were monitored via daily phenotyping and multi-omics analyses of leaf samples comprising proteomics, targeted transcriptomics, metabolomics, and hormonomics at several timepoints during and after stress treatments. Additionally, critical metabolites of tuber samples were analyzed at the end of the stress period. We performed integrative multi-omics data analysis using a bioinformatic pipeline that we established based on machine learning and knowledge networks. Waterlogging produced the most immediate and dramatic effects on potato plants, interestingly activating ABA responses similar to drought stress. In addition, we observed distinct stress signatures at multiple molecular levels in response to heat or drought and to a combination of both. In response to all treatments, we found a downregulation of photosynthesis at different molecular levels, an accumulation of minor amino acids, and diverse stress-induced hormones. Our integrative multi-omics analysis provides global insights into plant stress responses, facilitating improved breeding strategies toward climate-adapted potato varieties.
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Affiliation(s)
- Maja Zagorščak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Lamis Abdelhakim
- PSI (Photon Systems Instruments), spol. s r.o., Prumyslova 470, CZ-664 24 Drásov, Czech Republic
| | | | - Jitka Široká
- Laboratory of Growth Regulators, Palacký University in Olomouc & Institute of Experimental Botany AS CR, Šlechtitelů 27, Olomouc 779 00, Czech Republic
| | - Arindam Ghatak
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MOSYS), University Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Carissa Bleker
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Andrej Blejec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Jan Zrimec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Ondřej Novák
- Laboratory of Growth Regulators, Palacký University in Olomouc & Institute of Experimental Botany AS CR, Šlechtitelů 27, Olomouc 779 00, Czech Republic
| | - Aleš Pěnčík
- Laboratory of Growth Regulators, Palacký University in Olomouc & Institute of Experimental Botany AS CR, Šlechtitelů 27, Olomouc 779 00, Czech Republic
| | - Špela Baebler
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Lucia Perez Borroto
- Wageningen University and Research, Department of Plant Breeding, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Christian Schuy
- Department Biologie, Lehrstuhl für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudstr. 5, 91058 Erlangen, Germany
| | - Anže Županič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Leila Afjehi-Sadat
- Mass Spectrometry Unit, Research Support Facilities, Faculty of Life Sciences, University Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Bernhard Wurzinger
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MOSYS), University Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Wolfram Weckwerth
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MOSYS), University Vienna, Djerassiplatz 1, 1030 Vienna, Austria
- Vienna Metabolomics Center (VIME), University Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Maruša Pompe Novak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
- School for Viticulture and Enology, University of Nova Gorica, Gladni trg 8, 5271 Vipava, Slovenia
| | - Marc R Knight
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
| | - Miroslav Strnad
- Laboratory of Growth Regulators, Palacký University in Olomouc & Institute of Experimental Botany AS CR, Šlechtitelů 27, Olomouc 779 00, Czech Republic
| | - Christian Bachem
- Wageningen University and Research, Department of Plant Breeding, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Palak Chaturvedi
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MOSYS), University Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Sophia Sonnewald
- Department Biologie, Lehrstuhl für Biochemie, Friedrich-Alexander-Universität Erlangen-Nürnberg, Staudstr. 5, 91058 Erlangen, Germany
| | - Rashmi Sasidharan
- Plant Stress Resilience, Institute of Environmental Biology, Utrecht University, Heidelberglaan 8, 3584 CS Utrecht, The Netherlands
| | - Klára Panzarová
- PSI (Photon Systems Instruments), spol. s r.o., Prumyslova 470, CZ-664 24 Drásov, Czech Republic
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 121, 1000 Ljubljana, Slovenia
| | - Markus Teige
- Department of Functional and Evolutionary Ecology, Molecular Systems Biology (MOSYS), University Vienna, Djerassiplatz 1, 1030 Vienna, Austria
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Honda K, Tasaki M, Yamano T, Ueda M, Naiki H, Tanaka N, Morinaga Y, Miyagawa-Hayashino A. High frequency of occult transthyretin and apolipoprotein AI-type amyloid in aortic valves removed by valve replacement for aortic stenosis. Amyloid 2025; 32:22-28. [PMID: 39526702 DOI: 10.1080/13506129.2024.2426508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 10/01/2024] [Accepted: 11/04/2024] [Indexed: 11/16/2024]
Abstract
BACKGROUND A high incidence of valvular involvement of amyloid in the setting of aortic stenosis (AS) has been reported. Amyloid derived from ApoAI (AApoAI) can form local amyloid deposits in the aortic valve. Although a high prevalence of concomitant severe AS and cardiac transthyretin-type amyloidosis (ATTR) has been reported, the prevalence of valvular involvement by ATTR and AApoAI is unclear. METHODS Using immunostaining and mass spectrometry, we analysed amyloid proteins in 97 aortic valves removed for valve replacement due to AS at Kyoto Prefectural University of Medicine between 2014 and 2021. Clinical information was also reviewed. RESULTS Amyloid deposits were found in 44 cases (45%), of which 30 cases (68%) involved ATTR and 33 cases (75%) AApoAI. Statistical analysis showed significantly lower age and E/e' among amyloid-positive cases compared with amyloid-negative cases and significantly lower brain natriuretic peptide, higher fractional shortening, and higher left ventricular ejection fraction among ATTR-positive cases compared with ATTR-negative cases. Seven recent patients underwent bone scintigraphy and ATTR cardiomyopathy was observed in only one case. CONCLUSIONS AS symptoms can manifest earlier in patients with amyloid or ATTR deposition in the aortic valve than in patients without such deposition, even though left ventricular function is preserved.
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Affiliation(s)
- Kohei Honda
- Department of Surgical Pathology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masayoshi Tasaki
- Department of Clinical Biosciences, Graduate School of Health Sciences, Kumamoto University, Kumamoto, Japan
| | - Tetsuhiro Yamano
- Department of Infection Control and Molecular Laboratory Medicine/Department of Cardiovascular Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Mitsuharu Ueda
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Hironobu Naiki
- Department of Molecular Pathology, Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| | - Noriyuki Tanaka
- Department of Surgical Pathology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yukiko Morinaga
- Department of Surgical Pathology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Aya Miyagawa-Hayashino
- Department of Surgical Pathology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
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9
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Goubran H, Ahmed S, Ragab G, Seghatchian J, Burnouf T. Platelet proteomics: Clinical implications - Decoding the black box! Transfus Apher Sci 2025; 64:104060. [PMID: 39719751 DOI: 10.1016/j.transci.2024.104060] [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] [Indexed: 12/26/2024]
Abstract
Platelets are anucleate blood cells traditionally associated with hemostasis but now increasingly recognized for their multifaceted roles in immunity, inflammation, and tissue repair. Advances in platelet proteomics, employing high-throughput techniques such as mass spectrometry, have significantly enhanced our understanding of platelet biology and its clinical implications in transfusion medicine. Platelet proteomics offers a retrospective view of physiological and pathological changes over the platelet's 7-10-day lifespan, making it a unique tool for studying cumulative biological events. Recent applications include the identification of biomarkers for cardiovascular, infectious, autoimmune diseases and cancer. In neurodegeneration and aging, platelets have been explored for their shared molecular pathways with neurons, with findings implicating Tau, amyloid-beta, and alpha-synuclein as potential biomarkers. Proteomics is also emerging as an important factor in the development of evidence-based, tailor-made platelet-derived therapies. While promising, platelet proteomics requires further standardization and computational advances to support transitioning from research to routine clinical practice.
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Affiliation(s)
- Hadi Goubran
- Saskatoon Cancer Centre, Saskatoon, SK, Canada; Department of Oncology, College of Medicine, University of Saskatchewan, Saskatchewan, Canada
| | - Shahid Ahmed
- Saskatoon Cancer Centre, Saskatoon, SK, Canada; Department of Oncology, College of Medicine, University of Saskatchewan, Saskatchewan, Canada
| | - Gaafar Ragab
- Rheumatology and Immunology Unit, Internal Medicine Department, Cairo University, Egypt
| | - Jerard Seghatchian
- International Consultancy in Modern Personalized Blood Components Therapies and Innovative DDR Strategies, London, England, UK
| | - Thierry Burnouf
- Graduate Institute of Biological Materials and Tissue Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, Taiwan; International PhD Program in Biomedical Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, Taiwan.
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10
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Routray D, Ghatak A, Chaturvedi P, Petijová L, Weckwerth W, Ručová D, Bačkor M, Lang I, Goga M. Comparative analysis of geotypic variations in the proteome of Nostoc commune. PLANT SIGNALING & BEHAVIOR 2024; 19:2370719. [PMID: 38913942 PMCID: PMC11197914 DOI: 10.1080/15592324.2024.2370719] [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: 05/09/2024] [Accepted: 06/02/2024] [Indexed: 06/26/2024]
Abstract
Cyanobacterium Nostoc commune is a filamentous terrestrial prokaryotic organism widely distributed, which suggest its high adaptive potential to environmental or abiotic stress. Physiological parameters and proteomic analysis were performed in two accession of N. commune with the aim to elucidate the differences of physiological trails between distant geotypes, namely Antarctic (AN) and central European (CE). The result obtained clearly showed that the AN geotype demonstrates elevated levels of total phenols, flavonoids, carotenoids, and phycobiliproteins, indicative of its adaptation to environmental stress as referred by comparison to CE sample. Additionally, we employed LC-MS analysis to investigate the proteomes of N. commune from AN and CE geotypes. In total, 1147 proteins were identified, among which 646 proteins expressed significant (up-regulation) changes in both accessions. In the AN geotype, 83 exclusive proteins were identified compared to 25 in the CE geotype. Functional classification of the significant proteins showed a large fraction involved in photosynthesis, amino acid metabolism, carbohydrate metabolism and protein biosynthesis. Further analysis revealed some defense-related proteins such as, superoxide dismutase (SOD) and glutathione reductase, which are rather explicitly expressed in the AN N. commune. The last two proteins suggest a more stressful condition in AN N. commune. In summary, our findings highlight biochemical processes that safeguard the AN geotype of N. commune from extreme environmental challenges, not recorded in CE accession, probably due to less stressful environment in Europe. This study brings the first ever proteomic analysis of N. commune, emphasizing the need for additional investigations into the climate adaptation of this species with rather plastic genome.
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Affiliation(s)
- Deepti Routray
- Department of Plant Biology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
| | - Arindam Ghatak
- Molecular Systems Biology Lab, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
| | - Palak Chaturvedi
- Molecular Systems Biology Lab, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Linda Petijová
- Department of Genetics, Faculty of Science, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
| | - Dajana Ručová
- Department of Plant Biology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
| | - Martin Bačkor
- Department of Plant Biology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
- Institute of Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Nitra, Slovakia
| | - Ingeborg Lang
- Molecular Systems Biology Lab, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Michal Goga
- Department of Plant Biology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Košice, Slovakia
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11
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Powell T, Widdowson P, Nägeli A, Ebner M, Creese A. GingisREX: A Complementary Enzyme for the Detection of Bacterial Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2024; 35:2790-2794. [PMID: 39392299 PMCID: PMC11622235 DOI: 10.1021/jasms.4c00347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Revised: 09/30/2024] [Accepted: 10/09/2024] [Indexed: 10/12/2024]
Abstract
Reliable enzymatic digestion underscores successful mass-spectrometry-based proteomics experiments. In this study, we compare the use of the arginine-specific protease, GingisREX, against a more traditional approach in the identification of Escherichia coli proteins. An increased number of protein identifications were noted when GingisREX was used compared to a trypsin/lys-C mixture. This improvement was attributed to the generation of fewer peptides per protein, resulting in a simpler peptide mixture. Furthermore, GingisREX exhibited increased digestion efficiency, fewer missed cleavages, and improved MS/MS data quality for higher molecular weight peptides. The data here establish GingisREX to be a protease complementary to trypsin for enhanced detection of bacterial proteins. With further optimization, GingisREX could prove to be an effective alternative to trypsin for identifying host cell proteins in biotherapeutics.
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Affiliation(s)
- Thomas Powell
- Immunocore
Limited, 92 Park Drive, Milton Park, Abingdon, OX14 4RY, United
Kingdom
| | | | | | - Martin Ebner
- Immunocore
Limited, 92 Park Drive, Milton Park, Abingdon, OX14 4RY, United
Kingdom
| | - Andrew Creese
- Immunocore
Limited, 92 Park Drive, Milton Park, Abingdon, OX14 4RY, United
Kingdom
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12
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Bedi M, Das S, Das J, Mukherjee S, Basu A, Saha S, Ghosh A. Mitochondrial proteome analysis reveals that an augmented cytochrome c oxidase assembly and activity potentiates respiratory capacity in sarcoma. Biochem Biophys Res Commun 2024; 736:150501. [PMID: 39116681 DOI: 10.1016/j.bbrc.2024.150501] [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: 06/13/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 08/10/2024]
Abstract
Mitochondrial oxidative phosphorylation (OXPHOS) is an obligatory process in sarcoma. Despite that, the metabolic programming of sarcoma mitochondria is still unknown. To obtain a comprehensive metabolic insight of mitochondria, we developed a mouse fibrosarcoma model by injecting 3-methylcholanthrene and compared mitochondrial proteomes between sarcoma and its contralateral normal muscle using mass spectrometry. Our study identified ∼449 proteins listed in the SwissProt databases, and all the data sets are available via ProteomeXchange with the identifier PXD044903. In sarcoma, 49 mitochondrial proteins were found differentially expressed, including 36 proteins up-regulated and 13 proteins down-regulated, with the significance of p-value <0.05 and the log2[fold change] > 1 and < -1 as compared to normal muscle. Our data revealed that various anaplerotic reactions actively replenish the TCA cycle in sarcoma. The comparative expression profile and Western blotting analysis of OXPHOS subunits showed that complex-IV subunits, MT-CO3 and COX6A1, were significantly up-regulated in sarcoma vs. normal muscle. Further, biochemical and physiological assays confirmed enhanced complex-IV specific enzymatic and supercomplex activities with a concomitant increase of oxygen consumption rate in sarcoma mitochondria compared to normal muscle. Validation with human post-operative sarcoma tissues also confirms an increased MT-CO3 expression compared to normal tissue counterparts. Thus, our data comprehensively analyses the mitochondrial proteome and identifies augmented complex-IV assembly and activity in sarcoma.
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Affiliation(s)
- Minakshi Bedi
- Department of Biochemistry, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, India
| | - Surajit Das
- Department of Biochemistry, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, India
| | - Jagannath Das
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, India
| | - Soumyajit Mukherjee
- Department of Biochemistry, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, India
| | - Abhimanyu Basu
- IPGME&R and SSKM Hospital, 244, A.J.C. Bose Road, Kolkata, 700020, India
| | - Sudipto Saha
- Department of Biological Sciences, Bose Institute, Kolkata, 700091, India
| | - Alok Ghosh
- Department of Biochemistry, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, India.
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13
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Plouhinec L, Bonnin E, Kielbasa M, Armengaud J, Neugnot V, Berrin JG, Lafond M. A time-course analysis of Aspergillus terreus secretomes reveals the importance of pectin-degrading enzymes to increase the digestibility of soybean meal. Appl Environ Microbiol 2024; 90:e0215323. [PMID: 39162561 PMCID: PMC11409638 DOI: 10.1128/aem.02153-23] [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: 11/29/2023] [Accepted: 07/29/2024] [Indexed: 08/21/2024] Open
Abstract
Considering an ever-growing global population, which hit 8 billion people in the fall of 2022, it is essential to find solutions to avoid croplands competition between human food and animal feed. Agricultural co-products such as soybean meals have become important components of the circular economy thanks to their use in animal feed. Their implementation was made possible by the addition of exogenous enzymes in the diet of monogastric animals, especially fungal carbohydrate-active enzymes (CAZymes). Here, we describe a time-course production and analysis of Aspergillus terreus secretomes for the identification of CAZymes able to enhance the digestibility of soybean meals. Functional assays revealed that the release of nutrients and the degradation of pectins in soybean meals can be tightly interconnected. Using a comparative proteomics approach, we identified several fungal pectin-degrading enzymes leading to increased assimilable nutrients in the soluble fraction of soybean meals. Our results reinforce the importance of deconstructing pectic polysaccharides in feedstuffs and contribute to sharpen our understanding of the fungal enzymatic interplays involved in pectin hydrolysis.IMPORTANCEIn the present study, we developed a strategy to identify the key fungal enzymatic activities involved in the improvement of soybean meal (SBM) digestibility. Our data unravel the importance of pectin degradation for the release of nutrients from SBM and provide some insights regarding the degradation of rhamnogalacturonan-I (RG-I) by ascomycetes. Indeed, the hydrolysis of pectins and RG-I by human microbiota is well documented in the literature, but our knowledge of the fungal CAZymes at play for the degradation of soybean pectins remains hitherto underexplored. Due to its wide use in animal feed, improving the digestibility of SBM by enzymatic treatments is a current challenge for feed additive suppliers. Since non-starch polysaccharides and pectins have often been reported for their anti-nutritional role in SBM, we believe this study will provide new avenues toward the improvement of enzymatic cocktails for animal nutrition and health.
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Affiliation(s)
- Lauriane Plouhinec
- INRAE, Aix-Marseille Université, UMR 1163 Biodiversité et Biotechnologie Fongiques, Marseille, France
- Adisseo France S.A.S, CINAbio, INSA Toulouse, Toulouse, France
| | - Estelle Bonnin
- INRAE, Université de Nantes, UR 1268 Biopolymères Interactions Assemblage, Nantes, France
| | - Mélodie Kielbasa
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, Bagnols sur Cèze, France
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), Université Paris-Saclay, CEA, INRAE, Bagnols sur Cèze, France
| | | | - Jean-Guy Berrin
- INRAE, Aix-Marseille Université, UMR 1163 Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - Mickael Lafond
- INRAE, Aix-Marseille Université, UMR 1163 Biodiversité et Biotechnologie Fongiques, Marseille, France
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14
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Jalan M, Sharma A, Pei X, Weinhold N, Buechelmaier ES, Zhu Y, Ahmed-Seghir S, Ratnakumar A, Di Bona M, McDermott N, Gomez-Aguilar J, Anderson KS, Ng CKY, Selenica P, Bakhoum SF, Reis-Filho JS, Riaz N, Powell SN. RAD52 resolves transcription-replication conflicts to mitigate R-loop induced genome instability. Nat Commun 2024; 15:7776. [PMID: 39237529 PMCID: PMC11377823 DOI: 10.1038/s41467-024-51784-x] [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: 12/15/2023] [Accepted: 08/15/2024] [Indexed: 09/07/2024] Open
Abstract
Collisions of the transcription and replication machineries on the same DNA strand can pose a significant threat to genomic stability. These collisions occur in part due to the formation of RNA-DNA hybrids termed R-loops, in which a newly transcribed RNA molecule hybridizes with the DNA template strand. This study investigated the role of RAD52, a known DNA repair factor, in preventing collisions by directing R-loop formation and resolution. We show that RAD52 deficiency increases R-loop accumulation, exacerbating collisions and resulting in elevated DNA damage. Furthermore, RAD52's ability to interact with the transcription machinery, coupled with its capacity to facilitate R-loop dissolution, highlights its role in preventing collisions. Lastly, we provide evidence of an increased mutational burden from double-strand breaks at conserved R-loop sites in human tumor samples, which is increased in tumors with low RAD52 expression. In summary, this study underscores the importance of RAD52 in orchestrating the balance between replication and transcription processes to prevent collisions and maintain genome stability.
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Affiliation(s)
- Manisha Jalan
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA.
| | - Aman Sharma
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA
| | - Xin Pei
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA
| | - Nils Weinhold
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA
| | | | - Yingjie Zhu
- Department of Pathology and Laboratory Medicine, MSKCC, New York, NY, 10065, USA
| | | | | | - Melody Di Bona
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA
- Human Oncology and Pathogenesis, MSKCC, New York, NY, 10065, USA
| | - Niamh McDermott
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA
| | | | - Kyrie S Anderson
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA
| | - Charlotte K Y Ng
- Department for BioMedical Research, University of Bern, Bern, CH, 3008, Switzerland
- SIB, Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland
| | - Pier Selenica
- Department of Pathology and Laboratory Medicine, MSKCC, New York, NY, 10065, USA
| | - Samuel F Bakhoum
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA
- Human Oncology and Pathogenesis, MSKCC, New York, NY, 10065, USA
| | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, MSKCC, New York, NY, 10065, USA
- AstraZeneca, Gaithersburg, MD, 20878, USA
| | - Nadeem Riaz
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA
| | - Simon N Powell
- Department of Radiation Oncology, MSKCC, New York, NY, 10065, USA.
- Molecular Biology Program, MSKCC, New York, NY, 10065, USA.
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15
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Bhola M, Abe K, Orozco P, Rahnamoun H, Avila-Lopez P, Taylor E, Muhammad N, Liu B, Patel P, Marko JF, Starner AC, He C, Van Nostrand EL, Mondragón A, Lauberth SM. RNA interacts with topoisomerase I to adjust DNA topology. Mol Cell 2024; 84:3192-3208.e11. [PMID: 39173639 PMCID: PMC11380577 DOI: 10.1016/j.molcel.2024.07.032] [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: 09/28/2022] [Revised: 07/07/2023] [Accepted: 07/31/2024] [Indexed: 08/24/2024]
Abstract
Topoisomerase I (TOP1) is an essential enzyme that relaxes DNA to prevent and dissipate torsional stress during transcription. However, the mechanisms underlying the regulation of TOP1 activity remain elusive. Using enhanced cross-linking and immunoprecipitation (eCLIP) and ultraviolet-cross-linked RNA immunoprecipitation followed by total RNA sequencing (UV-RIP-seq) in human colon cancer cells along with RNA electrophoretic mobility shift assays (EMSAs), biolayer interferometry (BLI), and in vitro RNA-binding assays, we identify TOP1 as an RNA-binding protein (RBP). We show that TOP1 directly binds RNA in vitro and in cells and that most RNAs bound by TOP1 are mRNAs. Using a TOP1 RNA-binding mutant and topoisomerase cleavage complex sequencing (TOP1cc-seq) to map TOP1 catalytic activity, we reveal that RNA opposes TOP1 activity as RNA polymerase II (RNAPII) commences transcription of active genes. We further demonstrate the inhibitory role of RNA in regulating TOP1 activity by employing DNA supercoiling assays and magnetic tweezers. These findings provide insight into the coordinated actions of RNA and TOP1 in regulating DNA topological stress intrinsic to RNAPII-dependent transcription.
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Affiliation(s)
- Mannan Bhola
- Simpson Querrey Institute for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Kouki Abe
- Simpson Querrey Institute for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Paola Orozco
- Section of Molecular Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Homa Rahnamoun
- Section of Molecular Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Pedro Avila-Lopez
- Simpson Querrey Institute for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Elijah Taylor
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208-3108, USA
| | - Nefertiti Muhammad
- Simpson Querrey Institute for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Bei Liu
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
| | - Prachi Patel
- Simpson Querrey Institute for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - John F Marko
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208-3108, USA
| | - Anne C Starner
- Verna & Marrs McLean Department of Biochemistry & Molecular Pharmacology and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA; Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Eric L Van Nostrand
- Verna & Marrs McLean Department of Biochemistry & Molecular Pharmacology and Therapeutic Innovation Center, Baylor College of Medicine, Houston, TX, USA
| | - Alfonso Mondragón
- Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208-3108, USA
| | - Shannon M Lauberth
- Simpson Querrey Institute for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA; Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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16
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O’Brien MJ, Schrader JM, Ansari A. TFIIB-Termination Factor Interaction Affects Termination of Transcription on Genome-Wide Scale. Int J Mol Sci 2024; 25:8643. [PMID: 39201330 PMCID: PMC11354755 DOI: 10.3390/ijms25168643] [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: 07/05/2024] [Revised: 08/02/2024] [Accepted: 08/06/2024] [Indexed: 09/02/2024] Open
Abstract
Apart from its well-established role in the initiation of transcription, the general transcription factor TFIIB has been implicated in the termination step as well. The ubiquity of TFIIB involvement in termination as well as mechanistic details of its termination function, however, remain largely unexplored. Using GRO-seq analyses, we compared the terminator readthrough phenotype in the sua7-1 mutant (TFIIBsua7-1) and the isogenic wild type (TFIIBWT) strains. Approximately 74% of genes analyzed exhibited a 2-3-fold increase in readthrough of the poly(A)-termination signal in the TFIIBsua7-1 mutant compared to TFIIBWT cells. To understand the mechanistic basis of TFIIB's role in termination, we performed the mass spectrometry of TFIIB-affinity purified from chromatin and soluble cellular fractions-from TFIIBsua7-1 and TFIIBWT cells. TFIIB purified from the chromatin fraction of TFIIBWT cells exhibited significant enrichment of CF1A and Rat1 termination complexes. There was, however, a drastic decrease in TFIIB interaction with CF1A and Rat1 complexes in the TFIIBsua7-1 mutant. ChIP assays revealed about a 90% decline in the recruitment of termination factors in the TFIIBsua7-1 mutant compared to wild type cells. The overall conclusion of these results is that TFIIB affects the termination of transcription on a genome-wide scale, and the TFIIB-termination factor interaction plays a crucial role in the process.
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Affiliation(s)
| | | | - Athar Ansari
- Department of Biological Science, 5047 Gullen Mall, Wayne State University, Detroit, MI 48202, USA; (M.J.O.); (J.M.S.)
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17
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Chang G, Aroge FA, Venkateshappa R, Claydon TW, Sun B. Development of an Absolute Quantification Method for hERG Using PRM with Single Isotopologue in-Sample Calibration. ACS OMEGA 2024; 9:33972-33982. [PMID: 39130540 PMCID: PMC11308013 DOI: 10.1021/acsomega.4c04541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/20/2024] [Accepted: 06/21/2024] [Indexed: 08/13/2024]
Abstract
The human ether-à-go-go-related gene (KCNH2)-encoded protein hERG constitutes the α subunit of the Kv11.1 channel and contributes to the I kr current, which plays an important role in the cardiac action potential. Genetically and xenobiotically triggered malfunctions of hERG can cause arrhythmia. The expression of hERG in various study systems was assessed mainly as the fold change relative to the corresponding control. Here, we developed a simple and sensitive quantitation method using targeted mass spectrometry, i.e., the parallel reaction monitoring approach, to measure the absolute quantity of hERG in copy number. Such measurements do not require controls, and the obtained values can be compared with similar results for any other protein. To effectively avoid matrix effects, we used the heavy-match-light (HML) in-sample calibration approach that requires only a single isotopologue to achieve copy-number quantitation. No significant difference was observed in the results obtained by HML and by the classic standard addition in-sample calibration approach. Using four proteotypic peptides, we quantified the average number of copies of hERG in the HEK293T heterologous expression system as 3.6 ± 0.5 × 106 copies/cell, i.e., 1 million copies/cell for the fully assembled Kv11.1 channel.
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Affiliation(s)
- Ge Chang
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
| | - Fabusuyi A. Aroge
- School
of Mechatronic Systems Engineering, Simon
Fraser University, Surrey, British Columbia V3T0A3, Canada
| | - Ravichandra Venkateshappa
- Department
of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
| | - Tom W. Claydon
- Department
of Biomedical Physiology and Kinesiology, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
| | - Bingyun Sun
- Department
of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
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18
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Fernandes DC, Eto SF, Baldassi AC, Balbuena TS, Charlie-Silva I, de Andrade Belo MA, Pizauro JM. Meningitis caused by Aeromonas hydrophila in Oreochromis niloticus: Proteomics and druggability of virulence factors. FISH & SHELLFISH IMMUNOLOGY 2024; 151:109687. [PMID: 38866348 DOI: 10.1016/j.fsi.2024.109687] [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: 03/18/2024] [Revised: 05/30/2024] [Accepted: 06/08/2024] [Indexed: 06/14/2024]
Abstract
Meningitis caused by Gram-negative bacteria is a serious public health problem, causing morbidity and mortality in both children and adults. Here, we propose a novel experimental model using Nile tilapia (Oreochromis niloticus) to study neuroinflammation. The fish were infected with Aeromonas hydrophila, and the course of infection was monitored in the peripheral blood. Septicemia was obvious in the blood, while in the brain tissue, infection of the meninges was present. The histopathological examination showed suppurative meningitis, and the cellular immune response in the brain tissue during infection was mediated by microglia. These cells were morphologically characterized and phenotyped by MHC class II markers and CD68. The increased production of TNF-α, IL-1β and iNOS supported the infiltration of these cells during the neuroinflammatory process. In the proteomic analysis of A. hydrophila isolated from brain tissue, we found chemotactic and transport proteins, proteolytic enzymes and enzymes associated with the dismutation of nitric oxide (NO), as well as motor proteins and those responsible for cell division. After characterizing the most abundant proteins during the course of infection, we investigated the druggability index of these proteins and identified promising peptide sequences as molecular targets that are similar among bacteria. Thus, these findings deepened the understanding of the pathophysiology of meningitis caused by A. hydrophila. Moreover, through the proteomics analysis, important mechanisms and pathways used by the pathogen to subvert the host response were revealed, providing insights for the development of novel antibiotics and vaccines.
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Affiliation(s)
- Dayanne Carla Fernandes
- Institute of Chemistry, São Paulo State University (Unesp), Araraquara, Sao Paulo, SP, Brazil.
| | - Silas Fernandes Eto
- Laboratory Center of Excellence in New Target Discovery (CENTD) Special Laboratory, Butantan Institute, São Paulo, SP, Brazil
| | - Amanda Cristina Baldassi
- Department of Technology, School of Agrarian and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, Sao Paulo, SP, Brazil
| | - Thiago Santana Balbuena
- Department of Technology, School of Agrarian and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, Sao Paulo, SP, Brazil
| | - Ives Charlie-Silva
- Institute of Chemistry, São Paulo State University (Unesp), Araraquara, Sao Paulo, SP, Brazil
| | | | - João Martins Pizauro
- Department of Technology, School of Agrarian and Veterinary Sciences, São Paulo State University (Unesp), Jaboticabal, Sao Paulo, SP, Brazil
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19
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Zhao H, Li J, Xiang Y, Malik S, Vartak SV, Veronezi GMB, Young N, Riney M, Kalchschmidt J, Conte A, Jung SK, Ramachandran S, Roeder RG, Shi Y, Casellas R, Asturias FJ. An IDR-dependent mechanism for nuclear receptor control of Mediator interaction with RNA polymerase II. Mol Cell 2024; 84:2648-2664.e10. [PMID: 38955181 PMCID: PMC11283359 DOI: 10.1016/j.molcel.2024.06.006] [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: 06/28/2023] [Revised: 02/29/2024] [Accepted: 06/07/2024] [Indexed: 07/04/2024]
Abstract
The essential Mediator (MED) coactivator complex plays a well-understood role in regulation of basal transcription in all eukaryotes, but the mechanism underlying its role in activator-dependent transcription remains unknown. We investigated modulation of metazoan MED interaction with RNA polymerase II (RNA Pol II) by antagonistic effects of the MED26 subunit and the CDK8 kinase module (CKM). Biochemical analysis of CKM-MED showed that the CKM blocks binding of the RNA Pol II carboxy-terminal domain (CTD), preventing RNA Pol II interaction. This restriction is eliminated by nuclear receptor (NR) binding to CKM-MED, which enables CTD binding in a MED26-dependent manner. Cryoelectron microscopy (cryo-EM) and crosslinking-mass spectrometry (XL-MS) revealed that the structural basis for modulation of CTD interaction with MED relates to a large intrinsically disordered region (IDR) in CKM subunit MED13 that blocks MED26 and CTD interaction with MED but is repositioned upon NR binding. Hence, NRs can control transcription initiation by priming CKM-MED for MED26-dependent RNA Pol II interaction.
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Affiliation(s)
- Haiyan Zhao
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | - Jiaqin Li
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | - Yufei Xiang
- Center of Protein Engineering and Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sohail Malik
- Laboratory of Biochemistry and Molecular Biology, Rockefeller University, New York, NY 10065, USA
| | | | - Giovana M B Veronezi
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | - Natalie Young
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | - McKayla Riney
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | | | - Andrea Conte
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Seol Kyoung Jung
- Biodata Mining and Discovery Section, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Srinivas Ramachandran
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular Biology, Rockefeller University, New York, NY 10065, USA
| | - Yi Shi
- Center of Protein Engineering and Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Rafael Casellas
- Lymphocyte Nuclear Biology, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Francisco J Asturias
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical School, Aurora, CO 80045, USA.
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20
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O’Brien MJ, Schrader J, Ansari A. Genome-wide analysis of TFIIB's role in termination of transcription. RESEARCH SQUARE 2024:rs.3.rs-4619136. [PMID: 39070618 PMCID: PMC11276024 DOI: 10.21203/rs.3.rs-4619136/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
This study provides evidence that the role of TFIIB extends beyond initiation to include the termination step of transcription. Using GRO-seq analyses, we compared terminator readthrough phenotype in sua7-1 mutant (TFIIB sua7-1 ) and the isogenic wild type (TFIIB WT ) strains. Approximately 74% of genes analyzed exhibited a 2-3-fold increase in readthrough of the poly(A)-termination signal in the TFIIB sua7-1 mutant compared to TFIIB WT cells. Mass spectrometry of affinity purified TFIIB from chromatin fraction found TFIIB exhibiting interaction with CF1A and Rat1 termination complexes in TFIIB WT cells. There was, however, a drastic decrease in TFIIB interaction with CF1A and Rat1 termination complexes in the TFIIB sua7-1 mutant. ChIP assays revealed about 90% decline in recruitment of termination factors in TFIIB sua7-1 mutant compared to wild type cells. The overall conclusion of these results is that TFIIB affects termination of transcription on a genome-wide scale, and TFIIB-termination factor interaction may play a crucial role in the process.
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Affiliation(s)
- Michael J. O’Brien
- Department of Biological Science, 5047 Gullen Mall, Wayne State University, Detroit, MI 48202
| | - Jared Schrader
- Department of Biological Science, 5047 Gullen Mall, Wayne State University, Detroit, MI 48202
| | - Athar Ansari
- Department of Biological Science, 5047 Gullen Mall, Wayne State University, Detroit, MI 48202
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21
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Goto S, Hosojima M, Kabasawa H, Arai K, Takemoto K, Aoki H, Komochi K, Kobayashi R, Sugita N, Endo T, Kaseda R, Yoshida Y, Narita I, Hirayama Y, Saito A. Megalin-related mechanism of hemolysis-induced acute kidney injury and the therapeutic strategy. J Pathol 2024; 263:315-327. [PMID: 38721910 DOI: 10.1002/path.6284] [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: 10/03/2023] [Revised: 02/08/2024] [Accepted: 03/15/2024] [Indexed: 06/12/2024]
Abstract
Hemolysis-induced acute kidney injury (AKI) is attributed to heme-mediated proximal tubule epithelial cell (PTEC) injury and tubular cast formation due to intratubular protein condensation. Megalin is a multiligand endocytic receptor for proteins, peptides, and drugs in PTECs and mediates the uptake of free hemoglobin and the heme-scavenging protein α1-microglobulin. However, understanding of how megalin is involved in the development of hemolysis-induced AKI remains elusive. Here, we investigated the megalin-related pathogenesis of hemolysis-induced AKI and a therapeutic strategy using cilastatin, a megalin blocker. A phenylhydrazine-induced hemolysis model developed in kidney-specific mosaic megalin knockout (MegKO) mice confirmed megalin-dependent PTEC injury revealed by the co-expression of kidney injury molecule-1 (KIM-1). In the hemolysis model in kidney-specific conditional MegKO mice, the uptake of hemoglobin and α1-microglobulin as well as KIM-1 expression in PTECs was suppressed, but tubular cast formation was augmented, likely due to the nonselective inhibition of protein reabsorption in PTECs. Quartz crystal microbalance analysis revealed that cilastatin suppressed the binding of megalin with hemoglobin and α1-microglobulin. Cilastatin also inhibited the specific uptake of fluorescent hemoglobin by megalin-expressing rat yolk sac tumor-derived L2 cells. In a mouse model of hemolysis-induced AKI, repeated cilastatin administration suppressed PTEC injury by inhibiting the uptake of hemoglobin and α1-microglobulin and also prevented cast formation. Hemopexin, another heme-scavenging protein, was also found to be a novel ligand of megalin, and its binding to megalin and uptake by PTECs in the hemolysis model were suppressed by cilastatin. Mass spectrometry-based semiquantitative analysis of urinary proteins in cilastatin-treated C57BL/6J mice indicated that cilastatin suppressed the reabsorption of a limited number of megalin ligands in PTECs, including α1-microglobulin and hemopexin. Collectively, cilastatin-mediated selective megalin blockade is an effective therapeutic strategy to prevent both heme-mediated PTEC injury and cast formation in hemolysis-induced AKI. © 2024 The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Sawako Goto
- Department of Applied Molecular Medicine, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Michihiro Hosojima
- Department of Clinical Nutrition Science, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hideyuki Kabasawa
- Department of Clinical Nutrition Science, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kaho Arai
- Department of Applied Molecular Medicine, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Kazuya Takemoto
- Department of Applied Molecular Medicine, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Hiroyuki Aoki
- Department of Clinical Nutrition Science, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Koichi Komochi
- Department of Clinical Nutrition Science, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ryota Kobayashi
- Department of Clinical Nutrition Science, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Nanako Sugita
- Department of Clinical Nutrition Science, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Taeko Endo
- Department of Applied Molecular Medicine, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ryohei Kaseda
- Division of Clinical Nephrology and Rheumatology, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yutaka Yoshida
- Department of Bacteriology, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ichiei Narita
- Division of Clinical Nephrology and Rheumatology, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | | | - Akihiko Saito
- Department of Applied Molecular Medicine, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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22
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Chen L, Shao F, Chen K, Wu N, Sun B, Ge D, Wang G, Wang H, Yang Q. Organized assembly of chitosan into mechanically strong bio-composite by introducing a recombinant insect structural protein OfCPH-1. Carbohydr Polym 2024; 334:122044. [PMID: 38553240 DOI: 10.1016/j.carbpol.2024.122044] [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: 12/16/2023] [Revised: 02/06/2024] [Accepted: 03/11/2024] [Indexed: 04/02/2024]
Abstract
Chitosan, known for its appealing biological properties in packaging and biomedical applications, faces challenges in achieving a well-organized crystalline structure for mechanical excellence under mild conditions. Herein, we propose a facile and mild bioengineering approach to induce organized assembly of amorphous chitosan into mechanically strong bio-composite via incorporating a genetically engineered insect structural protein, the cuticular protein hypothetical-1 from the Ostrinia furnacalis (OfCPH-1). OfCPH-1 exhibits high binding affinity to chitosan via hydrogen-bonding interactions. Simply mixing a small proportion (0.5 w/w%) of bioengineered OfCPH-1 protein with acidic chitosan precursor induces the amorphous chitosan chains to form fibrous networks with hydrated chitosan crystals, accompanied with a solution-to-gel transition. We deduce that the water shell destruction driven by strong protein-chitosan interactions, triggers the formation of well-organized crystalline chitosan, which therefore offers the chitosan with significantly enhanced swelling resistance, and strength and modulus that outperforms that of most reported chitosan-based materials as well as petroleum-based plastics. Moreover, the composite exhibits a stretch-strengthening behavior similar to the training living muscles on cyclic load. Our work provides a route for harnessing the OfCPH-1-chitosan interaction in order to form a high-performance, sustainably sourced bio-composite.
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Affiliation(s)
- Lei Chen
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, No 97 Buxin Road, Shenzhen 518120, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Beijing 100193, China
| | - Fei Shao
- School of Bioengineering, School of Chemical Engineering and State Key Laboratory of Fine Chemicals, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, China
| | - Kaiwen Chen
- School of Bioengineering, School of Chemical Engineering and State Key Laboratory of Fine Chemicals, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, China
| | - Nan Wu
- School of Bioengineering, School of Chemical Engineering and State Key Laboratory of Fine Chemicals, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, China
| | - Bingbing Sun
- School of Bioengineering, School of Chemical Engineering and State Key Laboratory of Fine Chemicals, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, China
| | - Dan Ge
- School of Bioengineering, School of Chemical Engineering and State Key Laboratory of Fine Chemicals, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, China
| | - Guirong Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, No 97 Buxin Road, Shenzhen 518120, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Beijing 100193, China
| | - Huanan Wang
- School of Bioengineering, School of Chemical Engineering and State Key Laboratory of Fine Chemicals, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, China.
| | - Qing Yang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, No 97 Buxin Road, Shenzhen 518120, China; State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, No. 2 West Yuanmingyuan Road, Beijing 100193, China; School of Bioengineering, School of Chemical Engineering and State Key Laboratory of Fine Chemicals, Dalian University of Technology, No. 2 Linggong Road, Dalian 116024, China.
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23
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O'Brien MJ, Schrader J, Ansari A. Genome-wide analysis of TFIIB's role in termination of transcription. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.22.581640. [PMID: 38915573 PMCID: PMC11195087 DOI: 10.1101/2024.02.22.581640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Apart from its well-established role in initiation of transcription, the general transcription factor TFIIB has been implicated in the termination step as well. The ubiquity of TFIIB involvement in termination as well as mechanistic details of its termination function, however, remains largely unexplored. To determine the prevalence of TFIIB's role in termination, we performed GRO-seq analyses in sua7-1 mutant (TFIIB sua7-1 ) and the isogenic wild type (TFIIB WT ) strains of yeast. Almost a three-fold increase in readthrough of the poly(A)-termination signal was observed in TFIIB sua7-1 mutant compared to the TFIIB WT cells. Of all genes analyzed in this study, nearly 74% genes exhibited a statistically significant increase in terminator readthrough in the mutant. To gain an understanding of the mechanistic basis of TFIIB involvement in termination, we performed mass spectrometry of TFIIB, affinity purified from chromatin and soluble cellular fractions, from TFIIB sua7-1 and TFIIB WT cells. TFIIB purified from the chromatin fraction of TFIIB WT cells exhibited significant enrichment of CF1A and Rat1 termination complexes. There was, however, a drastic decrease in TFIIB interaction with both CF1A and Rat1 termination complexes in TFIIB sua7-1 mutant. ChIP assay revealed that the recruitment of Pta1 subunit of CPF complex, Rna15 subunit of CF1 complex and Rat1 subunit of Rat1 complex registered nearly 90% decline in the mutant over wild type cells. The overall conclusion of these results is that TFIIB affects termination of transcription on a genome-wide scale, and TFIIB-termination factor interaction may play a crucial role in the process.
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24
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Goto S, Tsutsumi A, Lee Y, Hosojima M, Kabasawa H, Komochi K, Nagatoishi S, Takemoto K, Tsumoto K, Nishizawa T, Kikkawa M, Saito A. Cryo-EM structures elucidate the multiligand receptor nature of megalin. Proc Natl Acad Sci U S A 2024; 121:e2318859121. [PMID: 38771880 PMCID: PMC11145282 DOI: 10.1073/pnas.2318859121] [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: 10/30/2023] [Accepted: 04/19/2024] [Indexed: 05/23/2024] Open
Abstract
Megalin (low-density lipoprotein receptor-related protein 2) is a giant glycoprotein of about 600 kDa, mediating the endocytosis of more than 60 ligands, including those of proteins, peptides, and drug compounds [S. Goto, M. Hosojima, H. Kabasawa, A. Saito, Int. J. Biochem. Cell Biol. 157, 106393 (2023)]. It is expressed predominantly in renal proximal tubule epithelial cells, as well as in the brain, lungs, eyes, inner ear, thyroid gland, and placenta. Megalin is also known to mediate the endocytosis of toxic compounds, particularly those that cause renal and hearing disorders [Y. Hori et al., J. Am. Soc. Nephrol. 28, 1783-1791 (2017)]. Genetic megalin deficiency causes Donnai-Barrow syndrome/facio-oculo-acoustico-renal syndrome in humans. However, it is not known how megalin interacts with such a wide variety of ligands and plays pathological roles in various organs. In this study, we elucidated the dimeric architecture of megalin, purified from rat kidneys, using cryoelectron microscopy. The maps revealed the densities of endogenous ligands bound to various regions throughout the dimer, elucidating the multiligand receptor nature of megalin. We also determined the structure of megalin in complex with receptor-associated protein, a molecular chaperone for megalin. The results will facilitate further studies on the pathophysiology of megalin-dependent multiligand endocytic pathways in multiple organs and will also be useful for the development of megalin-targeted drugs for renal and hearing disorders, Alzheimer's disease [B. V. Zlokovic et al., Proc. Natl. Acad. Sci. U.S.A. 93, 4229-4234 (1996)], and other illnesses.
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Affiliation(s)
- Sawako Goto
- Department of Applied Molecular Medicine, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata City951-8510, Japan
| | - Akihisa Tsutsumi
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo113-0033, Japan
| | - Yongchan Lee
- Department of the Biological Membrane Dynamics, Graduate School of Medical Life Science, Yokohama City University, Yokohama230-0045, Japan
| | - Michihiro Hosojima
- Department of Clinical Nutrition Science, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata City951-8510, Japan
| | - Hideyuki Kabasawa
- Department of Clinical Nutrition Science, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata City951-8510, Japan
| | - Koichi Komochi
- Department of Clinical Nutrition Science, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata City951-8510, Japan
| | - Satoru Nagatoishi
- Medical Device Development and Regulation Research Center, School of Engineering, The University of Tokyo, Tokyo113-8656, Japan
| | - Kazuya Takemoto
- Department of Applied Molecular Medicine, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata City951-8510, Japan
| | - Kouhei Tsumoto
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo113-8656, Japan
| | - Tomohiro Nishizawa
- Department of the Biological Membrane Dynamics, Graduate School of Medical Life Science, Yokohama City University, Yokohama230-0045, Japan
| | - Masahide Kikkawa
- Department of Cell Biology and Anatomy, Graduate School of Medicine, The University of Tokyo, Tokyo113-0033, Japan
| | - Akihiko Saito
- Department of Applied Molecular Medicine, Kidney Research Center, Niigata University Graduate School of Medical and Dental Sciences, Niigata City951-8510, Japan
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25
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Liu X, Abad L, Chatterjee L, Cristea IM, Varjosalo M. Mapping protein-protein interactions by mass spectrometry. MASS SPECTROMETRY REVIEWS 2024:10.1002/mas.21887. [PMID: 38742660 PMCID: PMC11561166 DOI: 10.1002/mas.21887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 04/22/2024] [Indexed: 05/16/2024]
Abstract
Protein-protein interactions (PPIs) are essential for numerous biological activities, including signal transduction, transcription control, and metabolism. They play a pivotal role in the organization and function of the proteome, and their perturbation is associated with various diseases, such as cancer, neurodegeneration, and infectious diseases. Recent advances in mass spectrometry (MS)-based protein interactomics have significantly expanded our understanding of the PPIs in cells, with techniques that continue to improve in terms of sensitivity, and specificity providing new opportunities for the study of PPIs in diverse biological systems. These techniques differ depending on the type of interaction being studied, with each approach having its set of advantages, disadvantages, and applicability. This review highlights recent advances in enrichment methodologies for interactomes before MS analysis and compares their unique features and specifications. It emphasizes prospects for further improvement and their potential applications in advancing our knowledge of PPIs in various biological contexts.
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Affiliation(s)
- Xiaonan Liu
- Department of Physiology, Faculty of Medical Sciences in Katowice, Medical University of Silesia in Katowice, Katowice, Poland
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Lawrence Abad
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Lopamudra Chatterjee
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Ileana M. Cristea
- Department of Molecular Biology, Princeton University, Princeton, New Jersey, USA
| | - Markku Varjosalo
- Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- iCAN Digital Precision Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
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26
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kammoun I, Miotello G, Ben Slama K, Armengaud J, Ghodhbane-Gtari F, Gtari M. The impact of Elaeagnus angustifolia root exudates on Parafrankia soli NRRL B-16219 exoproteome. J Genomics 2024; 12:58-70. [PMID: 38751381 PMCID: PMC11093716 DOI: 10.7150/jgen.93243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 04/21/2024] [Indexed: 05/18/2024] Open
Abstract
Root exudates from host plant species are known to play a critical role in the establishment and maintenance of symbiotic relationships with soil bacteria. In this study, we investigated the impact of root exudates from compatible host plant species; Elaeagnus angustifolia on the exoproteome of Parafrankia soli strain NRRL B-16219. A total of 565 proteins were evidenced as differentially abundant, with 32 upregulated and 533 downregulated in presence of the plant exudates. Analysis of the function of these proteins suggests that the bacterial strain is undergoing a complex metabolic reprogramming towards a new developmental phase elicited in presence of host plant root exudates. The upregulation of Type II/IV secretion system proteins among the differentially expressed proteins indicates their possible role in infecting the host plant, as shown for some rhizobia. Additionally, EF-Tu, proteins upregulated in this study, may function as an effector for the T4SSs and trigger plant defense responses. These findings suggest that Parafrankia soli may use EF-Tu to infect the actinorhizal host plant and pave the way for further investigations of the molecular mechanisms underlying the establishment of symbiotic relationships.
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Affiliation(s)
- Ikram kammoun
- Department of Biological and Chemical Engineering USCR Molecular Bacteriology and & Genomics, National Institute of Applied Sciences and Technology, University of Carthage, Tunis, Tunisia
| | - Guylaine Miotello
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, Université Paris-Saclay, SPI, 30200 Bagnols sur Cèze, France
| | - Karim Ben Slama
- Higher Institute of Applied Biological Sciences, Laboratory of Bioresources, Environment, and Biotechnology, University of Tunis El Manar, Tunis, Tunisia
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, Université Paris-Saclay, SPI, 30200 Bagnols sur Cèze, France
| | - Faten Ghodhbane-Gtari
- Department of Biological and Chemical Engineering USCR Molecular Bacteriology and & Genomics, National Institute of Applied Sciences and Technology, University of Carthage, Tunis, Tunisia
- Higher Institute of Biotechnology of Sidi Thabet, University of La Manouba, Sidi Thabet, Tunisia
| | - Maher Gtari
- Department of Biological and Chemical Engineering USCR Molecular Bacteriology and & Genomics, National Institute of Applied Sciences and Technology, University of Carthage, Tunis, Tunisia
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27
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Skurat AV, Segvich DM, Contreras CJ, Hu YC, Hurley TD, DePaoli-Roach AA, Roach PJ. Impaired malin expression and interaction with partner proteins in Lafora disease. J Biol Chem 2024; 300:107271. [PMID: 38588813 PMCID: PMC11063907 DOI: 10.1016/j.jbc.2024.107271] [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: 02/17/2024] [Revised: 03/25/2024] [Accepted: 03/27/2024] [Indexed: 04/10/2024] Open
Abstract
Lafora disease (LD) is an autosomal recessive myoclonus epilepsy with onset in the teenage years leading to death within a decade of onset. LD is characterized by the overaccumulation of hyperphosphorylated, poorly branched, insoluble, glycogen-like polymers called Lafora bodies. The disease is caused by mutations in either EPM2A, encoding laforin, a dual specificity phosphatase that dephosphorylates glycogen, or EMP2B, encoding malin, an E3-ubiquitin ligase. While glycogen is a widely accepted laforin substrate, substrates for malin have been difficult to identify partly due to the lack of malin antibodies able to detect malin in vivo. Here we describe a mouse model in which the malin gene is modified at the C-terminus to contain the c-myc tag sequence, making an expression of malin-myc readily detectable. Mass spectrometry analyses of immunoprecipitates using c-myc tag antibodies demonstrate that malin interacts with laforin and several glycogen-metabolizing enzymes. To investigate the role of laforin in these interactions we analyzed two additional mouse models: malin-myc/laforin knockout and malin-myc/LaforinCS, where laforin was either absent or the catalytic Cys was genomically mutated to Ser, respectively. The interaction of malin with partner proteins requires laforin but is not dependent on its catalytic activity or the presence of glycogen. Overall, the results demonstrate that laforin and malin form a complex in vivo, which stabilizes malin and enhances interaction with partner proteins to facilitate normal glycogen metabolism. They also provide insights into the development of LD and the rescue of the disease by the catalytically inactive phosphatase.
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Affiliation(s)
- Alexander V Skurat
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA; Lafora Epilepsy Cure Initiative, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Dyann M Segvich
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA; Lafora Epilepsy Cure Initiative, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Christopher J Contreras
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA; Lafora Epilepsy Cure Initiative, University of Kentucky College of Medicine, Lexington, Kentucky, USA
| | - Yueh-Chiang Hu
- Division of Developmental Biology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Thomas D Hurley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA; Lafora Epilepsy Cure Initiative, University of Kentucky College of Medicine, Lexington, Kentucky, USA.
| | - Anna A DePaoli-Roach
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA; Lafora Epilepsy Cure Initiative, University of Kentucky College of Medicine, Lexington, Kentucky, USA.
| | - Peter J Roach
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana, USA; Lafora Epilepsy Cure Initiative, University of Kentucky College of Medicine, Lexington, Kentucky, USA
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Molinelli L, Drula E, Gaillard JC, Navarro D, Armengaud J, Berrin JG, Tron T, Tarrago L. Methionine oxidation of carbohydrate-active enzymes during white-rot wood decay. Appl Environ Microbiol 2024; 90:e0193123. [PMID: 38376171 PMCID: PMC10952391 DOI: 10.1128/aem.01931-23] [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: 10/27/2023] [Accepted: 01/24/2024] [Indexed: 02/21/2024] Open
Abstract
White-rot fungi employ secreted carbohydrate-active enzymes (CAZymes) along with reactive oxygen species (ROS), like hydrogen peroxide (H2O2), to degrade lignocellulose in wood. H2O2 serves as a co-substrate for key oxidoreductases during the initial decay phase. While the degradation of lignocellulose by CAZymes is well documented, the impact of ROS on the oxidation of the secreted proteins remains unclear, and the identity of the oxidized proteins is unknown. Methionine (Met) can be oxidized to Met sulfoxide (MetO) or Met sulfone (MetO2) with potential deleterious, antioxidant, or regulatory effects. Other residues, like proline (Pro), can undergo carbonylation. Using the white-rot Pycnoporus cinnabarinus grown on aspen wood, we analyzed the Met content of the secreted proteins and their susceptibility to oxidation combining H218O2 with deep shotgun proteomics. Strikingly, their overall Met content was significantly lower (1.4%) compared to intracellular proteins (2.1%), a feature conserved in fungi but not in metazoans or plants. We evidenced that a catalase, widespread in white-rot fungi, protects the secreted proteins from oxidation. Our redox proteomics approach allowed the identification of 49 oxidizable Met and 40 oxidizable Pro residues within few secreted proteins, mostly CAZymes. Interestingly, many of them had several oxidized residues localized in hotspots. Some Met, including those in GH7 cellobiohydrolases, were oxidized up to 47%, with a substantial percentage of sulfone (13%). These Met are conserved in fungal homologs, suggesting important functional roles. Our findings reveal that white-rot fungi safeguard their secreted proteins by minimizing their Met content and by scavenging ROS and pinpoint redox-active residues in CAZymes.IMPORTANCEThe study of lignocellulose degradation by fungi is critical for understanding the ecological and industrial implications of wood decay. While carbohydrate-active enzymes (CAZymes) play a well-established role in lignocellulose degradation, the impact of hydrogen peroxide (H2O2) on secreted proteins remains unclear. This study aims at evaluating the effect of H2O2 on secreted proteins, focusing on the oxidation of methionine (Met). Using the model white-rot fungi Pycnoporus cinnabarinus grown on aspen wood, we showed that fungi protect their secreted proteins from oxidation by reducing their Met content and utilizing a secreted catalase to scavenge exogenous H2O2. The research identified key oxidizable Met within secreted CAZymes. Importantly, some Met, like those of GH7 cellobiohydrolases, undergone substantial oxidation levels suggesting important roles in lignocellulose degradation. These findings highlight the adaptive mechanisms employed by white-rot fungi to safeguard their secreted proteins during wood decay and emphasize the importance of these processes in lignocellulose breakdown.
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Affiliation(s)
- Lise Molinelli
- />Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille Université, Marseille, France
- Centrale Marseille, CNRS, ISM2, Aix Marseille Université, Marseille, France
| | - Elodie Drula
- />Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille Université, Marseille, France
- Architecture et Fonction des Macromolécules Biologiques (AFMB), CNRS, Aix-Marseille Université, Marseille, France
| | - Jean-Charles Gaillard
- Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, CEA, INRAE, Bagnols-sur-Cèze, France
| | - David Navarro
- />Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille Université, Marseille, France
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), SPI, Université Paris-Saclay, CEA, INRAE, Bagnols-sur-Cèze, France
| | - Jean-Guy Berrin
- />Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille Université, Marseille, France
| | - Thierry Tron
- Centrale Marseille, CNRS, ISM2, Aix Marseille Université, Marseille, France
| | - Lionel Tarrago
- />Biodiversité et Biotechnologie Fongiques, INRAE, Aix Marseille Université, Marseille, France
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Kudapa H, Ghatak A, Barmukh R, Chaturvedi P, Khan A, Kale S, Fragner L, Chitikineni A, Weckwerth W, Varshney RK. Integrated multi-omics analysis reveals drought stress response mechanism in chickpea (Cicer arietinum L.). THE PLANT GENOME 2024; 17:e20337. [PMID: 37165696 DOI: 10.1002/tpg2.20337] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 03/04/2023] [Accepted: 03/09/2023] [Indexed: 05/12/2023]
Abstract
Drought is one of the major constraints limiting chickpea productivity. To unravel complex mechanisms regulating drought response in chickpea, we generated transcriptomics, proteomics, and metabolomics datasets from root tissues of four contrasting drought-responsive chickpea genotypes: ICC 4958, JG 11, and JG 11+ (drought-tolerant), and ICC 1882 (drought-sensitive) under control and drought stress conditions. Integration of transcriptomics and proteomics data identified enriched hub proteins encoding isoflavone 4'-O-methyltransferase, UDP-d-glucose/UDP-d-galactose 4-epimerase, and delta-1-pyrroline-5-carboxylate synthetase. These proteins highlighted the involvement of pathways such as antibiotic biosynthesis, galactose metabolism, and isoflavonoid biosynthesis in activating drought stress response mechanisms. Subsequently, the integration of metabolomics data identified six metabolites (fructose, galactose, glucose, myoinositol, galactinol, and raffinose) that showed a significant correlation with galactose metabolism. Integration of root-omics data also revealed some key candidate genes underlying the drought-responsive "QTL-hotspot" region. These results provided key insights into complex molecular mechanisms underlying drought stress response in chickpea.
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Affiliation(s)
- Himabindu Kudapa
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Arindam Ghatak
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Rutwik Barmukh
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Palak Chaturvedi
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Aamir Khan
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sandip Kale
- The Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Lena Fragner
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Centre (VIME), University of Vienna, Vienna, Austria
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Centre for Crop & Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
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Zhang S, Ghatak A, Mohammadi Bazargani M, Kramml H, Zang F, Gao S, Ramšak Ž, Gruden K, Varshney RK, Jiang D, Chaturvedi P, Weckwerth W. Cell-type proteomic and metabolomic resolution of early and late grain filling stages of wheat endosperm. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:555-571. [PMID: 38050335 PMCID: PMC12047074 DOI: 10.1111/pbi.14203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/21/2023] [Accepted: 10/03/2023] [Indexed: 12/06/2023]
Abstract
The nutritional value of wheat grains, particularly their protein and metabolite composition, is a result of the grain-filling process, especially in the endosperm. Here, we employ laser microdissection (LMD) combined with shotgun proteomics and metabolomics to generate a cell type-specific proteome and metabolome inventory of developing wheat endosperm at the early (15 DAA) and late (26 DAA) grain-filling stages. We identified 1803 proteins and 41 metabolites from four different cell types (aleurone (AL), sub-aleurone (SA), starchy endosperm (SE) and endosperm transfer cells (ETCs). Differentially expressed proteins were detected, 67 in the AL, 31 in the SA, 27 in the SE and 50 in the ETCs between these two-time points. Cell-type accumulation of specific SUT and GLUT transporters, sucrose converting and starch biosynthesis enzymes correlate well with the respective sugar metabolites, suggesting sugar upload and starch accumulation via nucellar projection and ETC at 15 DAA in contrast to the later stage at 26 DAA. Changes in various protein levels between AL, SA and ETC support this metabolic switch from 15 to 26 DAA. The distinct spatial and temporal abundances of proteins and metabolites revealed a contrasting activity of nitrogen assimilation pathways, e.g. for GOGAT, GDH and glutamic acid, in the different cell types from 15 to 26 DAA, which can be correlated with specific protein accumulation in the endosperm. The integration of cell-type specific proteome and metabolome data revealed a complex metabolic interplay of the different cell types and a functional switch during grain development and grain-filling processes.
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Affiliation(s)
- Shuang Zhang
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop EcophysiologyMinistry of Agriculture/Nanjing Agricultural UniversityNanjingChina
| | - Arindam Ghatak
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
- Vienna Metabolomics Center (VIME)University of ViennaViennaAustria
| | | | - Hannes Kramml
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
| | - Fujuan Zang
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop EcophysiologyMinistry of Agriculture/Nanjing Agricultural UniversityNanjingChina
| | - Shuang Gao
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop EcophysiologyMinistry of Agriculture/Nanjing Agricultural UniversityNanjingChina
| | - Živa Ramšak
- Department of Systems Biology and Biotechnology, National Institute of BiologyLjubljanaSlovenia
| | - Kristina Gruden
- Department of Systems Biology and Biotechnology, National Institute of BiologyLjubljanaSlovenia
| | - Rajeev K. Varshney
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures InstituteMurdoch UniversityMurdochWAAustralia
| | - Dong Jiang
- National Technique Innovation Center for Regional Wheat Production/Key Laboratory of Crop EcophysiologyMinistry of Agriculture/Nanjing Agricultural UniversityNanjingChina
| | - Palak Chaturvedi
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary EcologyUniversity of ViennaViennaAustria
- Vienna Metabolomics Center (VIME)University of ViennaViennaAustria
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31
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Hollin T, Abel S, Banks C, Hristov B, Prudhomme J, Hales K, Florens L, Stafford Noble W, Le Roch KG. Proteome-Wide Identification of RNA-dependent proteins and an emerging role for RNAs in Plasmodium falciparum protein complexes. Nat Commun 2024; 15:1365. [PMID: 38355719 PMCID: PMC10866993 DOI: 10.1038/s41467-024-45519-1] [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: 04/11/2023] [Accepted: 01/26/2024] [Indexed: 02/16/2024] Open
Abstract
Ribonucleoprotein complexes are composed of RNA, RNA-dependent proteins (RDPs) and RNA-binding proteins (RBPs), and play fundamental roles in RNA regulation. However, in the human malaria parasite, Plasmodium falciparum, identification and characterization of these proteins are particularly limited. In this study, we use an unbiased proteome-wide approach, called R-DeeP, a method based on sucrose density gradient ultracentrifugation, to identify RDPs. Quantitative analysis by mass spectrometry identifies 898 RDPs, including 545 proteins not yet associated with RNA. Results are further validated using a combination of computational and molecular approaches. Overall, this method provides the first snapshot of the Plasmodium protein-protein interaction network in the presence and absence of RNA. R-DeeP also helps to reconstruct Plasmodium multiprotein complexes based on co-segregation and deciphers their RNA-dependence. One RDP candidate, PF3D7_0823200, is functionally characterized and validated as a true RBP. Using enhanced crosslinking and immunoprecipitation followed by high-throughput sequencing (eCLIP-seq), we demonstrate that this protein interacts with various Plasmodium non-coding transcripts, including the var genes and ap2 transcription factors.
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Affiliation(s)
- Thomas Hollin
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Steven Abel
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Charles Banks
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Borislav Hristov
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Jacques Prudhomme
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA
| | - Kianna Hales
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - William Stafford Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Karine G Le Roch
- Department of Molecular, Cell and Systems Biology, University of California Riverside, Riverside, CA, USA.
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Yamaguchi A, Tasaki M, Ueda M, Ando Y, Naiki H. Epidemiological study of the subtype frequency of systemic amyloidosis listed in the Annual of the Pathological Autopsy Cases in Japan. Pathol Int 2024; 74:68-76. [PMID: 38088470 PMCID: PMC11551829 DOI: 10.1111/pin.13395] [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: 10/19/2023] [Revised: 11/20/2023] [Accepted: 11/26/2023] [Indexed: 02/03/2024]
Abstract
Clinical presentation of systemic amyloidosis differs among subtypes, and accurate subtype classification is important for choosing the treatment. Amyloid transthyretin (ATTR) amyloidosis was the predominant among the recently consulted amyloidosis cases in Japan. To reveal the latest subtype frequency of systemic amyloidosis among autopsy cases in Japan. We analyzed systemic amyloidosis cases autopsied from January 2017 to December 2018, that were listed in the Annuals of the Pathological Autopsy Cases in Japan, Volumes 60 and 61. When the subtype was unclear, we performed a questionnaire survey, immunohistochemistry with in-house rabbit polyclonal anti-κ116 - 133 , anti-λ118 -134 , and anti-transthyretin115 -124 antibodies, and proteomic analysis. Out of 481 systemic amyloidosis cases listed in the Annuals, 411 cases were available for analysis (85.4%). We classified 399 of these systemic amyloidosis cases. ATTR was the most common subtype (44.4%, n = 177), followed by amyloid immunoglobulin light chain (AL) (38.8%, n = 155). Amyloid A and amyloid β2 -microglobulin were 9.3% (n = 37) and 6.0% (n = 24), respectively. Double deposition of amyloid was identified in 1.6% (n = 6). In 168 cases (42.1%), systemic amyloidosis was the main cause of death. Of these cases, AL was the most common subtype (47.6%, n = 80), followed by ATTR (41.1%, n = 69). ATTR is the most predominant subtype among the current autopsy cases in Japan.
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Affiliation(s)
- Aina Yamaguchi
- Department of Molecular PathologyUniversity of FukuiFukuiJapan
| | - Masayoshi Tasaki
- Department of Neurology, Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
- Department of Biomedical Laboratory Sciences, Graduate School of Health SciencesKumamoto UniversityKumamotoJapan
| | - Mitsuharu Ueda
- Department of Neurology, Graduate School of Medical SciencesKumamoto UniversityKumamotoJapan
| | - Yukio Ando
- Department of Amyloidosis ResearchNagasaki International UniversitySaseboJapan
| | - Hironobu Naiki
- Department of Molecular PathologyUniversity of FukuiFukuiJapan
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O'Brien MJ, Ansari A. Protein interaction network revealed by quantitative proteomic analysis links TFIIB to multiple aspects of the transcription cycle. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140968. [PMID: 37863410 PMCID: PMC10872477 DOI: 10.1016/j.bbapap.2023.140968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 10/22/2023]
Abstract
Although TFIIB is widely regarded as an initiation factor, recent reports have implicated it in multiple aspects of eukaryotic transcription. To investigate the broader role of TFIIB in transcription, we performed quantitative proteomic analysis of yeast TFIIB. We purified two different populations of TFIIB; one from soluble cell lysate, which is not engaged in transcription, and the other from the chromatin fraction which yields the transcriptionally active form of the protein. TFIIB purified from the chromatin exhibits several interactions that explain its non-canonical roles in transcription. RNAPII, TFIIF and TFIIH were the only components of the preinitiation complex with a significant presence in chromatin TFIIB. A notable feature was enrichment of all subunits of CF1 and Rat1 3' end processing-termination complexes in chromatin-TFIIB preparation. Subunits of the CPF termination complex were also detected in both chromatin and soluble derived TFIIB preparations. These results may explain the presence of TFIIB at the 3' end of genes during transcription as well as its role in promoter-termination interaction.
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Affiliation(s)
- Michael J O'Brien
- Department of Biological Science, 5047 Gullen Mall, Wayne State University, Detroit, MI 48202, United States of America
| | - Athar Ansari
- Department of Biological Science, 5047 Gullen Mall, Wayne State University, Detroit, MI 48202, United States of America.
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Shanmugam T, Chaturvedi P, Streit D, Ghatak A, Bergelt T, Simm S, Weckwerth W, Schleiff E. Low dose ribosomal DNA P-loop mutation affects development and enforces autophagy in Arabidopsis. RNA Biol 2024; 21:1-15. [PMID: 38156797 PMCID: PMC10761087 DOI: 10.1080/15476286.2023.2298532] [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] [Revised: 12/14/2023] [Accepted: 12/14/2023] [Indexed: 01/03/2024] Open
Abstract
Arabidopsis contains hundreds of ribosomal DNA copies organized within the nucleolar organizing regions (NORs) in chromosomes 2 and 4. There are four major types of variants of rDNA, VAR1-4, based on the polymorphisms of 3' external transcribed sequences. The variants are known to be differentially expressed during plant development. We created a mutant by the CRISPR-Cas9-mediated excision of ~ 25 nt from predominantly NOR4 ribosomal DNA copies, obtaining mosaic mutational events on ~ 5% of all rDNA copies. The excised region consists of P-loop and Helix-82 segments of 25S rRNA. The mutation led to allelic, dosage-dependent defects marked by lateral root inhibition, reduced size, and pointy leaves, all previously observed for defective ribosomal function. The mutation in NOR4 led to dosage compensation from the NOR2 copies by elevated expression of VAR1 in mutants and further associated single-nucleotide variants, thus, resulting in altered rRNA sub-population. Furthermore, the mutants exhibited rRNA maturation defects specifically in the minor pathway typified by 32S pre-rRNA accumulation. Density-gradient fractionation and subsequent RT-PCR of rRNA analyses revealed that mutated copies were not incorporated into the translating ribosomes. The mutants in addition displayed an elevated autophagic flux as shown by the autophagic marker GFP-ATG8e, likely related to ribophagy.
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Affiliation(s)
- Thiruvenkadam Shanmugam
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Palak Chaturvedi
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Deniz Streit
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Arindam Ghatak
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Thorsten Bergelt
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Stefan Simm
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Enrico Schleiff
- Molecular Cell Biology of Plants, Institute for Molecular Biosciences & Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany
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Xu H, Akinyemi IA, Haley J, McIntosh MT, Bhaduri-McIntosh S. ATM, KAP1 and the Epstein-Barr virus polymerase processivity factor direct traffic at the intersection of transcription and replication. Nucleic Acids Res 2023; 51:11104-11122. [PMID: 37852757 PMCID: PMC10639065 DOI: 10.1093/nar/gkad823] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/09/2023] [Accepted: 09/20/2023] [Indexed: 10/20/2023] Open
Abstract
The timing of transcription and replication must be carefully regulated for heavily-transcribed genomes of double-stranded DNA viruses: transcription of immediate early/early genes must decline as replication ramps up from the same genome-ensuring efficient and timely replication of viral genomes followed by their packaging by structural proteins. To understand how the prototypic DNA virus Epstein-Barr virus tackles the logistical challenge of switching from transcription to DNA replication, we examined the proteome at viral replication forks. Specifically, to transition from transcription, the viral DNA polymerase-processivity factor EA-D is SUMOylated by the epigenetic regulator and E3 SUMO-ligase KAP1/TRIM28. KAP1's SUMO2-ligase function is triggered by phosphorylation via the PI3K-related kinase ATM and the RNA polymerase II-associated helicase RECQ5 at the transcription machinery. SUMO2-EA-D then recruits the histone loader CAF1 and the methyltransferase SETDB1 to silence the parental genome via H3K9 methylation, prioritizing replication. Thus, a key viral protein and host DNA repair, epigenetic and transcription-replication interference pathways orchestrate the handover from transcription-to-replication, a fundamental feature of DNA viruses.
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Affiliation(s)
- Huanzhou Xu
- Division of Infectious Diseases, Department of Pediatrics, University of Florida, Gainesville, FL 32610, USA
| | - Ibukun A Akinyemi
- Child Health Research Institute, Department of Pediatrics, University of Florida, Gainesville, FL 32610, USA
| | - John Haley
- Department of Pathology and Stony Brook Proteomics Center, Stony Brook University, Stony Brook, NY 11794, USA
| | - Michael T McIntosh
- Child Health Research Institute, Department of Pediatrics, University of Florida, Gainesville, FL 32610, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
| | - Sumita Bhaduri-McIntosh
- Division of Infectious Diseases, Department of Pediatrics, University of Florida, Gainesville, FL 32610, USA
- Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA
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Seregin AA, Smirnova LP, Dmitrieva EM, Zavialova MG, Simutkin GG, Ivanova SA. Differential Expression of Proteins Associated with Bipolar Disorder as Identified Using the PeptideShaker Software. Int J Mol Sci 2023; 24:15250. [PMID: 37894929 PMCID: PMC10607299 DOI: 10.3390/ijms242015250] [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: 07/28/2023] [Revised: 09/29/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
The prevalence of bipolar disorder (BD) in modern society is growing rapidly, but due to the lack of paraclinical criteria, its differential diagnosis with other mental disorders is somewhat challenging. In this regard, the relevance of proteomic studies is increasing due to the development of methods for processing large data arrays; this contributes to the discovery of protein patterns of pathological processes and the creation of new methods of diagnosis and treatment. It seems promising to search for proteins involved in the pathogenesis of BD in an easily accessible material-blood serum. Sera from BD patients and healthy individuals were purified via affinity chromatography to isolate 14 major proteins and separated using 1D SDS-PAGE. After trypsinolysis, the proteins in the samples were identified via HPLC/mass spectrometry. Mass spectrometric data were processed using the OMSSA and X!Tandem search algorithms using the UniProtKB database, and the results were analyzed using PeptideShaker. Differences in proteomes were assessed via an unlabeled NSAF-based analysis using a two-tailed Bonferroni-adjusted t-test. When comparing the blood serum proteomes of BD patients and healthy individuals, 10 proteins showed significant differences in NSAF values. Of these, four proteins were predominantly present in BD patients with the maximum NSAF value: 14-3-3 protein zeta/delta; ectonucleoside triphosphate diphosphohydrolase 7; transforming growth factor-beta-induced protein ig-h3; and B-cell CLL/lymphoma 9 protein. Further exploration of the role of these proteins in BD is warranted; conducting such studies will help develop new paraclinical criteria and discover new targets for BD drug therapy.
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Affiliation(s)
- Alexander A. Seregin
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk 634014, Russia; (A.A.S.)
| | - Liudmila P. Smirnova
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk 634014, Russia; (A.A.S.)
| | - Elena M. Dmitrieva
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk 634014, Russia; (A.A.S.)
| | | | - German G. Simutkin
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk 634014, Russia; (A.A.S.)
| | - Svetlana A. Ivanova
- Mental Health Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk 634014, Russia; (A.A.S.)
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37
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Wang H, Dai C, Pfeuffer J, Sachsenberg T, Sanchez A, Bai M, Perez-Riverol Y. Tissue-based absolute quantification using large-scale TMT and LFQ experiments. Proteomics 2023; 23:e2300188. [PMID: 37488995 DOI: 10.1002/pmic.202300188] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 07/26/2023]
Abstract
Relative and absolute intensity-based protein quantification across cell lines, tissue atlases and tumour datasets is increasingly available in public datasets. These atlases enable researchers to explore fundamental biological questions, such as protein existence, expression location, quantity and correlation with RNA expression. Most studies provide MS1 feature-based label-free quantitative (LFQ) datasets; however, growing numbers of isobaric tandem mass tags (TMT) datasets remain unexplored. Here, we compare traditional intensity-based absolute quantification (iBAQ) proteome abundance ranking to an analogous method using reporter ion proteome abundance ranking with data from an experiment where LFQ and TMT were measured on the same samples. This new TMT method substitutes reporter ion intensities for MS1 feature intensities in the iBAQ framework. Additionally, we compared LFQ-iBAQ values to TMT-iBAQ values from two independent large-scale tissue atlas datasets (one LFQ and one TMT) using robust bottom-up proteomic identification, normalisation and quantitation workflows.
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Affiliation(s)
- Hong Wang
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Chengxin Dai
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing, China
| | - Julianus Pfeuffer
- Algorithmic Bioinformatics, Freie Universität Berlin, Berlin, Germany
| | - Timo Sachsenberg
- Department of Computer Science, Applied Bioinformatics, University of Tübingen, Tübingen, Germany
- Institute for Biological and Medical Informatics, University of Tübingen, Tübingen, Germany
| | - Aniel Sanchez
- Section for Clinical Chemistry, Department of Translational Medicine, Lund University, Skåne University Hospital Malmö, Malmö, Sweden
| | - Mingze Bai
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Life Omics, Beijing, China
| | - Yasset Perez-Riverol
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, UK
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Packard JE, Williams MR, Fromuth DP, Dembowski JA. Proliferating cell nuclear antigen inhibitors block distinct stages of herpes simplex virus infection. PLoS Pathog 2023; 19:e1011539. [PMID: 37486931 PMCID: PMC10399828 DOI: 10.1371/journal.ppat.1011539] [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: 04/18/2023] [Revised: 08/03/2023] [Accepted: 07/05/2023] [Indexed: 07/26/2023] Open
Abstract
Proliferating cell nuclear antigen (PCNA) forms a homotrimer that encircles replicating DNA and is bound by DNA polymerases to add processivity to cellular DNA synthesis. In addition, PCNA acts as a scaffold to recruit DNA repair and chromatin remodeling proteins to replicating DNA via its interdomain connecting loop (IDCL). Despite encoding a DNA polymerase processivity factor UL42, it was previously found that PCNA associates with herpes simplex virus type 1 (HSV-1) replication forks and is necessary for productive HSV-1 infection. To define the role that PCNA plays during viral DNA replication or a replication-coupled process, we investigated the effects that two mechanistically distinct PCNA inhibitors, PCNA-I1 and T2AA, have on the HSV-1 infectious cycle. PCNA-I1 binds at the interface between PCNA monomers, stabilizes the homotrimer, and may interfere with protein-protein interactions. T2AA inhibits select protein-protein interactions within the PCNA IDCL. Here we demonstrate that PCNA-I1 treatment results in reduced HSV-1 DNA replication, late gene expression, and virus production, while T2AA treatment results in reduced late viral gene expression and infectious virus production. To pinpoint the mechanisms by which PCNA inhibitors affect viral processes and protein recruitment to replicated viral DNA, we performed accelerated native isolation of proteins on nascent DNA (aniPOND). Results indicate that T2AA inhibits recruitment of the viral uracil glycosylase UL2 and transcription regulatory factors to viral DNA, likely leading to a defect in viral base excision repair and the observed defect in late viral gene expression and infectious virus production. In addition, PCNA-I1 treatment results in decreased association of the viral DNA polymerase UL30 and known PCNA-interacting proteins with viral DNA, consistent with the observed block in viral DNA replication and subsequent processes. Together, we conclude that inhibitors of cellular PCNA block recruitment of key viral and cellular factors to viral DNA to inhibit viral DNA synthesis and coupled processes.
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Affiliation(s)
- Jessica E. Packard
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, United States of America
| | - Maya R. Williams
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, United States of America
| | - Daniel P. Fromuth
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, United States of America
| | - Jill A. Dembowski
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, United States of America
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Cheng A, Zhang Y, Sun J, Huang D, Sulaiman JE, Huang X, Wu L, Ye W, Wu C, Lam H, Shi Y, Qian PY. Pterosin sesquiterpenoids from Pteris laeta Wall. ex Ettingsh. protect cells from glutamate excitotoxicity by modulating mitochondrial signals. JOURNAL OF ETHNOPHARMACOLOGY 2023; 308:116308. [PMID: 36822346 DOI: 10.1016/j.jep.2023.116308] [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: 12/21/2022] [Revised: 02/09/2023] [Accepted: 02/19/2023] [Indexed: 06/18/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE The genus Pteris (Pteridaceae) has been used as a traditional herb for a long time. In particular, Pteris laeta Wall. ex Ettingsh. has been widely used in traditional Chinese medicine to treat nervous system diseases and some pterosin sesquiterpenes from Pteris show neuroprotective activity, but their underlying molecular mechanisms remain elusive. Therefore, to investigate the neuroprotective activity and working mechanism of pterosin sesquiterpenes from P. laeta Wall. ex Ettingsh. will provide a better understanding and guidance in using P. laeta Wall. ex Ettingsh. as a traditional Chinese medicine. AIM OF THE STUDY We aim to develop effective treatments for neurodegenerative diseases from pterosin sesquiterpenes by evaluating their neuroprotective activity and investigating their working mechanisms. MATERIALS AND METHODS Primary screening on the glutamate-induced excitotoxicity cell model was assessed by 3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide (MTT) assay. Fluorescent-activated cell sorting (FACS) was used to analyze the activation level of glutamate receptors and mitochondria membrane potential after treatment. Transcriptomics and proteomics analysis was performed to identify possible targets of pterosin B. The key pathways were enriched by the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis through the Database for Annotation, Visualization, and Integrated Discovery (DAVID). The core targets were visualized by a protein-protein interaction network using STRING. The mRNA and protein expressions were evaluated using real-time quantitative polymerase chain reaction (Q-PCR) and western blot, respectively. Immunocytochemistry was performed to monitor mitochondrial and apoptotic proteins. Cellular reactive oxygen species (ROS) were measured by ROS assay, and Ca2+ was stained with Fluo-4 AM to quantify intracellular Ca2+ levels. RESULTS We found pterosin B from Pteris laeta Wall. ex Ettingsh. showed significant neuroprotective activity against glutamate excitotoxicity, enhancing cell viability from 43.8% to 105% (p-value: <0.0001). We demonstrated that pterosin B worked on the downstream signaling pathways of glutamate excitotoxicity rather than directly blocking the activation of glutamate receptors. Pterosin B restored mitochondria membrane potentials, alleviated intracellular calcium overload from 107.4% to 95.47% (p-value: 0.0006), eliminated cellular ROS by 36.55% (p-value: 0.0143), and partially secured cells from LPS-induced inflammation by increasing cell survival from 46.75% to 58.5% (p-value: 0.0114). Notably, pterosin B enhanced the expression of nuclear factor-erythroid factor 2-related factor 2 (NRF2) and heme oxygenase-1 (HO-1) by 2.86-fold (p-value: 0.0006) and 4.24-fold (p-value: 0.0012), and down-regulated Kelch-like ECH-associated protein 1 (KEAP1) expression by 2.5-fold (p-value: 0.0107), indicating that it possibly promotes mitochondrial biogenesis and mitophagy to maintain mitochondria quality control and homeostasis, and ultimately inhibits apoptotic cell death. CONCLUSIONS Our work revealed that pterosin B protected cells from glutamate excitotoxicity by targeting the downstream mitochondrial signals, making it a valuable candidate for developing potential therapeutic agents in treating neurodegenerative diseases.
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Affiliation(s)
- Aifang Cheng
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China; Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, 999077, China
| | - Yan Zhang
- School of Traditional Chinese Medicine, Southern Medical University, Guangzhou, 510515, China; Institute for Advancing Translational Medicine in Bone and Joint Diseases (TMBJ), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, 999077, China
| | - Jin Sun
- Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Duli Huang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China; Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, 999077, China
| | - Jordy Evan Sulaiman
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, 999077, China
| | - Xin Huang
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China; Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, 999077, China
| | - Long Wu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, 999077, China
| | - Wenkang Ye
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China; Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, 999077, China; SZU-HKUST Joint Ph.D. Program in Marine Environmental Science, Shenzhen University, Shenzhen, 518060, China
| | - Chuanhai Wu
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China; Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, 999077, China
| | - Henry Lam
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Hong Kong, 999077, China
| | - Yusheng Shi
- National-Local Joint Engineering Research Center for Drug-Research and Development (R&D) of Neurodegenerative Diseases, Dalian Medical University, Dalian, 116044, China; Academy of Integrative Medicine, Dalian Medical University, Dalian, 116044, China.
| | - Pei-Yuan Qian
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458, China; Department of Ocean Science and Hong Kong Branch of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong, 999077, China.
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Stout AJ, Rittenberg ML, Shub M, Saad MK, Mirliani AB, Dolgin J, Kaplan DL. A Beefy-R culture medium: Replacing albumin with rapeseed protein isolates. Biomaterials 2023; 296:122092. [PMID: 36965281 PMCID: PMC10111969 DOI: 10.1016/j.biomaterials.2023.122092] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 03/03/2023] [Accepted: 03/12/2023] [Indexed: 03/27/2023]
Abstract
The development of cost-effective serum-free media is essential for the economic viability of cultured meat. A key challenge facing this goal is the high-cost of recombinant albumin which is necessary in many serum-free media formulations, including a recently developed serum-free medium for bovine satellite cell (BSC) culture termed Beefy-9. Here we alter Beefy-9 by replacing recombinant albumin with rapeseed protein isolate (RPI), a bulk-protein solution obtained from agricultural waste through alkali extraction (pH 12.5), isoelectric protein precipitation (pH 4.5), dissolution of physiologically soluble proteins (pH 7.2), and concentration of proteins through 3 kDa ultrafiltration. This new medium, termed Beefy-R, was then used to culture BSCs over four passages, during which cells grew with an average doubling time of 26.6 h, showing improved growth compared with Beefy-9. In Beefy-R, BSCs maintained cell phenotype and myogenicity. Together, these results offer an effective, low-cost, and sustainable alternative to albumin for serum-free culture of muscle stem cells, thereby addressing a key hurdle facing cultured meat production.
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Affiliation(s)
- Andrew J Stout
- Biomedical Engineering Department, Tissue Engineering Resource Center, Tufts University, Medford, MA, USA
| | - Miriam L Rittenberg
- Biomedical Engineering Department, Tissue Engineering Resource Center, Tufts University, Medford, MA, USA; Biological Engineering Department, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michelle Shub
- Biomedical Engineering Department, Tissue Engineering Resource Center, Tufts University, Medford, MA, USA
| | - Michael K Saad
- Biomedical Engineering Department, Tissue Engineering Resource Center, Tufts University, Medford, MA, USA
| | - Addison B Mirliani
- Biomedical Engineering Department, Tissue Engineering Resource Center, Tufts University, Medford, MA, USA
| | - James Dolgin
- Biomedical Engineering Department, Tissue Engineering Resource Center, Tufts University, Medford, MA, USA
| | - David L Kaplan
- Biomedical Engineering Department, Tissue Engineering Resource Center, Tufts University, Medford, MA, USA.
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Suzuki H, Furugori K, Abe R, Ogawa S, Ito S, Akiyama T, Horiuchi K, Takahashi H. MED26-containing Mediator may orchestrate multiple transcription processes through organization of nuclear bodies. Bioessays 2023; 45:e2200178. [PMID: 36852638 DOI: 10.1002/bies.202200178] [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: 09/07/2022] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 03/01/2023]
Abstract
Mediator is a coregulatory complex that plays essential roles in multiple processes of transcription regulation. One of the human Mediator subunits, MED26, has a role in recruitment of the super elongation complex (SEC) to polyadenylated genes and little elongation complex (LEC) to non-polyadenylated genes, including small nuclear RNAs (snRNAs) and replication-dependent histone (RDH) genes. MED26-containing Mediator plays a role in 3' Pol II pausing at the proximal region of transcript end sites in RDH genes through recruitment of Cajal bodies (CBs) to histone locus bodies (HLBs). This finding suggests that Mediator is involved in the association of CBs with HLBs to facilitate 3' Pol II pausing and subsequent 3'-end processing by supplying 3'-end processing factors from CBs. Thus, we argue the possibility that Mediator is involved in the organization of nuclear bodies to orchestrate multiple processes of gene transcription.
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Affiliation(s)
- Hidefumi Suzuki
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Kazuki Furugori
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Ryota Abe
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Shintaro Ogawa
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Sayaka Ito
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Tomohiko Akiyama
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Keiko Horiuchi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
| | - Hidehisa Takahashi
- Department of Molecular Biology, Yokohama City University Graduate School of Medical Science, Yokohama, Kanagawa, Japan
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Bhattacharyya A, Sadhasivam S, Sinha M, Gupta S, Saini S, Singh H, Khurana A, Sachdeva S, Sardana K, Ghosh S. Treatment of recalcitrant cases of tinea corporis/cruris caused by T. mentagrophytes - interdigitale complex with mutations in ERG11 ERG 3, ERG4, MDR1 MFS genes & SQLE and their potential implications. Int J Dermatol 2023; 62:637-648. [PMID: 36929499 DOI: 10.1111/ijd.16622] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 01/10/2023] [Accepted: 02/07/2023] [Indexed: 03/18/2023]
Abstract
BACKGROUND Recalcitrant dermatophyte infections are being reported from various parts of the world due to varied causes including strain variation, steroid misuse, SQLE mutations, and variable quality of itraconazole pellet formulations. The oral drug preferred in endemic areas is itraconazole, to which MIC levels remain low, and clinical failures to itraconazole reported defy a sound scientific explanation. OBJECTIVES The objective of the study was to conduct a proteomic and genomic analysis on isolates from therapeutically recalcitrant case with isolation of gene mutations and enzymatic abnormalities to explain azole failures. METHODS Trichophyton mentagrophyte interdigitale complex strains were isolated from seven clinically non-responding tinea corporis/cruris patients, who had failed a sequential course of 6 weeks of terbinafine 250 mg QD and itraconazole 100 mg BID. After AFST 1 strain, KA01 with high MIC to most drugs was characterized using whole genome sequencing, comparative proteomic profiling, and total sterol quantification. RESULTS Sterol quantification showed that the standard strain of Trichophyton mentagrophytes (MTCC-7687) had half the ergosterol content than the resistant KA01 strain. Genomic analysis revealed mutations in SQLE, ERG4, ERG11, MDR1, MFS genes, and a novel ERG3 mutation. Proteomic analysis established the aberrant expression of acetyl Co-A transferase in the resistant strain and upregulation of thioredoxin reductase and peroxiredoxin. CONCLUSION Our findings demonstrate possible reasons for multidrug resistance in the prevalent strain with mutations in genes that predict terbinafine (SQLE) and azole actions (ERG4, ERG11, ERG3) apart from efflux pumps (MDR1, MFS) that can explain multidrug clinical failures.
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Affiliation(s)
| | | | - Mau Sinha
- Vyome Therapeutics Limited, New Delhi, India
| | - Swati Gupta
- Vyome Therapeutics Limited, New Delhi, India
| | | | | | - Ananta Khurana
- Department of Dermatology, Venereology and Leprosy, Dr. Ram Manohar Lohia Hospital, Atal Bihari Vajpayee Institute of Medical Sciences, New Delhi, India
| | - Soumya Sachdeva
- Saraswathi Institute of Medical Sciences, Anwarpur, Uttar Pradesh, India
| | - Kabir Sardana
- Department of Dermatology, Venereology and Leprosy, Dr. Ram Manohar Lohia Hospital, Atal Bihari Vajpayee Institute of Medical Sciences, New Delhi, India
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Wong TY, Yan N, Kwan KKL, Pan Y, Liu J, Xiao Y, Wu L, Lam H. Comparative proteomic analysis reveals the different hepatotoxic mechanisms of human hepatocytes exposed to silver nanoparticles. JOURNAL OF HAZARDOUS MATERIALS 2023; 445:130599. [PMID: 37055998 DOI: 10.1016/j.jhazmat.2022.130599] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/30/2022] [Accepted: 12/11/2022] [Indexed: 06/19/2023]
Abstract
Silver nanoparticles (AgNPs), which have been used extensively in consuming products and eventually released into the natural environment, have aroused concerns recently because of their potentially harmful effects on human beings following various routes of exposure. As the liver is one of the largest accumulation and deposition sites of circulatory AgNPs, it is important to evaluate the hepatotoxicity induced by AgNPs. However, the acting mechanisms of AgNPs-induced hepatotoxicity are still elusive to a great extent. Herein, we investigated the hepatotoxic effects of AgNPs using a comparative proteomics approach. First, we evaluated the cytotoxicity of different-sized AgNPs and found that the cancerous liver cells were generally more sensitive than the normal liver cells. Next, proteomics results suggested that HepG2 and L02 cells showed distinct adaptive responses upon AgNPs exposure. HepG2 cells respond to stresses by adapting energy metabolism, upregulating metallothionein expression and increasing the expression of antioxidants, while L02 cells protect themselves by increasing DNA repair and macro-autophagy. Besides, mitochondrial ROS has been identified as one of the causes of AgNPs-induced hepatotoxicity. Collectively, our results revealed that hepatic cancer cells and normal cells cope with AgNPs in notably different pathways, providing new insights into mechanisms underlying AgNPs-induced hepatotoxicity. DATA AVAILABILITY: The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium (Deutsch et al. (2020)) via the PRIDE (Perez-Riverol et al. (2019)) partner repository with the dataset identifier PXD029511.
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Affiliation(s)
- Tin Yan Wong
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Neng Yan
- School of Environmental Studies, China University of Geosciences, 430074, Wuhan, China.
| | | | - Yanrong Pan
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Jingjing Liu
- Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016, China
| | - Yao Xiao
- Department of Ocean Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Long Wu
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Henry Lam
- Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
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Misumi Y, Tabata Y, Tasaki M, Obayashi K, Yamakawa S, Nomura T, Ueda M. Binding of serum-derived amyloid-associated proteins to amyloid fibrils. Amyloid 2023; 30:67-73. [PMID: 36094798 DOI: 10.1080/13506129.2022.2120800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
BACKGROUND Amyloid signature proteins such as serum amyloid P component, apolipoprotein E (ApoE), and ApoA-IV generally co-localise with amyloid, regardless of the types of amyloid precursor protein or the organs. Most of these proteins derive from serum and have reportedly been involved in amyloid fibril formation and stabilisation, as well as in excretion and degradation of amyloid precursor proteins. However, the processes and mechanisms by which these specific proteins deposit together with amyloid fibrils have not been clarified. METHODS We analysed the binding of serum proteins to amyloid fibrils derived from amyloid β and insulin in vitro by using liquid chromatography-tandem mass spectrometry (LC-MS/MS). RESULTS Specific serum proteins including ApoA-I, ApoE, ApoA-IV, ApoC-III and vitronectin adhered to amyloid fibrils at high concentrations in vitro. In addition, the profile of these proteins commonly occurred in both amyloid β and insulin amyloid fibrils and was mostly consistent with the composition of amyloid signature proteins. We also showed that high concentrations of serum proteins can adhere to amyloid fibrils in a short time. CONCLUSIONS Our in vitro results suggest that amyloid signature proteins coexist with amyloid primarily dependent on the binding of each serum protein, in the extracellular fluid, to amyloid fibrils.
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Affiliation(s)
- Yohei Misumi
- Department of Neurology, Kumamoto University, Kumamoto, Japan
| | - Yuri Tabata
- Department of Neurology, Kumamoto University, Kumamoto, Japan
| | - Masayoshi Tasaki
- Department of Neurology, Kumamoto University, Kumamoto, Japan.,Department of Biomedical Laboratory Sciences, Kumamoto University, Kumamoto, Japan
| | - Konen Obayashi
- Department of Morphological and Physiological Sciences, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Shiori Yamakawa
- Department of Neurology, Kumamoto University, Kumamoto, Japan
| | - Toshiya Nomura
- Department of Neurology, Kumamoto University, Kumamoto, Japan
| | - Mitsuharu Ueda
- Department of Neurology, Kumamoto University, Kumamoto, Japan
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Shen S, Wang X, Zhu X, Rasam S, Ma M, Huo S, Qian S, Zhang M, Qu M, Hu C, Jin L, Tian Y, Sethi S, Poulsen D, Wang J, Tu C, Qu J. High-quality and robust protein quantification in large clinical/pharmaceutical cohorts with IonStar proteomics investigation. Nat Protoc 2023; 18:700-731. [PMID: 36494494 PMCID: PMC10673696 DOI: 10.1038/s41596-022-00780-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 09/22/2022] [Indexed: 12/14/2022]
Abstract
Robust, reliable quantification of large sample cohorts is often essential for meaningful clinical or pharmaceutical proteomics investigations, but it is technically challenging. When analyzing very large numbers of samples, isotope labeling approaches may suffer from substantial batch effects, and even with label-free methods, it becomes evident that low-abundance proteins are not reliably measured owing to unsufficient reproducibility for quantification. The MS1-based quantitative proteomics pipeline IonStar was designed to address these challenges. IonStar is a label-free approach that takes advantage of the high sensitivity/selectivity attainable by ultrahigh-resolution (UHR)-MS1 acquisition (e.g., 120-240k full width at half maximum at m/z = 200) which is now widely available on ultrahigh-field Orbitrap instruments. By selectively and accurately procuring quantitative features of peptides within precisely defined, very narrow m/z windows corresponding to the UHR-MS1 resolution, the method minimizes co-eluted interferences and substantially enhances signal-to-noise ratio of low-abundance species by decreasing noise level. This feature results in high sensitivity, selectivity, accuracy and precision for quantification of low-abundance proteins, as well as fewer missing data and fewer false positives. This protocol also emphasizes the importance of well-controlled, robust experimental procedures to achieve high-quality quantification across a large cohort. It includes a surfactant cocktail-aided sample preparation procedure that achieves high/reproducible protein/peptide recoveries among many samples, and a trapping nano-liquid chromatography-mass spectrometry strategy for sensitive and reproducible acquisition of UHR-MS1 peptide signal robustly across a large cohort. Data processing and quality evaluation are illustrated using an example dataset ( http://proteomecentral.proteomexchange.org ), and example results from pharmaceutical project and one clinical project (patients with acute respiratory distress syndrome) are shown. The complete IonStar pipeline takes ~1-2 weeks for a sample cohort containing ~50-100 samples.
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Affiliation(s)
- Shichen Shen
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Xue Wang
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA
- AbbVie Bioresearch Center, Worcester, MA, USA
| | - Xiaoyu Zhu
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Sailee Rasam
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Min Ma
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Shihan Huo
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Shuo Qian
- Department of Cell Stress Biology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Ming Zhang
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Miao Qu
- Department of Neurology, Xuanwu Hospital, Beijing, China
| | - Chenqi Hu
- AbbVie Bioresearch Center, Worcester, MA, USA
| | - Liang Jin
- AbbVie Bioresearch Center, Worcester, MA, USA
| | - Yu Tian
- AbbVie Bioresearch Center, Worcester, MA, USA
| | - Sanjay Sethi
- Department of Medicine, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - David Poulsen
- Department of Neurosurgery, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA
| | - Jianmin Wang
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Chengjian Tu
- BioProduction Group, Thermo Fisher Scientific, Buffalo, NY, USA
| | - Jun Qu
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY, USA.
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46
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Hadjeras L, Bartel J, Maier LK, Maaß S, Vogel V, Svensson SL, Eggenhofer F, Gelhausen R, Müller T, Alkhnbashi OS, Backofen R, Becher D, Sharma CM, Marchfelder A. Revealing the small proteome of Haloferax volcanii by combining ribosome profiling and small-protein optimized mass spectrometry. MICROLIFE 2023; 4:uqad001. [PMID: 37223747 PMCID: PMC10117724 DOI: 10.1093/femsml/uqad001] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/29/2022] [Accepted: 01/13/2023] [Indexed: 05/25/2023]
Abstract
In contrast to extensively studied prokaryotic 'small' transcriptomes (encompassing all small noncoding RNAs), small proteomes (here defined as including proteins ≤70 aa) are only now entering the limelight. The absence of a complete small protein catalogue in most prokaryotes precludes our understanding of how these molecules affect physiology. So far, archaeal genomes have not yet been analyzed broadly with a dedicated focus on small proteins. Here, we present a combinatorial approach, integrating experimental data from small protein-optimized mass spectrometry (MS) and ribosome profiling (Ribo-seq), to generate a high confidence inventory of small proteins in the model archaeon Haloferax volcanii. We demonstrate by MS and Ribo-seq that 67% of the 317 annotated small open reading frames (sORFs) are translated under standard growth conditions. Furthermore, annotation-independent analysis of Ribo-seq data showed ribosomal engagement for 47 novel sORFs in intergenic regions. A total of seven of these were also detected by proteomics, in addition to an eighth novel small protein solely identified by MS. We also provide independent experimental evidence in vivo for the translation of 12 sORFs (annotated and novel) using epitope tagging and western blotting, underlining the validity of our identification scheme. Several novel sORFs are conserved in Haloferax species and might have important functions. Based on our findings, we conclude that the small proteome of H. volcanii is larger than previously appreciated, and that combining MS with Ribo-seq is a powerful approach for the discovery of novel small protein coding genes in archaea.
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Affiliation(s)
- Lydia Hadjeras
- Department of Molecular Infection Biology II, Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Straße 2 / D15, 97080 Würzburg, Germany
| | - Jürgen Bartel
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany
| | | | - Sandra Maaß
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany
| | - Verena Vogel
- Biology II, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Sarah L Svensson
- Department of Molecular Infection Biology II, Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Straße 2 / D15, 97080 Würzburg, Germany
| | - Florian Eggenhofer
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Rick Gelhausen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Teresa Müller
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
| | - Omer S Alkhnbashi
- Information and Computer Science Department, King Fahd University of Petroleum and Minerals, Dhahran 31261, Saudi Arabia
| | - Rolf Backofen
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany
| | - Dörte Becher
- Department of Microbial Proteomics, Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Str. 8, 17489 Greifswald, Germany
| | - Cynthia M Sharma
- Department of Molecular Infection Biology II, Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Straße 2 / D15, 97080 Würzburg, Germany
| | - Anita Marchfelder
- Biology II, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
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47
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Kumar R, Ghatak A, Goyal I, Sarkar NK, Weckwerth W, Grover A, Chaturvedi P. Heat-induced proteomic changes in anthers of contrasting rice genotypes under variable stress regimes. FRONTIERS IN PLANT SCIENCE 2023; 13:1083971. [PMID: 36756226 PMCID: PMC9901367 DOI: 10.3389/fpls.2022.1083971] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 12/02/2022] [Indexed: 06/18/2023]
Abstract
Heat stress drastically affects anther tissues resulting in poor plant fertility, necessitating an urgent need to determine the key proteome regulation associated with mature anther in response to heat stress. We identified several genotype - specific protein alterations in rice anthers of Moroberekan (Japonica, heat sensitive), IR64 (Indica, moderately heat tolerant), and Nagina22 (Aus, heat tolerant) in the short-term (ST_HS; one cycle of 42°C, 4 hours before anthesis) and long-term (LT_HS; 6 cycles of 38°C, 6 hours before anthesis) heat stress. The proteins upregulated in long-term heat stress in Nagina22 were enriched in biological processes related to unfolded protein binding and carboxylic acid metabolism, including amino acid metabolism. In short-term heat stress, Nagina22 anthers were enriched in proteins associated with vitamin E biosynthesis and GTPase activator activity. In contrast, downregulated proteins were related to ribosomal proteins. The expression of different Hsp20 and DnaJ was genotype specific. Overall, the heat response in Nagina22 was associated with its capacity for adequate metabolic control and cellular homeostasis, which may be critical for its higher reproductive thermotolerance. This study improves our understanding of thermotolerance mechanisms in rice anthers during anthesis and lays a foundation for breeding thermotolerant varieties via molecular breeding.
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Affiliation(s)
- Ritesh Kumar
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Arindam Ghatak
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Isha Goyal
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Neelam K. Sarkar
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Wolfram Weckwerth
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Anil Grover
- Department of Plant Molecular Biology, University of Delhi, New Delhi, India
| | - Palak Chaturvedi
- Molecular Systems Biology Lab (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
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48
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Preston SEJ, Richard VR, Del Rincón SV, Borchers CH, Zahedi RP. Proteomic Assessment of the Murine Mammary Gland Extracellular Matrix. Methods Mol Biol 2023; 2614:261-271. [PMID: 36587130 DOI: 10.1007/978-1-0716-2914-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The extracellular matrix (ECM) is a molecular scaffold mainly comprising fibrous proteins, glycoproteins, proteoglycans, and polysaccharides. Aside from acting as a structural support, the ECM's composition dictates cell-matrix interactions at the biochemical and biophysical level. In the context of cancer, the ECM is a critical component of the tumor microenvironment (TME) and dysregulation of its deposition and remodelling has been shown to promote tumor onset, progression, and metastasis. Here, we describe a robust protocol for the isolation and subsequent proteomic analysis of the ECM of murine mammary glands, for downstream assays studying the role of the ECM in breast cancer. The protocol yields sufficient protein amounts to enable not only the global quantitation of protein expression but furthermore the enrichment and quantitative analysis of post-translationally modified peptides to study aberrant signalling.
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Affiliation(s)
- Samuel E J Preston
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada.,Segal Cancer Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
| | - Vincent R Richard
- Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.,Segal Cancer Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
| | - Sonia V Del Rincón
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada.,Segal Cancer Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
| | - Christoph H Borchers
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada. .,Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada. .,Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada. .,Department of Pathology, Jewish General Hospital, McGill University, Montreal, Canada. .,Segal Cancer Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada.
| | - René P Zahedi
- Manitoba Centre for Proteomics and Systems Biology, Winnipeg, MB, Canada. .,Department of Internal Medicine, University of Manitoba, Winnipeg, MB, Canada. .,Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, MB, Canada.
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49
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Pible O, Petit P, Steinmetz G, Rivasseau C, Armengaud J. Taxonomical composition and functional analysis of biofilms sampled from a nuclear storage pool. Front Microbiol 2023; 14:1148976. [PMID: 37125163 PMCID: PMC10133526 DOI: 10.3389/fmicb.2023.1148976] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Abstract
Sampling small amounts of biofilm from harsh environments such as the biofilm present on the walls of a radioactive material storage pool offers few analytical options if taxonomic characterization and estimation of the different biomass contributions are the objectives. Although 16S/18S rRNA amplification on extracted DNA and sequencing is the most widely applied method, its reliability in terms of quantitation has been questioned as yields can be species-dependent. Here, we propose a tandem-mass spectrometry proteotyping approach consisting of acquiring peptide data and interpreting then against a generalist database without any a priori. The peptide sequence information is transformed into useful taxonomical information that allows to obtain the different biomass contributions at different taxonomical ranks. This new methodology is applied for the first time to analyze the composition of biofilms from minute quantities of material collected from a pool used to store radioactive sources in a nuclear facility. For these biofilms, we report the identification of three genera, namely Sphingomonas, Caulobacter, and Acidovorax, and their functional characterization by metaproteomics which shows that these organisms are metabolic active. Differential expression of Gene Ontology GOslim terms between the two main microorganisms highlights their metabolic specialization.
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Affiliation(s)
- Olivier Pible
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, France
| | - Pauline Petit
- Université Grenoble Alpes, CEA, CNRS, IRIG, Grenoble, France
| | - Gérard Steinmetz
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, France
| | - Corinne Rivasseau
- Université Grenoble Alpes, CEA, CNRS, IRIG, Grenoble, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Jean Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, Bagnols-sur-Cèze, France
- *Correspondence: Jean Armengaud,
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50
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Zhang X, Jiang Q, Li J, Zhang S, Cao Y, Xia X, Cai D, Tan J, Chen J, Han JDJ. KCNQ1OT1 promotes genome-wide transposon repression by guiding RNA-DNA triplexes and HP1 binding. Nat Cell Biol 2022; 24:1617-1629. [PMID: 36266489 DOI: 10.1038/s41556-022-01008-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 09/07/2022] [Indexed: 01/18/2023]
Abstract
Transposon (de)repression and heterochromatin reorganization are dynamically regulated during cell fate determination and are hallmarks of cellular senescence. However, whether they are sequence specifically regulated remains unknown. Here we uncover that the KCNQ1OT1 lncRNA, by sequence-specific Hoogsteen base pairing with double-stranded genomic DNA via its repeat-rich region and binding to the heterochromatin protein HP1α, guides, induces and maintains epigenetic silencing at specific repetitive DNA elements. Repressing KCNQ1OT1 or deleting its repeat-rich region reduces DNA methylation and H3K9me3 on KCNQ1OT1-targeted transposons. Engineering a fusion KCNQ1OT1 with an ectopically targeting guiding triplex sequence induces de novo DNA methylation at the target site. Phenotypically, repressing KCNQ1OT1 induces senescence-associated heterochromatin foci, transposon activation and retrotransposition as well as cellular senescence, demonstrating an essential role of KCNQ1OT1 to safeguard against genome instability and senescence.
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Affiliation(s)
- Xiaoli Zhang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
| | - Quanlong Jiang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiyang Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Shiqiang Zhang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yaqiang Cao
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xian Xia
- Department of Pharmacology, Nanjing University of Chinese Medicine, Nanjing, China
| | - Donghong Cai
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiaqi Tan
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
| | - Jiekai Chen
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China.
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