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Wang YP, Wu EJ, Lurwanu Y, Ding JP, He DC, Waheed A, Nkurikiyimfura O, Liu ST, Li WY, Wang ZH, Yang L, Zhan J. Evidence for a synergistic effect of post-translational modifications and genomic composition of eEF-1α on the adaptation of Phytophthora infestans. Ecol Evol 2021; 11:5484-5496. [PMID: 34026022 PMCID: PMC8131795 DOI: 10.1002/ece3.7442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 02/19/2021] [Accepted: 02/21/2021] [Indexed: 12/18/2022] Open
Abstract
Genetic variation plays a fundamental role in pathogen's adaptation to environmental stresses. Pathogens with low genetic variation tend to survive and proliferate more poorly due to their lack of genotypic/phenotypic polymorphisms in responding to fluctuating environments. Evolutionary theory hypothesizes that the adaptive disadvantage of genes with low genomic variation can be compensated for structural diversity of proteins through post-translation modification (PTM) but this theory is rarely tested experimentally and its implication to sustainable disease management is hardly discussed. In this study, we analyzed nucleotide characteristics of eukaryotic translation elongation factor-1α (eEF-lα) gene from 165 Phytophthora infestans isolates and the physical and chemical properties of its derived proteins. We found a low sequence variation of eEF-lα protein, possibly attributable to purifying selection and a lack of intra-genic recombination rather than reduced mutation. In the only two isoforms detected by the study, the major one accounted for >95% of the pathogen collection and displayed a significantly higher fitness than the minor one. High lysine representation enhances the opportunity of the eEF-1α protein to be methylated and the absence of disulfide bonds is consistent with the structural prediction showing that many disordered regions are existed in the protein. Methylation, structural disordering, and possibly other PTMs ensure the ability of the protein to modify its functions during biological, cellular and biochemical processes, and compensate for its adaptive disadvantage caused by sequence conservation. Our results indicate that PTMs may function synergistically with nucleotide codes to regulate the adaptive landscape of eEF-1α, possibly as well as other housekeeping genes, in P. infestans. Compensatory evolution between pre- and post-translational phase in eEF-1α could enable pathogens quickly adapting to disease management strategies while efficiently maintaining critical roles of the protein playing in biological, cellular, and biochemical activities. Implications of these results to sustainable plant disease management are discussed.
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Affiliation(s)
- Yan-Ping Wang
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
| | - E-Jiao Wu
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
| | - Yahuza Lurwanu
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
- Department of Crop Protection Bayero University Kano Kano Nigeria
| | - Ji-Peng Ding
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
| | - Dun-Chun He
- School of Economics and Trade Fujian Jiangxia University Fuzhou China
| | - Abdul Waheed
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
| | - Oswald Nkurikiyimfura
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
| | - Shi-Ting Liu
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
| | - Wen-Yang Li
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
| | - Zong-Hua Wang
- Fujian University Key Laboratory for Plant-Microbe Interaction College of Life Sciences Fujian Agriculture and Forestry University Fuzhou China
- Institute of Oceanography Minjiang University Fuzhou China
| | - Lina Yang
- Key lab for Bio pesticide and Chemical Biology Ministry of Education Fujian Agriculture and Forestry University Fuzhou China
- Institute of Oceanography Minjiang University Fuzhou China
| | - Jiasui Zhan
- Department of Forest Mycology and Plant Pathology Swedish University of Agricultural Sciences Uppsala Sweden
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Chauhan D, Shames SR. Pathogenicity and Virulence of Legionella: Intracellular replication and host response. Virulence 2021; 12:1122-1144. [PMID: 33843434 PMCID: PMC8043192 DOI: 10.1080/21505594.2021.1903199] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Bacteria of the genus Legionella are natural pathogens of amoebae that can cause a severe pneumonia in humans called Legionnaires’ Disease. Human disease results from inhalation of Legionella-contaminated aerosols and subsequent bacterial replication within alveolar macrophages. Legionella pathogenicity in humans has resulted from extensive co-evolution with diverse genera of amoebae. To replicate intracellularly, Legionella generates a replication-permissive compartment called the Legionella-containing vacuole (LCV) through the concerted action of hundreds of Dot/Icm-translocated effector proteins. In this review, we present a collective overview of Legionella pathogenicity including infection mechanisms, secretion systems, and translocated effector function. We also discuss innate and adaptive immune responses to L. pneumophila, the implications of Legionella genome diversity and future avenues for the field.
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Affiliation(s)
- Deepika Chauhan
- Division of Biology, Kansas State University, Manhattan, Kansas, USA
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Selvaraju S, Ramya L, Parthipan S, Swathi D, Binsila BK, Kolte AP. Deciphering the complexity of sperm transcriptome reveals genes governing functional membrane and acrosome integrities potentially influence fertility. Cell Tissue Res 2021; 385:207-222. [PMID: 33783607 DOI: 10.1007/s00441-021-03443-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 03/01/2021] [Indexed: 12/14/2022]
Abstract
Deciphering sperm transcriptome is the key to understanding the molecular mechanisms governing peri-fertilization, embryonic development, and pregnancy establishment. This study aimed to profile sperm transcriptome to identify signature transcripts regulating male fertility. Semen samples were collected from 47 bulls with varied fertility rates. The sperm total RNA was isolated (n = 8) and subjected to transcriptome sequencing. Based on the expression pattern obtained from RNA profiling, the bulls were grouped (p = 0.03) into high-fertile and sub-fertile, and signature transcripts controlling sperm functions and fertility were identified. The results were validated using the OMIM database, qPCR, and sperm function tests. The sperm contains 1100 to 1700 intact transcripts, of which BCL2L11 and CAPZA3 were abundant and associated (p < 0.05) with spermatogenesis and post-embryonic organ morphogenesis. The upregulated genes in the acrosome integrity and functional membrane integrity groups had a close association with the fertility rate. The biological functions of these upregulated genes (p < 0.05) in the high-fertile bulls were associated with spermatogenesis (AFF4 and BRIP1), sperm motility (AK6 and ATP6V1G3), capacitation and zona binding (AGFG1), embryo development (TCF7 and AKIRIN2), and placental development (KRT19). The transcripts involved in pathways regulating embryonic development such as translation (EEF1B2 and MTIF3, p = 8.87E-05) and nonsense-mediated decay (RPL23 and RPL7A, p = 5.01E-27) were upregulated in high-fertile bulls. The identified transcripts may significantly impact oocyte function, embryogenesis, trophectoderm development, and pregnancy establishment. In addition, the study also reveals that the genes governing sperm functional membrane integrity and acrosome integrity have a prospective effect on male fertility.
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Affiliation(s)
- Sellappan Selvaraju
- Reproductive Physiology Laboratory, Animal Physiology Division, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India.
| | - Laxman Ramya
- Reproductive Physiology Laboratory, Animal Physiology Division, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
| | - Sivashanmugam Parthipan
- Reproductive Physiology Laboratory, Animal Physiology Division, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
| | - Divakar Swathi
- Reproductive Physiology Laboratory, Animal Physiology Division, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
| | - Bala Krishnan Binsila
- Reproductive Physiology Laboratory, Animal Physiology Division, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
| | - Atul P Kolte
- Omics Laboratory, Animal Nutrition Division, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
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Wu A, Tang J, Guo Z, Dai Y, Nie J, Hu W, Liu N, Ye C, Li S, Pei H, Zhou G. Long Non-Coding RNA CRYBG3 Promotes Lung Cancer Metastasis via Activating the eEF1A1/MDM2/MTBP Axis. Int J Mol Sci 2021; 22:3211. [PMID: 33809929 PMCID: PMC8048704 DOI: 10.3390/ijms22063211] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/12/2021] [Accepted: 03/18/2021] [Indexed: 12/14/2022] Open
Abstract
The occurrence of distant tumor metastases is a major barrier in non-small cell lung cancer (NSCLC) therapy, and seriously affects clinical treatment and patient prognosis. Recently, long non-coding RNAs (lncRNAs) have been demonstrated to be crucial regulators of metastasis in lung cancer. The aim of this study was to reveal the underlying mechanisms of a novel lncRNA LNC CRYBG3 in regulating NSCLC metastasis. Experimental results showed that LNC CRYBG3 was upregulated in NSCLC cells compared with normal tissue cells, and its level was involved in these cells' metastatic ability. Exogenously overexpressed LNC CRYBG3 increased the metastatic ability and the protein expression level of the metastasis-associated proteins Snail and Vimentin in low metastatic lung cancer HCC827 cell line. In addition, LNC CRYBG3 contributed to HCC827 cell metastasis in vivo. Mechanistically, LNC CRYBG3 could directly combine with eEF1A1 and promote it to move into the nucleus to enhance the transcription of MDM2. Overexpressed MDM2 combined with MDM2 binding protein (MTBP) to reduce the binding of MTBP with ACTN4 and consequently increased cell migration mediated by ACTN4. In conclusion, the LNC CRYBG3/eEF1A1/MDM2/MTBP axis is a novel signaling pathway regulating tumor metastasis and may be a potential therapeutic target for NSCLC treatment.
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Affiliation(s)
- Anqing Wu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, China; (A.W.); (J.T.); (Z.G.); (Y.D.); (J.N.); (W.H.); (N.L.); (C.Y.); (S.L.)
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou 215123, China
| | - Jiaxin Tang
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, China; (A.W.); (J.T.); (Z.G.); (Y.D.); (J.N.); (W.H.); (N.L.); (C.Y.); (S.L.)
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou 215123, China
| | - Ziyang Guo
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, China; (A.W.); (J.T.); (Z.G.); (Y.D.); (J.N.); (W.H.); (N.L.); (C.Y.); (S.L.)
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou 215123, China
| | - Yingchu Dai
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, China; (A.W.); (J.T.); (Z.G.); (Y.D.); (J.N.); (W.H.); (N.L.); (C.Y.); (S.L.)
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou 215123, China
| | - Jing Nie
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, China; (A.W.); (J.T.); (Z.G.); (Y.D.); (J.N.); (W.H.); (N.L.); (C.Y.); (S.L.)
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou 215123, China
| | - Wentao Hu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, China; (A.W.); (J.T.); (Z.G.); (Y.D.); (J.N.); (W.H.); (N.L.); (C.Y.); (S.L.)
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou 215123, China
| | - Ningang Liu
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, China; (A.W.); (J.T.); (Z.G.); (Y.D.); (J.N.); (W.H.); (N.L.); (C.Y.); (S.L.)
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou 215123, China
| | - Caiyong Ye
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, China; (A.W.); (J.T.); (Z.G.); (Y.D.); (J.N.); (W.H.); (N.L.); (C.Y.); (S.L.)
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou 215123, China
| | - Shihong Li
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, China; (A.W.); (J.T.); (Z.G.); (Y.D.); (J.N.); (W.H.); (N.L.); (C.Y.); (S.L.)
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou 215123, China
| | - Hailong Pei
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, China; (A.W.); (J.T.); (Z.G.); (Y.D.); (J.N.); (W.H.); (N.L.); (C.Y.); (S.L.)
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou 215123, China
| | - Guangming Zhou
- State Key Laboratory of Radiation Medicine and Protection, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, China; (A.W.); (J.T.); (Z.G.); (Y.D.); (J.N.); (W.H.); (N.L.); (C.Y.); (S.L.)
- Collaborative Innovation Center of Radiological Medicine of Jiangsu Higher Education Institutions, Suzhou 215123, China
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Yamada K, Nishimura T, Wakiya M, Satoh E, Fukuda T, Amaya K, Bando Y, Hirano H, Ishikawa T. Protein co-expression networks identified from HOT lesions of ER+HER2-Ki-67high luminal breast carcinomas. Sci Rep 2021; 11:1705. [PMID: 33462336 PMCID: PMC7814020 DOI: 10.1038/s41598-021-81509-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/05/2021] [Indexed: 01/20/2023] Open
Abstract
Patients with estrogen receptor-positive/human epidermal growth factor receptor 2-negative/Ki-67-high (ER+HER2-Ki-67high) luminal breast cancer have a worse prognosis and do not respond to hormonal treatment and chemotherapy. This study sought to identify disease-related protein networks significantly associated with this subtype, by assessing in-depth proteomes of 10 lesions of high and low Ki-67 values (HOT, five; COLD, five) microdissected from the five tumors. Weighted correlation network analysis screened by over-representative analysis identified the five modules significantly associated with the HOT lesions. Pathway enrichment analysis, together with causal network analysis, revealed pathways of ribosome-associated quality controls, heat shock response by oxidative stress and hypoxia, angiogenesis, and oxidative phosphorylation. A semi-quantitative correlation of key-protein expressions, protein co-regulation analysis, and multivariate correlation analysis suggested co-regulations via network-network interaction among the four HOT-characteristic modules. Predicted highly activated master and upstream regulators were most characteristic to ER-positive breast cancer and associated with oncogenic transformation, as well as resistance to chemotherapy and endocrine therapy. Interestingly, inhibited intervention causal networks of numerous chemical inhibitors were predicted within the top 10 lists for the WM2 and WM5 modules, suggesting involvement of potential therapeutic targets in those data-driven networks. Our findings may help develop therapeutic strategies to benefit patients.
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Affiliation(s)
- Kimito Yamada
- Department of Breast Surgery, Tokyo Medical University Hachioji Medical Centre, Tokyo, 193-0998, Japan
- Department of Breast Surgery, Tokyo Medical University Hospital, Tokyo, 160-0023, Japan
| | - Toshihide Nishimura
- Department of Translational Medicine Informatics, St. Marianna University School of Medicine, Kanagawa, 216-8511, Japan.
| | - Midori Wakiya
- Department of Diagnostic Pathology, Tokyo Medical University Hachioji Medical Centre, Tokyo, 193-0998, Japan
| | - Eiichi Satoh
- Department of Pathology, Institute of Medical Science, Tokyo Medical University, Tokyo, 160-0023, Japan
| | - Tetsuya Fukuda
- Research and Development, Biosys Technologies Inc, Tokyo, 152-0031, Japan
| | - Keigo Amaya
- Department of Breast Surgery, Tokyo Medical University Hachioji Medical Centre, Tokyo, 193-0998, Japan
| | - Yasuhiko Bando
- Research and Development, Biosys Technologies Inc, Tokyo, 152-0031, Japan
| | - Hiroshi Hirano
- Department of Diagnostic Pathology, Tokyo Medical University Hachioji Medical Centre, Tokyo, 193-0998, Japan
| | - Takashi Ishikawa
- Department of Breast Surgery, Tokyo Medical University Hospital, Tokyo, 160-0023, Japan
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Transcriptomic analysis of early stages of intestinal regeneration in Holothuria glaberrima. Sci Rep 2021; 11:346. [PMID: 33431961 PMCID: PMC7801731 DOI: 10.1038/s41598-020-79436-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 12/04/2020] [Indexed: 01/29/2023] Open
Abstract
Echinoderms comprise a group of animals with impressive regenerative capabilities. They can replace complex internal organs following injury or autotomy. In holothurians or sea cucumbers, cellular processes of intestinal regeneration have been extensively studied. The molecular machinery behind this faculty, however, remains to be understood. Here we assembled and annotated a de novo transcriptome using RNA-seq data consisting of regenerating and non-regenerating intestinal tissues from the sea cucumber Holothuria glaberrima. Comparisons of differential expression were made using the mesentery as a reference against 24 h and 3 days regenerating intestine, revealing a large number of differentially expressed transcripts. Gene ontology and pathway enrichment analysis showed evidence of increasing transcriptional activity. Further analysis of transcripts associated with transcription factors revealed diverse expression patterns with mechanisms involving developmental and cancer-related activity that could be related to the regenerative process. Our study demonstrates the broad and diversified gene expression profile during the early stages of the process using the mesentery as the focal point of intestinal regeneration. It also establishes the genes that are the most important candidates in the cellular processes that underlie regenerative responses.
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Bowden TJ, Kraev I, Lange S. Extracellular Vesicles and Post-Translational Protein Deimination Signatures in Mollusca-The Blue Mussel ( Mytilus edulis), Soft Shell Clam ( Mya arenaria), Eastern Oyster ( Crassostrea virginica) and Atlantic Jacknife Clam ( Ensis leei). BIOLOGY 2020; 9:biology9120416. [PMID: 33255637 PMCID: PMC7760292 DOI: 10.3390/biology9120416] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 12/20/2022]
Abstract
Simple Summary Oysters and clams form an important component of the food chain and food security and are of considerable commercial value worldwide. They are affected by pollution and climate change, as well as a range of infections, some of which are opportunistic. For aquaculture purposes they are furthermore of great commercial value and changes in their immune responses can also serve as indicators of changes in ocean environments. Therefore, studies into understanding new factors in their immune systems may aid new biomarker discovery and are of considerable value. This study assessed new biomarkers relating to changes in protein function in four economically important marine molluscs, the blue mussel, soft shell clam, Eastern oyster, and Atlantic jacknife clam. These findings indicate novel regulatory mechanisms of important metabolic and immunology related pathways in these mollusks. The findings provide new understanding to how these pathways function in diverse ways in different animal species as well as aiding new biomarker discovery for Mollusca aquaculture. Abstract Oysters and clams are important for food security and of commercial value worldwide. They are affected by anthropogenic changes and opportunistic pathogens and can be indicators of changes in ocean environments. Therefore, studies into biomarker discovery are of considerable value. This study aimed at assessing extracellular vesicle (EV) signatures and post-translational protein deimination profiles of hemolymph from four commercially valuable Mollusca species, the blue mussel (Mytilus edulis), soft shell clam (Mya arenaria), Eastern oyster (Crassostrea virginica), and Atlantic jacknife clam (Ensis leei). EVs form part of cellular communication by transporting protein and genetic cargo and play roles in immunity and host–pathogen interactions. Protein deimination is a post-translational modification caused by peptidylarginine deiminases (PADs), and can facilitate protein moonlighting in health and disease. The current study identified hemolymph-EV profiles in the four Mollusca species, revealing some species differences. Deiminated protein candidates differed in hemolymph between the species, with some common targets between all four species (e.g., histone H3 and H4, actin, and GAPDH), while other hits were species-specific; in blue mussel these included heavy metal binding protein, heat shock proteins 60 and 90, 2-phospho-D-glycerate hydrolyase, GTP cyclohydrolase feedback regulatory protein, sodium/potassium-transporting ATPase, and fibrinogen domain containing protein. In soft shell clam specific deimination hits included dynein, MCM3-associated protein, and SCRN. In Eastern oyster specific deimination hits included muscle LIM protein, beta-1,3-glucan-binding protein, myosin heavy chain, thaumatin-like protein, vWFA domain-containing protein, BTB domain-containing protein, amylase, and beta-catenin. Deiminated proteins specific to Atlantic jackknife clam included nacre c1q domain-containing protein and PDZ domain-containing protein In addition, some proteins were common as deiminated targets between two or three of the Bivalvia species under study (e.g., EP protein, C1q domain containing protein, histone H2B, tubulin, elongation factor 1-alpha, dominin, extracellular superoxide dismutase). Protein interaction network analysis for the deiminated protein hits revealed major pathways relevant for immunity and metabolism, providing novel insights into post-translational regulation via deimination. The study contributes to EV characterization in diverse taxa and understanding of roles for PAD-mediated regulation of immune and metabolic pathways throughout phylogeny.
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Affiliation(s)
- Timothy J. Bowden
- Aquaculture Research Institute, School of Food & Agriculture, University of Maine, Orono, ME 04469-5735, USA;
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science, Technology, Engineering and Mathematics, Open University, Milton Keynes MK7 6AA, UK;
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London W1W 6UW, UK
- Correspondence: ; Tel.: +44-(0)207-911-5000
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Bowden TJ, Kraev I, Lange S. Extracellular vesicles and post-translational protein deimination signatures in haemolymph of the American lobster (Homarus americanus). FISH & SHELLFISH IMMUNOLOGY 2020; 106:79-102. [PMID: 32731012 DOI: 10.1016/j.fsi.2020.06.053] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/21/2020] [Accepted: 06/27/2020] [Indexed: 06/11/2023]
Abstract
The American lobster (Homarus americanus) is a commercially important crustacean with an unusual long life span up to 100 years and a comparative animal model of longevity. Therefore, research into its immune system and physiology is of considerable importance both for industry and comparative immunology studies. Peptidylarginine deiminases (PADs) are a phylogenetically conserved enzyme family that catalyses post-translational protein deimination via the conversion of arginine to citrulline. This can lead to structural and functional protein changes, sometimes contributing to protein moonlighting, in health and disease. PADs also regulate the cellular release of extracellular vesicles (EVs), which is an important part of cellular communication, both in normal physiology and in immune responses. Hitherto, studies on EVs in Crustacea are limited and neither PADs nor associated protein deimination have been studied in a Crustacean species. The current study assessed EV and deimination signatures in haemolymph of the American lobster. Lobster EVs were found to be a poly-dispersed population in the 10-500 nm size range, with the majority of smaller EVs, which fell within 22-115 nm. In lobster haemolymph, 9 key immune and metabolic proteins were identified to be post-translationally deiminated, while further 41 deiminated protein hits were identified when searching against a Crustacean database. KEGG (Kyoto encyclopedia of genes and genomes) and GO (gene ontology) enrichment analysis of these deiminated proteins revealed KEGG and GO pathways relating to a number of immune, including anti-pathogenic (viral, bacterial, fungal) and host-pathogen interactions, as well as metabolic pathways, regulation of vesicle and exosome release, mitochondrial function, ATP generation, gene regulation, telomerase homeostasis and developmental processes. The characterisation of EVs, and post-translational deimination signatures, reported in lobster in the current study, and the first time in Crustacea, provides insights into protein moonlighting functions of both species-specific and phylogenetically conserved proteins and EV-mediated communication in this long-lived crustacean. The current study furthermore lays foundation for novel biomarker discovery for lobster aquaculture.
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Affiliation(s)
- Timothy J Bowden
- Aquaculture Research Institute, School of Food & Agriculture, University of Maine, Orono, ME, USA.
| | - Igor Kraev
- Electron Microscopy Suite, Faculty of Science,Technology, Engineering and Mathematics, Open University, Milton Keynes, MK7 6AA, UK.
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London, W1W 6UW, UK.
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Wang Q, Hao X, Liu K, Feng B, Li S, Zhang Z, Tang L, Mahboob S, Shao C. Early response to heat stress in Chinese tongue sole (Cynoglossus semilaevis): performance of different sexes, candidate genes and networks. BMC Genomics 2020; 21:745. [PMID: 33109079 PMCID: PMC7590793 DOI: 10.1186/s12864-020-07157-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/15/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Temperature is known to affect living organisms and alter the expression of responsive genes, which affects a series of life processes, such as development, reproduction and metabolism. Several genes and gene families have been involved in high temperature responses, such as heat shock protein (hsp) family, Jumonji family and genes related to cortisol synthesis. Gonad is a vital organ related to the existence of a species. However, the comprehensive understanding of gonadal responses to environmental temperature is limited. RESULTS To explore the effects of environmental temperature on genes and gene networks in gonads, we performed acute heat treatment (48 h) on Chinese tongue sole (Cynoglossus semilaevis). Gonadal transcriptome analysis was conducted on females, pseudomales and males exposed to high (28 °C) and normal (22 °C) temperatures. A total of 1226.24 million clean reads were obtained from 18 libraries. Principal component analysis (PCA) and differentially expressed gene (DEG) analysis revealed different performance of sex responses to heat stress. There were 4565, 790 and 1117 specific genes altered their expression level in females, pseudomales and males, respectively. Of these, genes related to hsp gene family, cortisol synthesis and metabolism and epigenetic regulation were involved in early heat response. Furthermore, a total of 1048 DEGs were shared among females, pesudomales and males, which may represent the inherent difference between high and normal temperatures. Genes, such as eef1akmt3, eef1akmt4, pnmt and hsp family members, were found. CONCLUSIONS Our results depicted for the first time the gonadal gene expression under acute high temperature treatment in Chinese tongue sole. The findings may provide a clue for understanding the responses of genes and networks to environmental temperature.
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Affiliation(s)
- Qian Wang
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
| | - Xiancai Hao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Kaiqiang Liu
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
| | - Bo Feng
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Shuo Li
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China.,State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China
| | - Zhihua Zhang
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Lili Tang
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
| | - Shahid Mahboob
- Department of Zoology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Changwei Shao
- Key Lab of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Nanjing Road 106, Qingdao, 266071, China. .,Laboratory for Marine Fisheries Science and Food Production Processes, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China.
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60
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Omer A, Patel D, Moran JL, Lian XJ, Di Marco S, Gallouzi IE. Autophagy and heat-shock response impair stress granule assembly during cellular senescence. Mech Ageing Dev 2020; 192:111382. [PMID: 33049246 DOI: 10.1016/j.mad.2020.111382] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/21/2020] [Accepted: 10/05/2020] [Indexed: 01/08/2023]
Abstract
Stress granules (SGs) are membraneless organelles formed in response to insult. These granules are related to pathological granules found in age-related neurogenerative diseases such as Parkinson's and Alzheimer's. Previously, we demonstrated that senescent cells, which accumulate with age, exposed to chronic oxidative stress, are unable to form SGs. Here, we show that the senescent cells' inability to form SGs correlates with an upregulation in both the heat-shock response and autophagy pathways, both of which are well-established promoters of SG disassembly. Our data also reveals that the knockdown of HSP70 and ATG5, important components of the heat-shock response and autophagy pathways, respectively, restores the number of SGs formed in senescent cells exposed to chronic oxidative stress. Surprisingly, under these conditions, the depletion of HSP70 or ATG5 did not affect the clearance of these SGs during their recovery from chronic stress. These data reveal that senescent cells possess a unique heat-shock and autophagy-dependent ability to impair the formation of SGs in response to chronic stress, thereby expanding the existing understanding of SG dynamics in senescent cells and their potential contribution to age-related neurodegenerative diseases.
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Affiliation(s)
- Amr Omer
- McGill University, Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, Montreal, Quebec, Canada.
| | - Devang Patel
- McGill University, Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, Montreal, Quebec, Canada
| | - Julian Lucas Moran
- McGill University, Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, Montreal, Quebec, Canada
| | - Xian Jin Lian
- McGill University, Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, Montreal, Quebec, Canada
| | - Sergio Di Marco
- McGill University, Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, Montreal, Quebec, Canada
| | - Imed-Eddine Gallouzi
- McGill University, Department of Biochemistry, Rosalind and Morris Goodman Cancer Centre, Montreal, Quebec, Canada.
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61
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Skariah G, Todd PK. Translational control in aging and neurodegeneration. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1628. [PMID: 32954679 DOI: 10.1002/wrna.1628] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 08/19/2020] [Accepted: 09/07/2020] [Indexed: 12/13/2022]
Abstract
Protein metabolism plays central roles in age-related decline and neurodegeneration. While a large body of research has explored age-related changes in protein degradation, alterations in the efficiency and fidelity of protein synthesis with aging are less well understood. Age-associated changes occur in both the protein synthetic machinery (ribosomal proteins and rRNA) and within regulatory factors controlling translation. At the same time, many of the interventions that prolong lifespan do so in part by pre-emptively decreasing protein synthesis rates to allow better harmonization to age-related declines in protein catabolism. Here we review the roles of translation regulation in aging, with a specific focus on factors implicated in age-related neurodegeneration. We discuss how emerging technologies such as ribosome profiling and superior mass spectrometric approaches are illuminating age-dependent mRNA-specific changes in translation rates across tissues to reveal a critical interplay between catabolic and anabolic pathways that likely contribute to functional decline. These new findings point to nodes in posttranscriptional gene regulation that both contribute to aging and offer targets for therapy. This article is categorized under: Translation > Translation Regulation Translation > Ribosome Biogenesis Translation > Translation Mechanisms.
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Affiliation(s)
- Geena Skariah
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
| | - Peter K Todd
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
- Ann Arbor VA Healthcare System, Department of Veterans Affairs, Ann Arbor, Michigan, USA
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62
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Ray J, Kruse A, Ozer A, Kajitani T, Johnson R, MacCoss M, Heck M, Lis JT. RNA aptamer capture of macromolecular complexes for mass spectrometry analysis. Nucleic Acids Res 2020; 48:e90. [PMID: 32609809 PMCID: PMC7470977 DOI: 10.1093/nar/gkaa542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 06/03/2020] [Accepted: 06/27/2020] [Indexed: 12/25/2022] Open
Abstract
Specific genomic functions are dictated by macromolecular complexes (MCs) containing multiple proteins. Affinity purification of these complexes, often using antibodies, followed by mass spectrometry (MS) has revolutionized our ability to identify the composition of MCs. However, conventional immunoprecipitations suffer from contaminating antibody/serum-derived peptides that limit the sensitivity of detection for low-abundant interacting partners using MS. Here, we present AptA-MS (aptamer affinity-mass spectrometry), a robust strategy primarily using a specific, high-affinity RNA aptamer against Green Fluorescent Protein (GFP) to identify interactors of a GFP-tagged protein of interest by high-resolution MS. Utilizing this approach, we have identified the known molecular chaperones that interact with human Heat Shock Factor 1 (HSF1), and observed an increased association with several proteins upon heat shock, including translation elongation factors and histones. HSF1 is known to be regulated by multiple post-translational modifications (PTMs), and we observe both known and new sites of modifications on HSF1. We show that AptA-MS provides a dramatic target enrichment and detection sensitivity in evolutionarily diverse organisms and allows identification of PTMs without the need for modification-specific enrichments. In combination with the expanding libraries of GFP-tagged cell lines, this strategy offers a general, inexpensive, and high-resolution alternative to conventional approaches for studying MCs.
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Affiliation(s)
- Judhajeet Ray
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Angela Kruse
- Department of Plant Pathology and Plant-microbe Biology, Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute, Ithaca, NY, USA
| | - Abdullah Ozer
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Takuya Kajitani
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Richard Johnson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Michael MacCoss
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Michelle Heck
- Department of Plant Pathology and Plant-microbe Biology, Cornell University, Ithaca, NY, USA
- Boyce Thompson Institute, Ithaca, NY, USA
- Emerging Pests and Pathogens Research Unit, Robert W. Holley Center, United States Department of Agriculture Agricultural Research Service (USDA ARS), Ithaca, NY, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
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63
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Nishimura T, Nakamura H, Tan KT, Zhuo DW, Fujii K, Koizumi H, Naruki S, Takagi M, Furuya N, Kato Y, Chen SJ, Kato H, Saji H. A proteogenomic profile of early lung adenocarcinomas by protein co-expression network and genomic alteration analysis. Sci Rep 2020; 10:13604. [PMID: 32788598 PMCID: PMC7423934 DOI: 10.1038/s41598-020-70578-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 07/24/2020] [Indexed: 12/15/2022] Open
Abstract
The tumourigenesis of early lung adenocarcinomas, including adenocarcinoma in situ (AIS), minimally invasive adenocarcinoma (MIA), and lepidic predominant invasive adenocarcinoma (LPA), remains unclear. This study aimed to capture disease-related molecular networks characterising each subtype and tumorigenesis by assessing 14 lung adenocarcinomas (AIS, five; MIA, five; LPA, four). Protein-protein interaction networks significant to the three subtypes were elucidated by weighted gene co-expression network analysis and pairwise G-statistics based analysis. Pathway enrichment analysis for AIS involved extracellular matrix proteoglycans and neutrophil degranulation pathway relating to tumour growth and angiogenesis. Whereas no direct networks were found for MIA, proteins significant to MIA were involved in oncogenic transformation, epithelial-mesenchymal transition, and detoxification in the lung. LPA was associated with pathways of HSF1-mediated heat shock response regulation, DNA damage repair, cell cycle regulation, and mitosis. Genomic alteration analysis suggested that LPA had both somatic mutations with loss of function and copy number gains more frequent than MIA. Oncogenic drivers were detected in both MIA and LPA, and also LPA had a higher degree of copy number loss than MIA. Our findings may help identifying potential therapeutic targets and developing therapeutic strategies to improve patient outcomes.
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Affiliation(s)
- Toshihide Nishimura
- Department of Translational Medicine Informatics, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan.
- Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan.
| | - Haruhiko Nakamura
- Department of Translational Medicine Informatics, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan
- Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan
| | | | | | - Kiyonaga Fujii
- Department of Translational Medicine Informatics, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan
- Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan
| | - Hirotaka Koizumi
- Department of Pathology, St. Marianna University Hospital, Kawasaki, Kanagawa, 216-8511, Japan
| | - Saeko Naruki
- Department of Pathology, St. Marianna University Hospital, Kawasaki, Kanagawa, 216-8511, Japan
| | - Masayuki Takagi
- Department of Pathology, St. Marianna University Hospital, Kawasaki, Kanagawa, 216-8511, Japan
| | - Naoki Furuya
- Division of Respiratory Medicine, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan
| | - Yasufumi Kato
- Department of Thoracic Surgery, Kanto Central Hospital, Tokyo, 158-8531, Japan
| | | | - Harubumi Kato
- Tokyo Medical University, Tokyo, 160-0023, Japan
- International University of Health and Welfare, Tokyo, 107-8402, Japan
| | - Hisashi Saji
- Department of Chest Surgery, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan
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Lunin S, Khrenov M, Glushkova O, Parfenyuk S, Novoselova T, Novoselova E. Precursors of thymic peptides as stress sensors. Expert Opin Biol Ther 2020; 20:1461-1475. [PMID: 32700610 DOI: 10.1080/14712598.2020.1800636] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
INTRODUCTION A large volume of data indicates that the known thymic hormones, thymulin, thymopoietin, thymosin-α, thymosin-β, and thymic humoral factor-y2, exhibit different spectra of activities. Although large in volume, available data are rather fragmented, resulting in a lack of understanding of the role played by thymic hormones in immune homeostasis. AREA COVERED Existing data compartmentalizes the effect of thymic peptides into 2 categories: influence on immune cells and interconnection with neuroendocrine systems. The current study draws attention to a third aspect of the thymic peptide effect that has not been clarified yet, wherein ubiquitous and highly abundant intranuclear precursors of so called 'thymic peptides' play a fundamental role in all somatic cells. EXPERT OPINION Our analysis indicated that, under certain stress-related conditions, these precursors are cleaved to form immunologically active peptides that rapidly leave the nucleus and intracellular spaces, to send 'distress signals' to the immune system, thereby acting as stress sensors. We propose that these peptides may form a link between somatic cells and immune as well as neuroendocrine systems. This model may provide a better understanding of the mechanisms underlying immune homeostasis, leading thereby to the development of new therapeutic regimes utilizing the characteristics of thymic peptides.
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Affiliation(s)
- Sergey Lunin
- Laboratory of Reception Mechanisms, Institute of Cell Biophysics of the Russian Academy of Sciences, PSCBR RAS , Pushchino, Russia
| | - Maxim Khrenov
- Laboratory of Reception Mechanisms, Institute of Cell Biophysics of the Russian Academy of Sciences, PSCBR RAS , Pushchino, Russia
| | - Olga Glushkova
- Laboratory of Reception Mechanisms, Institute of Cell Biophysics of the Russian Academy of Sciences, PSCBR RAS , Pushchino, Russia
| | - Svetlana Parfenyuk
- Laboratory of Reception Mechanisms, Institute of Cell Biophysics of the Russian Academy of Sciences, PSCBR RAS , Pushchino, Russia
| | - Tatyana Novoselova
- Laboratory of Reception Mechanisms, Institute of Cell Biophysics of the Russian Academy of Sciences, PSCBR RAS , Pushchino, Russia
| | - E Novoselova
- Laboratory of Reception Mechanisms, Institute of Cell Biophysics of the Russian Academy of Sciences, PSCBR RAS , Pushchino, Russia
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Najm R, Zalocusky KA, Zilberter M, Yoon SY, Hao Y, Koutsodendris N, Nelson M, Rao A, Taubes A, Jones EA, Huang Y. In Vivo Chimeric Alzheimer's Disease Modeling of Apolipoprotein E4 Toxicity in Human Neurons. Cell Rep 2020; 32:107962. [PMID: 32726626 PMCID: PMC7430173 DOI: 10.1016/j.celrep.2020.107962] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 05/15/2020] [Accepted: 07/03/2020] [Indexed: 02/08/2023] Open
Abstract
Despite its clear impact on Alzheimer's disease (AD) risk, apolipoprotein (apo) E4's contributions to AD etiology remain poorly understood. Progress in answering this and other questions in AD research has been limited by an inability to model human-specific phenotypes in an in vivo environment. Here we transplant human induced pluripotent stem cell (hiPSC)-derived neurons carrying normal apoE3 or pathogenic apoE4 into human apoE3 or apoE4 knockin mouse hippocampi, enabling us to disentangle the effects of apoE4 produced in human neurons and in the brain environment. Using single-nucleus RNA sequencing (snRNA-seq), we identify key transcriptional changes specific to human neuron subtypes in response to endogenous or exogenous apoE4. We also find that Aβ from transplanted human neurons forms plaque-like aggregates, with differences in localization and interaction with microglia depending on the transplant and host apoE genotype. These findings highlight the power of in vivo chimeric disease modeling for studying AD.
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Affiliation(s)
- Ramsey Najm
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kelly A Zalocusky
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Gladstone Center for Translational Advancement, San Francisco, CA 94158, USA
| | - Misha Zilberter
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
| | - Seo Yeon Yoon
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA
| | - Yanxia Hao
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Gladstone Center for Translational Advancement, San Francisco, CA 94158, USA
| | - Nicole Koutsodendris
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Maxine Nelson
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Antara Rao
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alice Taubes
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Emily A Jones
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yadong Huang
- Gladstone Institute of Neurological Disease, San Francisco, CA 94158, USA; Developmental and Stem Cell Biology Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Gladstone Center for Translational Advancement, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Departments of Neurology and Pathology, University of California, San Francisco, San Francisco, CA 94143, USA.
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EEF1A1 deacetylation enables transcriptional activation of remyelination. Nat Commun 2020; 11:3420. [PMID: 32647127 PMCID: PMC7347577 DOI: 10.1038/s41467-020-17243-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 06/19/2020] [Indexed: 12/14/2022] Open
Abstract
Remyelination of the peripheral and central nervous systems (PNS and CNS, respectively) is a prerequisite for functional recovery after lesion. However, this process is not always optimal and becomes inefficient in the course of multiple sclerosis. Here we show that, when acetylated, eukaryotic elongation factor 1A1 (eEF1A1) negatively regulates PNS and CNS remyelination. Acetylated eEF1A1 (Ac-eEF1A1) translocates into the nucleus of myelinating cells where it binds to Sox10, a key transcription factor for PNS and CNS myelination and remyelination, to drag Sox10 out of the nucleus. We show that the lysine acetyltransferase Tip60 acetylates eEF1A1, whereas the histone deacetylase HDAC2 deacetylates eEF1A1. Promoting eEF1A1 deacetylation maintains the activation of Sox10 target genes and increases PNS and CNS remyelination efficiency. Taken together, these data identify a major mechanism of Sox10 regulation, which appears promising for future translational studies on PNS and CNS remyelination. The molecular mechanisms regulating remyelination are unclear. Here, the authors show that promoting deacetylation of eEF1A1 prevents the translocation of Sox10 outside the nucleus, contributing to maintaining the expression of Sox10 target genes and increasing remyelination efficiency.
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67
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Zhang X, Antonelo D, Hendrix J, To V, Campbell Y, Von Staden M, Li S, Suman SP, Zhai W, Chen J, Zhu H, Schilling W. Proteomic Characterization of Normal and Woody Breast Meat from Broilers of Five Genetic Strains. MEAT AND MUSCLE BIOLOGY 2020. [DOI: 10.22175/mmb.8759] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Woody breast (WB) is an emergent broiler myopathy that is macroscopically characterized by hardened areas of the Pectoralis major muscle. Five genetic strains (strains 1–5) of mixed-sex broilers were fed either a control or an amino acid (AA)-reduced diet (20% reduction of digestible lysine, total sulfur AAs, and threonine) for 8 wk. Differences between whole-muscle proteome profiles of normal breast (NB; n = 6 gels) and WB tissue (n = 6 gels) were characterized for (1) broiler strains 1–5 that were fed with a control diet and collected at 0 min; (2) strain 5 (control diet) that were collected at 15 min, 4 h, and 24 h; (3) strain 5 (0 min) that were fed with a control and an AA-reduced diet. Birds that yielded WB were heavier and had a greater pH at death (pH0min) than normal birds. Results indicated that 21 proteins were more abundant (P < 0.05) and 3 proteins were less abundant (P < 0.05) in WB compared with NB. The differentially abundant proteins in each comparison were consistently upregulated or downregulated in WB tissue although the different protein profiles were noticed for each comparison. Strains 2 and 5 had more protein profile differences between WB and NB meat than strains 1, 3, and 4, which potentially indicates a stronger genetic component for strains 2 and 5 with respect to WB formation. The proteins that were more abundant in WB compared to NB are involved in carbohydrate metabolism, oxidative stress, cytoskeleton structure, and transport and signaling. Ingenuity Pathway Analysis indicated that regulated pathways in WB were mainly related to carbohydrate metabolism, cellular repair, cellular organization and maintenance, and cell death and survival. The results support the potential causes of WB myopathy, including the presence of hypoxia, oxidative stress, increased apoptosis, misfolded proteins, and inflammation.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Wes Schilling
- Mississippi State University Department of Food Science, Nutrition and Health Promotion
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68
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The Legionella pneumophila Metaeffector Lpg2505 (MesI) Regulates SidI-Mediated Translation Inhibition and Novel Glycosyl Hydrolase Activity. Infect Immun 2020; 88:IAI.00853-19. [PMID: 32122942 DOI: 10.1128/iai.00853-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/27/2020] [Indexed: 12/19/2022] Open
Abstract
Legionella pneumophila, the etiological agent of Legionnaires' disease, employs an arsenal of hundreds of Dot/Icm-translocated effector proteins to facilitate replication within eukaryotic phagocytes. Several effectors, called metaeffectors, function to regulate the activity of other Dot/Icm-translocated effectors during infection. The metaeffector Lpg2505 is essential for L. pneumophila intracellular replication only when its cognate effector, SidI, is present. SidI is a cytotoxic effector that interacts with the host translation factor eEF1A and potently inhibits eukaryotic protein translation by an unknown mechanism. Here, we evaluated the impact of Lpg2505 on SidI-mediated phenotypes and investigated the mechanism of SidI function. We determined that Lpg2505 binds with nanomolar affinity to SidI and suppresses SidI-mediated inhibition of protein translation. SidI binding to eEF1A and Lpg2505 is not mutually exclusive, and the proteins bind distinct regions of SidI. We also discovered that SidI possesses GDP-dependent glycosyl hydrolase activity and that this activity is regulated by Lpg2505. We have therefore renamed Lpg2505 MesI (metaeffector of SidI). This work reveals novel enzymatic activity for SidI and provides insight into how intracellular replication of L. pneumophila is regulated by a metaeffector.
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Chalorak P, Dharmasaroja P, Meemon K. Downregulation of eEF1A/EFT3-4 Enhances Dopaminergic Neurodegeneration After 6-OHDA Exposure in C. elegans Model. Front Neurosci 2020; 14:303. [PMID: 32425742 PMCID: PMC7212436 DOI: 10.3389/fnins.2020.00303] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 03/16/2020] [Indexed: 12/12/2022] Open
Abstract
Parkinson’s disease (PD) is a neurodegenerative disorder characterized by the aggregation of α-synuclein protein and selective death of dopaminergic (DA) neurons in the substantia nigra of the midbrain. Although the molecular pathogenesis of PD is not completely understood, a recent study has reported that eukaryotic translation elongation factor 1 alpha (eEF1A) declined in the PD-affected brain. Therefore, the roles of eEF1A1 and eEF1A2 in the prevention of DA neuronal cell death in PD are aimed to be investigated. Herein, by using Caenorhabditis elegans as a PD model, we investigated the role of eft-3/eft-4, the worm homolog of eEF1A1/eEF1A2, on 6-hydroxydopamine (6-OHDA)-induced DA neuron degeneration. Our results demonstrated that the expressions of eft-3 and eft-4 were decreased in the 6-OHDA-induced worms. RNA interference (RNAi) of eft-3 and eft-4 resulted in dramatic exacerbation of DA neurodegeneration induced by 6-OHDA, as well as aggravated the food-sensing behavior, ethanol avoidance, and decreased lifespan when compared with only 6-OHDA-induced worms. Moreover, downregulation of eft-3/4 in 6-OHDA-induced worms suppressed the expression of the anti-apoptotic genes, including PI3K/age-1, PDK-1/pdk-1, mTOR/let-363, and AKT-1,2/akt-1,2, promoting the expression of apoptotic genes such as BH3/egl-1 and Caspase-9/ced-3. Collectively, these findings indicate that eEF1A plays an important role in the 6-OHDA-induced neurodegeneration through the phosphatidylinositol 3-kinase (PI3K)/serine/threonine protein kinase (Akt)/mammalian target of rapamycin (mTOR) pathway and that eEF1A isoforms may be a novel and effective pro-survival factor in protective DA neurons against toxin-induced neuronal death.
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Affiliation(s)
- Pawanrat Chalorak
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Krai Meemon
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
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Carvill GL, Helbig KL, Myers CT, Scala M, Huether R, Lewis S, Kruer TN, Guida BS, Bakhtiari S, Sebe J, Tang S, Stickney H, Oktay SU, Bhandiwad AA, Ramsey K, Narayanan V, Feyma T, Rohena LO, Accogli A, Severino M, Hollingsworth G, Gill D, Depienne C, Nava C, Sadleir LG, Caruso PA, Lin AE, Jansen FE, Koeleman B, Brilstra E, Willemsen MH, Kleefstra T, Sa J, Mathieu ML, Perrin L, Lesca G, Striano P, Casari G, Scheffer IE, Raible D, Sattlegger E, Capra V, Padilla-Lopez S, Mefford HC, Kruer MC. Damaging de novo missense variants in EEF1A2 lead to a developmental and degenerative epileptic-dyskinetic encephalopathy. Hum Mutat 2020; 41:1263-1279. [PMID: 32196822 DOI: 10.1002/humu.24015] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 02/14/2020] [Accepted: 03/13/2020] [Indexed: 11/08/2022]
Abstract
Heterozygous de novo variants in the eukaryotic elongation factor EEF1A2 have previously been described in association with intellectual disability and epilepsy but never functionally validated. Here we report 14 new individuals with heterozygous EEF1A2 variants. We functionally validate multiple variants as protein-damaging using heterologous expression and complementation analysis. Our findings allow us to confirm multiple variants as pathogenic and broaden the phenotypic spectrum to include dystonia/choreoathetosis, and in some cases a degenerative course with cerebral and cerebellar atrophy. Pathogenic variants appear to act via a haploinsufficiency mechanism, disrupting both the protein synthesis and integrated stress response functions of EEF1A2. Our studies provide evidence that EEF1A2 is highly intolerant to variation and that de novo pathogenic variants lead to an epileptic-dyskinetic encephalopathy with both neurodevelopmental and neurodegenerative features. Developmental features may be driven by impaired synaptic protein synthesis during early brain development while progressive symptoms may be linked to an impaired ability to handle cytotoxic stressors.
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Affiliation(s)
- Gemma L Carvill
- Ken and Ruth Davee Department of Neurology, Northwestern University, Chicago, Illinois
| | - Katherine L Helbig
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania.,The Epilepsy NeuroGenetics Initiative, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Candace T Myers
- Division of Genetic Medicine, Department of Pediatrics, Seattle, Washington
| | - Marcello Scala
- Department of Pediatric Neurology & Muscular Disorders, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università degli Studi di Genova, Genoa, Italy
| | - Robert Huether
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, California
| | - Sara Lewis
- Barrow Neurological Institute, Department of Neurology, Phoenix Children's Hospital, Phoenix, Arizona.,Departments of Child Health, Cellular & Molecular Medicine, and Neurology and Program in Genetics, University of Arizona College of Medicine Phoenix, Phoenix, Arizona
| | - Tyler N Kruer
- Barrow Neurological Institute, Department of Neurology, Phoenix Children's Hospital, Phoenix, Arizona.,Departments of Child Health, Cellular & Molecular Medicine, and Neurology and Program in Genetics, University of Arizona College of Medicine Phoenix, Phoenix, Arizona
| | - Brandon S Guida
- Barrow Neurological Institute, Department of Neurology, Phoenix Children's Hospital, Phoenix, Arizona.,Departments of Child Health, Cellular & Molecular Medicine, and Neurology and Program in Genetics, University of Arizona College of Medicine Phoenix, Phoenix, Arizona
| | - Somayeh Bakhtiari
- Barrow Neurological Institute, Department of Neurology, Phoenix Children's Hospital, Phoenix, Arizona.,Departments of Child Health, Cellular & Molecular Medicine, and Neurology and Program in Genetics, University of Arizona College of Medicine Phoenix, Phoenix, Arizona
| | - Joy Sebe
- Department of Biology, University of Washington, Seattle, Washington.,Department of Biological Structure, University of Washington, Seattle, Washington
| | - Sha Tang
- Division of Clinical Genomics, Ambry Genetics, Aliso Viejo, California
| | - Heather Stickney
- Department of Biological Structure, University of Washington, Seattle, Washington
| | - Sehribani Ulusoy Oktay
- Department of Biology, University of Washington, Seattle, Washington.,Department of Biological Structure, University of Washington, Seattle, Washington
| | - Ashwin A Bhandiwad
- Department of Biological Structure, University of Washington, Seattle, Washington
| | - Keri Ramsey
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders, Translational Genomics Research Institute, Phoenix, Arizona
| | - Timothy Feyma
- Department of Neurology, Gillette Children's Specialty Healthcare, St. Paul, Minnesota
| | - Luis O Rohena
- Department of Pediatrics, Division of Genetics, San Antonio Military Medical Center, San Antonio, Texas.,Department of Pediatrics, Long School of Medicine, University of Texas, San Antonio, Texas
| | - Andrea Accogli
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università degli Studi di Genova, Genoa, Italy.,Medical Genetics Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Mariasavina Severino
- Department of Pediatric Neurology & Muscular Disorders, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini, Genoa, Italy
| | - Georgina Hollingsworth
- Departments of Medicine and Paediatrics, University of Melbourne and Austin Health Royal Children's Hospital, Melbourne, Australia
| | - Deepak Gill
- Ty Nelson Department of Neurology, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Christel Depienne
- INSERM UMR 975, Institut du Cerveau et de la Moelle Epinière, Hôpital Pitié-Salpêtrière, Paris, France
| | - Caroline Nava
- INSERM UMR 975, Institut du Cerveau et de la Moelle Epinière, Hôpital Pitié-Salpêtrière, Paris, France
| | - Lynette G Sadleir
- Department of Paediatrics and Child Health, University of Otago Wellington, Wellington South, New Zealand
| | - Paul A Caruso
- Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston
| | - Angela E Lin
- Medical Genetics, Department of Pediatrics, MassGeneral Hospital for Children, Harvard Medical School, Boston, Massachusetts
| | - Floor E Jansen
- Department of Pediatric Neurology, University Medical Center, Utrecht, The Netherlands
| | - Bobby Koeleman
- Department of Pediatric Neurology, University Medical Center, Utrecht, The Netherlands
| | - Eva Brilstra
- Department of Genetics, Utrecht University, Utrecht, The Netherlands
| | - Marjolein H Willemsen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Joaquim Sa
- Serviço de Genética Médica, Centro Hospitalar e Universitário de Coimbra, Coimbra, Portugal
| | - Marie-Laure Mathieu
- Neuropaediatrics Department, Femme Mère Enfant Hospital, Lyon, France.,Claude Bernard Lyon 1 University, Lyon, France
| | - Laurine Perrin
- Department of Paediatric Physical Medicine and Rehabilitation, CHU Saint-Etienne, Hôpital Bellevue, Saint-Étienne, France
| | - Gaetan Lesca
- CRNL Inserm U1028-CNRS UMR5292-Claude Bernard University Lyon 1, Lyon, France.,Department of Medical Genetics, Lyon University Hospital, Lyon, France
| | - Pasquale Striano
- Department of Pediatric Neurology & Muscular Disorders, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università degli Studi di Genova, Genoa, Italy
| | - Giorgio Casari
- Department of Pediatric Neurology & Muscular Disorders, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini, Genoa, Italy.,Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, Università degli Studi di Genova, Genoa, Italy
| | - Ingrid E Scheffer
- Departments of Medicine and Paediatrics, University of Melbourne and Austin Health Royal Children's Hospital, Melbourne, Australia
| | - David Raible
- Department of Biology, University of Washington, Seattle, Washington.,Department of Biological Structure, University of Washington, Seattle, Washington
| | - Evelyn Sattlegger
- School of Natural & Computational Sciences, Massey University, Auckland, New Zealand
| | - Valeria Capra
- Department of Pediatric Neurology & Muscular Disorders, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini, Genoa, Italy
| | - Sergio Padilla-Lopez
- Barrow Neurological Institute, Department of Neurology, Phoenix Children's Hospital, Phoenix, Arizona.,Departments of Child Health, Cellular & Molecular Medicine, and Neurology and Program in Genetics, University of Arizona College of Medicine Phoenix, Phoenix, Arizona
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Pediatrics, Seattle, Washington
| | - Michael C Kruer
- Barrow Neurological Institute, Department of Neurology, Phoenix Children's Hospital, Phoenix, Arizona.,Departments of Child Health, Cellular & Molecular Medicine, and Neurology and Program in Genetics, University of Arizona College of Medicine Phoenix, Phoenix, Arizona
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71
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Sato H, Das S, Singer RH, Vera M. Imaging of DNA and RNA in Living Eukaryotic Cells to Reveal Spatiotemporal Dynamics of Gene Expression. Annu Rev Biochem 2020; 89:159-187. [PMID: 32176523 DOI: 10.1146/annurev-biochem-011520-104955] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
This review focuses on imaging DNA and single RNA molecules in living cells to define eukaryotic functional organization and dynamic processes. The latest advances in technologies to visualize individual DNA loci and RNAs in real time are discussed. Single-molecule fluorescence microscopy provides the spatial and temporal resolution to reveal mechanisms regulating fundamental cell functions. Novel insights into the regulation of nuclear architecture, transcription, posttranscriptional RNA processing, and RNA localization provided by multicolor fluorescence microscopy are reviewed. A perspective on the future use of live imaging technologies and overcoming their current limitations is provided.
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Affiliation(s)
- Hanae Sato
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA; , ,
| | - Sulagna Das
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA; , ,
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA; , , .,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Maria Vera
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA; , , .,Department of Biochemistry, McGill University, Montreal, Quebec H3G 1Y6, Canada;
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72
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Alfares A, Alfadhel M, Mujamammi A, Alotaibi B, Albahkali S, Al Balwi M, Benabdelkamel H, Masood A, Ali R, Almuaysib A, Al Mahri S, Mohammad S, Alanazi IO, Alfadda A, AlGhamdi S, Alrfaei BM. Proteomic and Molecular Assessment of the Common Saudi Variant in ACADVL Gene Through Mesenchymal Stem Cells. Front Cell Dev Biol 2020; 7:365. [PMID: 32010688 PMCID: PMC6979051 DOI: 10.3389/fcell.2019.00365] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/13/2019] [Indexed: 11/13/2022] Open
Abstract
Very-long-chain acyl-coenzyme A dehydrogenase (VLCAD) is a coenzyme encoded by ACADVL that converts very-long-chain fatty acids into energy. This process is disrupted by c.65C > A; p.Ser22∗ mutation. To clarify mechanisms by which this mutation leads to VLCAD deficiency, we evaluated differences in molecular and cellular functions between mesenchymal stem cells with normal and mutant VLCAD. Saudi Arabia have a high incidence of this form of mutation. Stem cells with mutant VLCAD were isolated from skin of two patients. Metabolic activity and proliferation were evaluated. The Same evaluation was repeated on normal stem cells introduced with same mutation by CRISPR. Mitochondrial depiction was done by electron microscope and proteomic analysis was done on patients' cells. Metabolic activity and proliferation were significantly lower in patients' cells. Introducing the same mutation into normal stem cells resulted in the same defects. We detected mitochondrial abnormalities by electron microscopy in addition to poor wound healing and migration processes in mutant cells. Furthermore, in a proteomic analysis, we identified several upregulated or downregulated proteins related to hypoglycemia, liver disorder, and cardiac and muscle involvement. We concluded experimental assays of mutant ACADVL (c.65C > A; p.Ser22∗) contribute to severe neonatal disorders with hypoglycemia, liver disorder, and cardiac and muscle involvement.
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Affiliation(s)
- Ahmad Alfares
- Department of Pediatrics, College of Medicine, Qassim University, Al-Qassim, Saudi Arabia.,Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, MNGHA, Riyadh, Saudi Arabia
| | - Majid Alfadhel
- Division of Genetics, Department of Pediatrics, King Abdullah Specialized Children Hospital, King Abdulaziz Medical City, MNGHA, Riyadh, Saudi Arabia.,Medical Genomics Research Department, King Abdullah International Medical Research Center, MNGHA, Riyadh, Saudi Arabia.,College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, MNGHA, Riyadh, Saudi Arabia
| | - Ahmed Mujamammi
- Unit of Clinical Biochemistry/Medical Biochemistry, Department of Pathology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Batoul Alotaibi
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, MNGHA, Riyadh, Saudi Arabia.,Stem Cells Unit, Department of Cellular Therapy, King Abdullah International Medical Research Center, MNGHA, Riyadh, Saudi Arabia
| | - Sarah Albahkali
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, MNGHA, Riyadh, Saudi Arabia.,Stem Cells Unit, Department of Cellular Therapy, King Abdullah International Medical Research Center, MNGHA, Riyadh, Saudi Arabia
| | - Mohammed Al Balwi
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, MNGHA, Riyadh, Saudi Arabia.,Medical Genomics Research Department, King Abdullah International Medical Research Center, MNGHA, Riyadh, Saudi Arabia.,College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, MNGHA, Riyadh, Saudi Arabia
| | - Hicham Benabdelkamel
- Proteomics Resource Unit, Obesity Research Center, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Afshan Masood
- Proteomics Resource Unit, Obesity Research Center, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Rizwan Ali
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, MNGHA, Riyadh, Saudi Arabia.,Medical Core Facility and Platforms Department, King Abdullah International Medical Research Center, MNGHA, Riyadh, Saudi Arabia
| | - Amani Almuaysib
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, MNGHA, Riyadh, Saudi Arabia.,Stem Cells Unit, Department of Cellular Therapy, King Abdullah International Medical Research Center, MNGHA, Riyadh, Saudi Arabia
| | - Saeed Al Mahri
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, MNGHA, Riyadh, Saudi Arabia.,Department of Experimental Medicine, King Abdullah International Medical Research Center, MNGHA, Riyadh, Saudi Arabia
| | - Sameer Mohammad
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, MNGHA, Riyadh, Saudi Arabia.,Department of Experimental Medicine, King Abdullah International Medical Research Center, MNGHA, Riyadh, Saudi Arabia
| | - Ibrahim O Alanazi
- National Centre for Biotechnology, Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Assim Alfadda
- Proteomics Resource Unit, Obesity Research Center, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | - Saleh AlGhamdi
- Medical Genomics Research Department, King Abdullah International Medical Research Center, MNGHA, Riyadh, Saudi Arabia.,Clinical Research Department, Research Center, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Bahauddeen M Alrfaei
- College of Medicine, King Saud Bin Abdulaziz University for Health Sciences, MNGHA, Riyadh, Saudi Arabia.,Stem Cells Unit, Department of Cellular Therapy, King Abdullah International Medical Research Center, MNGHA, Riyadh, Saudi Arabia
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73
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Kuta R, Larochelle N, Fernandez M, Pal A, Minotti S, Tibshirani M, St Louis K, Gentil BJ, Nalbantoglu JN, Hermann A, Durham HD. Depending on the stress, histone deacetylase inhibitors act as heat shock protein co-inducers in motor neurons and potentiate arimoclomol, exerting neuroprotection through multiple mechanisms in ALS models. Cell Stress Chaperones 2020; 25:173-191. [PMID: 31900865 PMCID: PMC6985055 DOI: 10.1007/s12192-019-01064-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/12/2019] [Accepted: 12/20/2019] [Indexed: 12/13/2022] Open
Abstract
Upregulation of heat shock proteins (HSPs) is an approach to treatment of neurodegenerative disorders with impaired proteostasis. Many neurons, including motor neurons affected in amyotrophic lateral sclerosis (ALS), are relatively resistant to stress-induced upregulation of HSPs. This study demonstrated that histone deacetylase (HDAC) inhibitors enable the heat shock response in cultured spinal motor neurons, in a stress-dependent manner, and can improve the efficacy of HSP-inducing drugs in murine spinal cord cultures subjected to thermal or proteotoxic stress. The effect of particular HDAC inhibitors differed with the stress paradigm. The HDAC6 (class IIb) inhibitor, tubastatin A, acted as a co-inducer of Hsp70 (HSPA1A) expression with heat shock, but not with proteotoxic stress induced by expression of mutant SOD1 linked to familial ALS. Certain HDAC class I inhibitors (the pan inhibitor, SAHA, or the HDAC1/3 inhibitor, RGFP109) were HSP co-inducers comparable to the hydroxyamine arimoclomol in response to proteotoxic stress, but not thermal stress. Regardless, stress-induced Hsp70 expression could be enhanced by combining an HDAC inhibitor with either arimoclomol or with an HSP90 inhibitor that constitutively induced HSPs. HDAC inhibition failed to induce Hsp70 in motor neurons expressing ALS-linked mutant FUS, in which the heat shock response was suppressed; yet SAHA, RGFP109, and arimoclomol did reduce loss of nuclear FUS, a disease hallmark, and HDAC inhibition rescued the DNA repair response in iPSC-derived motor neurons carrying the FUSP525Lmutation, pointing to multiple mechanisms of neuroprotection by both HDAC inhibiting drugs and arimoclomol.
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Affiliation(s)
- Rachel Kuta
- Department of Neurology and Neurosurgery and Montreal Neurological Institute, McGill University, 3801 University St., Montreal, QC, H3A 2B4, Canada
| | - Nancy Larochelle
- Department of Neurology and Neurosurgery and Montreal Neurological Institute, McGill University, 3801 University St., Montreal, QC, H3A 2B4, Canada
| | - Mario Fernandez
- Department of Neurology and Neurosurgery and Montreal Neurological Institute, McGill University, 3801 University St., Montreal, QC, H3A 2B4, Canada
| | - Arun Pal
- Department Neurology, Technische Universität Dresden, Fetscherstr. 74, 01307, Dresden, Germany
| | - Sandra Minotti
- Department of Neurology and Neurosurgery and Montreal Neurological Institute, McGill University, 3801 University St., Montreal, QC, H3A 2B4, Canada
| | - Michael Tibshirani
- Department of Neurology and Neurosurgery and Montreal Neurological Institute, McGill University, 3801 University St., Montreal, QC, H3A 2B4, Canada
| | - Kyle St Louis
- Department of Neurology and Neurosurgery and Montreal Neurological Institute, McGill University, 3801 University St., Montreal, QC, H3A 2B4, Canada
| | - Benoit J Gentil
- Department of Neurology and Neurosurgery and Montreal Neurological Institute, McGill University, 3801 University St., Montreal, QC, H3A 2B4, Canada
| | - Josephine N Nalbantoglu
- Department of Neurology and Neurosurgery and Montreal Neurological Institute, McGill University, 3801 University St., Montreal, QC, H3A 2B4, Canada
| | - Andreas Hermann
- Translational Neurodegeneration Section "Albrecht-Kossel", Department of Neurology and Center for Transdisciplinary Neuroscience (CTNR), University Medical Center Rostock, University of Rostock, Rostock, Germany and German Center for Neurodegenerative Diseases (DZNE) Rostock, Rostock, Germany
| | - Heather D Durham
- Department of Neurology and Neurosurgery and Montreal Neurological Institute, McGill University, 3801 University St., Montreal, QC, H3A 2B4, Canada.
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74
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Venkata Subbaiah KC, Hedaya O, Wu J, Jiang F, Yao P. Mammalian RNA switches: Molecular rheostats in gene regulation, disease, and medicine. Comput Struct Biotechnol J 2019; 17:1326-1338. [PMID: 31741723 PMCID: PMC6849081 DOI: 10.1016/j.csbj.2019.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 09/30/2019] [Accepted: 10/07/2019] [Indexed: 01/12/2023] Open
Abstract
Alteration of RNA structure by environmental signals is a fundamental mechanism of gene regulation. For example, the riboswitch is a noncoding RNA regulatory element that binds a small molecule and causes a structural change in the RNA, thereby regulating transcription, splicing, or translation of an mRNA. The role of riboswitches in metabolite sensing and gene regulation in bacteria and other lower species was reported almost two decades ago, but riboswitches have not yet been discovered in mammals. An analog of the riboswitch, the protein-directed RNA switch (PDRS), has been identified as an important regulatory mechanism of gene expression in mammalian cells. RNA-binding proteins and microRNAs are two major executors of PDRS via their interaction with target transcripts in mammals. These protein-RNA interactions influence cellular functions by integrating environmental signals and intracellular pathways from disparate stimuli to modulate stability or translation of specific mRNAs. The discovery of a riboswitch in eukaryotes that is composed of a single class of thiamine pyrophosphate (TPP) suggests that additional ligand-sensing RNAs may be present to control eukaryotic or mammalian gene expression. In this review, we focus on protein-directed RNA switch mechanisms in mammals. We offer perspectives on the potential discovery of mammalian protein-directed and compound-dependent RNA switches that are related to human disease and medicine.
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Affiliation(s)
- Kadiam C Venkata Subbaiah
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States
| | - Omar Hedaya
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States.,Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States
| | - Jiangbin Wu
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States
| | - Feng Jiang
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States.,Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States
| | - Peng Yao
- Aab Cardiovascular Research Institute, Department of Medicine, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States.,Department of Biochemistry & Biophysics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States.,The Center for RNA Biology, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States.,The Center for Biomedical Informatics, University of Rochester School of Medicine & Dentistry, Rochester, NY 14586, United States
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75
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Magnadóttir B, Kraev I, Guðmundsdóttir S, Dodds AW, Lange S. Extracellular vesicles from cod (Gadus morhua L.) mucus contain innate immune factors and deiminated protein cargo. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 99:103397. [PMID: 31108150 DOI: 10.1016/j.dci.2019.103397] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/16/2019] [Accepted: 05/16/2019] [Indexed: 06/09/2023]
Abstract
Extracellular vesicles are released from cells and participate in cell communication via transfer of protein and genetic cargo derived from the parent cells. EVs play roles in normal physiology and immunity and are also linked to various pathological processes. Peptidylarginine deiminases (PADs) are phylogenetically conserved enzymes with physiological and pathophysiological roles. PADs cause post-translational protein deimination, resulting in structural and, in some cases, functional changes in target proteins and are also linked to EV biogenesis. This study describes for the first time EVs isolated from cod mucosa. Mucosal EVs were characterised by electron microscopy, nanoparticle tracking analysis and EV-specific surface markers. Cod mucosal EVs were found to carry PAD, complement component C3 and C-reactive proteins. C3 was found to be deiminated in both whole mucus and mucosal EVs, with some differences, and further 6 deiminated immune and cytoskeletal proteins were identified in EVs by LC-MS/MS analysis. As mucosal surfaces of teleost fish reflect human mucosal surfaces, these findings may provide useful insights into roles of EVs in mucosal immunity throughout phylogeny.
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Affiliation(s)
- Bergljót Magnadóttir
- Institute for Experimental Pathology, University of Iceland, Keldur V. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Igor Kraev
- School of Life, Health and Chemical Sciences, The Open University, Walton Hall, MK7 6AA, UK.
| | - Sigríður Guðmundsdóttir
- Institute for Experimental Pathology, University of Iceland, Keldur V. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Alister W Dodds
- MRC Immunochemistry Unit, Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, Department of Biomedical Sciences, University of Westminster, London, W1W 6UW, UK.
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76
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Yang Y, Liu D, Wu L, Huang W, Yang S, Xia J, Liu X, Meng Z. Comparative transcriptome analyses reveal changes of gene expression in fresh and cryopreserved yellow catfish (Pelteobagrus fulvidraco) sperm and the effects of Cryoprotectant Me 2SO. Int J Biol Macromol 2019; 133:457-465. [PMID: 31002905 DOI: 10.1016/j.ijbiomac.2019.04.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 04/08/2019] [Accepted: 04/08/2019] [Indexed: 10/27/2022]
Abstract
This study, for the first time in fish, compared the transcriptome of fresh and frozen-thawed sperm, and would help to better understand the effect of cryopreservation on fish sperm and then better preserve the aquatic germplasm resources. Here, we employed high-throughput sequencing technology to obtain the transcriptome of yellow catfish from fresh sperm, cryopreserved sperm with and without cryoprotectant. When cryoprotectant (Me2SO) was excluded, down-regulated genes were significantly enriched into calcium ion binding, cytoskeletal protein binding, microfilament motor activity, calmodulin binding and carnitine O-acyltransferase activity, which affected Ca2+ regulation, cellular morphology, motility and metabolism. Moreover, heat shock proteins and genes associated with regulation of cholesterol, HCO3- and protein tyrosine phosphorylation (PTP) were down-regulated, and thus would impair ability against stress, membrane rigidity, pH regulation and signal transduction of cryopreserved sperm. After Me2SO was added, the amounts of DEGs decreased significantly and down-regulation of genes were found mainly in cytoskeleton and heat shock proteins, thereby suggesting that Me2SO effectively reduced the impact caused by low temperature on gene expression. Whether adding Me2SO or not, the up-regulated genes were mainly found in ribosomal proteins genes. However, when Me2SO was added, over-expression of some genes might contribute to maintain normal function of cryopreserved sperm.
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Affiliation(s)
- Yang Yang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Dongqing Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lina Wu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Wenhua Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Sen Yang
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Junhong Xia
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Xiaochun Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.
| | - Zining Meng
- School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.
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77
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Alriquet M, Martínez-Limón A, Hanspach G, Hengesbach M, Tartaglia GG, Calloni G, Vabulas RM. Assembly of Proteins by Free RNA during the Early Phase of Proteostasis Stress. J Proteome Res 2019; 18:2835-2847. [PMID: 31244213 DOI: 10.1021/acs.jproteome.9b00143] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
At any stage of their lifecycle, mRNAs are coated by specialized proteins. One of few circumstances when free mRNA appears in the cytosol is the disassembly of polysomes during the stress-induced shutdown of protein synthesis. Using quantitative mass spectrometry, we sought to identify the free RNA-interacting cellular machinery in heat-shocked mammalian cells. Free RNA-associated proteins displayed higher disorder and larger size, which supports the role of multivalent interactions during the initial phase of the association with RNAs during stress. Structural features of the free RNA interactors defined them as a subset of RNA-binding proteins. The interaction between these assembled proteins in vivo required RNA. Reconstitution of the association process in vitro indicated a multimolecular basis for increased binding to RNA upon heat shock in the cytosol. Our study represents a step toward understanding how free RNA is processed in the cytosol during proteostasis stress.
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Affiliation(s)
- Marion Alriquet
- Buchmann Institute for Molecular Life Sciences , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany.,Institute of Biophysical Chemistry , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany
| | - Adrían Martínez-Limón
- Buchmann Institute for Molecular Life Sciences , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany.,Institute of Biophysical Chemistry , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany
| | - Gerd Hanspach
- Institute for Organic Chemistry and Chemical Biology , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany
| | - Gian G Tartaglia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology , Universitat Pompeu Fabra (UPF), Institucio Catalana de Recerca i Estudis Avançats (ICREA) , 08002 Barcelona , Spain
| | - Giulia Calloni
- Buchmann Institute for Molecular Life Sciences , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany.,Institute of Biophysical Chemistry , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany
| | - R Martin Vabulas
- Buchmann Institute for Molecular Life Sciences , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany.,Institute of Biophysical Chemistry , Goethe University Frankfurt , 60438 Frankfurt am Main , Germany
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79
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Li X, Chen N, Zhou L, Wang C, Wen X, Jia L, Cui J, Hoffman AR, Hu JF, Li W. Genome-wide target interactome profiling reveals a novel EEF1A1 epigenetic pathway for oncogenic lncRNA MALAT1 in breast cancer. Am J Cancer Res 2019; 9:714-729. [PMID: 31105998 PMCID: PMC6511647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 03/14/2019] [Indexed: 06/09/2023] Open
Abstract
Breast cancer is the most common cancer in women worldwide, accounting for approximately 500,000 deaths each year. MALAT1 is a highly conserved long noncoding RNA (lncRNA), and its increased expression is associated with relapse and metastatic progression in breast cancer. We performed RNA reverse transcription-associated trap sequencing (RAT-seq) to characterize the genome-wide target interaction network for MALAT1 and showed that MALAT1 interacted with multiple pathway target genes that are closely related to tumor progression and metastasis. Notably, MALAT1 bound to the promoter regulatory element of the translation elongation factor 1-alpha 1 gene EEF1A1. Knockdown of MALAT1 by shRNA caused significant downregulation of EEF1A1 in breast cancer MDA-MB231 and SKRB3 cells. Using a luciferase reporter assay, we showed that knockdown of MALAT1 reduced the promoter activity of EEF1A1 in these two breast cancer cells. Chromatin immunoprecipitation (ChIP) assay indicated that MALAT1 regulated EEF1A1 by altering the histone 3 lysine 4 (H3K4) epigenotype in the gene promoter. MALAT1 was overexpressed in breast cancer tissues and breast cancer cells. Knockdown of MALAT1 reduced cell proliferation and invasion by arresting cells at the G0/G1 phase. Ectopic overexpression of EEF1A1 reversed the altered tumor phenotypes induced by MALAT1 shRNA treatment. These data suggest an epigenetic mechanism by which MALAT1 lncRNA facilitates a pro-metastatic phenotype in breast cancer by trans-regulating EEF1A1.
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Affiliation(s)
- Xueli Li
- Stem Cell and Cancer Center, The First Hospital of Jilin University71 Xinmin Street, Changchun 130021, Jilin, China
| | - Naifei Chen
- Stem Cell and Cancer Center, The First Hospital of Jilin University71 Xinmin Street, Changchun 130021, Jilin, China
| | - Lei Zhou
- Stem Cell and Cancer Center, The First Hospital of Jilin University71 Xinmin Street, Changchun 130021, Jilin, China
- Stanford University Medical School, Palo Alto Veterans Institute for ResearchPalo Alto, CA 94304, USA
| | - Cong Wang
- Stem Cell and Cancer Center, The First Hospital of Jilin University71 Xinmin Street, Changchun 130021, Jilin, China
| | - Xue Wen
- Stem Cell and Cancer Center, The First Hospital of Jilin University71 Xinmin Street, Changchun 130021, Jilin, China
| | - Lin Jia
- Stem Cell and Cancer Center, The First Hospital of Jilin University71 Xinmin Street, Changchun 130021, Jilin, China
- Stanford University Medical School, Palo Alto Veterans Institute for ResearchPalo Alto, CA 94304, USA
| | - Jiuwei Cui
- Stem Cell and Cancer Center, The First Hospital of Jilin University71 Xinmin Street, Changchun 130021, Jilin, China
| | - Andrew R Hoffman
- Stanford University Medical School, Palo Alto Veterans Institute for ResearchPalo Alto, CA 94304, USA
| | - Ji-Fan Hu
- Stem Cell and Cancer Center, The First Hospital of Jilin University71 Xinmin Street, Changchun 130021, Jilin, China
- Stanford University Medical School, Palo Alto Veterans Institute for ResearchPalo Alto, CA 94304, USA
| | - Wei Li
- Stem Cell and Cancer Center, The First Hospital of Jilin University71 Xinmin Street, Changchun 130021, Jilin, China
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80
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eEF1A demonstrates paralog specific effects on HIV-1 reverse transcription efficiency. Virology 2019; 530:65-74. [DOI: 10.1016/j.virol.2019.01.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 01/25/2019] [Accepted: 01/28/2019] [Indexed: 11/23/2022]
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81
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Magnadóttir B, Bragason BT, Bricknell IR, Bowden T, Nicholas AP, Hristova M, Guðmundsdóttir S, Dodds AW, Lange S. Peptidylarginine deiminase and deiminated proteins are detected throughout early halibut ontogeny - Complement components C3 and C4 are post-translationally deiminated in halibut (Hippoglossus hippoglossus L.). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2019; 92:1-19. [PMID: 30395876 DOI: 10.1016/j.dci.2018.10.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 10/30/2018] [Accepted: 10/30/2018] [Indexed: 06/08/2023]
Abstract
Post-translational protein deimination is mediated by peptidylarginine deiminases (PADs), which are calcium dependent enzymes conserved throughout phylogeny with physiological and pathophysiological roles. Protein deimination occurs via the conversion of protein arginine into citrulline, leading to structural and functional changes in target proteins. In a continuous series of early halibut development from 37 to 1050° d, PAD, total deiminated proteins and deiminated histone H3 showed variation in temporal and spatial detection in various organs including yolksac, muscle, skin, liver, brain, eye, spinal cord, chondrocytes, heart, intestines, kidney and pancreas throughout early ontogeny. For the first time in any species, deimination of complement components C3 and C4 is shown in halibut serum, indicating a novel mechanism of complement regulation in immune responses and homeostasis. Proteomic analysis of deiminated target proteins in halibut serum further identified complement components C5, C7, C8 C9 and C1 inhibitor, as well as various other immunogenic, metabolic, cytoskeletal and nuclear proteins. Post-translational deimination may facilitate protein moonlighting, an evolutionary conserved phenomenon, allowing one polypeptide chain to carry out various functions to meet functional requirements for diverse roles in immune defences and tissue remodelling.
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Affiliation(s)
- Bergljót Magnadóttir
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Birkir Thor Bragason
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Ian R Bricknell
- Aquaculture Research Institute School of Marine Sciences, University of Maine, Orono, ME, USA.
| | - Timothy Bowden
- Aquaculture Research Institute School of Food & Agriculture, University of Maine, University of Maine, Orono, ME, USA.
| | - Anthony P Nicholas
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Mariya Hristova
- Perinatal Brain Protection and Repair Group, EGA Institute for Women's Health, University College London, London, WC1E 6HX, UK.
| | - Sigríður Guðmundsdóttir
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Alister W Dodds
- MRC Immunochemistry Unit, Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, School of Life Sciences, University of Westminster, London, W1W 6UW, UK.
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82
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Lü D, Sun S, Zhang F, Luo C, Zheng L, Wu Y, Li N, Zhang C, Wang C, Chen Q, Long M. Microgravity-induced hepatogenic differentiation of rBMSCs on board the SJ-10 satellite. FASEB J 2018; 33:4273-4286. [PMID: 30521385 DOI: 10.1096/fj.201802075r] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Bone marrow-derived mesenchymal stem cells (BMSCs) are able to differentiate into functional hepatocytelike cells, which are expected to serve as a potential cell source in regenerative medicine, tissue engineering, and clinical treatment of liver injury. Little is known about whether and how space microgravity is able to direct the hepatogenic differentiation of BMSCs in the actual space microenvironment. In this study, we examined the effects of space microgravity on BMSC hepatogenic differentiation on board the SJ-10 Recoverable Scientific Satellite. Rat BMSCs were cultured and induced in hepatogenic induction medium for 3 and 10 d in custom-made space cell culture hardware. Cell growth was monitored periodically in orbit, and the fixed cells and collected supernatants were retrieved back to the Earth for further analyses. Data indicated that space microgravity improves the differentiating capability of the cells by up-regulating hepatocyte-specific albumin and cytokeratin 18. The resulting cells tended to be maturated, with an in-orbit period of up to 10 d. In space, mechanosensitive molecules of β1-integrin, β-actin, α-tubulin, and Ras homolog gene family member A presented enhanced expression, whereas those of cell-surface glycoprotein CD44, intercellular adhesion molecule 1, vascular cell adhesion molecule 1, vinculin, cell division control protein 42 homolog, and Rho-associated coiled-coil kinase yielded reduced expression. Also observed in space were the depolymerization of actin filaments and the accumulation of microtubules and vimentin through the altered expression and location of focal adhesion complexes, Rho guanosine 5'-triphosphatases, as well as the enhanced exosome-mediated mRNA transfer. This work furthers the understanding of the underlying mechanisms of space microgravity in directing hepatogenic differentiation of BMSCs.-Lü, D., Sun, S., Zhang, F., Luo, C., Zheng, L., Wu, Y., Li, N., Zhang, C., Wang, C., Chen, Q., Long, M. Microgravity-induced hepatogenic differentiation of rBMSCs on board the SJ-10 satellite.
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Affiliation(s)
- Dongyuan Lü
- Key Laboratory of Microgravity, Center of Biomechanics and Bioengineering, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China.,Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China; and.,School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Shujin Sun
- Key Laboratory of Microgravity, Center of Biomechanics and Bioengineering, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China.,Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China; and.,School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Fan Zhang
- Key Laboratory of Microgravity, Center of Biomechanics and Bioengineering, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China.,Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China; and.,School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chunhua Luo
- Key Laboratory of Microgravity, Center of Biomechanics and Bioengineering, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China.,Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China; and
| | - Lu Zheng
- Key Laboratory of Microgravity, Center of Biomechanics and Bioengineering, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China.,Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China; and.,School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yi Wu
- Key Laboratory of Microgravity, Center of Biomechanics and Bioengineering, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China.,Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China; and.,School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ning Li
- Key Laboratory of Microgravity, Center of Biomechanics and Bioengineering, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China.,Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China; and.,School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Chen Zhang
- Key Laboratory of Microgravity, Center of Biomechanics and Bioengineering, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China.,Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China; and
| | - Chengzhi Wang
- Key Laboratory of Microgravity, Center of Biomechanics and Bioengineering, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China.,Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China; and.,School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Qin Chen
- Key Laboratory of Microgravity, Center of Biomechanics and Bioengineering, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China.,Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China; and
| | - Mian Long
- Key Laboratory of Microgravity, Center of Biomechanics and Bioengineering, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China.,Beijing Key Laboratory of Engineered Construction and Mechanobiology, Institute of Mechanics, Chinese Academy of Sciences, Beijing, China; and.,School of Engineering Sciences, University of Chinese Academy of Sciences, Beijing, China
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83
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Ali A, Biswas A, Pal M. HSF1 mediated TNF‐α production during proteotoxic stress response pioneers proinflammatory signal in human cells. FASEB J 2018; 33:2621-2635. [DOI: 10.1096/fj.201801482r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Asif Ali
- Division of Molecular MedicineBose InstituteKolkataIndia
| | | | - Mahadeb Pal
- Division of Molecular MedicineBose InstituteKolkataIndia
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84
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Magnadóttir B, Hayes P, Hristova M, Bragason BT, Nicholas AP, Dodds AW, Guðmundsdóttir S, Lange S. Post-translational protein deimination in cod (Gadus morhua L.) ontogeny novel roles in tissue remodelling and mucosal immune defences? DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2018; 87:157-170. [PMID: 29908202 DOI: 10.1016/j.dci.2018.06.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Revised: 06/12/2018] [Accepted: 06/12/2018] [Indexed: 06/08/2023]
Abstract
Peptidylarginine deiminases (PADs) are calcium dependent enzymes with physiological and pathophysiological roles conserved throughout phylogeny. PADs promote post-translational deimination of protein arginine to citrulline, altering the structure and function of target proteins. Deiminated proteins were detected in the early developmental stages of cod from 11 days post fertilisation to 70 days post hatching. Deiminated proteins were present in mucosal surfaces and in liver, pancreas, spleen, gut, muscle, brain and eye during early cod larval development. Deiminated protein targets identified in skin mucosa included nuclear histones; cytoskeletal proteins such as tubulin and beta-actin; metabolic and immune related proteins such as galectin, mannan-binding lectin, toll-like receptor, kininogen, Beta2-microglobulin, aldehyde dehydrogenase, bloodthirsty and preproapolipoprotein A-I. Deiminated histone H3, a marker for anti-pathogenic neutrophil extracellular traps, was particularly elevated in mucosal tissues in immunostimulated cod larvae. PAD-mediated protein deimination may facilitate protein moonlighting, allowing the same protein to exhibit a range of biological functions, in tissue remodelling and mucosal immune defences in teleost ontogeny.
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Affiliation(s)
- Bergljót Magnadóttir
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Polly Hayes
- Department of Biomedical Sciences, University of Westminster, London, W1W 6UW, UK.
| | - Mariya Hristova
- Perinatal Brain Protection and Repair Group, EGA Institute for Women's Health, University College London, WC1E 6HX, London, UK.
| | - Birkir Thor Bragason
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Anthony P Nicholas
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA.
| | - Alister W Dodds
- MRC Immunochemistry Unit, Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Sigríður Guðmundsdóttir
- Institute for Experimental Pathology, University of Iceland, Keldur v. Vesturlandsveg, 112 Reykjavik, Iceland.
| | - Sigrun Lange
- Tissue Architecture and Regeneration Research Group, Department of Biomedical Sciences, University of Westminster, London, W1W 6UW, UK.
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85
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Contradictory mRNA and protein misexpression of EEF1A1 in ductal breast carcinoma due to cell cycle regulation and cellular stress. Sci Rep 2018; 8:13904. [PMID: 30224719 PMCID: PMC6141510 DOI: 10.1038/s41598-018-32272-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 09/05/2018] [Indexed: 02/08/2023] Open
Abstract
Encoded by EEF1A1, the eukaryotic translation elongation factor eEF1α1 strongly promotes the heat shock response, which protects cancer cells from proteotoxic stress, following for instance oxidative stress, hypoxia or aneuploidy. Unexpectedly, therefore, we find that EEF1A1 mRNA levels are reduced in virtually all breast cancers, in particular in ductal carcinomas. Univariate and multivariate analyses indicate that EEF1A1 mRNA underexpression independently predicts poor patient prognosis for estrogen receptor-positive (ER+) cancers. EEF1A1 mRNA levels are lowest in the most invasive, lymph node-positive, advanced stage and postmenopausal tumors. In sharp contrast, immunohistochemistry on 100 ductal breast carcinomas revealed that at the protein level eEF1α1 is ubiquitously overexpressed, especially in ER+ , progesterone receptor-positive and lymph node-negative tumors. Explaining this paradox, we find that EEF1A1 mRNA levels in breast carcinomas are low due to EEF1A1 allelic copy number loss, found in 27% of tumors, and cell cycle-specific expression, because mRNA levels are high in G1 and low in proliferating cells. This also links estrogen-induced cell proliferation to clinical observations. In contrast, high eEF1α1 protein levels protect tumor cells from stress-induced cell death. These observations suggest that, by obviating EEF1A1 transcription, cancer cells can rapidly induce the heat shock response following proteotoxic stress, and survive.
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86
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O-GlcNAc modification of eIF4GI acts as a translational switch in heat shock response. Nat Chem Biol 2018; 14:909-916. [PMID: 30127386 DOI: 10.1038/s41589-018-0120-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 07/10/2018] [Indexed: 11/09/2022]
Abstract
Heat shock response (HSR) is an ancient signaling pathway leading to thermoprotection of nearly all living organisms. Emerging evidence suggests that intracellular O-linked β-N-acetylglucosamine (O-GlcNAc) serves as a molecular 'thermometer' by reporting ambient temperature fluctuations. Whether and how O-GlcNAc modification regulates HSR remains unclear. Here we report that, upon heat shock stress, the key translation initiation factor eIF4GI undergoes dynamic O-GlcNAcylation at the N-terminal region. Without O-GlcNAc modification, the preferential translation of stress mRNAs is impaired. Unexpectedly, stress mRNAs are entrapped within stress granules (SGs) that are no longer dissolved during stress recovery. Mechanistically, we show that stress-induced eIF4GI O-GlcNAcylation repels poly(A)-binding protein 1 and promotes SG disassembly, thereby licensing stress mRNAs for selective translation. Using various eIF4GI mutants created by CRISPR/Cas9, we demonstrate that eIF4GI acts as a translational switch via reversible O-GlcNAcylation. Our study reveals a central mechanism linking heat stress sensing, protein remodeling, SG dynamics and translational reprogramming.
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87
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Kachaev ZM, Lebedeva LA, Kozlov EN, Toropygin IY, Schedl P, Shidlovskii YV. Paip2 is localized to active promoters and loaded onto nascent mRNA in Drosophila. Cell Cycle 2018; 17:1708-1720. [PMID: 29995569 DOI: 10.1080/15384101.2018.1496738] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Paip2 (Poly(A)-binding protein - interacting protein 2) is a conserved metazoan-specific protein that has been implicated in regulating the translation and stability of mRNAs. However, we have found that Paip2 is not restricted to the cytoplasm but is also found in the nucleus in Drosophila embryos, salivary glands, testes, and tissue culture cells. Nuclear Paip2 is associated with chromatin, and in chromatin immunoprecipitation experiments it maps to the promoter regions of active genes. However, this chromatin association is indirect, as it is RNA-dependent. Thus, Paip2 is one more item in the growing list of translation factors that are recruited to mRNAs co-transcriptionally.
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Affiliation(s)
- Zaur M Kachaev
- a Laboratory of Gene Expression Regulation in Development , Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia
| | - Lyubov A Lebedeva
- a Laboratory of Gene Expression Regulation in Development , Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia
| | - Eugene N Kozlov
- a Laboratory of Gene Expression Regulation in Development , Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia
| | - Ilya Y Toropygin
- d Center of Common Use "Human Proteome" , V.I. Orekhovich Research Institute of Biomedical Chemistry , Moscow , Russia
| | - Paul Schedl
- a Laboratory of Gene Expression Regulation in Development , Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia.,b Department of Molecular Biology , Princeton University , Princeton , NJ , USA
| | - Yulii V Shidlovskii
- a Laboratory of Gene Expression Regulation in Development , Institute of Gene Biology, Russian Academy of Sciences , Moscow , Russia.,c Department of Biology and General Genetics , I.M. Sechenov First Moscow State Medical University , Moscow , Russia
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88
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Rebl A, Verleih M, Nipkow M, Altmann S, Bochert R, Goldammer T. Gradual and Acute Temperature Rise Induces Crossing Endocrine, Metabolic, and Immunological Pathways in Maraena Whitefish ( Coregonus maraena). Front Genet 2018; 9:241. [PMID: 30073015 PMCID: PMC6060367 DOI: 10.3389/fgene.2018.00241] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/19/2018] [Indexed: 12/17/2022] Open
Abstract
The complex and still poorly understood nature of thermoregulation in various fish species complicates the determination of the physiological status on the basis of diagnostic marker genes and indicative molecular pathways. The present study aimed to compare the physiological impacts of both gradual and acute temperature rise from 18 to 24°C on maraena whitefish in aquaculture. Microarray-based transcriptome profiles in the liver, spleen and kidney of heat-stressed maraena whitefish revealed the modulation of a significantly higher number of genes in those groups exposed to gradually rising temperatures compared with the acutely stressed groups, which might reflect early adaptation mechanisms. Moreover, we suggest a common set of 11 differentially expressed genes that indicate thermal stress induced by gradual or acute temperature rise in the three selected tissues. Besides the two pathways regulated in both data sets unfolded protein response and aldosterone signaling in epithelial cells, we identified unique tissue- and stress type-specific pathways reflecting the crossroads between signal transduction, metabolic and immunologic pathways to cope with thermal stress. In addition, comparing lists of differentially regulated genes with meta-analyzed published data sets revealed that “acute temperature rise”-responding genes that encode members of the HSP70, HSP90, and HSP40 families; their functional homologs; co-chaperones and stress-signal transducers are well-conserved across different species, tissues and/or cell types and experimental approaches.
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Affiliation(s)
- Alexander Rebl
- Fish Genetics Unit, Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Marieke Verleih
- Fish Genetics Unit, Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Mareen Nipkow
- Fish Genetics Unit, Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Simone Altmann
- Fish Genetics Unit, Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Ralf Bochert
- Research Station Aquaculture Born, Institute of Fisheries, Mecklenburg-Vorpommern Research Centre for Agriculture and Fisheries (LFA MV), Born, Germany
| | - Tom Goldammer
- Fish Genetics Unit, Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
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89
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Dai C. The heat-shock, or HSF1-mediated proteotoxic stress, response in cancer: from proteomic stability to oncogenesis. Philos Trans R Soc Lond B Biol Sci 2018; 373:rstb.2016.0525. [PMID: 29203710 DOI: 10.1098/rstb.2016.0525] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2017] [Indexed: 12/17/2022] Open
Abstract
The heat-shock, or HSF1-mediated proteotoxic stress, response (HSR/HPSR) is characterized by induction of heat-shock proteins (HSPs). As molecular chaperones, HSPs facilitate the folding, assembly, transportation and degradation of other proteins. In mammals, heat shock factor 1 (HSF1) is the master regulator of this ancient transcriptional programme. Upon proteotoxic insults, the HSR/HPSR is essential to proteome homeostasis, or proteostasis, thereby resisting stress and antagonizing protein misfolding diseases and ageing. Contrasting with these benefits, an unexpected pro-oncogenic role of the HSR/HPSR is unfolding. Whereas HSF1 remains latent in primary cells without stress, it becomes constitutively activated within malignant cells, rendering them addicted to HSF1 for their growth and survival. Highlighting the HSR/HPSR as an integral component of the oncogenic network, several key pathways governing HSF1 activation by environmental stressors are causally implicated in malignancy. Importantly, HSF1 impacts the cancer proteome systemically. By suppressing tumour-suppressive amyloidogenesis, HSF1 preserves cancer proteostasis to support the malignant state, both providing insight into how HSF1 enables tumorigenesis and suggesting disruption of cancer proteostasis as a therapeutic strategy. This review provides an overview of the role of HSF1 in oncogenesis, mechanisms underlying its constitutive activation within cancer cells and its pro-oncogenic action, as well as potential HSF1-targeting strategies.This article is part of the theme issue 'Heat shock proteins as modulators and therapeutic targets of chronic disease: an integrated perspective'.
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Affiliation(s)
- Chengkai Dai
- Mouse Cancer Genetics Program, Center for Cancer Research NCI-Frederick, Building 560, Room 32-31b, 1050 Boyles Street, Frederick, MD 21702, USA
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90
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George G, Singh S, Lokappa SB, Varkey J. Gene co-expression network analysis for identifying genetic markers in Parkinson's disease - a three-way comparative approach. Genomics 2018; 111:819-830. [PMID: 29852216 DOI: 10.1016/j.ygeno.2018.05.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 04/16/2018] [Accepted: 05/06/2018] [Indexed: 12/30/2022]
Abstract
Parkinson's disease (PD) is a neurodegenerative disorder involving progressive deterioration of dopaminergic neurons. Although few genetic markers for familial PD are known, the etiology of sporadic PD remains poorly understood. Microarray data was analysed for induced pluripotent stem cells (iPSCs) derived from PD patients and mature neuronal cells (mDA) differentiated from these iPSCs. Combining expression and semantic similarity, a highly-correlated PD interactome was constructed that included interactions of established Parkinson's disease marker genes. A novel three-way comparative approach was employed, delineating topologically and functionally important genes. These genes showed involvement in pathways like Parkin-ubiquitin proteosomal system (UPS), immune associated biological processes and apoptosis. Of interest are three genes, eEF1A1, CASK, and PSMD6 that are linked to PARK2 activity in the cell and thereby form attractive candidate genes for understanding PD. Network biology approach delineated in this study can be applied to other neurodegenerative disorders for identification of important genetic regulators.
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Affiliation(s)
- Gincy George
- Department of Bioinformatics, Karunya University, Karunya Nagar, Tamil Nadu 641114, India
| | - Sachidanand Singh
- Department of Bioinformatics, Karunya University, Karunya Nagar, Tamil Nadu 641114, India; Institute of Bio-Sciences and Technology, Shri Ramswaroop Memorial University, Deva Road, Uttar Pradesh 225003, India
| | - Sowmya Bekshe Lokappa
- Department of Bioinformatics, Karunya University, Karunya Nagar, Tamil Nadu 641114, India; Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA.
| | - Jobin Varkey
- Department of Bioinformatics, Karunya University, Karunya Nagar, Tamil Nadu 641114, India; Zilkha Neurogenetic Institute, University of Southern California, Los Angeles, CA 90033, USA.
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91
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Coppin L, Leclerc J, Vincent A, Porchet N, Pigny P. Messenger RNA Life-Cycle in Cancer Cells: Emerging Role of Conventional and Non-Conventional RNA-Binding Proteins? Int J Mol Sci 2018; 19:ijms19030650. [PMID: 29495341 PMCID: PMC5877511 DOI: 10.3390/ijms19030650] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/16/2018] [Accepted: 02/19/2018] [Indexed: 02/06/2023] Open
Abstract
Functional specialization of cells and tissues in metazoans require specific gene expression patterns. Biological processes, thus, need precise temporal and spatial coordination of gene activity. Regulation of the fate of messenger RNA plays a crucial role in this context. In the present review, the current knowledge related to the role of RNA-binding proteins in the whole mRNA life-cycle is summarized. This field opens up a new angle for understanding the importance of the post-transcriptional control of gene expression in cancer cells. The emerging role of non-classic RNA-binding proteins is highlighted. The goal of this review is to encourage readers to view, through the mRNA life-cycle, novel aspects of the molecular basis of cancer and the potential to develop RNA-based therapies.
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Affiliation(s)
- Lucie Coppin
- University of Lille, UMR-S 1172-JPARC-Jean-Pierre Aubert Research Center, F-59000 Lille, France.
- Inserm, UMR-S 1172, Team "Mucins, Epithelial Differentiation and Carcinogenesis", F-59000 Lille, Frances.
- CHU Lille, Service de Biochimie "Hormonologie, Métabolisme-Nutrition, Oncologie", F-59000 Lille, France.
| | - Julie Leclerc
- University of Lille, UMR-S 1172-JPARC-Jean-Pierre Aubert Research Center, F-59000 Lille, France.
- Inserm, UMR-S 1172, Team "Mucins, Epithelial Differentiation and Carcinogenesis", F-59000 Lille, Frances.
- CHU Lille, Service de Biochimie "Hormonologie, Métabolisme-Nutrition, Oncologie", F-59000 Lille, France.
| | - Audrey Vincent
- University of Lille, UMR-S 1172-JPARC-Jean-Pierre Aubert Research Center, F-59000 Lille, France.
- Inserm, UMR-S 1172, Team "Mucins, Epithelial Differentiation and Carcinogenesis", F-59000 Lille, Frances.
- CHU Lille, Service de Biochimie "Hormonologie, Métabolisme-Nutrition, Oncologie", F-59000 Lille, France.
| | - Nicole Porchet
- University of Lille, UMR-S 1172-JPARC-Jean-Pierre Aubert Research Center, F-59000 Lille, France.
- Inserm, UMR-S 1172, Team "Mucins, Epithelial Differentiation and Carcinogenesis", F-59000 Lille, Frances.
- CHU Lille, Service de Biochimie "Hormonologie, Métabolisme-Nutrition, Oncologie", F-59000 Lille, France.
| | - Pascal Pigny
- University of Lille, UMR-S 1172-JPARC-Jean-Pierre Aubert Research Center, F-59000 Lille, France.
- Inserm, UMR-S 1172, Team "Mucins, Epithelial Differentiation and Carcinogenesis", F-59000 Lille, Frances.
- CHU Lille, Service de Biochimie "Hormonologie, Métabolisme-Nutrition, Oncologie", F-59000 Lille, France.
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92
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Nelson VK, Ali A, Dutta N, Ghosh S, Jana M, Ganguli A, Komarov A, Paul S, Dwivedi V, Chatterjee S, Jana NR, Lakhotia SC, Chakrabarti G, Misra AK, Mandal SC, Pal M. Azadiradione ameliorates polyglutamine expansion disease in Drosophila by potentiating DNA binding activity of heat shock factor 1. Oncotarget 2018; 7:78281-78296. [PMID: 27835876 PMCID: PMC5346638 DOI: 10.18632/oncotarget.12930] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 08/21/2016] [Indexed: 01/14/2023] Open
Abstract
Aggregation of proteins with the expansion of polyglutamine tracts in the brain underlies progressive genetic neurodegenerative diseases (NDs) like Huntington's disease and spinocerebellar ataxias (SCA). An insensitive cellular proteotoxic stress response to non-native protein oligomers is common in such conditions. Indeed, upregulation of heat shock factor 1 (HSF1) function and its target protein chaperone expression has shown promising results in animal models of NDs. Using an HSF1 sensitive cell based reporter screening, we have isolated azadiradione (AZD) from the methanolic extract of seeds of Azadirachta indica, a plant known for its multifarious medicinal properties. We show that AZD ameliorates toxicity due to protein aggregation in cell and fly models of polyglutamine expansion diseases to a great extent. All these effects are correlated with activation of HSF1 function and expression of its target protein chaperone genes. Notably, HSF1 activation by AZD is independent of cellular HSP90 or proteasome function. Furthermore, we show that AZD directly interacts with purified human HSF1 with high specificity, and facilitates binding of HSF1 to its recognition sequence with higher affinity. These unique findings qualify AZD as an ideal lead molecule for consideration for drug development against NDs that affect millions worldwide.
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Affiliation(s)
- Vinod K Nelson
- Division of Molecular Medicine, Bose Institute, Kolkata, West Bengal, India.,Department of Pharmaceutical Technology, Pharmacognosy and Phytotherapy Laboratory, Jadavpur University, Jadavpur, West Bengal, India
| | - Asif Ali
- Division of Molecular Medicine, Bose Institute, Kolkata, West Bengal, India
| | - Naibedya Dutta
- Division of Molecular Medicine, Bose Institute, Kolkata, West Bengal, India
| | - Suvranil Ghosh
- Division of Molecular Medicine, Bose Institute, Kolkata, West Bengal, India
| | - Manas Jana
- Division of Molecular Medicine, Bose Institute, Kolkata, West Bengal, India
| | - Arnab Ganguli
- Dr. B. C. Guha Center for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, West Bengal, India
| | - Andrei Komarov
- Cellecta Inc, Mountain View, California, United States of America
| | - Soumyadip Paul
- Division of Molecular Medicine, Bose Institute, Kolkata, West Bengal, India
| | - Vibha Dwivedi
- Department of Zoology, Cytogenetics Laboratory, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | | | - Nihar R Jana
- Cellular and Molecular Neuroscience Laboratory, National Brain Research Institute, Manesar, Gurgaon, Haryana, India
| | - Subhash C Lakhotia
- Department of Zoology, Cytogenetics Laboratory, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Gopal Chakrabarti
- Dr. B. C. Guha Center for Genetic Engineering and Biotechnology, University of Calcutta, Kolkata, West Bengal, India
| | - Anup K Misra
- Division of Molecular Medicine, Bose Institute, Kolkata, West Bengal, India
| | - Subhash C Mandal
- Department of Pharmaceutical Technology, Pharmacognosy and Phytotherapy Laboratory, Jadavpur University, Jadavpur, West Bengal, India
| | - Mahadeb Pal
- Division of Molecular Medicine, Bose Institute, Kolkata, West Bengal, India
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93
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Hamey JJ, Wilkins MR. Methylation of Elongation Factor 1A: Where, Who, and Why? Trends Biochem Sci 2018; 43:211-223. [PMID: 29398204 DOI: 10.1016/j.tibs.2018.01.004] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 01/09/2018] [Accepted: 01/10/2018] [Indexed: 11/17/2022]
Abstract
Eukaryotic elongation factor 1A (eEF1A) is an essential and highly conserved protein involved in diverse cellular processes, including translation, cytoskeleton organisation, nuclear export, and proteasomal degradation. Recently, nine novel and site-specific methyltransferases were discovered that target eEF1A, five in yeast and four in human, making it the eukaryotic protein with the highest number of independent methyltransferases. Some of these methyltransferases show striking evolutionary conservation. Yet, they come from diverse methyltransferase families, indicating they confer competitive advantage through independent origins. As might be expected, the first functional studies of specific methylation sites found them to have distinct effects, notably on eEF1A-related processes of translation and tRNA aminoacylation. Further functional studies of sites will likely reveal other unique roles for this interesting modification.
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Affiliation(s)
- Joshua J Hamey
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, 2052, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, 2052, Australia.
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94
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eEF1A1 Overexpression Enhances Tumor Progression and Indicates Poor Prognosis in Hepatocellular Carcinoma. Transl Oncol 2017; 11:125-131. [PMID: 29248802 PMCID: PMC6002347 DOI: 10.1016/j.tranon.2017.11.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 11/03/2017] [Accepted: 11/06/2017] [Indexed: 12/12/2022] Open
Abstract
Liver is a major contributor of protein production physiologically. The aberrant state of protein synthesis leads to tumor progression. Eukaryotic elongation factor 1 alpha 1 (eEF1A1) is a major member of the eukaryotic elongation factor family that regulates protein synthesis. Although eEF1A1 plays an essential role in controlling the cell fate, its clinical significance in tumor development and progression has not been reported. Here, we aimed to uncover the expression and prognostic significance of eEF1A1 in hepatocellular carcinoma (HCC). Our data indicated that eEF1A1 expression was elevated in HCC cell lines and clinical samples at both the mRNA and protein levels. Immunohistochemistry revealed that eEF1A1 expression was upregulated in HCC samples compared with corresponding non-tumorous tissues. In 50 HCC cases with portal vein embolus, higher eEF1A1 immunoreactivity was detected in tumor metastases compared with the primary lesions. Kaplan–Meier analysis indicated that increased eEF1A1 expression was closely associated with unfavorable post-surgical overall and disease-free survival in 453 HCC patients. Moreover, multivariate analysis indicated eEF1A1 as an independent predictor for overall and disease-free survival. Collectively, our study suggests eEF1A1 as a novel prognostic biomarker and potential therapeutic target for HCC patients.
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95
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RNA polymerase II pausing and transcriptional regulation of the HSP70 expression. Eur J Cell Biol 2017; 96:739-745. [DOI: 10.1016/j.ejcb.2017.09.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 08/16/2017] [Accepted: 09/25/2017] [Indexed: 12/20/2022] Open
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96
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Intercellular mRNA trafficking via membrane nanotube-like extensions in mammalian cells. Proc Natl Acad Sci U S A 2017; 114:E9873-E9882. [PMID: 29078295 PMCID: PMC5699038 DOI: 10.1073/pnas.1706365114] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
mRNA molecules convey genetic information within cells, beginning from genes in the nucleus to ribosomes in the cell body, where they are translated into proteins. Here we show a mode of transferring genetic information from one cell to another. Contrary to previous publications suggesting that mRNAs transfer via extracellular vesicles, we provide visual and quantitative data showing that mRNAs transfer via membrane nanotubes and direct cell-to-cell contact. We predict that this process has a major role in regulating local cellular environments with respect to tissue development and maintenance and cellular responses to stress, interactions with parasites, tissue transplants, and the tumor microenvironment. RNAs have been shown to undergo transfer between mammalian cells, although the mechanism behind this phenomenon and its overall importance to cell physiology is not well understood. Numerous publications have suggested that RNAs (microRNAs and incomplete mRNAs) undergo transfer via extracellular vesicles (e.g., exosomes). However, in contrast to a diffusion-based transfer mechanism, we find that full-length mRNAs undergo direct cell–cell transfer via cytoplasmic extensions characteristic of membrane nanotubes (mNTs), which connect donor and acceptor cells. By employing a simple coculture experimental model and using single-molecule imaging, we provide quantitative data showing that mRNAs are transferred between cells in contact. Examples of mRNAs that undergo transfer include those encoding GFP, mouse β-actin, and human Cyclin D1, BRCA1, MT2A, and HER2. We show that intercellular mRNA transfer occurs in all coculture models tested (e.g., between primary cells, immortalized cells, and in cocultures of immortalized human and murine cells). Rapid mRNA transfer is dependent upon actin but is independent of de novo protein synthesis and is modulated by stress conditions and gene-expression levels. Hence, this work supports the hypothesis that full-length mRNAs undergo transfer between cells through a refined structural connection. Importantly, unlike the transfer of miRNA or RNA fragments, this process of communication transfers genetic information that could potentially alter the acceptor cell proteome. This phenomenon may prove important for the proper development and functioning of tissues as well as for host–parasite or symbiotic interactions.
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97
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Quiles JM, Narasimhan M, Mosbruger T, Shanmugam G, Crossman D, Rajasekaran NS. Identification of transcriptome signature for myocardial reductive stress. Redox Biol 2017; 13:568-580. [PMID: 28768233 PMCID: PMC5536881 DOI: 10.1016/j.redox.2017.07.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2017] [Revised: 07/20/2017] [Accepted: 07/20/2017] [Indexed: 12/20/2022] Open
Abstract
The nuclear factor erythroid 2 like 2 (Nfe2l2/Nrf2) is a master regulator of antioxidant gene transcription. We recently identified that constitutive activation of Nrf2 (CaNrf2) caused reductive stress (RS) in the myocardium. Here we investigate how chronic Nrf2 activation alters myocardial mRNA transcriptome in the hearts of CaNrf2 transgenic (TG-low and TG-high) mice using an unbiased integrated systems approach and next generation RNA sequencing followed by qRT-PCR methods. A total of 246 and 1031 differentially expressed genes (DEGs) were identified in the heart of TGL and TGH in relation to NTG littermates at ~ 6 months of age. Notably, the expression and validation of the transcripts were gene-dosage dependent and statistically significant. Ingenuity Pathway Analysis identified enriched biological processes and canonical pathways associated with myocardial RS in the CaNrf2-TG mice. In addition, an overrepresentation of xenobiotic metabolic signaling, glutathione-mediated detoxification, unfolded protein response, and protein ubiquitination was observed. Other, non-canonical signaling pathways identified include: eNOS, integrin-linked kinase, glucocorticoid receptor, PI3/AKT, actin cytoskeleton, cardiac hypertrophy, and the endoplasmic reticulum stress response. In conclusion, this mRNA profiling identified a "biosignature" for pro-reductive (TGL) and reductive stress (TGH) that can predict the onset, rate of progression, and clinical outcome of Nrf2-dependent myocardial complications. We anticipate that this global sequencing analysis will illuminate the undesirable effect of chronic Nrf2 signaling leading to RS-mediated pathogenesis besides providing important guidance for the application of Nrf2 activation-based cytoprotective strategies.
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Affiliation(s)
- Justin M Quiles
- Cardiac Aging & Redox Signaling Laboratory, Division of Molecular & Cellular Pathology, Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Madhusudhanan Narasimhan
- Department of Pharmacology and Neuroscience, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Timothy Mosbruger
- Division of Cardiovascular Medicine, Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Gobinath Shanmugam
- Cardiac Aging & Redox Signaling Laboratory, Division of Molecular & Cellular Pathology, Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - David Crossman
- Heflin Center for Genomic Sciences, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Namakkal S Rajasekaran
- Cardiac Aging & Redox Signaling Laboratory, Division of Molecular & Cellular Pathology, Department of Pathology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA; Division of Cardiovascular Medicine, Department of Medicine, University of Utah School of Medicine, Salt Lake City, UT 84132, USA; Center for Free Radical Biology, The University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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98
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Activation of tissue plasminogen activator by metastasis-inducing S100P protein. Biochem J 2017; 474:3227-3240. [PMID: 28798096 DOI: 10.1042/bcj20170578] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 08/08/2017] [Accepted: 08/09/2017] [Indexed: 12/25/2022]
Abstract
S100P protein in human breast cancer cells is associated with reduced patient survival and, in a model system of metastasis, it confers a metastatic phenotype upon benign mammary tumour cells. S100P protein possesses a C-terminal lysine residue. Using a multiwell in vitro assay, S100P is now shown for the first time to exhibit a strong, C-terminal lysine-dependent activation of tissue plasminogen activator (tPA), but not of urokinase-catalysed plasminogen activation. The presence of 10 μM calcium ions stimulates tPA activation of plasminogen 2-fold in an S100P-dependent manner. S100P physically interacts with both plasminogen and tPA in vitro, but not with urokinase. Cells constitutively expressing S100P exhibit detectable S100P protein on the cell surface, and S100P-containing cells show enhanced activation of plasminogen compared with S100P-negative control cells. S100P shows C-terminal lysine-dependent enhancement of cell invasion. An S100P antibody, when added to the culture medium, reduced the rate of invasion of wild-type S100P-expressing cells, but not of cells expressing mutant S100P proteins lacking the C-terminal lysine, suggesting that S100P functions outside the cell. The protease inhibitors, aprotinin or α-2-antiplasmin, reduced the invasion of S100P-expressing cells, but not of S100P-negative control cells, nor cells expressing S100P protein lacking the C-terminal lysine. It is proposed that activation of tPA via the C-terminal lysine of S100P contributes to the enhancement of cell invasion by S100P and thus potentially to its metastasis-promoting activity.
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99
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Structural rationale for the cross-resistance of tumor cells bearing the A399V variant of elongation factor eEF1A1 to the structurally unrelated didemnin B, ternatin, nannocystin A and ansatrienin B. J Comput Aided Mol Des 2017; 31:915-928. [DOI: 10.1007/s10822-017-0066-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Accepted: 09/08/2017] [Indexed: 01/24/2023]
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100
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Hamey JJ, Wienert B, Quinlan KGR, Wilkins MR. METTL21B Is a Novel Human Lysine Methyltransferase of Translation Elongation Factor 1A: Discovery by CRISPR/Cas9 Knockout. Mol Cell Proteomics 2017; 16:2229-2242. [PMID: 28663172 DOI: 10.1074/mcp.m116.066308] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 06/28/2017] [Indexed: 02/03/2023] Open
Abstract
Lysine methylation is widespread on human proteins, however the enzymes that catalyze its addition remain largely unknown. This limits our capacity to study the function and regulation of this modification. Here we used the CRISPR/Cas9 system to knockout putative protein methyltransferases METTL21B and METTL23 in K562 cells, to determine if they methylate elongation factor eEF1A. The known eEF1A methyltransferase EEF1AKMT1 was also knocked out as a control. Targeted mass spectrometry revealed the loss of lysine 165 methylation upon knockout of METTL21B, and the expected loss of lysine 79 methylation on knockout of EEF1AKMT1 No loss of eEF1A methylation was seen in the METTL23 knockout. Recombinant METTL21B was shown in vitro to catalyze methylation on lysine 165 in eEF1A1 and eEF1A2, confirming it as the methyltransferase responsible for this methylation site. Proteomic analysis by SILAC revealed specific upregulation of large ribosomal subunit proteins in the METTL21B knockout, and changes to further processes related to eEF1A function in knockouts of both METTL21B and EEF1AKMT1 This indicates that the methylation of lysine 165 in human eEF1A has a very specific role. METTL21B exists only in vertebrates, with its target lysine showing similar evolutionary conservation. We suggest METTL21B be renamed eEF1A-KMT3. This is the first study to specifically generate CRISPR/Cas9 knockouts of putative protein methyltransferase genes, for substrate discovery and site mapping. Our approach should prove useful for the discovery of further novel methyltransferases, and more generally for the discovery of sites for other protein-modifying enzymes.
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Affiliation(s)
- Joshua J Hamey
- From the ‡School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, 2052, Australia
| | - Beeke Wienert
- From the ‡School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, 2052, Australia
| | - Kate G R Quinlan
- From the ‡School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, 2052, Australia
| | - Marc R Wilkins
- From the ‡School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, 2052, Australia
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