Mouse Zygote-Specific Proteasome Assembly Chaperone Important for Maternal-To-Zygotic Transition
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From Bipotent Neuromesodermal Progenitors to Neural-Mesodermal Interactions During Embryonic Development
International Journal of Molecular Sciences Review From Bipotent Neuromesodermal Progenitors to Neural-Mesodermal Interactions during Embryonic Development Nitza Kahane and Chaya Kalcheim * Department of Medical Neurobiology, Institute of Medical Research Israel-Canada (IMRIC) and the Edmond and Lily Safra Center for Brain Sciences (ELSC), Hebrew University of Jerusalem-Hadassah Medical School, P.O. Box 12272, Jerusalem 9112102, Israel; [email protected] * Correspondence: [email protected] Abstract: To ensure the formation of a properly patterned embryo, multiple processes must operate harmoniously at sequential phases of development. This is implemented by mutual interactions between cells and tissues that together regulate the segregation and specification of cells, their growth and morphogenesis. The formation of the spinal cord and paraxial mesoderm derivatives exquisitely illustrate these processes. Following early gastrulation, while the vertebrate body elongates, a pop- ulation of bipotent neuromesodermal progenitors resident in the posterior region of the embryo generate both neural and mesodermal lineages. At later stages, the somitic mesoderm regulates aspects of neural patterning and differentiation of both central and peripheral neural progenitors. Reciprocally, neural precursors influence the paraxial mesoderm to regulate somite-derived myogen- esis and additional processes by distinct mechanisms. Central to this crosstalk is the activity of the axial notochord, which, via sonic hedgehog signaling, plays pivotal roles in neural, skeletal muscle and cartilage ontogeny. Here, we discuss the cellular and molecular basis underlying this complex Citation: Kahane, N.; Kalcheim, C. developmental plan, with a focus on the logic of sonic hedgehog activities in the coordination of the From Bipotent Neuromesodermal Progenitors to Neural-Mesodermal neural-mesodermal axis. -
Degradation and Beyond: Control of Androgen Receptor Activity by the Proteasome System
CELLULAR & MOLECULAR BIOLOGY LETTERS Volume 11, (2006) pp 109 – 131 http://www.cmbl.org.pl DOI: 10.2478/s11658-006-0011-9 Received: 06 December 2005 Revised form accepted: 31 January 2006 © 2006 by the University of Wrocław, Poland DEGRADATION AND BEYOND: CONTROL OF ANDROGEN RECEPTOR ACTIVITY BY THE PROTEASOME SYSTEM TOMASZ JAWORSKI Department of Cellular Biochemistry, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093 Warsaw, Poland Abstract: The androgen receptor (AR) is a transcription factor belonging to the family of nuclear receptors which mediates the action of androgens in the development of urogenital structures. AR expression is regulated post- * Corresponding author: e-mail: [email protected] Abbreviations used: AATF – apoptosis antagonizing factor; APIS complex – AAA proteins independent of 20S; ARA54 – AR-associated protein 54; ARA70 – AR-associated protein 70; ARE – androgen responsive element; ARNIP – AR N-terminal interacting protein; bFGF – basic fibroblast growth factor; CARM1 – coactivator-associated arginine methyltransferase 1; CHIP – C-terminus Hsp70 interacting protein; DBD – DNA binding domain; E6-AP – E6-associated protein; GRIP-1 – glucocorticoid receptor interacting protein 1; GSK3β – glycogen synthase kinase 3β; HDAC1 – histone deacetylase 1; HECT – homologous to the E6-AP C-terminus; HEK293 – human embryonal kidney cell line; HepG2 – human hepatoma cell line; Hsp90 – heat shock protein 90; IGF-1 – insulin-like growth factor 1; IL-6 – interleukin 6; KLK2 – -
Deubiquitinase UCHL1 Maintains Protein Homeostasis Through PSMA7-APEH- Proteasome Axis in High-Grade Serous Ovarian Carcinoma
bioRxiv preprint doi: https://doi.org/10.1101/2020.09.28.316810; this version posted October 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Deubiquitinase UCHL1 Maintains Protein Homeostasis through PSMA7-APEH- Proteasome Axis in High-Grade Serous Ovarian Carcinoma Apoorva Tangri1*, Kinzie Lighty1*, Jagadish Loganathan1, Fahmi Mesmar2, Ram Podicheti3, Chi Zhang1, Marcin Iwanicki4, Harikrishna Nakshatri1,5, Sumegha Mitra1,5,# 1 Indiana University School of Medicine, Indianapolis, IN, USA 2 Indiana University, Bloomington, IN, USA 3Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, USA 4Stevens Institute of Technology, Hoboken, NJ, USA 5Indiana University Melvin & Bren Simon Cancer Center, Indianapolis, USA *Equal contribution # corresponding author; to whom correspondence may be addressed. E-mail: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.09.28.316810; this version posted October 9, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract High-grade serous ovarian cancer (HGSOC) is characterized by chromosomal instability, DNA damage, oxidative stress, and high metabolic demand, which exacerbate misfolded, unfolded and damaged protein burden resulting in increased proteotoxicity. However, the underlying mechanisms that maintain protein homeostasis to promote HGSOC growth remain poorly understood. In this study, we report that the neuronal deubiquitinating enzyme, ubiquitin carboxyl-terminal hydrolase L1 (UCHL1) is overexpressed in HGSOC and maintains protein homeostasis. UCHL1 expression was markedly increased in HGSOC patient tumors and serous tubal intraepithelial carcinoma (HGSOC precursor lesions). -
Role of Phytochemicals in Colon Cancer Prevention: a Nutrigenomics Approach
Role of phytochemicals in colon cancer prevention: a nutrigenomics approach Marjan J van Erk Promotor: Prof. Dr. P.J. van Bladeren Hoogleraar in de Toxicokinetiek en Biotransformatie Wageningen Universiteit Co-promotoren: Dr. Ir. J.M.M.J.G. Aarts Universitair Docent, Sectie Toxicologie Wageningen Universiteit Dr. Ir. B. van Ommen Senior Research Fellow Nutritional Systems Biology TNO Voeding, Zeist Promotiecommissie: Prof. Dr. P. Dolara University of Florence, Italy Prof. Dr. J.A.M. Leunissen Wageningen Universiteit Prof. Dr. J.C. Mathers University of Newcastle, United Kingdom Prof. Dr. M. Müller Wageningen Universiteit Dit onderzoek is uitgevoerd binnen de onderzoekschool VLAG Role of phytochemicals in colon cancer prevention: a nutrigenomics approach Marjan Jolanda van Erk Proefschrift ter verkrijging van graad van doctor op gezag van de rector magnificus van Wageningen Universiteit, Prof.Dr.Ir. L. Speelman, in het openbaar te verdedigen op vrijdag 1 oktober 2004 des namiddags te vier uur in de Aula Title Role of phytochemicals in colon cancer prevention: a nutrigenomics approach Author Marjan Jolanda van Erk Thesis Wageningen University, Wageningen, the Netherlands (2004) with abstract, with references, with summary in Dutch ISBN 90-8504-085-X ABSTRACT Role of phytochemicals in colon cancer prevention: a nutrigenomics approach Specific food compounds, especially from fruits and vegetables, may protect against development of colon cancer. In this thesis effects and mechanisms of various phytochemicals in relation to colon cancer prevention were studied through application of large-scale gene expression profiling. Expression measurement of thousands of genes can yield a more complete and in-depth insight into the mode of action of the compounds. -
Salivary Biomarkers for Diagnosis of Inflammatory Bowel Diseases
International Journal of Molecular Sciences Review Salivary Biomarkers for Diagnosis of Inflammatory Bowel Diseases: A Systematic Review Kacper Nijakowski * and Anna Surdacka Department of Conservative Dentistry and Endodontics, Poznan University of Medical Sciences, 60-812 Poznan, Poland; [email protected] * Correspondence: [email protected] Received: 24 September 2020; Accepted: 6 October 2020; Published: 10 October 2020 Abstract: Saliva as a biological fluid has a remarkable potential in the non-invasive diagnostics of several systemic disorders. Inflammatory bowel diseases are chronic inflammatory disorders of the gastrointestinal tract. This systematic review was designed to answer the question “Are salivary biomarkers reliable for the diagnosis of inflammatory bowel diseases?”. Following the inclusion and exclusion criteria, eleven studies were included (according to PRISMA statement guidelines). Due to their heterogeneity, the potential salivary markers for IBD were divided into four groups: oxidative status markers, inflammatory cytokines, microRNAs and other biomarkers. Active CD patients manifest decreased activity of antioxidants (e.g., glutathione, catalase) and increased lipid peroxidation. Therefore, malondialdehyde seems to be a good diagnostic marker of CD. Moreover, elevated concentrations of proinflammatory cytokines (such as interleukin 1β, interleukin 6 or tumour necrosis factor α) are associated with the activity of IBD. Additionaly, selected miRNAs are altered in saliva (overexpressed miR-101 in CD; overexpressed miR-21, miR-31, miR-142-3p and underexpressed miR-142-5p in UC). Among other salivary biomarkers, exosomal PSMA7, α-amylase and calprotectin are detected. In conclusion, saliva contains several biomarkers which can be used credibly for the early diagnosis and regular monitoring of IBD. However, further investigations are necessary to validate these findings, as well as to identify new reliable salivary biomarkers. -
Table 1. Swine Proteins Identified As Differentially Expressed at 24Dpi in OURT 88/3 Infected Animals
Table 1. swine proteins identified as differentially expressed at 24dpi in OURT 88/3 infected animals. Gene name Protein ID Protein Name -Log p-value control vs A_24DPI Difference control Vs A_24DPI F8 K7GL28 Coagulation factor VIII 2.123919902 5.42533493 PPBP F1RUL6 C-X-C motif chemokine 3.219079808 4.493174871 SDPR I3LDR9 Caveolae associated protein 2 2.191007299 4.085711161 IGHG L8B0X5 IgG heavy chain 2.084611488 -4.282530149 LOC100517145 F1S3H9 Complement C3 (LOC100517145) 3.885740476 -4.364484406 GOLM1 F1S4I1 Golgi membrane protein 1 1.746130664 -4.767168681 FCN2 I3L5W3 Ficolin-2 2.937884686 -6.029483795 Table 2. swine proteins identified as differentially expressed at 7dpi in Benin ΔMGF infected animals. Gene name Protein ID Protein Name -Log p-value control vs B_7DPI Difference control Vs B_7DPI A0A075B7I5 Ig-like domain-containing protein 1.765578164 -3.480728149 ATP5A1 F1RPS8_PIG ATP synthase subunit alpha 2.270386995 3.270935059 LOC100627396 F1RX35_PIG Fibrinogen C-terminal domain-containing protein 2.211242648 3.967363358 LOC100514666;LOC102158263 F1RX36_PIG Fibrinogen alpha chain 2.337934993 3.758180618 FGB F1RX37_PIG Fibrinogen beta chain 2.411948004 4.03753376 PSMA8 F1SBA5_PIG Proteasome subunit alpha type 1.473601007 -3.815182686 ACAN F1SKR0_PIG Aggrecan core protein 1.974489764 -3.726634026 TFG F1SL01_PIG PB1 domain-containing protein 1.809215274 -3.131304741 LOC100154408 F1SSL6_PIG Proteasome subunit alpha type 1.701949053 -3.944885254 PSMA4 F2Z528_PIG Proteasome subunit alpha type 2.045768185 -4.502977371 PSMA5 F2Z5K2_PIG -
Comparative Transcriptomics Identifies Potential Stemness-Related Markers for Mesenchymal Stromal/Stem Cells
bioRxiv preprint doi: https://doi.org/10.1101/2021.05.25.445659; this version posted May 26, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Comparative Transcriptomics Identifies Potential Stemness-Related Markers for Mesenchymal Stromal/Stem Cells Authors Myret Ghabriel 1, Ahmed El Hosseiny 1, 2, Ahmed Moustafa*1, 2 and Asma Amleh*1, 2 Affiliations 1Biotechnology Program, American University in Cairo, New Cairo 11835, Egypt 2Department of Biology, American University in Cairo, New Cairo 11835, Egypt *Corresponding authors: Ahmed Moustafa [email protected] Asma Amleh [email protected]. Abstract Mesenchymal stromal/stem cells (MSCs) are multipotent cells residing in multiple tissues with the capacity for self-renewal and differentiation into various cell types. These properties make them promising candidates for regenerative therapies. MSC identification is critical in yielding pure populations for successful therapeutic applications; however, the criteria for MSC identification proposed by the International Society for Cellular Therapy (ISCT) is inconsistent across different tissue sources. In this study, we aimed to identify potential markers to be used together with the ISCT’s criteria to provide a more accurate means of MSC identification. Thus, we carried out a comparative analysis of the expression of human and mouse MSCs derived from multiple tissues to identify the common differentially expressed genes. We show that six members of the proteasome degradation system are similarly expressed across MSCs derived from bone marrow, adipose tissue, amnion, and umbilical cord. -
Genes for Extracellular Matrix-Degrading Metalloproteinases and Their Inhibitor, TIMP, Are Expressed During Early Mammalian Development
Downloaded from genesdev.cshlp.org on September 23, 2021 - Published by Cold Spring Harbor Laboratory Press Genes for extracellular matrix-degrading metalloproteinases and their inhibitor, TIMP, are expressed during early mammalian development Carol A. Brenner, 1 Richard R. Adler, 2 Daniel A. Rappolee, Roger A. Pedersen, and Zena Werb 3 Laboratory of Radiobiology and Environmental Health, and Department of Anatomy, University of California, San Francisco, California 94143-0750 USA Extracellular matrix (ECM) remodeling accompanies cell migration, cell--cell interactions, embryo expansion, uterine implantation, and tissue invasion during mammalian embryogenesis. We have found that mouse embryos secrete functional ECM-degrading metalloproteinases, including collagenase and stromelysin, that are inhibitable by the tissue inhibitor of metalloproteinases (TIMP) and that are regulated during peri-implantation development and endoderm differentiation, mRNA transcripts for collagenase, stromelysin, and TIMP were detected as maternal transcripts in the unfertilized egg, were present at the zygote and cleavage stages, and increased at the blastocyst stage and with endoderm differentiation. These data suggest that metalloproteinases function in cell-ECM interactions during growth, development, and implantation of mammalian embryos. [Key Words: Collagenase; stromelysin; polymerase chain reaction; tissue inhibitor of metalloproteinases; maternal mRNA; endoderm differentiation] January 31, 1989; revised version accepted March 15, 1989. The extracellular matrix (ECM) forms a substrate for cell 1988}. The activity of these proteinases is regulated by attachment and migration and directs cell form and the tissue inhibitor of metalloproteinases {TIMPI function through cell-ECM interactions. ECM macro- (Murphy et al. 1985; Herron et al. 1986a, b; Gavrilovic et molecules first appear in the mammalian embryo in the al. -
Deubiquitinase UCHL1 Maintains Protein Homeostasis Through the PSMA7-APEH- Proteasome Axis in High-Grade Serous Ovarian Carcinoma
Author Manuscript Published OnlineFirst on March 22, 2021; DOI: 10.1158/1541-7786.MCR-20-0883 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. Deubiquitinase UCHL1 Maintains Protein Homeostasis through the PSMA7-APEH- Proteasome Axis in High-Grade Serous Ovarian Carcinoma Apoorva Tangri1*, Kinzie Lighty1*, Jagadish Loganathan1, Fahmi Mesmar2, Ram Podicheti3, Chi Zhang4, Marcin Iwanicki5, Ronny Drapkin6, Harikrishna Nakshatri7,8, Sumegha Mitra1,8,# 1Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN, USA 2Department of Intelligent Systems Engineering, Indiana University, Bloomington, IN, USA 3Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN, USA 4Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA 5Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, NJ, USA 6Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA 7Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA 8Indiana University Simon Comprehensive Cancer Center, Indianapolis, USA *Equal contribution Running title: UCHL1 mediates protein homeostasis in HGSOC Conflict of interest disclosure statement: None #Corresponding author Sumegha Mitra, Ph.D. Assistant Professor of Obstetrics and Gynecology Indiana University School of Medicine C547 Joseph E. Walther Hall (R3) 980 W Walnut Street, Indianapolis, IN 46202 317-274-3967 (office) 317-944-7417 (fax) [email protected] 1 Downloaded from mcr.aacrjournals.org on October 1, 2021. © 2021 American Association for Cancer Research. Author Manuscript Published OnlineFirst on March 22, 2021; DOI: 10.1158/1541-7786.MCR-20-0883 Author manuscripts have been peer reviewed and accepted for publication but have not yet been edited. -
Proteasome Biology: Chemistry and Bioengineering Insights
polymers Review Proteasome Biology: Chemistry and Bioengineering Insights Lucia Raˇcková * and Erika Csekes Centre of Experimental Medicine, Institute of Experimental Pharmacology and Toxicology, Slovak Academy of Sciences, Dúbravská cesta 9, 841 04 Bratislava, Slovakia; [email protected] * Correspondence: [email protected] or [email protected] Received: 28 September 2020; Accepted: 23 November 2020; Published: 4 December 2020 Abstract: Proteasomal degradation provides the crucial machinery for maintaining cellular proteostasis. The biological origins of modulation or impairment of the function of proteasomal complexes may include changes in gene expression of their subunits, ubiquitin mutation, or indirect mechanisms arising from the overall impairment of proteostasis. However, changes in the physico-chemical characteristics of the cellular environment might also meaningfully contribute to altered performance. This review summarizes the effects of physicochemical factors in the cell, such as pH, temperature fluctuations, and reactions with the products of oxidative metabolism, on the function of the proteasome. Furthermore, evidence of the direct interaction of proteasomal complexes with protein aggregates is compared against the knowledge obtained from immobilization biotechnologies. In this regard, factors such as the structures of the natural polymeric scaffolds in the cells, their content of reactive groups or the sequestration of metal ions, and processes at the interface, are discussed here with regard to their -
The Ubiquitin-Proteasome System
Review The ubiquitin-proteasome system DIPANKAR NANDI*, PANKAJ TAHILIANI, ANUJITH KUMAR and DILIP CHANDU Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India *Corresponding author (Fax, 91-80-23600814; Email, [email protected]) The 2004 Nobel Prize in chemistry for the discovery of protein ubiquitination has led to the recognition of cellular proteolysis as a central area of research in biology. Eukaryotic proteins targeted for degradation by this pathway are first ‘tagged’ by multimers of a protein known as ubiquitin and are later proteolyzed by a giant enzyme known as the proteasome. This article recounts the key observations that led to the discovery of ubiquitin-proteasome system (UPS). In addition, different aspects of proteasome biology are highlighted. Finally, some key roles of the UPS in different areas of biology and the use of inhibitors of this pathway as possible drug targets are discussed. [Nandi D, Tahiliani P, Kumar A and Chandu D 2006 The ubiquitin-proteasome system; J. Biosci. 31 137–155] 1. Introduction biological processes, e.g. transcription, cell cycle, antigen processing, cellular defense, signalling etc. is now well In an incisive article, J Goldstein, the 1985 Nobel laureate established (Ciechanover and Iwai 2004; Varshavsky 2005). for the regulation of cholesterol metabolism (together with During the early days in the field of cytosolic protein M Brown) and Chair for the Jury for the Lasker awards, degradation, cell biologists were intrigued by the requirement laments the fact that it is hard to pick out truly original dis- of ATP in this process as it is well known that peptide bond coveries among the plethora of scientific publications hydrolysis does not require metabolic energy. -
Transcriptome Analysis Reveals Possible Immunomodulatory Activity Mechanism of Chlorella Sp
marine drugs Article Transcriptome Analysis Reveals Possible Immunomodulatory Activity Mechanism of Chlorella sp. Exopolysaccharides on RAW264.7 Macrophages Siwei Wu, Hongquan Liu * , Siyu Li, Han Sun, Xiumiao He, Ying Huang and Han Long Guangxi Key Laboratory for Polysaccharide Materials and Modifications, School of Marine and Biotechnology, GuangXi University for Nationalities, Nanning 530006, China; [email protected] (S.W.); [email protected] (S.L.); [email protected] (H.S.); [email protected] (X.H.); [email protected] (Y.H.); [email protected] (H.L.) * Correspondence: [email protected] Abstract: In this study, the exopolysaccharides of Chlorella sp. (CEP) were isolated to obtain the purified fraction CEP4. Characterization results showed that CEP4 was a sulfated heteropolysaccha- ride. The main monosaccharide components of CEP4 are glucosamine hydrochloride (40.8%) and glucuronic acid (21.0%). The impact of CEP4 on the immune activity of RAW264.7 macrophage cy- tokines was detected, and the results showed that CEP4 induced the production of nitric oxide (NO), TNF-α, and IL-6 in a dose-dependent pattern within a range of 6 µg/mL. A total of 4824 differentially expressed genes (DEGs) were obtained from the results of RNA-seq. Gene enrichment analysis showed that immune-related genes such as NFKB1, IL-6, and IL-1b were significantly upregulated, while the genes RIPK1 and TLR4 were significantly downregulated. KEGG pathway enrichment analysis showed that DEGs were significantly enriched in immune-related biological processes, Citation: Wu, S.; Liu, H.; Li, S.; including toll-like receptor (TLR) signaling pathway, cytosolic DNA-sensing pathway, and C-type Sun, H.; He, X.; Huang, Y.; Long, H.