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Liu Y, Peng L, Chen J, Chen L, Wu Y, Cheng M, Chen M, Ye X, Jin Y. EIF5A2 specifically regulates the transcription of aging-related genes in human neuroblastoma cells. BMC Geriatr 2023; 23:83. [PMID: 36750933 PMCID: PMC9906866 DOI: 10.1186/s12877-023-03793-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
BACKGROUND Post-transcriptional regulation plays a critical role in controlling biological processes such as aging. Previous studies have shown that eukaryotic initiation factor 5A (EIF5A) might play a crucial role in aging. It is unknown whether EIF5A2, a second isoform of EIF5A, could impact aging through post-transcriptional regulation. METHODS In the present study, EIF5A2 overexpression (EIF5A2-OE) was induced in SH-SY5Y cells. RNA-seq, bioinformatics analysis and RT-qPCR validation experiments were then performed to explore the molecular mechanism of EIF5A2-mediated transcriptional regulation. Cell viability, proportion of senescent cells and the cell cycle were respectively determined by Cell Counting Kit-8, SA-β‑galactosidase and flow cytometry to evaluate the cell senescence. RESULTS A total of 190 downregulated and 126 upregulated genes related to EIF5A2-OE were identified. Genes closely related to cellular aging processes such as unfolded protein response (UPR), cell adhesion and calcium signaling pathway were under global transcriptional regulation. Moreover, EIF5A2-OE promoted the viability of SH-SY5Y cells and reduced cell senescence in vitro. Among 30 genes with the most significant expression differences in EIF5A2-OE cells, we identified eight genes, including ASNS, ATF3, ATF4, CEBPB, DDIT3, HERPUD1, HSPA5 and XBP1, enriched in the UPR. Through EIF5A2-tanscription factors (TFs)-targets regulation network in EIF5A2-OE cells, we found three TFs, BHLHE40, RHOXF1 and TBX20, that targeted at these eight UPR-related genes. Verification test via the published database of human glial cell tissue showed only BHLHE40 and RHOXF1 were significantly associated with EIF5A2. CONCLUSIONS Our findings suggest that EIF5A2 may alleviate cell senescence in vitro and mediate UPR-related genes via specific TFs. Thus, EIF5A2 could function as a regulator of aging via the regulation of transcription, which greatly expands the current understanding of the mechanisms of EIF5A2-mediated gene regulation.
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Affiliation(s)
- Yuwei Liu
- grid.49470.3e0000 0001 2331 6153Department of Internal Medicine and Geriatrics, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei China ,grid.49470.3e0000 0001 2331 6153Department of General Practice, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei China
| | - Li Peng
- grid.49470.3e0000 0001 2331 6153Department of Internal Medicine and Geriatrics, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei China ,grid.49470.3e0000 0001 2331 6153Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei China
| | - Jing Chen
- grid.49470.3e0000 0001 2331 6153Department of Internal Medicine and Geriatrics, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei China
| | - Ling Chen
- grid.49470.3e0000 0001 2331 6153Department of Internal Medicine and Geriatrics, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei China
| | - Ying Wu
- grid.49470.3e0000 0001 2331 6153Department of Internal Medicine and Geriatrics, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei China
| | - Mengxin Cheng
- grid.49470.3e0000 0001 2331 6153Department of Internal Medicine and Geriatrics, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei China
| | - Min Chen
- grid.49470.3e0000 0001 2331 6153Department of Internal Medicine and Geriatrics, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei China
| | - Xujun Ye
- Department of Internal Medicine and Geriatrics, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, China.
| | - Yalei Jin
- Department of General Practice, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, Hubei, China.
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Fiches GN, Wu Z, Zhou D, Biswas A, Li TW, Kong W, Jean M, Santoso NG, Zhu J. Polyamine biosynthesis and eIF5A hypusination are modulated by the DNA tumor virus KSHV and promote KSHV viral infection. PLoS Pathog 2022; 18:e1010503. [PMID: 35486659 PMCID: PMC9094511 DOI: 10.1371/journal.ppat.1010503] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 05/11/2022] [Accepted: 04/05/2022] [Indexed: 12/12/2022] Open
Abstract
Polyamines are critical metabolites involved in various cellular processes and often dysregulated in cancers. Kaposi’s sarcoma-associated Herpesvirus (KSHV), a defined human oncogenic virus, leads to profound alterations of host metabolic landscape to favor development of KSHV-associated malignancies. In our studies, we identified that polyamine biosynthesis and eIF5A hypusination are dynamically regulated by KSHV infection through modulation of key enzymes (ODC1 and DHPS) of these pathways. During KSHV latency, ODC1 and DHPS are upregulated along with increase of hypusinated eIF5A (hyp-eIF5A), while hyp-eIF5A is further induced along with reduction of ODC1 and intracellular polyamines during KSHV lytic reactivation. In return these metabolic pathways are required for both KSHV lytic reactivation and de novo infection. Further analysis unraveled that synthesis of critical KSHV latent and lytic proteins (LANA, RTA) depends on hypusinated-eIF5A. We also demonstrated that KSHV infection can be efficiently and specifically suppressed by inhibitors targeting these pathways. Collectively, our results illustrated that the dynamic and profound interaction of a DNA tumor virus (KSHV) with host polyamine biosynthesis and eIF5A hypusination pathways promote viral propagation, thus defining new therapeutic targets to treat KSHV-associated malignancies. Understanding virus-host interactions is crucial to develop and improve therapies. Kaposi’s sarcoma associated Herpesvirus (KSHV) is a human gamma-herpesvirus which deeply modulates the host metabolism and is associated with various cancers of endothelial and lymphoid origin. Polyamines are critical metabolites often dysregulated in cancers. In this study we demonstrated KSHV dynamically modulates polyamine metabolism to favor eIF5A hypusination and translation of critical KSHV latent and lytic proteins (LANA, RTA). Consequently, we found KSHV lytic switch from latency and de novo infection were dependent on polyamines and hypusination and pharmacological inhibition efficiently and specifically restricted KSHV infection. Our study provides new insights into KSHV alteration of the host metabolism and describe new therapeutic targets to treat KSHV-associated malignancies.
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Affiliation(s)
- Guillaume N. Fiches
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Zhenyu Wu
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Dawei Zhou
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Ayan Biswas
- Department of Genetics, School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Tai-Wei Li
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Weili Kong
- Gladstone Institute of Virology and Immunology, University of California, San Francisco, California, United States of America
| | - Maxime Jean
- Department of Neurology, University of Rochester Medical center, Rochester, New York, United States of America
| | - Netty G. Santoso
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
| | - Jian Zhu
- Department of Pathology, Ohio State University College of Medicine, Columbus, Ohio, United States of America
- * E-mail:
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Agboigba E, Kuchaev E, Garaeva N, Klochkova E, Varfolomeev A, Usachev K, Yusupov M, Validov S. ORF19.2286 Gene: Isolation and Purification of Deoxyhypusine Hydroxylase from the Human Pathogenic Yeast Candida albicans. Mol Biol 2022. [DOI: 10.1134/s0026893322020029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Proteomic Research on the Antitumor Properties of Medicinal Mushrooms. Molecules 2021; 26:molecules26216708. [PMID: 34771120 PMCID: PMC8588050 DOI: 10.3390/molecules26216708] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/27/2021] [Accepted: 11/02/2021] [Indexed: 12/22/2022] Open
Abstract
Medicinal mushrooms are increasingly being recognized as an important therapeutic modality in complementary oncology. Until now, more than 800 mushroom species have been known to possess significant pharmacological properties, of which antitumor and immunomodulatory properties have been the most researched. Besides a number of medicinal mushroom preparations being used as dietary supplements and nutraceuticals, several isolates from mushrooms have been used as official antitumor drugs in clinical settings for several decades. Various proteomic approaches allow for the identification of a large number of differentially regulated proteins serendipitously, thereby providing an important platform for a discovery of new potential therapeutic targets and approaches as well as biomarkers of malignant disease. This review is focused on the current state of proteomic research into antitumor mechanisms of some of the most researched medicinal mushroom species, including Phellinus linteus, Ganoderma lucidum, Auricularia auricula, Agrocybe aegerita, Grifola frondosa, and Lentinus edodes, as whole body extracts or various isolates, as well as of complex extract mixtures.
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5
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Lindner B, Martin E, Steininger M, Bundalo A, Lenter M, Zuber J, Schuler M. A genome-wide CRISPR/Cas9 screen to identify phagocytosis modulators in monocytic THP-1 cells. Sci Rep 2021; 11:12973. [PMID: 34155263 PMCID: PMC8217514 DOI: 10.1038/s41598-021-92332-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 06/02/2021] [Indexed: 01/23/2023] Open
Abstract
Phagocytosis of microbial pathogens, dying or dead cells, and cell debris is essential to maintain tissue homeostasis. Impairment of these processes is associated with autoimmunity, developmental defects and toxic protein accumulation. However, the underlying molecular mechanisms of phagocytosis remain incompletely understood. Here, we performed a genome-wide CRISPR knockout screen to systematically identify regulators involved in phagocytosis of Staphylococcus (S.) aureus by human monocytic THP-1 cells. The screen identified 75 hits including known regulators of phagocytosis, e.g. members of the actin cytoskeleton regulation Arp2/3 and WAVE complexes, as well as genes previously not associated with phagocytosis. These novel genes are involved in translational control (EIF5A and DHPS) and the UDP glycosylation pathway (SLC35A2, SLC35A3, UGCG and UXS1) and were further validated by single gene knockout experiments. Whereas the knockout of EIF5A and DHPS impaired phagocytosis, knocking out SLC35A2, SLC35A3, UGCG and UXS1 resulted in increased phagocytosis. In addition to S. aureus phagocytosis, the above described genes also modulate phagocytosis of Escherichia coli and yeast-derived zymosan A. In summary, we identified both known and unknown genetic regulators of phagocytosis, the latter providing a valuable resource for future studies dissecting the underlying molecular and cellular mechanisms and their role in human disease.
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Affiliation(s)
- Benjamin Lindner
- Department of Drug Discovery Science, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorferstr. 65, 88397, Biberach an der Riss, Germany.
| | - Eva Martin
- Department of Drug Discovery Science, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorferstr. 65, 88397, Biberach an der Riss, Germany
| | - Monika Steininger
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Aleksandra Bundalo
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Martin Lenter
- Department of Drug Discovery Science, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorferstr. 65, 88397, Biberach an der Riss, Germany
| | - Johannes Zuber
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), 1030, Vienna, Austria
- Medical University of Vienna, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Michael Schuler
- Department of Drug Discovery Science, Boehringer Ingelheim Pharma GmbH & Co. KG, Birkendorferstr. 65, 88397, Biberach an der Riss, Germany
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6
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D'Agostino M, Motta S, Romagnoli A, Orlando P, Tiano L, La Teana A, Di Marino D. Insights Into the Binding Mechanism of GC7 to Deoxyhypusine Synthase in Sulfolobus solfataricus: A Thermophilic Model for the Design of New Hypusination Inhibitors. Front Chem 2021; 8:609942. [PMID: 33392152 PMCID: PMC7773846 DOI: 10.3389/fchem.2020.609942] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 11/16/2020] [Indexed: 12/18/2022] Open
Abstract
Translation factor 5A (eIF5A) is one of the most conserved proteins involved in protein synthesis. It plays a key role during the elongation of polypeptide chains, and its activity is critically dependent on hypusination, a post-translational modification of a specific lysine residue through two consecutive enzymatic steps carried out by deoxyhypusine synthase (DHS), with spermidine as substrate, and deoxyhypusine hydroxylase (DOHH). It is well-established that eIF5A is overexpressed in several cancer types, and it is involved in various diseases such as HIV-1 infection, malaria, and diabetes; therefore, the development of inhibitors targeting both steps of the hypusination process is considered a promising and challenging therapeutic strategy. One of the most efficient inhibitors of the hypusination process is the spermidine analog N1-guanyl-1,7-diaminoheptane (GC7). GC7 interacts in a specific binding pocket of the DHS completely blocking its activity; however, its therapeutic use is limited by poor selectivity and restricted bioavailability. Here we have performed a comparative study between human DHS (hDHS) and archaeal DHS from crenarchaeon Sulfolobus solfataricus (aDHS) to understand the structural and dynamical features of the GC7 inhibition. The advanced metadynamics (MetaD) classical molecular dynamics simulations show that the GC7 interaction is less stable in the thermophilic enzyme compared to hDHS that could underlie a lower inhibitory capacity of the hypusination process in Sulfolobus solfataricus. To confirm this hypothesis, we have tested GC7 activity on S. solfataricus by measuring cellular growth, and results have shown the lack of inhibition of aIF5A hypusination in contrast to the established effect on eukaryotic cellular growth. These results provide, for the first time, detailed molecular insights into the binding mechanism of GC7 to aDHS generating the basis for the design of new and more specific DHS inhibitors.
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Affiliation(s)
- Mattia D'Agostino
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Stefano Motta
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Milan, Italy
| | - Alice Romagnoli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy.,New York-Marche Structural Biology Center (Ny-Masbic), Polytechnic University of Marche, Ancona, Italy
| | - Patrick Orlando
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Luca Tiano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Anna La Teana
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy.,New York-Marche Structural Biology Center (Ny-Masbic), Polytechnic University of Marche, Ancona, Italy
| | - Daniele Di Marino
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy.,New York-Marche Structural Biology Center (Ny-Masbic), Polytechnic University of Marche, Ancona, Italy
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7
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Li X, He J, Ren X, Zhao H, Zhao H. Circ_0003998 enhances doxorubicin resistance in hepatocellular carcinoma by regulating miR-218-5p/EIF5A2 pathway. Diagn Pathol 2020; 15:141. [PMID: 33308276 PMCID: PMC7733254 DOI: 10.1186/s13000-020-01056-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Accepted: 11/29/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The involvement of circular RNAs (circRNAs) in chemoresistance of tumors has been identified. Herein, this study aims to investigate the role and the underlying mechanism of circ_0003998 in doxorubicin (DOX) resistance in hepatocellular carcinoma (HCC). METHODS The expression of circ_0003998 and microRNA (miR)-218-5p and eukaryotic translation initiation factor 5A-2 (EIF5A2) mRNA was detected using quantitative real-time polymerase chain reaction. Cell viability, migration and invasion were analyzed using cell counting kit-8, colony formation and transwell assay, respectively. The levels of matrix metallopeptidase 9 (MMP-9), E-cadherin, Vimentin, N-cadherin and EIF5A2 protein were detected using western blot. The interaction between miR-218-5p and circ_0003998 or EIF5A2 was confirmed by dual-luciferase reporter assay. In vivo experiments were performed using murine xenograft models. RESULTS Circ_0003998 was elevated in HCC tissues, DOX-resistant tissues and cells, and circ_0003998 knockdown promoted DOX-sensitivity in HCC by inhibiting resistant cell viability, migration, invasion and EMT in vitro and enhanced DOX cytotoxicity in vivo. Bioinformatics analysis revealed circ_0003998 inhibited miR-218-5p expression, which was clarified to be a target of circ_0003998, and circ_0003998 knockdown sensitized HCC cell to DOX by sponging miR-218-5p. EIF5A2 was a target of miR-218-5p, and miR-218-5p mitigated DOX resistance in HCC cells through modulating EIF5A2 expression. Additionally, circ_0003998 served as a competing endogenous RNA for miR-218-5p to regulate EIF5A2 expression. CONCLUSION Circ_0003998 knockdown sensitized HCC cell to DOX by regulating miR-218-5p/EIF5A2 axis, indicating new markers of poor response to DOX and potential therapeutic strategies for the chemotherapy of HCC.
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Affiliation(s)
- Xiaomin Li
- Shanxi Medical University, Taiyuan, Shanxi, China
- Department of General Surgery, Shanxi Bethune Hospital, No. 99 Longcheng Street, Xiaodian District, Taiyuan, 030032, Shanxi, China
| | - Jiefeng He
- Department of General Surgery, Shanxi Bethune Hospital, No. 99 Longcheng Street, Xiaodian District, Taiyuan, 030032, Shanxi, China
| | - Xiaojing Ren
- Department of General Surgery, Shanxi Bethune Hospital, No. 99 Longcheng Street, Xiaodian District, Taiyuan, 030032, Shanxi, China
| | - Haichao Zhao
- Department of General Surgery, Shanxi Bethune Hospital, No. 99 Longcheng Street, Xiaodian District, Taiyuan, 030032, Shanxi, China
| | - Haoliang Zhao
- Department of General Surgery, Shanxi Bethune Hospital, No. 99 Longcheng Street, Xiaodian District, Taiyuan, 030032, Shanxi, China.
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8
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Zhao K, Ye Z, Li Y, Li C, Yang X, Chen Q, Xing C. LncRNA FTX Contributes to the Progression of Colorectal Cancer Through Regulating miR-192-5p/EIF5A2 Axis. Onco Targets Ther 2020; 13:2677-2688. [PMID: 32280242 PMCID: PMC7127817 DOI: 10.2147/ott.s241011] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 02/29/2020] [Indexed: 12/11/2022] Open
Abstract
Background Long non-coding RAN five prime to Xist (LncRNA FTX) has been revealed to be a cancer-related lncRNA and implicated in the progression of colorectal cancer (CRC). Besides, miR-192-5p (miR-192) or eukaryotic initiation factor 5A2 (EIF5A2) also was identified to link with the tumorigenesis of CRC. Here, we further explored the function of FTX and the regulatory relationship among FTX, miR-192 and EIF5A2 in CRC progression. Methods Levels of FTX, miR-192-5p and EIF5A2 were detected by quantitative real-time polymerase chain reaction (qRT-PCR) or Western blot, respectively. Cell proliferation, apoptosis, migration and invasion were analyzed using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, flow cytometry or transwell assay, respectively. The interaction between miR-192-5p and FTX or EIF5A2 was confirmed by dual-luciferase reporter and pull-down assay. Murine xenograft model was established using LoVo cells transfected with sh-FTX. Results FTX was up-regulated in CRC tissues and cell lines, knockdown of FTX inhibited CRC cell proliferation, migration and invasion in vitro as well as suppressed CRC tumor growth in vivo. FTX was confirmed to directly bind to miR-192-5p and negatively regulated miR-192-5p expression in CRC cells. Besides that overexpressed FTX positively modulated EIF5A2, a direct target of miR-192-5p, via miR-192-5p in CRC cells. Importantly, the inhibitory activities on CRC progression mediated by FTX deletion were reversed miR-192-5p down-regulation or EIF5A2 up-regulation. Conclusion LncRNA FTX functioned as an oncogene to contribute to CRC progression by regulating miR-192-5p/EIF5A2 axis, providing a novel insight into the pathogenesis of CRC and a promising therapeutic target for CRC treatment.
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Affiliation(s)
- Kui Zhao
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Soochow University, Suzhou 215004, Jiangsu, People's Republic of China
| | - Zhenyu Ye
- Department of Hepatobiliary and Pancreatic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou 215004, Jiangsu, People's Republic of China
| | - Yecheng Li
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Soochow University, Suzhou 215004, Jiangsu, People's Republic of China
| | - Chunyan Li
- Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, Jiangsu, People's Republic of China
| | - Xiaodong Yang
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Soochow University, Suzhou 215004, Jiangsu, People's Republic of China
| | - Qiang Chen
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Soochow University, Suzhou 215004, Jiangsu, People's Republic of China
| | - Chungen Xing
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Soochow University, Suzhou 215004, Jiangsu, People's Republic of China
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Zhang H, Alsaleh G, Feltham J, Sun Y, Napolitano G, Riffelmacher T, Charles P, Frau L, Hublitz P, Yu Z, Mohammed S, Ballabio A, Balabanov S, Mellor J, Simon AK. Polyamines Control eIF5A Hypusination, TFEB Translation, and Autophagy to Reverse B Cell Senescence. Mol Cell 2019; 76:110-125.e9. [PMID: 31474573 PMCID: PMC6863385 DOI: 10.1016/j.molcel.2019.08.005] [Citation(s) in RCA: 183] [Impact Index Per Article: 36.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 04/30/2019] [Accepted: 08/02/2019] [Indexed: 02/08/2023]
Abstract
Failure to make adaptive immune responses is a hallmark of aging. Reduced B cell function leads to poor vaccination efficacy and a high prevalence of infections in the elderly. Here we show that reduced autophagy is a central molecular mechanism underlying immune senescence. Autophagy levels are specifically reduced in mature lymphocytes, leading to compromised memory B cell responses in old individuals. Spermidine, an endogenous polyamine metabolite, induces autophagy in vivo and rejuvenates memory B cell responses. Mechanistically, spermidine post-translationally modifies the translation factor eIF5A, which is essential for the synthesis of the autophagy transcription factor TFEB. Spermidine is depleted in the elderly, leading to reduced TFEB expression and autophagy. Spermidine supplementation restored this pathway and improved the responses of old human B cells. Taken together, our results reveal an unexpected autophagy regulatory mechanism mediated by eIF5A at the translational level, which can be harnessed to reverse immune senescence in humans.
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Affiliation(s)
- Hanlin Zhang
- The Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
| | - Ghada Alsaleh
- The Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
| | - Jack Feltham
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Yizhe Sun
- The Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
| | - Gennaro Napolitano
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy; Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Via Pansini 5, 80131, Naples, Italy
| | - Thomas Riffelmacher
- The Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
| | - Philip Charles
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK; Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Lisa Frau
- The Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK
| | - Philip Hublitz
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, OX3 9DS, UK
| | - Zhanru Yu
- Target Discovery Institute, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Shabaz Mohammed
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Andrea Ballabio
- Telethon Institute of Genetics and Medicine (TIGEM), Via Campi Flegrei 34, 80078, Pozzuoli, Naples, Italy; Medical Genetics Unit, Department of Medical and Translational Science, Federico II University, Via Pansini 5, 80131, Naples, Italy; Department of Molecular and Human Genetics and Neurological Research Institute, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stefan Balabanov
- Division of Haematology, University Hospital and University of Zürich, 8091, Zürich, Switzerland
| | - Jane Mellor
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Anna Katharina Simon
- The Kennedy Institute of Rheumatology, University of Oxford, Roosevelt Drive, Oxford, OX3 7FY, UK.
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10
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Golubev AA, Validov SZ, Usachev KS, Yusupov MM. Elongation Factor P: New Mechanisms of Function and an Evolutionary Diversity of Translation Regulation. Mol Biol 2019. [DOI: 10.1134/s0026893319040034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Structural dynamics of a spinlabeled ribosome elongation factor P (EF-P) from Staphylococcus aureus by EPR spectroscopy. SN APPLIED SCIENCES 2019. [DOI: 10.1007/s42452-019-0468-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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12
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Meneguello L, Barbosa NM, Pereira KD, Proença ARG, Tamborlin L, Simabuco FM, Iwai LK, Zanelli CF, Valentini SR, Luchessi AD. The polyproline-motif of S6K2: eIF5A translational dependence and importance for protein-protein interactions. J Cell Biochem 2019; 120:6015-6025. [PMID: 30320934 DOI: 10.1002/jcb.27888] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 09/20/2018] [Indexed: 12/18/2022]
Abstract
Ribosomal S6 kinase 1 (S6K1) and S6K2 proteins are effectors of the mammalian target of rapamycin complex 1 pathway, which control the process of protein synthesis in eukaryotes. S6K2 is associated with tumor progression and has a conserved C-terminus polyproline rich motif predicted to be important for S6K2 interactions. It is noteworthy that the translation of proteins containing sequential prolines has been proposed to be dependent of eukaryotic translation initiation factor 5A (eIF5A) translation factor. Therefore, we investigated the importance of polyproline-rich region of the S6K2 for its intrinsic phosphorylation activity, protein-protein interaction and eIF5A role in S6K2 translation. In HeLa cell line, replacing S6K2 polyproline by the homologous S6K1-sequence did not affect its kinase activity and the S6K2 endogenous content was maintained after eIF5A gene silencing, even after near complete depletion of eIF5A protein. Moreover, no changes in S6K2 transcript content was observed, ruling out the possibility of compensatory regulation by increasing the mRNA content. However, in the budding yeast model, we observed that S6K2 production was impaired when compared with S6K2∆Pro, after reduction of eIF5A protein content. These results suggest that although the polyproline region of S6K2 is capable of generating ribosomal stalling, the depletion of eIF5A in HeLa cells seems to be insufficient to cause an expressive decrease in the content of endogenous S6K2. Finally, coimmunoprecipitation assays revealed that the replacement of the polyproline motif of S6K2 alters its interactome and impairs its interaction with RPS6, a key modulator of ribosome activity. These results evidence the importance of S6K2 polyproline motif in the context of S6Ks function.
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Affiliation(s)
- Leticia Meneguello
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas (UNICAMP), Limeira, Brazil
- Institute of Biosciences, Department of Biology, São Paulo State University (UNESP), Rio Claro, Brazil
| | - Natália M Barbosa
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Brazil
| | - Karina D Pereira
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas (UNICAMP), Limeira, Brazil
- Institute of Biosciences, Department of Biology, São Paulo State University (UNESP), Rio Claro, Brazil
| | - André R G Proença
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas (UNICAMP), Limeira, Brazil
| | - Leticia Tamborlin
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas (UNICAMP), Limeira, Brazil
- Institute of Biosciences, Department of Biology, São Paulo State University (UNESP), Rio Claro, Brazil
| | - Fernando M Simabuco
- Laboratory of Functional Properties in Foods, School of Applied Sciences, University of Campinas (UNICAMP), Limeira, Brazil
| | - Leo K Iwai
- Special Laboratory of Applied Toxinology, Center of Toxins, Immune-Response and Cell Signaling, LETA/ CeTICS, Butantan Institute, Butanta, Brazil
| | - Cleslei F Zanelli
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Brazil
| | - Sandro R Valentini
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Brazil
| | - Augusto D Luchessi
- Laboratory of Biotechnology, School of Applied Sciences, University of Campinas (UNICAMP), Limeira, Brazil
- Institute of Biosciences, Department of Biology, São Paulo State University (UNESP), Rio Claro, Brazil
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13
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Park MH, Wolff EC. Hypusine, a polyamine-derived amino acid critical for eukaryotic translation. J Biol Chem 2018; 293:18710-18718. [PMID: 30257869 DOI: 10.1074/jbc.tm118.003341] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The natural amino acid hypusine (N ϵ-4-amino-2-hydroxybutyl(lysine)) is derived from the polyamine spermidine, and occurs only in a single family of cellular proteins, eukaryotic translation factor 5A (eIF5A) isoforms. Hypusine is formed by conjugation of the aminobutyl moiety of spermidine to a specific lysine residue of this protein. The posttranslational synthesis of hypusine involves two enzymatic steps, catalyzed by deoxyhypusine synthase (DHPS) and deoxyhypusine hydroxylase (DOHH). Hypusine is essential for eIF5A activity. Inactivation of either the eIF5A or the DHPS gene is lethal in yeast and mouse, underscoring the vital role of eIF5A hypusination in eukaryotic cell growth and animal development. The long and basic side chain of the hypusine residue promotes eIF5A-mediated translation elongation by facilitating peptide bond formation at polyproline stretches and at many other ribosome-pausing sites. It also enhances translation termination by stimulating peptide release. By promoting translation, the hypusine modification of eIF5A provides a key link between polyamines and cell growth regulation. eIF5A has been implicated in several human pathological conditions. Recent genetic data suggest that eIF5A haploinsufficiency or impaired deoxyhypusine synthase activity is associated with neurodevelopmental disorders in humans.
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Affiliation(s)
- Myung Hee Park
- From the NIDCR, National Institutes of Health, Bethesda, Maryland 20892
| | - Edith C Wolff
- From the NIDCR, National Institutes of Health, Bethesda, Maryland 20892
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14
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Bassani F, Romagnoli A, Cacciamani T, Amici A, Benelli D, Londei P, Märtens B, Bläsi U, La Teana A. Modification of translation factor aIF5A from Sulfolobus solfataricus. Extremophiles 2018; 22:769-780. [PMID: 30047030 PMCID: PMC6105217 DOI: 10.1007/s00792-018-1037-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/24/2018] [Indexed: 01/30/2023]
Abstract
Eukaryotic eIF5A and its bacterial orthologue EF-P are translation elongation factors whose task is to rescue ribosomes from stalling during the synthesis of proteins bearing particular sequences such as polyproline stretches. Both proteins are characterized by unique post-translational modifications, hypusination and lysinylation, respectively, which are essential for their function. An orthologue is present in all Archaea but its function is poorly understood. Here, we show that aIF5A of the crenarchaeum Sulfolobus solfataricus is hypusinated and forms a stable complex with deoxyhypusine synthase, the first enzyme of the hypusination pathway. The recombinant enzyme is able to modify its substrate in vitro resulting in deoxyhypusinated aIF5A. Moreover, with the aim to identify the enzyme involved in the second modification step, i.e. hypusination, a set of proteins interacting with aIF5A was identified.
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Affiliation(s)
- F Bassani
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - A Romagnoli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - T Cacciamani
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy.,New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy
| | - A Amici
- Department of Clinical Sciences, Section of Biochemistry, Polytechnic University of Marche, Via Ranieri 67, 60131, Ancona, Italy
| | - D Benelli
- Department of Cellular Biotechnologies and Haematology, Sapienza University of Rome, Via Regina Elena 324, 00161, Rome, Italy
| | - P Londei
- Department of Cellular Biotechnologies and Haematology, Sapienza University of Rome, Via Regina Elena 324, 00161, Rome, Italy
| | - B Märtens
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030, Vienna, Austria
| | - U Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030, Vienna, Austria
| | - A La Teana
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Via Brecce Bianche, 60131, Ancona, Italy.
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15
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The role of polyproline motifs in the histidine kinase EnvZ. PLoS One 2018; 13:e0199782. [PMID: 29953503 PMCID: PMC6023141 DOI: 10.1371/journal.pone.0199782] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 06/13/2018] [Indexed: 12/20/2022] Open
Abstract
Although distinct amino acid motifs containing consecutive prolines (polyP) cause ribosome stalling, which necessitates recruitment of the translation elongation factor P (EF-P), they occur strikingly often in bacterial proteomes. For example, polyP motifs are found in more than half of all histidine kinases in Escherichia coli K-12, which raises the question of their role(s) in receptor function. Here we have investigated the roles of two polyP motifs in the osmosensor and histidine kinase EnvZ. We show that the IPPPL motif in the HAMP domain is required for dimerization of EnvZ. Moreover, replacement of the prolines in this motif by alanines disables the receptor’s sensor function. The second motif, VVPPA, which is located in the periplasmic domain, was found to be required for interaction with the modulator protein MzrA. Our study also reveals that polyP-dependent stalling has little effect on EnvZ levels. Hence, both polyP motifs in EnvZ are primarily involved in protein-protein interaction. Furthermore, while the first motif occurs in almost all EnvZ homologues, the second motif is only found in species that have MzrA, indicating co-evolution of the two proteins.
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16
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Shirokikh NE, Preiss T. Translation initiation by cap-dependent ribosome recruitment: Recent insights and open questions. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1473. [PMID: 29624880 DOI: 10.1002/wrna.1473] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 02/02/2018] [Accepted: 02/14/2018] [Indexed: 12/14/2022]
Abstract
Gene expression universally relies on protein synthesis, where ribosomes recognize and decode the messenger RNA template by cycling through translation initiation, elongation, and termination phases. All aspects of translation have been studied for decades using the tools of biochemistry and molecular biology available at the time. Here, we focus on the mechanism of translation initiation in eukaryotes, which is remarkably more complex than prokaryotic initiation and is the target of multiple types of regulatory intervention. The "consensus" model, featuring cap-dependent ribosome entry and scanning of mRNA leader sequences, represents the predominantly utilized initiation pathway across eukaryotes, although several variations of the model and alternative initiation mechanisms are also known. Recent advances in structural biology techniques have enabled remarkable molecular-level insights into the functional states of eukaryotic ribosomes, including a range of ribosomal complexes with different combinations of translation initiation factors that are thought to represent bona fide intermediates of the initiation process. Similarly, high-throughput sequencing-based ribosome profiling or "footprinting" approaches have allowed much progress in understanding the elongation phase of translation, and variants of them are beginning to reveal the remaining mysteries of initiation, as well as aspects of translation termination and ribosomal recycling. A current view on the eukaryotic initiation mechanism is presented here with an emphasis on how recent structural and footprinting results underpin axioms of the consensus model. Along the way, we further outline some contested mechanistic issues and major open questions still to be addressed. This article is categorized under: Translation > Translation Mechanisms Translation > Translation Regulation RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Nikolay E Shirokikh
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
| | - Thomas Preiss
- EMBL-Australia Collaborating Group, Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
- Victor Chang Cardiac Research Institute, Darlinghurst, Australia
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17
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Fujimura K, Wang H, Watson F, Klemke RL. KRAS Oncoprotein Expression Is Regulated by a Self-Governing eIF5A-PEAK1 Feed-Forward Regulatory Loop. Cancer Res 2018; 78:1444-1456. [PMID: 29321164 PMCID: PMC5856625 DOI: 10.1158/0008-5472.can-17-2873] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/09/2017] [Accepted: 01/05/2018] [Indexed: 01/25/2023]
Abstract
There remains intense interest in tractable approaches to target or silence the KRAS oncoprotein as a rational therapeutic strategy to attack pancreatic ductal adenocarcinoma (PDAC) and other cancers that overexpress it. Here we provide evidence that accumulation of the KRAS oncoprotein is controlled by a self-regulating feed-forward regulatory loop that utilizes a unique hypusinated isoform of the translation elongation factor eIF5A and the tyrosine kinase PEAK1. Oncogenic activation of KRAS increased eIF5A-PEAK1 translational signaling, which in turn facilitated increased KRAS protein synthesis. Mechanistic investigations show that this feed-forward positive regulatory pathway was controlled by oncogenic KRAS-driven metabolic demands, operated independently of canonical mTOR signaling, and did not involve new KRAS gene transcription. Perturbing eIF5A-PEAK1 signaling, by genetic or pharmacologic strategies or by blocking glutamine synthesis, was sufficient to inhibit expression of KRAS, eIF5A, and PEAK1, to attenuate cancer cell growth and migration, and to block tumor formation in established preclinical mouse models of PDAC. Levels of KRAS, eIF5A, and PEAK1 protein increased during cancer progression with the highest levels of expression observed in metastatic cell populations. Combinatorial targeting of eIF5A hypusination and the RAS-ERK signaling pathway cooperated to attenuate KRAS expression and its downstream signaling along with cell growth in vitro and tumor formation in vivo Collectively, our findings highlight a new mechanistic strategy to attenuate KRAS expression as a therapeutic strategy to target PDAC and other human cancers driven by KRAS activation.Significance: These findings highlight a new mechanistic strategy to attenuate KRAS expression as a therapeutic strategy to target human cancers driven by KRAS activation. Cancer Res; 78(6); 1444-56. ©2018 AACR.
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Affiliation(s)
- Ken Fujimura
- Department of Pathology, University of California, San Diego, La Jolla, California
- Moores Cancer Center, University of California, San Diego, La Jolla, California
| | - Huawei Wang
- Department of Pathology, University of California, San Diego, La Jolla, California
- Moores Cancer Center, University of California, San Diego, La Jolla, California
| | - Felicia Watson
- Department of Pathology, University of California, San Diego, La Jolla, California
- Moores Cancer Center, University of California, San Diego, La Jolla, California
| | - Richard L Klemke
- Department of Pathology, University of California, San Diego, La Jolla, California.
- Moores Cancer Center, University of California, San Diego, La Jolla, California
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18
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Muthukumaran S, Bhuvanasundar R, Umashankar V, Sulochana KN. Insights on ornithine decarboxylase silencing as a potential strategy for targeting retinoblastoma. Biomed Pharmacother 2017; 98:23-28. [PMID: 29241071 DOI: 10.1016/j.biopha.2017.12.030] [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: 08/12/2017] [Revised: 11/27/2017] [Accepted: 12/07/2017] [Indexed: 01/26/2023] Open
Abstract
Ornithine Decarboxylase (ODC) is a key enzyme involved in polyamine synthesis and is reported to be up regulated in several cancers. However, the effect of ODC gene silencing in retinoblastoma is to be understood for utilization in therapeutic applications. Hence, in this study, a novel siRNA (small interference RNA) targeting ODC was designed and validated in Human Y79 retinoblastoma cells for its effects on intracellular polyamine levels, Matrix Metalloproteinase 2 & 9 activity and Cell cycle. The designed siRNA showed efficient silencing of ODC mRNA expression and protein levels in Y79 cells. It also showed significant reduction of intracellular polyamine levels and altered levels of oncogenic LIN28b expression. By this study, a regulatory loop is proposed, wherein, ODC silencing in Y79 cells to result in decreased polyamine levels, thereby, leading to altered protein levels of Lin28b, MMP-2 and MMP-9, which falls in line with earlier studies in neuroblastoma. Thus, by this study, we propose ODC silencing as a prospective strategy for targeting retinoblastoma.
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Affiliation(s)
- Sivashanmugam Muthukumaran
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, India; School of Chemical and Biotechnology, SASTRA University, Thanjavur, India
| | - Renganathan Bhuvanasundar
- R.S. Mehta Jain Department of Biochemistry and Cell Biology, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, India
| | - Vetrivel Umashankar
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, India.
| | - K N Sulochana
- R.S. Mehta Jain Department of Biochemistry and Cell Biology, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Chennai, India
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19
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Abstract
Polyamines are small, abundant, aliphatic molecules present in all mammalian cells. Within the context of the cell, they play a myriad of roles, from modulating nucleic acid conformation to promoting cellular proliferation and signaling. In addition, polyamines have emerged as important molecules in virus-host interactions. Many viruses have been shown to require polyamines for one or more aspects of their replication cycle, including DNA and RNA polymerization, nucleic acid packaging, and protein synthesis. Understanding the role of polyamines has become easier with the application of small-molecule inhibitors of polyamine synthesis and the use of interferon-induced regulators of polyamines. Here we review the diverse mechanisms in which viruses require polyamines and investigate blocking polyamine synthesis as a potential broad-spectrum antiviral approach.
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20
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Park MH, Mandal A, Mandal S, Wolff EC. A new non-radioactive deoxyhypusine synthase assay adaptable to high throughput screening. Amino Acids 2017; 49:1793-1804. [PMID: 28819816 DOI: 10.1007/s00726-017-2477-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 08/01/2017] [Indexed: 02/07/2023]
Abstract
Deoxyhypusine synthase (DHS) catalyzes the post-translational modification of eukaryotic translation factor 5A (eIF5A) by the polyamine, spermidine, that converts one specific lysine residue to deoxyhypusine [N ε -4-aminobutyl(lysine)], which is subsequently hydroxylated to hypusine [N ε -4-amino-2-hydroxybutyl(lysine)]. Hypusine synthesis represents the most critical function of polyamine. As eIF5A has been implicated in various human diseases, identification of specific inhibitors of hypusine modification is of vital importance. DHS catalyzes a complex reaction that occurs in two stages, first, the NAD-dependent cleavage of spermidine to form an enzyme-butylimine intermediate and enzyme-bound NADH, and second, the transfer of the butylimine moiety from the enzyme intermediate to the eIF5A precursor and subsequent reduction of the eIF5A-butylimine intermediate by enzyme-bound NADH to form deoxyhypusine [N ε -4-aminobutyl(lysine)]. Our data demonstrate that there is a measurable release of enzyme-bound NADH in the absence of eIF5A precursor and that the DHS activity can be determined by coupling the first phase reaction with the NADH-Glo assay in which the generation of luminescence is dependent on NADH derived from the DHS partial reaction. The conventional DHS assay that measures the incorporation of radioactivity from [1,8-3H]spermidine into the eIF5A precursor in the complete reaction cannot be readily adapted for high throughput screening (HTS). In contrast, the non-radioactive DHS/NADH-Glo coupled assay is highly specific, sensitive and reproducible and could be configured for HTS of small molecule libraries for the identification of new inhibitors of DHS. Furthermore, the coupled assay provides new insights into the dynamics of the DHS reaction especially regarding the fate of NADH.
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Affiliation(s)
- Myung Hee Park
- National Institute of Dental and Craniofacial Research (NIDCR), National Institutes of Health (NIH), Bethesda, MD, 20892-4340, USA.
| | - Ajeet Mandal
- National Institute of Dental and Craniofacial Research (NIDCR), National Institutes of Health (NIH), Bethesda, MD, 20892-4340, USA
| | - Swati Mandal
- National Institute of Dental and Craniofacial Research (NIDCR), National Institutes of Health (NIH), Bethesda, MD, 20892-4340, USA
| | - Edith C Wolff
- National Institute of Dental and Craniofacial Research (NIDCR), National Institutes of Health (NIH), Bethesda, MD, 20892-4340, USA
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21
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Olsen ME, Connor JH. Hypusination of eIF5A as a Target for Antiviral Therapy. DNA Cell Biol 2017; 36:198-201. [PMID: 28080131 PMCID: PMC5346904 DOI: 10.1089/dna.2016.3611] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 12/19/2016] [Indexed: 01/14/2023] Open
Affiliation(s)
- Michelle E Olsen
- Department of Microbiology, Boston University , Boston, Massachusetts
| | - John H Connor
- Department of Microbiology, Boston University , Boston, Massachusetts
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22
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Barbosa NM, Boldrin PEG, Rossi D, Yamamoto PA, Watanabe TF, Serrão VH, Hershey JWB, Fraser CS, Valentini SR, Zanelli CF. Mapping surface residues of eIF5A that are important for binding to the ribosome using alanine scanning mutagenesis. Amino Acids 2016; 48:2363-74. [PMID: 27388480 PMCID: PMC5897047 DOI: 10.1007/s00726-016-2279-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 06/11/2016] [Indexed: 01/15/2023]
Abstract
The translation elongation factor eIF5A is conserved through evolution and is necessary to rescue the ribosome during translation elongation of polyproline-containing proteins. Although the site of eIF5A binding to the ribosome is known, no systematic analysis has been performed so far to determine the important residues on the surface of eIF5A required for ribosome binding. In this study, we used clustered charged-to-alanine mutagenesis and structural modeling to address this question. We generated four new mutants of yeast eIF5A: tif51A-4, tif51A-6, tif51A-7 and tif51A-11, and complementation analysis revealed that tif51A-4 and tif51A-7 could not sustain cell growth in a strain lacking wild-type eIF5A. Moreover, the allele tif51A-4 also displayed negative dominance over wild-type eIF5A. Both in vivo GST-pulldowns and in vitro fluorescence anisotropy demonstrated that eIF5A from mutant tif51A-7 exhibited an importantly reduced affinity for the ribosome, implicating the charged residues in cluster 7 as determinant features on the eIF5A surface for contacting the ribosome. Notably, modified eIF5A from mutant tif51A-4, despite exhibiting the most severe growth phenotype, did not abolish ribosome interactions as with mutant tif51A-7. Taking into account the modeling eIF5A + 80S + P-tRNA complex, our data suggest that interactions of eIF5A with ribosomal protein L1 are more important to stabilize the interaction with the ribosome as a whole than the contacts with P-tRNA. Finally, the ability of eIF5A from tif51A-4 to bind to the ribosome while potentially blocking physical interaction with P-tRNA could explain its dominant negative phenotype.
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Affiliation(s)
- Natália M Barbosa
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University-UNESP, Rod Araraquara-Jaú Km01, Araraquara, SP, 14800-903, Brazil
| | - Paulo E G Boldrin
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University-UNESP, Rod Araraquara-Jaú Km01, Araraquara, SP, 14800-903, Brazil
| | - Danuza Rossi
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University-UNESP, Rod Araraquara-Jaú Km01, Araraquara, SP, 14800-903, Brazil
| | - Priscila A Yamamoto
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University-UNESP, Rod Araraquara-Jaú Km01, Araraquara, SP, 14800-903, Brazil
| | - Tatiana F Watanabe
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University-UNESP, Rod Araraquara-Jaú Km01, Araraquara, SP, 14800-903, Brazil
| | - Vitor H Serrão
- Physics and Interdisciplinary Science Department, Physics Institute of Sao Carlos, University of Sao Paulo-USP, Sao Carlos, SP, 13563-120, Brazil
| | - John W B Hershey
- Molecular and Cellular Biology Department, University of California, Davis, CA, 95616, USA
| | - Christopher S Fraser
- Molecular and Cellular Biology Department, University of California, Davis, CA, 95616, USA
| | - Sandro R Valentini
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University-UNESP, Rod Araraquara-Jaú Km01, Araraquara, SP, 14800-903, Brazil
| | - Cleslei F Zanelli
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University-UNESP, Rod Araraquara-Jaú Km01, Araraquara, SP, 14800-903, Brazil.
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23
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Cáceres CJ, Angulo J, Contreras N, Pino K, Vera-Otarola J, López-Lastra M. Targeting deoxyhypusine hydroxylase activity impairs cap-independent translation initiation driven by the 5'untranslated region of the HIV-1, HTLV-1, and MMTV mRNAs. Antiviral Res 2016; 134:192-206. [PMID: 27633452 DOI: 10.1016/j.antiviral.2016.09.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 09/12/2016] [Indexed: 12/14/2022]
Abstract
Replication of the human immunodeficiency virus type 1 (HIV-1) is dependent on eIF5A hypusination. Hypusine is formed post-translationally on the eIF5A precursor by two consecutive enzymatic steps; a reversible reaction involving the enzyme deoxyhypusine synthase (DHS) and an irreversible step involving the enzyme deoxyhypusine hydroxylase (DOHH). In this study we explored the effect of inhibiting DOHH activity and therefore eIF5A hypusination, on HIV-1 gene expression. Results show that the expression of proteins from an HIV-1 molecular clone is reduced when DOHH activity is inhibited by Deferiprone (DFP) or Ciclopirox (CPX). Next we evaluated the requirement of DOHH activity for internal ribosome entry site (IRES)-mediated translation initiation driven by the 5'untranslated region (5'UTR) of the full length HIV-1 mRNA. Results show that HIV-1 IRES activity relies on DOHH protein concentration and enzymatic activity. Similar results were obtained for IRES-dependent translation initiation mediated by 5'UTR of the human T-cell lymphotropic virus type 1 (HTLV-1) and the mouse mammary tumor virus (MMTV) mRNAs. Interestingly, activity of the poliovirus IRES, was less sensitive to the targeting of DOHH suggesting that not all viral IRESs are equally dependent on the cellular concentration or the activity of DOHH. In summary we present evidence indicating that the cellular concentration of DOHH and its enzymatic activity play a role in HIV-1, HTLV-1 and MMTV IRES-mediated translation initiation.
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Affiliation(s)
- C Joaquín Cáceres
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Jenniffer Angulo
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Nataly Contreras
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Karla Pino
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Jorge Vera-Otarola
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile
| | - Marcelo López-Lastra
- Laboratorio de Virología Molecular, Instituto Milenio de Inmunología e Inmunoterapia, Departamento de Enfermedades Infecciosas e Inmunología Pediátrica, Escuela de Medicina, Pontificia Universidad Católica de Chile, Marcoleta 391, Santiago, Chile.
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24
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Chu J, Cargnello M, Topisirovic I, Pelletier J. Translation Initiation Factors: Reprogramming Protein Synthesis in Cancer. Trends Cell Biol 2016; 26:918-933. [PMID: 27426745 DOI: 10.1016/j.tcb.2016.06.005] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 06/03/2016] [Accepted: 06/13/2016] [Indexed: 12/11/2022]
Abstract
Control of mRNA translation plays a crucial role in the regulation of gene expression and is critical for cellular homeostasis. Dysregulation of translation initiation factors has been documented in several pathologies including cancer. Aberrant function of translation initiation factors leads to translation reprogramming that promotes proliferation, survival, angiogenesis, and metastasis. In such context, understanding how altered levels (and presumably activity) of initiation factors can contribute to tumor initiation and/or maintenance is of major interest for the development of novel therapeutic strategies. In this review we provide an overview of translation initiation mechanisms and focus on recent findings describing the role of individual initiation factors and their aberrant activity in cancer.
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Affiliation(s)
- Jennifer Chu
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Marie Cargnello
- Lady Davis Institute, SMBD JGH, McGill University, Montreal, Quebec, Canada; Gerald Bronfman Department of Oncology, McGill University, Quebec, Canada
| | - Ivan Topisirovic
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada; Lady Davis Institute, SMBD JGH, McGill University, Montreal, Quebec, Canada; Gerald Bronfman Department of Oncology, McGill University, Quebec, Canada.
| | - Jerry Pelletier
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada; Gerald Bronfman Department of Oncology, McGill University, Quebec, Canada; The Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada.
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25
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The molecular choreography of protein synthesis: translational control, regulation, and pathways. Q Rev Biophys 2016; 49:e11. [PMID: 27658712 DOI: 10.1017/s0033583516000056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Translation of proteins by the ribosome regulates gene expression, with recent results underscoring the importance of translational control. Misregulation of translation underlies many diseases, including cancer and many genetic diseases. Decades of biochemical and structural studies have delineated many of the mechanistic details in prokaryotic translation, and sketched the outlines of eukaryotic translation. However, translation may not proceed linearly through a single mechanistic pathway, but likely involves multiple pathways and branchpoints. The stochastic nature of biological processes would allow different pathways to occur during translation that are biased by the interaction of the ribosome with other translation factors, with many of the steps kinetically controlled. These multiple pathways and branchpoints are potential regulatory nexus, allowing gene expression to be tuned at the translational level. As research focus shifts toward eukaryotic translation, certain themes will be echoed from studies on prokaryotic translation. This review provides a general overview of the dynamic data related to prokaryotic and eukaryotic translation, in particular recent findings with single-molecule methods, complemented by biochemical, kinetic, and structural findings. We will underscore the importance of viewing the process through the viewpoints of regulation, translational control, and heterogeneous pathways.
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26
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Katoh T, Wohlgemuth I, Nagano M, Rodnina MV, Suga H. Essential structural elements in tRNA(Pro) for EF-P-mediated alleviation of translation stalling. Nat Commun 2016; 7:11657. [PMID: 27216360 PMCID: PMC4890201 DOI: 10.1038/ncomms11657] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 04/18/2016] [Indexed: 12/23/2022] Open
Abstract
The ribosome stalls on translation of polyproline sequences due to inefficient peptide bond formation between consecutive prolines. The translation factor EF-P is able to alleviate this stalling by accelerating Pro-Pro formation. However, the mechanism by which EF-P recognizes the stalled complexes and accelerates peptide bond formation is not known. Here, we use genetic code reprogramming through a flexible in-vitro translation (FIT) system to investigate how mutations in tRNAPro affect EF-P function. We show that the 9-nt D-loop closed by the stable D-stem sequence in tRNAPro is a crucial recognition determinant for EF-P. Such D-arm structures are shared only among the tRNAPro isoacceptors and tRNAfMet in Escherichia coli, and the D-arm of tRNAfMet is essential for EF-P-induced acceleration of fMet–puromycin formation. Thus, the activity of EF-P is controlled by recognition elements in the tRNA D-arm. Ribosomes tend to stall during the translation of consecutive proline residues, which can be rescued by the co-translational factor EF-P. Here the authors identify a structural element of tRNAPro responsible for specific recognition by EF-P and stimulation of Pro-Pro peptide bond formation.
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Affiliation(s)
- Takayuki Katoh
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,JST, PRESTO, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Ingo Wohlgemuth
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Goettingen 37077, Germany
| | - Masanobu Nagano
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Goettingen 37077, Germany
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.,JST, CREST, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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27
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Mandal A, Mandal S, Park MH. Global quantitative proteomics reveal up-regulation of endoplasmic reticulum stress response proteins upon depletion of eIF5A in HeLa cells. Sci Rep 2016; 6:25795. [PMID: 27180817 PMCID: PMC4867578 DOI: 10.1038/srep25795] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/20/2016] [Indexed: 11/08/2022] Open
Abstract
The eukaryotic translation factor, eIF5A, is a translation factor essential for protein synthesis, cell growth and animal development. By use of a adenoviral eIF5A shRNA, we have achieved an effective depletion of eIF5A in HeLa cells and undertook in vivo comprehensive proteomic analyses to examine the effects of eIF5A depletion on the total proteome and to identify cellular pathways influenced by eIF5A. The proteome of HeLa cells transduced with eIF5A shRNA was compared with that of scramble shRNA-transduced counterpart by the iTRAQ method. We identified 972 proteins consistently detected in three iTRAQ experiments and 104 proteins with significantly altered levels (protein ratio ≥1.5 or ≤0.66, p-value ≤0.05) at 72 h and/or 96 h of Ad-eIF5A-shRNA transduction. The altered expression levels of key pathway proteins were validated by western blotting. Integration of functional ontology with expression data of the 104 proteins revealed specific biological processes that are prominently up- or down-regulated. Heatmap analysis and Cytoscape visualization of biological networks identified protein folding as the major cellular process affected by depletion of eIF5A. Our unbiased, quantitative, proteomic data demonstrate that the depletion of eIF5A leads to endoplasmic reticulum stress, an unfolded protein response and up-regulation of chaperone expression in HeLa cells.
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Affiliation(s)
- Ajeet Mandal
- Molecular and Cellular Biochemistry Section, Oral and Pharyngeal Cancer Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bldg.30 Rm. 3A300, Bethesda, MD 20892, USA
| | - Swati Mandal
- Molecular and Cellular Biochemistry Section, Oral and Pharyngeal Cancer Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bldg.30 Rm. 3A300, Bethesda, MD 20892, USA
| | - Myung Hee Park
- Molecular and Cellular Biochemistry Section, Oral and Pharyngeal Cancer Branch, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bldg.30 Rm. 3A300, Bethesda, MD 20892, USA
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28
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Rossi D, Barbosa NM, Galvão FC, Boldrin PEG, Hershey JWB, Zanelli CF, Fraser CS, Valentini SR. Evidence for a Negative Cooperativity between eIF5A and eEF2 on Binding to the Ribosome. PLoS One 2016; 11:e0154205. [PMID: 27115996 PMCID: PMC4845985 DOI: 10.1371/journal.pone.0154205] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/10/2016] [Indexed: 01/04/2023] Open
Abstract
eIF5A is the only protein known to contain the essential and unique amino acid residue hypusine. eIF5A functions in both translation initiation due to its stimulation of methionyl-puromycin synthesis and translation elongation, being highly required for peptide-bound formation of specific ribosome stalling sequences such as poly-proline. The functional interaction between eIF5A, tRNA, and eEF2 on the surface of the ribosome is further clarified herein. Fluorescence anisotropy assays were performed to determine the affinity of eIF5A to different ribosomal complexes and reveal its interaction exclusively and directly with the 60S ribosomal subunit in a hypusine-dependent manner (Ki60S-eIF5A-Hyp = 16 nM, Ki60S-eIF5A-Lys = 385 nM). A 3-fold increase in eIF5A affinity to the 80S is observed upon charged-tRNAiMet binding, indicating positive cooperativity between P-site tRNA binding and eIF5A binding to the ribosome. Previously identified conditional mutants of yeast eIF5A, eIF5AQ22H/L93F and eIF5AK56A, display a significant decrease in ribosome binding affinity. Binding affinity between ribosome and eIF5A-wild type or mutants eIF5AK56A, but not eIF5AQ22H/L93F, is impaired in the presence of eEF2 by 4-fold, consistent with negative cooperativity between eEF2 and eIF5A binding to the ribosome. Interestingly, high-copy eEF2 is toxic only to eIF5AQ22H/L93F and causes translation elongation defects in this mutant. These results suggest that binding of eEF2 to the ribosome alters its conformation, resulting in a weakened affinity of eIF5A and impairment of this interplay compromises cell growth due to translation elongation defects.
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Affiliation(s)
- Danuza Rossi
- School of Pharmaceutical Sciences, UNESP - Univ Estadual Paulista, Department of Biological Sciences, Araraquara, SP, Brazil, 14801
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA, United States of America, 95616
| | - Natalia M. Barbosa
- School of Pharmaceutical Sciences, UNESP - Univ Estadual Paulista, Department of Biological Sciences, Araraquara, SP, Brazil, 14801
| | - Fabio C. Galvão
- School of Pharmaceutical Sciences, UNESP - Univ Estadual Paulista, Department of Biological Sciences, Araraquara, SP, Brazil, 14801
| | - Paulo E. G. Boldrin
- School of Pharmaceutical Sciences, UNESP - Univ Estadual Paulista, Department of Biological Sciences, Araraquara, SP, Brazil, 14801
| | - John W. B. Hershey
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA, United States of America, 95616
| | - Cleslei F. Zanelli
- School of Pharmaceutical Sciences, UNESP - Univ Estadual Paulista, Department of Biological Sciences, Araraquara, SP, Brazil, 14801
| | - Christopher S. Fraser
- Department of Molecular and Cellular Biology, University of California Davis, Davis, CA, United States of America, 95616
| | - Sandro R. Valentini
- School of Pharmaceutical Sciences, UNESP - Univ Estadual Paulista, Department of Biological Sciences, Araraquara, SP, Brazil, 14801
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29
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Lee WB, Kang JS, Choi WY, Zhang Q, Kim CH, Choi UY, Kim-Ha J, Kim YJ. Mincle-mediated translational regulation is required for strong nitric oxide production and inflammation resolution. Nat Commun 2016; 7:11322. [PMID: 27089465 PMCID: PMC4837483 DOI: 10.1038/ncomms11322] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 03/14/2016] [Indexed: 12/21/2022] Open
Abstract
In response to persistent mycobacteria infection, the host induces a granuloma, which often fails to eradicate bacteria and results in tissue damage. Diverse host receptors are required to control the formation and resolution of granuloma, but little is known concerning their regulatory interactions. Here we show that Mincle, the inducible receptor for mycobacterial cord factor, is the key switch for the transition of macrophages from cytokine expression to high nitric oxide production. In addition to its stimulatory role on TLR-mediated transcription, Mincle enhanced the translation of key genes required for nitric oxide synthesis through p38 and eIF5A hypusination, leading to granuloma resolution. Thus, Mincle has dual functions in the promotion and subsequent resolution of inflammation during anti-mycobacterial defence using both transcriptional and translational controls.
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Affiliation(s)
- Wook-Bin Lee
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Ji-Seon Kang
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Won Young Choi
- Department of Integrated Omics for Biomedical Science, Graduate School, Yonsei University, Seoul 03722, Republic of Korea
| | - Quanri Zhang
- Department of Integrated Omics for Biomedical Science, Graduate School, Yonsei University, Seoul 03722, Republic of Korea
| | - Chul Han Kim
- Department of Integrated Omics for Biomedical Science, Graduate School, Yonsei University, Seoul 03722, Republic of Korea
| | - Un Yung Choi
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Jeongsil Kim-Ha
- Department of Integrative Bioscience and Biotechnology, College of Life Sciences, Sejong University, Seoul 05006, Republic of Korea
| | - Young-Joon Kim
- Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
- Department of Integrated Omics for Biomedical Science, Graduate School, Yonsei University, Seoul 03722, Republic of Korea
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30
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Lassak J, Wilson DN, Jung K. Stall no more at polyproline stretches with the translation elongation factors EF-P and IF-5A. Mol Microbiol 2015; 99:219-35. [PMID: 26416626 DOI: 10.1111/mmi.13233] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2015] [Indexed: 01/18/2023]
Abstract
Synthesis of polyproline proteins leads to translation arrest. To overcome this ribosome stalling effect, bacteria depend on a specialized translation elongation factor P (EF-P), being orthologous and functionally identical to eukaryotic/archaeal elongation factor e/aIF-5A (recently renamed 'EF5'). EF-P binds to the stalled ribosome between the peptidyl-tRNA binding and tRNA-exiting sites, and stimulates peptidyl-transferase activity, thus allowing translation to resume. In their active form, both EF-P and e/aIF-5A are post-translationally modified at a positively charged residue, which protrudes toward the peptidyl-transferase center when bound to the ribosome. While archaeal and eukaryotic IF-5A strictly depend on (deoxy-) hypusination (hypusinylation) of a conserved lysine, bacteria have evolved diverse analogous modification strategies to activate EF-P. In Escherichia coli and Salmonella enterica a lysine is extended by β-lysinylation and subsequently hydroxylated, whereas in Pseudomonas aeruginosa and Shewanella oneidensis an arginine in the equivalent position is rhamnosylated. Inactivation of EF-P, or the corresponding modification systems, reduces not only bacterial fitness, but also impairs virulence. Here, we review the function of EF-P and IF-5A and their unusual posttranslational protein modifications.
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Affiliation(s)
- Jürgen Lassak
- Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, D-81377, Munich, Germany.,Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, D-82152, Martinsried, Germany
| | - Daniel N Wilson
- Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, D-81377, Munich, Germany.,Gene Center, Department for Biochemistry, Ludwig-Maximilians-Universität München, 81377, Munich, Germany
| | - Kirsten Jung
- Center for Integrated Protein Science Munich, Ludwig-Maximilians-Universität München, D-81377, Munich, Germany.,Department of Biology I, Microbiology, Ludwig-Maximilians-Universität München, D-82152, Martinsried, Germany
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31
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Nguyen S, Leija C, Kinch L, Regmi S, Li Q, Grishin NV, Phillips MA. Deoxyhypusine Modification of Eukaryotic Translation Initiation Factor 5A (eIF5A) Is Essential for Trypanosoma brucei Growth and for Expression of Polyprolyl-containing Proteins. J Biol Chem 2015; 290:19987-98. [PMID: 26082486 PMCID: PMC4528157 DOI: 10.1074/jbc.m115.656785] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 05/18/2015] [Indexed: 11/06/2022] Open
Abstract
The eukaryotic protozoan parasite Trypanosoma brucei is the causative agent of human African trypanosomiasis. Polyamine biosynthesis is essential in T. brucei, and the polyamine spermidine is required for synthesis of a novel cofactor called trypanothione and for deoxyhypusine modification of eukaryotic translation initiation factor 5A (eIF5A). eIF5A promotes translation of proteins containing polyprolyl tracts in mammals and yeast. To evaluate the function of eIF5A in T. brucei, we used RNA interference (RNAi) to knock down eIF5A levels and found that it is essential for T. brucei growth. The RNAi-induced growth defect was complemented by expression of wild-type human eIF5A but not by a Lys-50 mutant that blocks modification by deoxyhypusine. Bioinformatics analysis showed that 15% of the T. brucei proteome contains 3 or more consecutive prolines and that actin-related proteins and cysteine proteases were highly enriched in the group. Steady-state protein levels of representative proteins containing 9 consecutive prolines that are involved in actin assembly (formin and CAP/Srv2p) were significantly reduced by knockdown of eIF5A. Several T. brucei polyprolyl proteins are involved in flagellar assembly. Knockdown of TbeIF5A led to abnormal cell morphologies and detached flagella, suggesting that eIF5A is important for translation of proteins needed for these processes. Potential specialized functions for eIF5A in T. brucei in translation of variable surface glycoproteins were also uncovered. Inhibitors of deoxyhypusination would be expected to cause a pleomorphic effect on multiple cell processes, suggesting that deoxyhypusine/hypusine biosynthesis could be a promising drug target in not just T. brucei but in other eukaryotic pathogens.
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MESH Headings
- Amino Acid Sequence
- Animals
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Flagella/genetics
- Flagella/metabolism
- Flagella/ultrastructure
- Gene Knockdown Techniques
- Humans
- Lysine/analogs & derivatives
- Lysine/metabolism
- Microfilament Proteins/genetics
- Microfilament Proteins/metabolism
- Molecular Sequence Data
- Peptide Initiation Factors/antagonists & inhibitors
- Peptide Initiation Factors/genetics
- Peptide Initiation Factors/metabolism
- Peptides/metabolism
- Protein Processing, Post-Translational
- Proteome/genetics
- Proteome/metabolism
- Protozoan Proteins/antagonists & inhibitors
- Protozoan Proteins/genetics
- Protozoan Proteins/metabolism
- RNA, Messenger/antagonists & inhibitors
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Protozoan/antagonists & inhibitors
- RNA, Protozoan/genetics
- RNA, Protozoan/metabolism
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- RNA-Binding Proteins/antagonists & inhibitors
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- Sequence Alignment
- Sequence Homology, Amino Acid
- Trypanosoma brucei brucei/genetics
- Trypanosoma brucei brucei/metabolism
- Trypanosoma brucei brucei/ultrastructure
- Eukaryotic Translation Initiation Factor 5A
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Affiliation(s)
| | | | | | | | - Qiong Li
- From the Departments of Pharmacology and
| | - Nick V Grishin
- Biophysics and Biochemistry and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9041
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32
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Mathews MB, Hershey JWB. The translation factor eIF5A and human cancer. BIOCHIMICA ET BIOPHYSICA ACTA 2015; 1849:836-44. [PMID: 25979826 PMCID: PMC4732523 DOI: 10.1016/j.bbagrm.2015.05.002] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 05/06/2015] [Indexed: 12/14/2022]
Abstract
The eukaryotic initiation factor eIF5A is a translation factor that, unusually, has been assigned functions in both initiation and elongation. Additionally, it is implicated in transcription, mRNA turnover and nucleocytoplasmic transport. Two eIF5A isoforms are generated from distinct but related genes. The major isoform, eIF5A1, is considered constitutive, is abundantly expressed in most cells, and is essential for cell proliferation. The second isoform, eIF5A2, is expressed in few normal tissues but is highly expressed in many cancers and has been designated a candidate oncogene. Elevated expression of either isoform carries unfavorable prognostic implications for several cancers, and both have been advanced as cancer biomarkers. The amino acid hypusine, a presumptively unique eIF5A post-translational modification, is required for most known eIF5A functions and it renders eIF5A susceptible to inhibitors of the modification pathway as therapeutic targets. eIF5A has been shown to regulate a number of gene products specifically, termed the eIF5A regulon, and its role in translating proline-rich sequences has recently been identified. A model is advanced that accommodates eIF5A in both the initiation and elongation phases of translation. We review here the biochemical functions of eIF5A, the relationship of its isoforms with human cancer, and evolving clinical applications. This article is part of a Special Issue entitled: Translation and Cancer.
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Affiliation(s)
- Michael B Mathews
- Department of Medicine, Rutgers New Jersey Medical School, Newark, NJ 07103, USA.
| | - John W B Hershey
- Department of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, Davis, CA 95616, USA.
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33
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Smircich P, Eastman G, Bispo S, Duhagon MA, Guerra-Slompo EP, Garat B, Goldenberg S, Munroe DJ, Dallagiovanna B, Holetz F, Sotelo-Silveira JR. Ribosome profiling reveals translation control as a key mechanism generating differential gene expression in Trypanosoma cruzi. BMC Genomics 2015; 16:443. [PMID: 26054634 PMCID: PMC4460968 DOI: 10.1186/s12864-015-1563-8] [Citation(s) in RCA: 95] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 04/22/2015] [Indexed: 12/02/2022] Open
Abstract
Background Due to the absence of transcription initiation regulation of protein coding genes transcribed by RNA polymerase II, posttranscriptional regulation is responsible for the majority of gene expression changes in trypanosomatids. Therefore, cataloging the abundance of mRNAs (transcriptome) and the level of their translation (translatome) is a key step to understand control of gene expression in these organisms. Results Here we assess the extent of regulation of the transcriptome and the translatome in the Chagas disease causing agent, Trypanosoma cruzi, in both the non-infective (epimastigote) and infective (metacyclic trypomastigote) insect’s life stages using RNA-seq and ribosome profiling. The observed steady state transcript levels support constitutive transcription and maturation implying the existence of distinctive posttranscriptional regulatory mechanisms controlling gene expression levels at those parasite stages. Meanwhile, the downregulation of a large proportion of the translatome indicates a key role of translation control in differentiation into the infective form. The previously described proteomic data correlate better with the translatomes than with the transcriptomes and translational efficiency analysis shows a wide dynamic range, reinforcing the importance of translatability as a regulatory step. Translation efficiencies for protein families like ribosomal components are diminished while translation of the transialidase virulence factors is upregulated in the quiescent infective metacyclic trypomastigote stage. Conclusions A large subset of genes is modulated at the translation level in two different stages of Trypanosoma cruzi life cycle. Translation upregulation of virulence factors and downregulation of ribosomal proteins indicates different degrees of control operating to prepare the parasite for an infective life form. Taking together our results show that translational regulation, in addition to regulation of steady state level of mRNA, is a major factor playing a role during the parasite differentiation. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1563-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Pablo Smircich
- Laboratory of Molecular Interactions, School of Sciences, Universidad de la República, Montevideo, Uruguay. .,Department of Genetics. School of Medicine, Universidad de la República, Montevideo, Uruguay.
| | - Guillermo Eastman
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia 3318, Montevideo, CP 11600, Uruguay.
| | - Saloe Bispo
- Laboratory of Gene Expression Regulation Studies Carlos Chagas Institute, FIOCRUZ, Curitiba, 81350-010, Brazil.
| | - María Ana Duhagon
- Laboratory of Molecular Interactions, School of Sciences, Universidad de la República, Montevideo, Uruguay. .,Department of Genetics. School of Medicine, Universidad de la República, Montevideo, Uruguay.
| | - Eloise P Guerra-Slompo
- Laboratory of Gene Expression Regulation Studies Carlos Chagas Institute, FIOCRUZ, Curitiba, 81350-010, Brazil.
| | - Beatriz Garat
- Laboratory of Molecular Interactions, School of Sciences, Universidad de la República, Montevideo, Uruguay.
| | - Samuel Goldenberg
- Laboratory of Gene Expression Regulation Studies Carlos Chagas Institute, FIOCRUZ, Curitiba, 81350-010, Brazil.
| | - David J Munroe
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.
| | - Bruno Dallagiovanna
- Laboratory of Gene Expression Regulation Studies Carlos Chagas Institute, FIOCRUZ, Curitiba, 81350-010, Brazil.
| | - Fabiola Holetz
- Laboratory of Gene Expression Regulation Studies Carlos Chagas Institute, FIOCRUZ, Curitiba, 81350-010, Brazil.
| | - Jose R Sotelo-Silveira
- Department of Genomics, Instituto de Investigaciones Biológicas Clemente Estable, Av. Italia 3318, Montevideo, CP 11600, Uruguay. .,Department of Cell and Molecular Biology, School of Sciences, Universidad de la Republica, Montevideo, Uruguay.
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Song A, Tom J, Yu Z, Pham V, Tan D, Zhang D, Fang G, Yu T, Deshayes K. Development of Orthogonally Protected Hypusine for Solid-Phase Peptide Synthesis. J Org Chem 2015; 80:3677-81. [DOI: 10.1021/acs.joc.5b00110] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aimin Song
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jeffrey Tom
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Zhiyong Yu
- International Discovery Service Unit, WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao
Free Trade Zone, Shanghai 200131, China
| | - Victoria Pham
- Department of Protein Chemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Dajin Tan
- International Discovery Service Unit, WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao
Free Trade Zone, Shanghai 200131, China
| | - Dengxiong Zhang
- International Discovery Service Unit, WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao
Free Trade Zone, Shanghai 200131, China
| | - Guoyong Fang
- Center for Peptide Service, WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao
Free Trade Zone, Shanghai 200131, China
| | - Tao Yu
- Center for Peptide Service, WuXi AppTec (Shanghai) Co., Ltd., 288 Fute Zhong Road, Waigaoqiao
Free Trade Zone, Shanghai 200131, China
| | - Kurt Deshayes
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
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Montenegro-Rodríguez C, Peirotén A, Sanchez-Jimenez A, Arqués JL, Landete JM. Analysis of gene expression of bifidobacteria using as the reporter an anaerobic fluorescent protein. Biotechnol Lett 2015; 37:1405-13. [DOI: 10.1007/s10529-015-1802-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 02/26/2015] [Indexed: 01/16/2023]
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Mandal A, Mandal S, Park MH. Genome-wide analyses and functional classification of proline repeat-rich proteins: potential role of eIF5A in eukaryotic evolution. PLoS One 2014; 9:e111800. [PMID: 25364902 PMCID: PMC4218817 DOI: 10.1371/journal.pone.0111800] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 10/06/2014] [Indexed: 12/16/2022] Open
Abstract
The eukaryotic translation factor, eIF5A has been recently reported as a sequence-specific elongation factor that facilitates peptide bond formation at consecutive prolines in Saccharomyces cerevisiae, as its ortholog elongation factor P (EF-P) does in bacteria. We have searched the genome databases of 35 representative organisms from six kingdoms of life for PPP (Pro-Pro-Pro) and/or PPG (Pro-Pro-Gly)-encoding genes whose expression is expected to depend on eIF5A. We have made detailed analyses of proteome data of 5 selected species, Escherichia coli, Saccharomyces cerevisiae, Drosophila melanogaster, Mus musculus and Homo sapiens. The PPP and PPG motifs are low in the prokaryotic proteomes. However, their frequencies markedly increase with the biological complexity of eukaryotic organisms, and are higher in newly derived proteins than in those orthologous proteins commonly shared in all species. Ontology classifications of S. cerevisiae and human genes encoding the highest level of polyprolines reveal their strong association with several specific biological processes, including actin/cytoskeletal associated functions, RNA splicing/turnover, DNA binding/transcription and cell signaling. Previously reported phenotypic defects in actin polarity and mRNA decay of eIF5A mutant strains are consistent with the proposed role for eIF5A in the translation of the polyproline-containing proteins. Of all the amino acid tandem repeats (≥3 amino acids), only the proline repeat frequency correlates with functional complexity of the five organisms examined. Taken together, these findings suggest the importance of proline repeat-rich proteins and a potential role for eIF5A and its hypusine modification pathway in the course of eukaryotic evolution.
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Affiliation(s)
- Ajeet Mandal
- Oral and Pharyngeal Cancer Branch, NIDCR, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Swati Mandal
- Oral and Pharyngeal Cancer Branch, NIDCR, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Myung Hee Park
- Oral and Pharyngeal Cancer Branch, NIDCR, National Institutes of Health, Bethesda, Maryland, United States of America
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Kobayashi K, Katz A, Rajkovic A, Ishii R, Branson OE, Freitas MA, Ishitani R, Ibba M, Nureki O. The non-canonical hydroxylase structure of YfcM reveals a metal ion-coordination motif required for EF-P hydroxylation. Nucleic Acids Res 2014; 42:12295-305. [PMID: 25274739 PMCID: PMC4231759 DOI: 10.1093/nar/gku898] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
EF-P is a bacterial tRNA-mimic protein, which accelerates the ribosome-catalyzed polymerization of poly-prolines. In Escherichia coli, EF-P is post-translationally modified on a conserved lysine residue. The post-translational modification is performed in a two-step reaction involving the addition of a β-lysine moiety and the subsequent hydroxylation, catalyzed by PoxA and YfcM, respectively. The β-lysine moiety was previously shown to enhance the rate of poly-proline synthesis, but the role of the hydroxylation is poorly understood. We solved the crystal structure of YfcM and performed functional analyses to determine the hydroxylation mechanism. In addition, YfcM appears to be structurally distinct from any other hydroxylase structures reported so far. The structure of YfcM is similar to that of the ribonuclease YbeY, even though they do not share sequence homology. Furthermore, YfcM has a metal ion-coordinating motif, similar to YbeY. The metal ion-coordinating motif of YfcM resembles a 2-His-1-carboxylate motif, which coordinates an Fe(II) ion and forms the catalytic site of non-heme iron enzymes. Our findings showed that the metal ion-coordinating motif of YfcM plays an essential role in the hydroxylation of the β-lysylated lysine residue of EF-P. Taken together, our results suggested the potential catalytic mechanism of hydroxylation by YfcM.
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Affiliation(s)
- Kan Kobayashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan Global Research Cluster, RIKEN, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Assaf Katz
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA
| | - Andrei Rajkovic
- Molecular, Cell, and Developmental Biology Program, Ohio State University, Columbus, OH 43210, USA
| | - Ryohei Ishii
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan Global Research Cluster, RIKEN, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Owen E Branson
- Department of Biochemistry, Ohio State University, Columbus, OH 43210, USA
| | - Michael A Freitas
- Comprehensive Cancer Center, Ohio State University, Columbus, OH 43210, USA Department of Molecular Virology, Immunology and Medical Genetics, Ohio State University, Columbus, OH 43210, USA
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan Global Research Cluster, RIKEN, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Michael Ibba
- Department of Microbiology, Ohio State University, Columbus, OH 43210, USA Ohio State Biochemistry Program, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan Global Research Cluster, RIKEN, 2-1, Hirosawa, Wako, Saitama, 351-0198, Japan
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EF-P dependent pauses integrate proximal and distal signals during translation. PLoS Genet 2014; 10:e1004553. [PMID: 25144653 PMCID: PMC4140641 DOI: 10.1371/journal.pgen.1004553] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 06/20/2014] [Indexed: 12/21/2022] Open
Abstract
Elongation factor P (EF-P) is required for the efficient synthesis of proteins with stretches of consecutive prolines and other motifs that would otherwise lead to ribosome pausing. However, previous reports also demonstrated that levels of most diprolyl-containing proteins are not altered by the deletion of efp. To define the particular sequences that trigger ribosome stalling at diprolyl (PPX) motifs, we used ribosome profiling to monitor global ribosome occupancy in Escherichia coli strains lacking EF-P. Only 2.8% of PPX motifs caused significant ribosomal pausing in the Δefp strain, with up to a 45-fold increase in ribosome density observed at the pausing site. The unexpectedly low fraction of PPX motifs that produce a pause in translation led us to investigate the possible role of sequences upstream of PPX. Our data indicate that EF-P dependent pauses are strongly affected by sequences upstream of the PPX pattern. We found that residues as far as 3 codons upstream of the ribosomal peptidyl-tRNA site had a dramatic effect on whether or not a particular PPX motif triggered a ribosomal pause, while internal Shine Dalgarno sequences upstream of the motif had no effect on EF-P dependent translation efficiency. Increased ribosome occupancy at particular stall sites did not reliably correlate with a decrease in total protein levels, suggesting that in many cases other factors compensate for the potentially deleterious effects of stalling on protein synthesis. These findings indicate that the ability of a given PPX motif to initiate an EF-P-alleviated stall is strongly influenced by its local context, and that other indirect post-transcriptional effects determine the influence of such stalls on protein levels within the cell. Elongation factor P (EF-P) is a well-conserved bacterial protein. Although it can enhance protein synthesis in vitro, it is generally regarded as an ancillary factor required for robust translation of transcripts with stretches of consecutive prolines. In this work we performed ribosome profiling to better understand the role of EF-P during translation. Our data confirmed that translational effects due to lack of EF-P are mainly confined to PPX–encoding genes. Wide variations in EF-P dependent translation of these PPXs led us to investigate the effect of sequences upstream of diproline-containing motifs. We found that amino acids encoded upstream of PPX play a key role in EF-P-dependent translation. Finally, comparison of ribosome profiling data to existing proteomic data indicates that although many PPX-containing patterns have increased ribosome occupancies, this does not necessarily lead to altered protein levels. Taken together these data show a direct role for EF-P during synthesis of PPX motifs, and indirect effects on other post-transcriptional regulators of gene expression.
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