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Akbudak MA, Cirik N, Erdeger SN, Filiz E, Dogu S, Bor M. GpEF1A: a novel lysine methyltransferase gene from Gypsophila perfoliata L. involved in boron homeostasis. PLANT BIOLOGY (STUTTGART, GERMANY) 2024; 26:727-734. [PMID: 38781082 DOI: 10.1111/plb.13658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 03/30/2024] [Indexed: 05/25/2024]
Abstract
Rapid accumulation of boron (B) leads to toxicity in plant tissues, and the narrow gap between deficiency and toxicity makes it difficult to adjust essential B levels in soil for plant productivity. Therefore, understanding different aspects of B tolerance is necessary to provide new and valid solutions to B toxicity. Gypsophila perfoliata stands out as a remarkable example of a B-tolerant plant, with a natural propensity to thrive in environments such as B mines and soils enriched with high levels of B. In this study, a yeast functional screening experiment was conducted using cDNA libraries from G. perfoliata leaf and root cells for B tolerance. Ten colonies from the leaf library grew in 80 mm boric acid, while none emerged from the root library. Analysis of isolated cDNAs showed identical sequences and a unique motif related to B tolerance. The gene GpEF1A was identified in the tolerant yeast colonies, with predicted structural features suggesting its role, and RT-qPCR indicating increased expression under B stress. A regulatory role for EF1A lysine methylation was proposed in mammalian cells and fungi because of its dynamic and inducible nature under environmental constraints. This could also be relevant for plant cells, as the high similarity of the GpEF1A gene in some salt-tolerant plants might indicate the upregulation of EF1A as a conserved way to cope with abiotic stress conditions. This report represents the first instance of involvement of GpEF1A in B tolerance, and further detailed studies are necessary to understand other components of this tolerance mechanism.
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Affiliation(s)
- M A Akbudak
- Department of Agricultural Biotechnology, Akdeniz University, Antalya, Türkiye
| | - N Cirik
- Department of Agricultural Biotechnology, Akdeniz University, Antalya, Türkiye
| | - S N Erdeger
- Department of Agricultural Biotechnology, Akdeniz University, Antalya, Türkiye
| | - E Filiz
- Cilimli Vocational School, Duzce University, Duzce, Türkiye
| | - S Dogu
- Meram Vocational School, Necmettin Erbakan University, Konya, Türkiye
| | - M Bor
- Department of Biology, Ege University, Izmir, Türkiye
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2
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Zhang W, Wang J, Shan C. The eEF1A protein in cancer: Clinical significance, oncogenic mechanisms, and targeted therapeutic strategies. Pharmacol Res 2024; 204:107195. [PMID: 38677532 DOI: 10.1016/j.phrs.2024.107195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/09/2024] [Accepted: 04/22/2024] [Indexed: 04/29/2024]
Abstract
Eukaryotic elongation factor 1A (eEF1A) is among the most abundant proteins in eukaryotic cells. Evolutionarily conserved across species, eEF1A is in charge of translation elongation for protein biosynthesis as well as a plethora of non-translational moonlighting functions for cellular homeostasis. In malignant cells, however, eEF1A becomes a pleiotropic driver of cancer progression via a broad diversity of pathways, which are not limited to hyperactive translational output. In the past decades, mounting studies have demonstrated the causal link between eEF1A and carcinogenesis, gaining deeper insights into its multifaceted mechanisms and corroborating its value as a prognostic marker in various cancers. On the other hand, an increasing number of natural and synthetic compounds were discovered as anticancer eEF1A-targeting inhibitors. Among them, plitidepsin was approved for the treatment of multiple myeloma whereas metarrestin was currently under clinical development. Despite significant achievements in these two interrelated fields, hitherto there lacks a systematic examination of the eEF1A protein in the context of cancer research. Therefore, the present work aims to delineate its clinical implications, molecular oncogenic mechanisms, and targeted therapeutic strategies as reflected in the ever expanding body of literature, so as to deepen mechanistic understanding of eEF1A-involved tumorigenesis and inspire the development of eEF1A-targeted chemotherapeutics and biologics.
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Affiliation(s)
- Weicheng Zhang
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, People's Republic of China.
| | - Jiyan Wang
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, People's Republic of China
| | - Changliang Shan
- The State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin, People's Republic of China.
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3
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Hamey JJ, Nguyen A, Haddad M, Vázquez-Campos X, Pfeiffer PG, Wilkins MR. Methylation of elongation factor 1A by yeast Efm4 or human eEF1A-KMT2 involves a beta-hairpin recognition motif and crosstalks with phosphorylation. J Biol Chem 2024; 300:105639. [PMID: 38199565 PMCID: PMC10844748 DOI: 10.1016/j.jbc.2024.105639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 12/13/2023] [Accepted: 01/01/2024] [Indexed: 01/12/2024] Open
Abstract
Translation elongation factor 1A (eEF1A) is an essential and highly conserved protein required for protein synthesis in eukaryotes. In both Saccharomyces cerevisiae and human, five different methyltransferases methylate specific residues on eEF1A, making eEF1A the eukaryotic protein targeted by the highest number of dedicated methyltransferases after histone H3. eEF1A methyltransferases are highly selective enzymes, only targeting eEF1A and each targeting just one or two specific residues in eEF1A. However, the mechanism of this selectivity remains poorly understood. To reveal how S. cerevisiae elongation factor methyltransferase 4 (Efm4) specifically methylates eEF1A at K316, we have used AlphaFold-Multimer modeling in combination with crosslinking mass spectrometry (XL-MS) and enzyme mutagenesis. We find that a unique beta-hairpin motif, which extends out from the core methyltransferase fold, is important for the methylation of eEF1A K316 in vitro. An alanine mutation of a single residue on this beta-hairpin, F212, significantly reduces Efm4 activity in vitro and in yeast cells. We show that the equivalent residue in human eEF1A-KMT2 (METTL10), F220, is also important for its activity towards eEF1A in vitro. We further show that the eEF1A guanine nucleotide exchange factor, eEF1Bα, inhibits Efm4 methylation of eEF1A in vitro, likely due to competitive binding. Lastly, we find that phosphorylation of eEF1A at S314 negatively crosstalks with Efm4-mediated methylation of K316. Our findings demonstrate how protein methyltransferases can be highly selective towards a single residue on a single protein in the cell.
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Affiliation(s)
- Joshua J Hamey
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, Australia.
| | - Amy Nguyen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, Australia
| | - Mahdi Haddad
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, Australia
| | - Xabier Vázquez-Campos
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, Australia
| | - Paige G Pfeiffer
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, New South Wales, Australia
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4
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Engelfriet ML, Małecki JM, Forsberg AF, Falnes PØ, Ciosk R. Characterization of the biochemical activity and tumor-promoting role of the dual protein methyltransferase METL-13/METTL13 in Caenorhabditis elegans. PLoS One 2023; 18:e0287558. [PMID: 37347777 PMCID: PMC10286969 DOI: 10.1371/journal.pone.0287558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/07/2023] [Indexed: 06/24/2023] Open
Abstract
The methyltransferase-like protein 13 (METTL13) methylates the eukaryotic elongation factor 1 alpha (eEF1A) on two locations: the N-terminal amino group and lysine 55. The absence of this methylation leads to reduced protein synthesis and cell proliferation in human cancer cells. Previous studies showed that METTL13 is dispensable in non-transformed cells, making it potentially interesting for cancer therapy. However, METTL13 has not been examined yet in whole animals. Here, we used the nematode Caenorhabditis elegans as a simple model to assess the functions of METTL13. Using methyltransferase assays and mass spectrometry, we show that the C. elegans METTL13 (METL-13) methylates eEF1A (EEF-1A) in the same way as the human protein. Crucially, the cancer-promoting role of METL-13 is also conserved and depends on the methylation of EEF-1A, like in human cells. At the same time, METL-13 appears dispensable for animal growth, development, and stress responses. This makes C. elegans a convenient whole-animal model for studying METL13-dependent carcinogenesis without the complications of interfering with essential wild-type functions.
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Affiliation(s)
- Melanie L. Engelfriet
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Jędrzej M. Małecki
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Anna F. Forsberg
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Pål Ø. Falnes
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - Rafal Ciosk
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
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5
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Hamey JJ, Wilkins MR. The protein methylation network in yeast: A landmark in completeness for a eukaryotic post-translational modification. Proc Natl Acad Sci U S A 2023; 120:e2215431120. [PMID: 37252976 PMCID: PMC10265986 DOI: 10.1073/pnas.2215431120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023] Open
Abstract
Defining all sites for a post-translational modification in the cell, and identifying their upstream modifying enzymes, is essential for a complete understanding of a modification's function. However, the complete mapping of a modification in the proteome and definition of its associated enzyme-substrate network is rarely achieved. Here, we present the protein methylation network for Saccharomyces cerevisiae. Through a formal process of defining and quantifying all potential sources of incompleteness, for both the methylation sites in the proteome and also protein methyltransferases, we prove that this protein methylation network is now near-complete. It contains 33 methylated proteins and 28 methyltransferases, comprising 44 enzyme-substrate relationships, and a predicted further three enzymes. While the precise molecular function of most methylation sites is unknown, and it remains possible that other sites and enzymes remain undiscovered, the completeness of this protein modification network is unprecedented and allows us to holistically explore the role and evolution of protein methylation in the eukaryotic cell. We show that while no single protein methylation event is essential in yeast, the vast majority of methylated proteins are themselves essential, being primarily involved in the core cellular processes of transcription, RNA processing, and translation. This suggests that protein methylation in lower eukaryotes exists to fine-tune proteins whose sequences are evolutionarily constrained, providing an improvement in the efficiency of their cognate processes. The approach described here, for the construction and evaluation of post-translational modification networks and their constituent enzymes and substrates, defines a formal process of utility for other post-translational modifications.
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Affiliation(s)
- Joshua J. Hamey
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW2052, Australia
| | - Marc R. Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW2052, Australia
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6
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Mealey-Farr R, Jeong J, Park J, Liu S, Hausmann S, Francis JW, Angulo Ibanez M, Cho J, Chua K, Mazur PK, Gozani O. Antibody toolkit to investigate eEF1A methylation dynamics in mRNA translation elongation. J Biol Chem 2023; 299:104747. [PMID: 37094697 PMCID: PMC10220242 DOI: 10.1016/j.jbc.2023.104747] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 04/26/2023] Open
Abstract
Protein synthesis is a fundamental step in gene expression, with modulation of mRNA translation at the elongation step emerging as an important regulatory node in shaping cellular proteomes. In this context, five distinct lysine methylation events on eukaryotic elongation factor 1A (eEF1A), a fundamental nonribosomal elongation factor, are proposed to influence mRNA translation elongation dynamics. However, a lack of affinity tools has hindered progress in fully understanding how eEF1A lysine methylation impacts protein synthesis. Here we develop and characterize a suite of selective antibodies to investigate eEF1A methylation and provide evidence that methylation levels decline in aged tissue. Determination of the methyl state and stoichiometry on eEF1A in various cell lines by mass spectrometry shows modest cell-to-cell variability. We also find by Western blot analysis that knockdown of individual eEF1A-specific lysine methyltransferases leads to depletion of the cognate lysine methylation event and indicates active crosstalk between different sites. Further, we find that the antibodies are specific in immunohistochemistry applications. Finally, application of the antibody toolkit suggests that several eEF1A methylation events decrease in aged muscle tissue. Together, our study provides a roadmap for leveraging methyl state and sequence-selective antibody reagents to accelerate discovery of eEF1A methylation-related functions and suggests a role for eEF1A methylation, via protein synthesis regulation, in aging biology.
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Affiliation(s)
| | - Jinho Jeong
- Department of Biology, Stanford University, Stanford, California, USA
| | - Juhyung Park
- Department of Biology, Stanford University, Stanford, California, USA
| | - Shuo Liu
- Department of Biology, Stanford University, Stanford, California, USA
| | - Simone Hausmann
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Joel W Francis
- Department of Biology, Stanford University, Stanford, California, USA
| | - Maria Angulo Ibanez
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA; Geriatric Research, Education, and Clinical Center, Veterans Affairs Palo Alto Health Care System, Palo Alto, California, USA
| | - Joonseok Cho
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA; Geriatric Research, Education, and Clinical Center, Veterans Affairs Palo Alto Health Care System, Palo Alto, California, USA
| | - Katrin Chua
- Department of Medicine, Stanford University School of Medicine, Stanford, California, USA; Geriatric Research, Education, and Clinical Center, Veterans Affairs Palo Alto Health Care System, Palo Alto, California, USA
| | - Pawel K Mazur
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, California, USA.
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7
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Liu J, Shao Y, Li D, Li C. N6-methyladenosine helps Apostichopus japonicus resist Vibrio splendidus infection by targeting coelomocyte autophagy via the AjULK-AjYTHDF/AjEEF-1α axis. Commun Biol 2023; 6:547. [PMID: 37210465 DOI: 10.1038/s42003-023-04929-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 05/11/2023] [Indexed: 05/22/2023] Open
Abstract
N6-Methyladenosine (m6A) modification is one of the most abundant post-transcriptional modifications that can mediate autophagy in various pathological processes. However, the functional role of m6A in autophagy regulation is not well-documented during Vibrio splendidus infection of Apostichopus japonicus. In this study, the inhibition of m6A level by knockdown of methyltransferase-like 3 (AjMETTL3) significantly decreased V. splendidus-induced coelomocyte autophagy and led to an increase in the intracellular V. splendidus burden. In this condition, Unc-51-like kinase 1 (AjULK) displayed the highest differential expression of m6A level. Moreover, knockdown of AjULK can reverse the V. splendidus-mediated autophagy in the condition of AjMETTL3 overexpression. Furthermore, knockdown of AjMETTL3 did not change the AjULK mRNA transcript levels but instead decreased protein levels. Additionally, YTH domain-containing family protein (AjYTHDF) was identified as a reader protein of AjULK and promoted AjULK expression in an m6A-dependent manner. Furthermore, the AjYTHDF-mediated AjULK expression depended on its interaction with translation elongation factor 1-alpha (AjEEF-1α). Altogether, our findings suggest that m6A is involved in resisting V. splendidus infection via facilitating coelomocyte autophagy in AjULK-AjYTHDF/AjEEF-1α-dependent manner, which provides a theoretical basis for disease prevention and therapy in A. japonicus.
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Affiliation(s)
- Jiqing Liu
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, P. R. China
| | - Yina Shao
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, P. R. China
| | - Dongdong Li
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, P. R. China
| | - Chenghua Li
- State Key Laboratory for Quality and Safety of Agro-products, Ningbo University, Ningbo, P. R. China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, P. R. China.
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Negrutskii B, Shalak V, Novosylna O, Porubleva L, Lozhko D, El'skaya A. The eEF1 family of mammalian translation elongation factors. BBA ADVANCES 2022; 3:100067. [PMID: 37082266 PMCID: PMC10074971 DOI: 10.1016/j.bbadva.2022.100067] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 12/03/2022] Open
Abstract
The eEF1 family of mammalian translation elongation factors is comprised of the two variants of eEF1A (eEF1A1 and eEF1A2), and the eEF1B complex. The latter consists of eEF1Bα, eEF1Bβ, and eEF1Bγ subunits. The two eEF1A variants have similar translation activity but may differ with respect to their secondary, "moonlighting" functions. This variability is underlined by the difference in the spatial organization of eEF1A1 and eEF1A2, and also possibly by the differences in their post-translational modifications. Here, we review the data on the spatial organization and post-translation modifications of eEF1A1 and eEF1A2, and provide examples of their involvement in various processes in addition to translation. We also describe the structural models of eEF1B subunits, their organization in the subcomplexes, and the trimeric model of the entire eEF1B complex. We discuss the functional consequences of such an assembly into a complex as well as the involvement of individual subunits in non-translational processes.
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Affiliation(s)
- B.S. Negrutskii
- Institute of Molecular Biology and Genetics, Acad. Zabolotnogo Str. 150, 03143 Kyiv, Ukraine
- Aarhus Institute of Advanced Sciences, Høegh-Guldbergs Gade 6B, DK–8000 Aarhus C, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, DK-8000 Aarhus C, Denmark
| | - V.F. Shalak
- Institute of Molecular Biology and Genetics, Acad. Zabolotnogo Str. 150, 03143 Kyiv, Ukraine
| | - O.V. Novosylna
- Institute of Molecular Biology and Genetics, Acad. Zabolotnogo Str. 150, 03143 Kyiv, Ukraine
| | - L.V. Porubleva
- Institute of Molecular Biology and Genetics, Acad. Zabolotnogo Str. 150, 03143 Kyiv, Ukraine
| | - D.M. Lozhko
- Institute of Molecular Biology and Genetics, Acad. Zabolotnogo Str. 150, 03143 Kyiv, Ukraine
| | - A.V. El'skaya
- Institute of Molecular Biology and Genetics, Acad. Zabolotnogo Str. 150, 03143 Kyiv, Ukraine
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Jiang H, Zhang Y, Liu B, Yang X, Wang Z, Han M, Li H, Luo J, Yao H. Dynamic regulation of eEF1A1 acetylation affects colorectal carcinogenesis. Biol Chem 2022; 404:585-599. [PMID: 36420535 DOI: 10.1515/hsz-2022-0180] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 11/07/2022] [Indexed: 11/25/2022]
Abstract
Abstract
The dysregulation of the translation elongation factor families which are responsible for reprogramming of mRNA translation has been shown to contribute to tumor progression. Here, we report that the acetylation of eukaryotic Elongation Factor 1 Alpha 1 (eEF1A1/EF1A1) is required for genotoxic stress response and maintaining the malignancy of colorectal cancer (CRC) cells. The evolutionarily conserved site K439 is identified as the key acetylation site. Tissue expression analysis demonstrates that the acetylation level of eEF1A1 K439 is higher than paired normal tissues. Most importantly, hyperacetylation of eEF1A1 at K439 negatively correlates with CRC patient survival. Mechanistically, CBP and SIRT1 are the major acetyltransferase and deacetylase of eEF1A1. Hyperacetylation of eEF1A1 at K439 shows a significant tumor-promoting effect by increasing the capacity of proliferation, migration, and invasion of CRC cells. Our findings identify the altered post-translational modification at the translation machines as a critical factor in stress response and susceptibility to colorectal carcinogenesis.
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Affiliation(s)
- Hongpeng Jiang
- Department of General Surgery, Beijing Friendship Hospital , Capital Medical University; Beijing Key Laboratory of Cancer Invasion and Metastasis Research and National Clinical Research Center for Digestive Diseases , 95 Yong-an Road, Xi-Cheng District , Beijing 100050 , P.R. China
| | - Yu Zhang
- Department of Medical Genetics, Center for Medical Genetics , Peking University Health Science Center , Beijing 100191 , P.R. China
| | - Boya Liu
- Department of Medical Genetics, Center for Medical Genetics , Peking University Health Science Center , Beijing 100191 , P.R. China
| | - Xin Yang
- Department of Medical Genetics, Center for Medical Genetics , Peking University Health Science Center , Beijing 100191 , P.R. China
| | - Zhe Wang
- Department of Medical Genetics, Center for Medical Genetics , Peking University Health Science Center , Beijing 100191 , P.R. China
| | - Meng Han
- MOE Key Laboratory of Bioinformatics, School of Life Sciences , Tsinghua University , Beijing 100084 , P.R. China
- College of Biological Sciences and Technology , Beijing Key Laboratory of Food Processing and Safety in Forest, Beijing Forestry University , Beijing 100083 , P.R. China
| | - Huiying Li
- College of Biological Sciences and Technology , Beijing Key Laboratory of Food Processing and Safety in Forest, Beijing Forestry University , Beijing 100083 , P.R. China
| | - Jianyuan Luo
- Department of Medical Genetics, Center for Medical Genetics , Peking University Health Science Center , Beijing 100191 , P.R. China
| | - Hongwei Yao
- Department of General Surgery, Beijing Friendship Hospital , Capital Medical University; Beijing Key Laboratory of Cancer Invasion and Metastasis Research and National Clinical Research Center for Digestive Diseases , 95 Yong-an Road, Xi-Cheng District , Beijing 100050 , P.R. China
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10
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Hapke R, Venton L, Rose KL, Sheng Q, Reddy A, Prather R, Jones A, Rathmell WK, Haake SM. SETD2 regulates the methylation of translation elongation factor eEF1A1 in clear cell renal cell carcinoma. KIDNEY CANCER JOURNAL : OFFICIAL JOURNAL OF THE KIDNEY CANCER ASSOCIATION 2022; 6:179-193. [PMID: 36684483 PMCID: PMC9851421 DOI: 10.3233/kca-220009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND SET domain-containing protein 2 (SETD2) is commonly mutated in renal cell carcinoma. SETD2 methylates histone H3 as well as a growing list of non-histone proteins. OBJECTIVE Initially, we sought to explore SETD2-dependent changes in lysine methylation of proteins in proximal renal tubule cells. Subsequently, we focused on changes in lysine methylation of the translation elongation factor eEF1A1. METHODS To accomplish these objectives, we initially performed a systems-wide analysis of protein lysine-methylation and expression in wild type (WT) and SETD2-knock out (KO) kidney cells and later focused our studies on eEF1A1 as well as the expression of lysine methyltransferases that regulate its lysine methylation. RESULTS We observed decreased lysine methylation of the translation elongation factor eEF1A1. EEF1AKMT2 and EEF1AKMT3 are known to methylate eEF1A1, and we show here that their expression is dependent on SET-domain function of SETD2. Globally, we observe differential expression of hundreds of proteins in WT versus SETD2-KO cells, including increased expression of many involved in protein translation. Finally, we observe decreased progression free survival and loss of EEF1AKMT2 gene expression in SETD2-mutated tumors predicted to have loss of function of the SET domain. CONCLUSION Overall, these data suggest that SETD2-mutated ccRCC, via loss of enzymatic function of the SET domain, displays dysregulation of protein translation as a potentially important component of the transformed phenotype.
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Affiliation(s)
- Robert Hapke
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Lindsay Venton
- Department of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kristie Lindsay Rose
- Mass Spectrometry Research Center, Proteomics Core Laboratory, Vanderbilt University, Nashville, TN, USA
| | - Quanhu Sheng
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Rebecca Prather
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Angela Jones
- Vanderbilt Technologies for Advanced Genomics (VANTAGE), Vanderbilt University Medical Center, Nashville, TN, USA
| | - W. Kimryn Rathmell
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Scott M. Haake
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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11
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Zhang Y, Wei J, Zhou H, Li B, Chen Y, Qian F, Liu J, Xie X, Xu H. Identification of two potential immune-related biomarkers of Graves' disease based on integrated bioinformatics analyses. Endocrine 2022; 78:306-314. [PMID: 35962894 DOI: 10.1007/s12020-022-03156-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/27/2022] [Indexed: 11/24/2022]
Abstract
BACKGROUND Graves' disease (GD) is an autoimmune disease, the incidence of which is increasing yearly. GD requires long-life therapy. Therefore, the potential immune-related biomarkers of GD need to be studied. METHOD In our study, differentially expressed genes (DEGs) were derived from the online Gene Expression Omnibus (GEO) microarray expression dataset GSE71956. Protein‒protein interaction (PPI) network analyses were used to identify hub genes, which were validated by qPCR. GSEA was used to screen potential pathways and related immune cells. Next, CIBERSORT analysis was used to further explore the immune subtype distribution pattern among hub genes. ROC curves were used to analyze the specificity and sensitivity of hub genes. RESULT 44 DEGs were screened from the GEO dataset. Two hub genes, EEF1A1 and EIF4B, were obtained from the PPI network and validated by qPCR (p < 0.05). GSEA was conducted to identify potential pathways and immune cells related to these the two hub genes. Immune cell subtype analysis revealed that hub genes had extensive associations with many different types of immune cells, particularly resting memory CD4+ T cells. AUCs of ROC analysis were 0.687 and 0.733 for EEF1A1 and EIF4B, respectively. CONCLUSION Our study revealed two hub genes, EEF1A1 and EIF4B, that are associated with resting memory CD4+ T cells and potential immune-related molecular biomarkers and therapeutic targets of GD.
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Affiliation(s)
- Yihan Zhang
- Department of Endocrinology and Metabolism, Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 100 Haining Road, Shanghai, 200080, China
| | - Jia Wei
- Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Hong Zhou
- Department of Endocrinology and Metabolism, Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 100 Haining Road, Shanghai, 200080, China
| | - Bingxin Li
- Department of Endocrinology and Metabolism, Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 100 Haining Road, Shanghai, 200080, China
| | - Ying Chen
- Department of Endocrinology and Metabolism, Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 100 Haining Road, Shanghai, 200080, China
| | - Feng Qian
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jingting Liu
- Engineering Research Center of Cell and Therapeutic Antibody, Ministry of Education, School of Pharmacy, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xin Xie
- Department of Endocrinology and Metabolism, Shanghai Traditional Chinese and Medicine Integrated Hospital, 18 Baoding Road, Hongkou District, Shanghai, 200080, China.
| | - Huanbai Xu
- Department of Endocrinology and Metabolism, Center for Microbiota and Immunological Diseases, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 100 Haining Road, Shanghai, 200080, China.
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12
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Kooverjee BB, Soma P, Van Der Nest MA, Scholtz MM, Neser FWC. Selection Signatures in South African Nguni and Bonsmara Cattle Populations Reveal Genes Relating to Environmental Adaptation. Front Genet 2022; 13:909012. [PMID: 35783284 PMCID: PMC9247466 DOI: 10.3389/fgene.2022.909012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022] Open
Abstract
Climate change is a major influencing factor in beef production. The greenhouse gases produced from livestock production systems contribute to the overall greenhouse gas emissions. The aim of this study was to identify selection signatures within and between Nguni and Bonsmara cattle in relation to production and adaptation. For this purpose, genomic 150 K single nucleotide polymorphism data from Nguni (n = 231) and Bonsmara (n = 252) cattle in South Africa were used. Extended haplotype homozygosity (EHH) based analysis was executed within each population using integrated haplotype score (iHS). The R package rehh was used for detecting selection signatures across the two populations with cross population EHH (XP-EHH). Total of 121 regions of selection signatures were detected (p < 0.0001) in the Bonsmara and Nguni populations. Several genes relating to DNA methylation, heat stress, feed efficiency and nitrogen metabolism were detected within and between each population. These regions also included QTLs associated with residual feed intake, residual gain, carcass weight, stature and body weight in the Bonsmara, while QTLs associated with conception rate, shear force, tenderness score, juiciness, temperament, heat tolerance, feed efficiency and age at puberty were identified in Nguni. Based on the results of the study it is recommended that the Nguni and Bonsmara be utilized in crossbreeding programs as they have beneficial traits that may allow them to perform better in the presence of climate change. Results of this study coincide with Nguni and Bonsmara breed characteristics and performance, and furthermore support informative crossbreeding programs to enhance livestock productivity in South Africa.
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Affiliation(s)
- Bhaveni B. Kooverjee
- Department of Animal Breeding and Genetics, Animal Production, Agricultural Research Council, Pretoria, South Africa
- Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
- *Correspondence: Bhaveni B. Kooverjee, ; Pranisha Soma,
| | - Pranisha Soma
- Department of Animal Breeding and Genetics, Animal Production, Agricultural Research Council, Pretoria, South Africa
- *Correspondence: Bhaveni B. Kooverjee, ; Pranisha Soma,
| | | | - Michiel M. Scholtz
- Department of Animal Breeding and Genetics, Animal Production, Agricultural Research Council, Pretoria, South Africa
- Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
| | - Frederick W. C. Neser
- Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
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13
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Alam M, Shima H, Matsuo Y, Long NC, Matsumoto M, Ishii Y, Sato N, Sugiyama T, Nobuta R, Hashimoto S, Liu L, Kaneko MK, Kato Y, Inada T, Igarashi K. mTORC1-independent translation control in mammalian cells by methionine adenosyltransferase 2A and S-adenosylmethionine. J Biol Chem 2022; 298:102084. [PMID: 35636512 PMCID: PMC9243181 DOI: 10.1016/j.jbc.2022.102084] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 11/21/2022] Open
Abstract
Methionine adenosyltransferase (MAT) catalyzes the synthesis of S-adenosylmethionine (SAM). As the sole methyl-donor for methylation of DNA, RNA, and proteins, SAM levels affect gene expression by changing methylation patterns. Expression of MAT2A, the catalytic subunit of isozyme MAT2, is positively correlated with proliferation of cancer cells; however, how MAT2A promotes cell proliferation is largely unknown. Given that the protein synthesis is induced in proliferating cells and that RNA and protein components of translation machinery are methylated, we tested here whether MAT2 and SAM are coupled with protein synthesis. By measuring ongoing protein translation via puromycin labeling, we revealed that MAT2A depletion or chemical inhibition reduced protein synthesis in HeLa and Hepa1 cells. Furthermore, overexpression of MAT2A enhanced protein synthesis, indicating that SAM is limiting under normal culture conditions. In addition, MAT2 inhibition did not accompany reduction in mechanistic target of rapamycin complex 1 activity but nevertheless reduced polysome formation. Polysome-bound RNA sequencing revealed that MAT2 inhibition decreased translation efficiency of some fraction of mRNAs. MAT2A was also found to interact with the proteins involved in rRNA processing and ribosome biogenesis; depletion or inhibition of MAT2 reduced 18S rRNA processing. Finally, quantitative mass spectrometry revealed that some translation factors were dynamically methylated in response to the activity of MAT2A. These observations suggest that cells possess an mTOR-independent regulatory mechanism that tunes translation in response to the levels of SAM. Such a system may acclimate cells for survival when SAM synthesis is reduced, whereas it may support proliferation when SAM is sufficient.
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Affiliation(s)
- Mahabub Alam
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan; Department of Animal Science and Nutrition, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Chattogram, Bangladesh
| | - Hiroki Shima
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yoshitaka Matsuo
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Nguyen Chi Long
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mitsuyo Matsumoto
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yusho Ishii
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Nichika Sato
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Takato Sugiyama
- Laboratory of Gene Regulation, Department of Molecular Biopharmacy and Genetics, Tohoku University Graduate School of Pharmaceutical Science, Sendai, Japan
| | - Risa Nobuta
- Laboratory of Gene Regulation, Department of Molecular Biopharmacy and Genetics, Tohoku University Graduate School of Pharmaceutical Science, Sendai, Japan
| | - Satoshi Hashimoto
- Laboratory of Gene Regulation, Department of Molecular Biopharmacy and Genetics, Tohoku University Graduate School of Pharmaceutical Science, Sendai, Japan
| | - Liang Liu
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mika K Kaneko
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Yukinari Kato
- Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, Sendai, Japan; Department of Molecular Pharmacology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Toshifumi Inada
- Division of RNA and Gene Regulation, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.
| | - Kazuhiko Igarashi
- Department of Biochemistry, Tohoku University Graduate School of Medicine, Sendai, Japan.
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14
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Lu J, Guo Y, Muhmood A, Zeng B, Qiu Y, Wang P, Ren L. Probing the antioxidant activity of functional proteins and bioactive peptides in Hermetia illucens larvae fed with food wastes. Sci Rep 2022; 12:2799. [PMID: 35181682 PMCID: PMC8857240 DOI: 10.1038/s41598-022-06668-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 01/27/2022] [Indexed: 11/09/2022] Open
Abstract
Food waste is becoming more prevalent, and managing it is one of the most important issues in terms of food safety. In this study, functional proteins and bioactive peptides produced from the enzymatic digestion of black soldier fly (Hermetia illucens L., BSF) fed with food wastes were characterized and quantified using proteomics-based analysis. The results revealed approximately 78 peptides and 57 proteins, including 40S ribosomal protein S4, 60S ribosomal protein L8, ATP synthase subunit alpha, ribosomal protein S3, Histone H2A, NADP-glutamate dehydrogenase, Fumarate hydratase, RNA helicase, Chitin binding Peritrophin-A, Lectin C-type protein, etc. were found in BSF. Furthermore, functional analysis of the proteins revealed that the 60S ribosomal protein L5 (RpL5) in BSF interacted with a variety of ribosomal proteins and played a key role in the glycolytic process (AT14039p). Higher antioxidant activity was found in peptide sequences such as GYGFGGGAGCLSMDTGAHLNR, VVPSANRAMVGIVAGGGRIDKPILK, AGLQFPVGR, GFKDQIQDVFK, and GFKDQIQDVFK. It was concluded that the bioconversion of food wastes by BSF brought about the generation of a variety of functional proteins and bioactive peptides with strong antioxidant activity. However, more studies are required to exploit BSF's potential in the value addition of food wastes.
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Affiliation(s)
- Jiaxin Lu
- School of Ecology and Environment, Beijing Technology and Business University, Beijing, 100048, China.,State Environmental Protection Key Laboratory of Food Chain Pollution Control, Beijing Technology and Business University, Beijing, 100048, China.,Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, Beijing Technology and Business University, Beijing, 100048, China
| | - Yuwen Guo
- School of Ecology and Environment, Beijing Technology and Business University, Beijing, 100048, China
| | - Atif Muhmood
- Institute of Soil Chemistry and Environmental Sciences, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Bei Zeng
- School of Ecology and Environment, Beijing Technology and Business University, Beijing, 100048, China
| | - Yizhan Qiu
- School of Ecology and Environment, Beijing Technology and Business University, Beijing, 100048, China
| | - Pan Wang
- School of Ecology and Environment, Beijing Technology and Business University, Beijing, 100048, China. .,State Environmental Protection Key Laboratory of Food Chain Pollution Control, Beijing Technology and Business University, Beijing, 100048, China. .,Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, Beijing Technology and Business University, Beijing, 100048, China.
| | - Lianhai Ren
- School of Ecology and Environment, Beijing Technology and Business University, Beijing, 100048, China. .,State Environmental Protection Key Laboratory of Food Chain Pollution Control, Beijing Technology and Business University, Beijing, 100048, China. .,Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, Beijing Technology and Business University, Beijing, 100048, China.
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15
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Xu B, Liu L, Song G. Functions and Regulation of Translation Elongation Factors. Front Mol Biosci 2022; 8:816398. [PMID: 35127825 PMCID: PMC8807479 DOI: 10.3389/fmolb.2021.816398] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/20/2021] [Indexed: 12/18/2022] Open
Abstract
Translation elongation is a key step of protein synthesis, during which the nascent polypeptide chain extends by one amino acid residue during one elongation cycle. More and more data revealed that the elongation is a key regulatory node for translational control in health and disease. During elongation, elongation factor Tu (EF-Tu, eEF1A in eukaryotes) is used to deliver aminoacyl-tRNA (aa-tRNA) to the A-site of the ribosome, and elongation factor G (EF-G, EF2 in eukaryotes and archaea) is used to facilitate the translocation of the tRNA2-mRNA complex on the ribosome. Other elongation factors, such as EF-Ts/eEF1B, EF-P/eIF5A, EF4, eEF3, SelB/EFsec, TetO/Tet(M), RelA and BipA, have been found to affect the overall rate of elongation. Here, we made a systematic review on the canonical and non-canonical functions and regulation of these elongation factors. In particular, we discussed the close link between translational factors and human diseases, and clarified how post-translational modifications control the activity of translational factors in tumors.
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Affiliation(s)
- Benjin Xu
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China
- *Correspondence: Benjin Xu, ; Guangtao Song,
| | - Ling Liu
- Department of Medical Laboratory Science, Fenyang College, Shanxi Medical University, Fenyang, China
| | - Guangtao Song
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- *Correspondence: Benjin Xu, ; Guangtao Song,
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16
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Gasparski AN, Mason DE, Moissoglu K, Mili S. Regulation and outcomes of localized RNA translation. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1721. [PMID: 35166036 PMCID: PMC9787767 DOI: 10.1002/wrna.1721] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/18/2022] [Accepted: 01/22/2022] [Indexed: 12/31/2022]
Abstract
Spatial segregation of mRNAs in the cytoplasm of cells is a well-known biological phenomenon that is widely observed in diverse species spanning different kingdoms of life. In mammalian cells, localization of mRNAs has been documented and studied quite extensively in highly polarized cells, most notably in neurons, where localized mRNAs function to direct protein production at sites that are quite distant from the soma. Recent studies have strikingly revealed that a large proportion of the cellular transcriptome exhibits polarized distributions even in cells that lack an obvious need for long-range transport, such as fibroblasts or epithelial cells. This review focuses on emerging concepts regarding the functional outcomes of mRNA targeting in the cytoplasm of such cells. We also discuss regulatory mechanisms controlling these events, with an emphasis on the role of cell mechanics and the organization of the cytoskeleton. This article is categorized under: Translation > Regulation RNA Export and Localization > RNA Localization.
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Affiliation(s)
- Alexander N. Gasparski
- Laboratory of Cellular and Molecular Biology, Center for Cancer ResearchNational Cancer Institute, NIHBethesdaMarylandUSA
| | - Devon E. Mason
- Laboratory of Cellular and Molecular Biology, Center for Cancer ResearchNational Cancer Institute, NIHBethesdaMarylandUSA
| | - Konstadinos Moissoglu
- Laboratory of Cellular and Molecular Biology, Center for Cancer ResearchNational Cancer Institute, NIHBethesdaMarylandUSA
| | - Stavroula Mili
- Laboratory of Cellular and Molecular Biology, Center for Cancer ResearchNational Cancer Institute, NIHBethesdaMarylandUSA
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17
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Liu S, Matsui TS, Kang N, Deguchi S. Analysis of senescence-responsive stress fiber proteome reveals reorganization of stress fibers mediated by elongation factor eEF2 in HFF-1 cells. Mol Biol Cell 2021; 33:ar10. [PMID: 34705524 PMCID: PMC8886821 DOI: 10.1091/mbc.e21-05-0229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Stress fibers (SFs), which are actomyosin structures, reorganize in response to various cues to maintain cellular homeostasis. Currently, the protein components of SFs are only partially identified, limiting our understanding of their responses. Here we isolate SFs from human fibroblasts HFF-1 to determine with proteomic analysis the whole protein components and how they change with replicative senescence (RS), a state where cells decline in the ability to replicate after repeated divisions. We found that at least 135 proteins are associated with SFs, and 63 of them are up-regulated with RS, by which SFs become larger in size. Among them, we focused on eEF2 (eukaryotic translation elongation factor 2) as it exhibited on RS the most significant increase in abundance. We show that eEF2 is critical to the reorganization and stabilization of SFs in senescent fibroblasts. Our findings provide a novel molecular basis for SFs to be reinforced to resist cellular senescence.
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Affiliation(s)
- Shiyou Liu
- Division of Bioengineering, Graduate School of Engineering Science, Osaka University, Japan
| | - Tsubasa S Matsui
- Division of Bioengineering, Graduate School of Engineering Science, Osaka University, Japan
| | - Na Kang
- Division of Bioengineering, Graduate School of Engineering Science, Osaka University, Japan
| | - Shinji Deguchi
- Division of Bioengineering, Graduate School of Engineering Science, Osaka University, Japan
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18
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Jakobsson ME. Structure, Activity and Function of the Dual Protein Lysine and Protein N-Terminal Methyltransferase METTL13. Life (Basel) 2021; 11:1121. [PMID: 34832997 PMCID: PMC8624817 DOI: 10.3390/life11111121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/18/2021] [Accepted: 10/18/2021] [Indexed: 02/07/2023] Open
Abstract
METTL13 (also known as eEF1A-KNMT and FEAT) is a dual methyltransferase reported to target the N-terminus and Lys55 in the eukaryotic translation elongation factor 1 alpha (eEF1A). METTL13-mediated methylation of eEF1A has functional consequences related to translation dynamics and include altered rate of global protein synthesis and translation of specific codons. Aberrant regulation of METTL13 has been linked to several types of cancer but the precise mechanisms are not yet fully understood. In this article, the current literature related to the structure, activity, and function of METTL13 is systematically reviewed and put into context. The links between METTL13 and diseases, mainly different types of cancer, are also summarized. Finally, key challenges and opportunities for METTL13 research are pinpointed in a prospective outlook.
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Affiliation(s)
- Magnus E Jakobsson
- Department of Immunotechnology, Lund University, Medicon Village, 22100 Lund, Sweden
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19
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Sohtome Y, Shimazu T, Shinkai Y, Sodeoka M. Propargylic Se-adenosyl-l-selenomethionine: A Chemical Tool for Methylome Analysis. Acc Chem Res 2021; 54:3818-3827. [PMID: 34612032 DOI: 10.1021/acs.accounts.1c00395] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Devising synthetic strategies to construct a covalent bond is a common research topic among synthetic chemists. A key driver of success is the high tunability of the conditions, including catalysts, reagents, solvents, and reaction temperature. Such flexibility of synthetic operations has allowed for the rapid exploration of a myriad of artificial synthetic transformations in recent decades. However, if we turn our attention to chemical reactions controlled in living cells, the situation is quite different; the number of hit substrates for the reaction-type is relatively small, while the crowded environment is chemically complex and inflexible to control.A specific objective of this Account is to introduce our chemical methylome analysis as an example of bridging the gap between chemistry and biology. Protein methylation, catalyzed by protein methyltransferases (MTases) using S-adenosyl-l-methionine (SAM or AdoMet) as a methyl donor, is a simple but important post-translational covalent modification. We aim to efficiently identify MTase substrates and methylation sites using activity-based protein profiling (ABPP) with propargylic Se-adenosyl-l-selenomethionine (ProSeAM, also called SeAdoYn). Specifically, we draw heavily from quantitative proteomics that yields information about the differences between two samples utilizing LC-MS/MS analysis. By exploiting the use of ProSeAM, we have prepared the requisite two samples for quantitative methylome analysis. The structural difference between ProSeAM and the parent SAM is so small that the quantity of modification of the protein substrate with this artificial cofactor reflects, to a large extent, levels of activity of the MTase of interest with SAM. First, we identified that the addition of exogenous recombinant MTase (methylation accel), a natural catalyst, enhances the generation of the corresponding propargylated product even in the cell lysate. Then, we applied the principle to isotope label-free quantification with HEK293T cell lysates. By comparing the intensity of LC-MS/MS signals in the absence and presence of the MTase, we have successfully correlated the MTase substrates. We have currently applied the concept to the stable isotope label-based quantification, SILAC (stable isotope labeling by amino acids in cell culture). The strategy merging ProSeAM/MTase/SILAC (PMS) is uniquely versatile and programmable. We can choose suitable cell lines, subcellular fractions (i.e.; whole lysate or mitochondria), and genotypes as required. In particular, we would like to emphasize that the use of cell lysates derived from disease-associated MTase knockouts (KOs) holds vast potential to discover functionally unknown but biologically important methylation events. By adding ProSeAM and a recombinant MTase to the lysates derived from KO cells, we successfully characterized unprecedented nonhistone substrates of several MTases. Furthermore, this chemoproteomic procedure can be applied to explore MTase inhibitors (methylation brake). The combined strategy with ProSeAM/inhibitor/SILAC (PIS) offers intriguing opportunities to explore nonhistone methylation inhibitors.Considering that SAM is the second most widely used enzyme-substrate following ATP, the interdisciplinary research between chemistry and biology using SAM analogs has a potentially huge impact on a wide range of research fields associated with biological methylation. We hope that this Account will help to further delineate the biological function of this important class of enzymatic reaction.
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Affiliation(s)
- Yoshihiro Sohtome
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Tadahiro Shimazu
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mikiko Sodeoka
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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20
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Jakobsson ME. Enzymology and significance of protein histidine methylation. J Biol Chem 2021; 297:101130. [PMID: 34461099 PMCID: PMC8446795 DOI: 10.1016/j.jbc.2021.101130] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/23/2021] [Accepted: 08/26/2021] [Indexed: 12/21/2022] Open
Abstract
Cells synthesize proteins using 20 standard amino acids and expand their biochemical repertoire through intricate enzyme-mediated post-translational modifications (PTMs). PTMs can either be static and represent protein editing events or be dynamically regulated as a part of a cellular response to specific stimuli. Protein histidine methylation (Hme) was an elusive PTM for over 5 decades and has only recently attracted considerable attention through discoveries concerning its enzymology, extent, and function. Here, we review the status of the Hme field and discuss the implications of Hme in physiological and cellular processes. We also review the experimental toolbox for analysis of Hme and discuss the strengths and weaknesses of different experimental approaches. The findings discussed in this review demonstrate that Hme is widespread across cells and tissues and functionally regulates key cellular processes such as cytoskeletal dynamics and protein translation. Collectively, the findings discussed here showcase Hme as a regulator of key cellular functions and highlight the regulation of this modification as an emerging field of biological research.
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21
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Shu X, Li X, Xiang X, Wang Q, Wu Q. METTL21B is a prognostic biomarker and potential therapeutic target in low-grade gliomas. Aging (Albany NY) 2021; 13:20661-20683. [PMID: 34446611 PMCID: PMC8436898 DOI: 10.18632/aging.203454] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/14/2021] [Indexed: 12/17/2022]
Abstract
A considerable amount of literature has demonstrated that eukaryotic translation elongation factor 1A (eEF1A) is closely related to tumors. As a newly identified lysine specific methyltransferase targeting eEF1A at Lys-165, too little attention has been paid to the function of METTL21B. To determine the potential significance and prognostic value of METTL21B in low grade glioma (LGG), we analyzed the expression, methylation level and copy number variations (CNV) of METTL21B and its effect on prognosis in patients with LGG by 4 public databases in conjunction with experimental examination of LGG patient samples. As a result, we found that high expression, hypomethylation and gain/amplification of CNV of METTL21B were associated with poor prognosis in LGG. The potential functions of METTL21B in LGG may be involved in cell adhesion, angiogenesis and cell proliferation of tumor by enrichment analysis. In addition, METTL21B may facilitate immune evasion of tumor and affect prognosis by mediating macrophage polarization from M1 to M2 and regulating expression of immune checkpoints. Nevertheless, patients with high METTL21B level are likely to have better response to immune checkpoints blockage therapy. Because of its substrate specificity, METTL21B is expected to be a promising target for the treatment of glioma.
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Affiliation(s)
- Xin Shu
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Xinquan Li
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Xiaochen Xiang
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Qiang Wang
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, Wuhan 430065, China
| | - Qingming Wu
- Institute of Infection, Immunology and Tumor Microenvironment, Hubei Province Key Laboratory of Occupational Hazard Identification and Control, Medical College, Wuhan University of Science and Technology, Wuhan 430065, China
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22
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Methyltransferase like 13 mediates the translation of Snail in head and neck squamous cell carcinoma. Int J Oral Sci 2021; 13:26. [PMID: 34381012 PMCID: PMC8357922 DOI: 10.1038/s41368-021-00130-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 01/06/2023] Open
Abstract
Methyltransferase like 13 (METTL13), a kind of methyltransferase, is implicated in protein binding and synthesis. The upregulation of METTL13 has been reported in a variety of tumors. However, little was known about its potential function in head and neck squamous cell carcinoma (HNSCC) so far. In this study, we found that METTL13 was significantly upregulated in HNSCC at both mRNA and protein level. Increased METTL13 was negatively associated with clinical prognosis. And METTL13 markedly affected HNSCC cellular phenotypes in vivo and vitro. Further mechanism study revealed that METTL13 could regulate EMT signaling pathway by mediating enhancing translation efficiency of Snail, the key transcription factor in EMT, hence regulating the progression of EMT. Furthermore, Snail was verified to mediate METTL13-induced HNSCC cell malignant phenotypes. Altogether, our study had revealed the oncogenic role of METTL13 in HNSCC, and provided a potential therapeutic strategy.
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23
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Mateyak MK, He D, Sharma P, Kinzy TG. Mutational analysis reveals potential phosphorylation sites in eukaryotic elongation factor 1A that are important for its activity. FEBS Lett 2021; 595:2208-2220. [PMID: 34293820 PMCID: PMC9292714 DOI: 10.1002/1873-3468.14164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 07/11/2021] [Accepted: 07/13/2021] [Indexed: 11/25/2022]
Abstract
Previous studies have suggested that phosphorylation of translation elongation factor 1A (eEF1A) can alter its function, and large‐scale phospho‐proteomic analyses in Saccharomyces cerevisiae have identified 14 eEF1A residues phosphorylated under various conditions. Here, a series of eEF1A mutations at these proposed sites were created and the effects on eEF1A activity were analyzed. The eEF1A‐S53D and eEF1A‐T430D phosphomimetic mutant strains were inviable, while corresponding alanine mutants survived but displayed defects in growth and protein synthesis. The activity of an eEF1A‐S289D mutant was significantly reduced in the absence of the guanine nucleotide exchange factor eEF1Bα and could be restored by an exchange‐deficient form of the protein, suggesting that eEF1Bα promotes eEF1A activity by a mechanism other than nucleotide exchange. Our data show that several of the phosphorylation sites identified by high‐throughput analysis are critical for eEF1A function.
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Affiliation(s)
- Maria K Mateyak
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Dongming He
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Pragati Sharma
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Terri Goss Kinzy
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Illinois State University, Normal, IL, USA
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24
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Waddington JC, Meng X, Illing PT, Tailor A, Adair K, Whitaker P, Hamlett J, Jenkins RE, Farrell J, Berry N, Purcell AW, Naisbitt DJ, Park BK. Identification of Flucloxacillin-Haptenated HLA-B*57:01 Ligands: Evidence of Antigen Processing and Presentation. Toxicol Sci 2021; 177:454-465. [PMID: 32726429 DOI: 10.1093/toxsci/kfaa124] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Flucloxacillin is a β-lactam antibiotic associated with a high incidence of drug-induced liver reactions. Although expression of human leukocyte antigen (HLA)-B*57:01 increases susceptibility, little is known of the pathological mechanisms involved in the induction of the clinical phenotype. Irreversible protein modification is suspected to drive the reaction through the modification of peptides that are presented by the risk allele. In this study, the binding of flucloxacillin to immune cells was characterized and the nature of the peptides presented by HLA-B*57:01 was analyzed using mass spectrometric-based immunopeptidomics methods. Flucloxacillin modification of multiple proteins was observed, providing a potential source of neoantigens for HLA presentation. Of the peptides eluted from flucloxacillin-treated C1R-B*57:01 cells, 6 putative peptides were annotated as flucloxacillin-modified HLA-B*57:01 peptide ligands (data are available via ProteomeXchange with identifier PXD020137). To conclude, we have characterized naturally processed drug-haptenated HLA ligands presented on the surface of antigen presenting cells that may drive drug-specific CD8+ T-cell responses.
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Affiliation(s)
- James C Waddington
- MRC Centre for Drug Safety Science, Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool L69 3GE, United Kingdom
| | - Xiaoli Meng
- MRC Centre for Drug Safety Science, Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool L69 3GE, United Kingdom
| | - Patricia T Illing
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Arun Tailor
- MRC Centre for Drug Safety Science, Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool L69 3GE, United Kingdom
| | - Kareena Adair
- MRC Centre for Drug Safety Science, Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool L69 3GE, United Kingdom
| | - Paul Whitaker
- Regional Adult Cystic Fibrosis Unit, St James's Hospital, Leeds LS9 7TF, United Kingdom
| | - Jane Hamlett
- MRC Centre for Drug Safety Science, Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool L69 3GE, United Kingdom
| | - Rosalind E Jenkins
- MRC Centre for Drug Safety Science, Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool L69 3GE, United Kingdom
| | - John Farrell
- MRC Centre for Drug Safety Science, Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool L69 3GE, United Kingdom
| | - Neil Berry
- Department of Chemistry, University of Liverpool, Liverpool L69 7ZD, United Kingdom
| | - Anthony W Purcell
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Dean J Naisbitt
- MRC Centre for Drug Safety Science, Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool L69 3GE, United Kingdom
| | - Brian Kevin Park
- MRC Centre for Drug Safety Science, Department of Molecular & Clinical Pharmacology, University of Liverpool, Liverpool L69 3GE, United Kingdom
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25
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Mills A, Gago F. On the Need to Tell Apart Fraternal Twins eEF1A1 and eEF1A2, and Their Respective Outfits. Int J Mol Sci 2021; 22:6973. [PMID: 34203525 PMCID: PMC8268798 DOI: 10.3390/ijms22136973] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/25/2021] [Accepted: 06/25/2021] [Indexed: 01/03/2023] Open
Abstract
eEF1A1 and eEF1A2 are paralogous proteins whose presence in most normal eukaryotic cells is mutually exclusive and developmentally regulated. Often described in the scientific literature under the collective name eEF1A, which stands for eukaryotic elongation factor 1A, their best known activity (in a monomeric, GTP-bound conformation) is to bind aminoacyl-tRNAs and deliver them to the A-site of the 80S ribosome. However, both eEF1A1 and eEF1A2 are endowed with multitasking abilities (sometimes performed by homo- and heterodimers) and can be located in different subcellular compartments, from the plasma membrane to the nucleus. Given the high sequence identity of these two sister proteins and the large number of post-translational modifications they can undergo, we are often confronted with the dilemma of discerning which is the particular proteoform that is actually responsible for the ascribed biochemical or cellular effects. We argue in this review that acquiring this knowledge is essential to help clarify, in molecular and structural terms, the mechanistic involvement of these two ancestral and abundant G proteins in a variety of fundamental cellular processes other than translation elongation. Of particular importance for this special issue is the fact that several de novo heterozygous missense mutations in the human EEF1A2 gene are associated with a subset of rare but severe neurological syndromes and cardiomyopathies.
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Affiliation(s)
| | - Federico Gago
- Department of Biomedical Sciences & “Unidad Asociada IQM-CSIC”, School of Medicine and Health Sciences, University of Alcalá, E-28805 Alcalá de Henares, Spain;
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26
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Liu R, Tearle R, Low WY, Chen T, Thomsen D, Smith TPL, Hiendleder S, Williams JL. Distinctive gene expression patterns and imprinting signatures revealed in reciprocal crosses between cattle sub-species. BMC Genomics 2021; 22:410. [PMID: 34082698 PMCID: PMC8176687 DOI: 10.1186/s12864-021-07667-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 04/21/2021] [Indexed: 01/06/2023] Open
Abstract
Background There are two genetically distinct subspecies of cattle, Bos taurus taurus and Bos taurus indicus, which arose from independent domestication events. The two types of cattle show substantial phenotypic differences, some of which emerge during fetal development and are reflected in birth outcomes, including birth weight. We explored gene expression profiles in the placenta and four fetal tissues at mid-gestation from one taurine (Bos taurus taurus; Angus) and one indicine (Bos taurus indicus; Brahman) breed and their reciprocal crosses. Results In total 120 samples were analysed from a pure taurine breed, an indicine breed and their reciprocal cross fetuses, which identified 6456 differentially expressed genes (DEGs) between the two pure breeds in at least one fetal tissue of which 110 genes were differentially expressed in all five tissues examined. DEGs shared across tissues were enriched for pathways related to immune and stress response functions. Only the liver had a substantial number of DEGs when reciprocal crossed were compared among which 310 DEGs were found to be in common with DEGs identified between purebred livers; these DEGs were significantly enriched for metabolic process GO terms. Analysis of DEGs across purebred and crossbred tissues suggested an additive expression pattern for most genes, where both paternal and maternal alleles contributed to variation in gene expression levels. However, expression of 5% of DEGs in each tissue was consistent with parent of origin effects, with both paternal and maternal dominance effects identified. Conclusions These data identify candidate genes potentially driving the tissue-specific differences between these taurine and indicine breeds and provide a biological insight into parental genome effects underlying phenotypic differences in bovine fetal development. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07667-2.
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Affiliation(s)
- Ruijie Liu
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Rick Tearle
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Wai Yee Low
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Tong Chen
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia
| | - Dana Thomsen
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia.,Robinson Research Institute, The University of Adelaide, Adelaide, Australia
| | - Timothy P L Smith
- USMARC, USDA-ARS-US Meat Animal Research Center, Clay Center, NE, USA
| | - Stefan Hiendleder
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia.,Robinson Research Institute, The University of Adelaide, Adelaide, Australia
| | - John L Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, Australia. .,Present address: Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Università Cattolica del Sacro Cuore, Piacenza, Italy.
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27
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Emery-Corbin SJ, Hamey JJ, Ansell BRE, Balan B, Tichkule S, Stroehlein AJ, Cooper C, McInerney BV, Hediyeh-Zadeh S, Vuong D, Crombie A, Lacey E, Davis MJ, Wilkins MR, Bahlo M, Svärd SG, Gasser RB, Jex AR. Eukaryote-Conserved Methylarginine Is Absent in Diplomonads and Functionally Compensated in Giardia. Mol Biol Evol 2021; 37:3525-3549. [PMID: 32702104 PMCID: PMC7743719 DOI: 10.1093/molbev/msaa186] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Methylation is a common posttranslational modification of arginine and lysine in eukaryotic proteins. Methylproteomes are best characterized for higher eukaryotes, where they are functionally expanded and evolved complex regulation. However, this is not the case for protist species evolved from the earliest eukaryotic lineages. Here, we integrated bioinformatic, proteomic, and drug-screening data sets to comprehensively explore the methylproteome of Giardia duodenalis-a deeply branching parasitic protist. We demonstrate that Giardia and related diplomonads lack arginine-methyltransferases and have remodeled conserved RGG/RG motifs targeted by these enzymes. We also provide experimental evidence for methylarginine absence in proteomes of Giardia but readily detect methyllysine. We bioinformatically infer 11 lysine-methyltransferases in Giardia, including highly diverged Su(var)3-9, Enhancer-of-zeste and Trithorax proteins with reduced domain architectures, and novel annotations demonstrating conserved methyllysine regulation of eukaryotic elongation factor 1 alpha. Using mass spectrometry, we identify more than 200 methyllysine sites in Giardia, including in species-specific gene families involved in cytoskeletal regulation, enriched in coiled-coil features. Finally, we use known methylation inhibitors to show that methylation plays key roles in replication and cyst formation in this parasite. This study highlights reduced methylation enzymes, sites, and functions early in eukaryote evolution, including absent methylarginine networks in the Diplomonadida. These results challenge the view that arginine methylation is eukaryote conserved and demonstrate that functional compensation of methylarginine was possible preceding expansion and diversification of these key networks in higher eukaryotes.
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Affiliation(s)
- Samantha J Emery-Corbin
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Joshua J Hamey
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Brendan R E Ansell
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Balu Balan
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.,Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Swapnil Tichkule
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Andreas J Stroehlein
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Crystal Cooper
- Central Analytical Research Facility (CARF), Institute for Future Environments, Queensland University of Technology, Brisbane, QLD, Australia
| | - Bernie V McInerney
- Australian Proteome Analysis Facility (APAF), Macquarie University, North Ryde, NSW, Australia
| | - Soroor Hediyeh-Zadeh
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.,Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Daniel Vuong
- Microbial Screening Technologies, Smithfield, NSW, Australia
| | - Andrew Crombie
- Microbial Screening Technologies, Smithfield, NSW, Australia
| | - Ernest Lacey
- Microbial Screening Technologies, Smithfield, NSW, Australia.,Chemistry and Biomolecular Sciences, Faculty of Science, Macquarie University, North Ryde, NSW, Australia
| | - Melissa J Davis
- Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.,Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Staffan G Svärd
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Aaron R Jex
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.,Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
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28
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Pan N, Bhatti MZ, Zhang W, Ni B, Fan X, Chen J. Transcriptome analysis reveals the encystment-related lncRNA expression profile and coexpressed mRNAs in Pseudourostyla cristata. Sci Rep 2021; 11:8274. [PMID: 33859278 PMCID: PMC8050308 DOI: 10.1038/s41598-021-87680-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 03/31/2021] [Indexed: 12/02/2022] Open
Abstract
Ciliated protozoans form dormant cysts for survival under adverse conditions. The molecular mechanisms regulating this process are critical for understanding how single-celled eukaryotes adapt to the environment. Despite the accumulated data on morphology and gene coding sequences, the molecular mechanism by which lncRNAs regulate ciliate encystment remains unknown. Here, we first detected and analyzed the lncRNA expression profile and coexpressed mRNAs in dormant cysts versus vegetative cells in the hypotrich ciliate Pseudourostyla cristata by high-throughput sequencing and qRT-PCR. A total of 853 differentially expressed lncRNAs were identified. Compared to vegetative cells, 439 and 414 lncRNAs were upregulated and downregulated, respectively, while 47 lncRNAs were specifically expressed in dormant cysts. A lncRNA-mRNA coexpression network was constructed, and the possible roles of lncRNAs were screened. Three of the identified lncRNAs, DN12058, DN20924 and DN30855, were found to play roles in fostering encystment via their coexpressed mRNAs. These lncRNAs can regulate a variety of physiological activities that are essential for encystment, including autophagy, protein degradation, the intracellular calcium concentration, microtubule-associated dynein and microtubule interactions, and cell proliferation inhibition. These findings provide the first insight into the potentially functional lncRNAs and their coexpressed mRNAs involved in the dormancy of ciliated protozoa and contribute new evidence for understanding the molecular mechanisms regulating encystment.
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Affiliation(s)
- Nan Pan
- School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Muhammad Zeeshan Bhatti
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, China.,Department of Biological Sciences, National University of Medical Sciences, Rawalpindi, 46000, Pakistan
| | - Wen Zhang
- School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Bing Ni
- School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Xinpeng Fan
- School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| | - Jiwu Chen
- School of Life Sciences, East China Normal University, Shanghai, 200241, China.
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29
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Chen F, Chen Z, Guan T, Zhou Y, Ge L, Zhang H, Wu Y, Jiang GM, He W, Li J, Wang H. N6 -Methyladenosine Regulates mRNA Stability and Translation Efficiency of KRT7 to Promote Breast Cancer Lung Metastasis. Cancer Res 2021; 81:2847-2860. [PMID: 33795252 DOI: 10.1158/0008-5472.can-20-3779] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 02/03/2021] [Accepted: 03/26/2021] [Indexed: 11/16/2022]
Abstract
The roles of RNA modification during organ metastasis of cancer cells are not known. Here we established breast cancer lung metastasis cells by three rounds of selection of lung metastatic subpopulations in vivo and designated them as BCLMF3 cells. In these cells, mRNA N6 -methyladenosine (m6A) and methyltransferase METTL3 were increased, while the demethylase FTO was decreased. Epi-transcriptome and transcriptome analyses together with functional studies identified keratin 7 (KRT7) as a key effector for m6A-induced breast cancer lung metastasis. Specifically, increased METTL3 methylated KRT7-AS at A877 to increase the stability of a KRT7-AS/KRT7 mRNA duplex via IGF2BP1/HuR complexes. Furthermore, YTHDF1/eEF-1 was involved in FTO-regulated translational elongation of KRT7 mRNA, with methylated A950 in KRT7 exon 6 as the key site for methylation. In vivo and clinical studies confirmed the essential roles of KRT7, KRT7-AS, and METTL3 for lung metastasis and clinical progression of breast cancer. Collectively, m6A promotes breast cancer lung metastasis by increasing the stability of a KRT7-AS/KRT7 mRNA duplex and translation of KRT7. SIGNIFICANCE: This study suggests that N6 -methyladenosine is a key driver and potential therapeutic target in breast cancer metastasis.
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Affiliation(s)
- Feng Chen
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhuojia Chen
- Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, China
| | - Tao Guan
- Shanxi Cancer Hospital, No. 3, Taiyuan, Shanxi Province, China
| | - Yan Zhou
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lichen Ge
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Haisheng Zhang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yingmin Wu
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Guan-Min Jiang
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Sun Yat-sen University, Zhuhai, Guangdong, China
| | - Weiling He
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Jiexin Li
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Hongsheng Wang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong, China.
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30
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Di Blasi R, Blyuss O, Timms JF, Conole D, Ceroni F, Whitwell HJ. Non-Histone Protein Methylation: Biological Significance and Bioengineering Potential. ACS Chem Biol 2021; 16:238-250. [PMID: 33411495 DOI: 10.1021/acschembio.0c00771] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Protein methylation is a key post-translational modification whose effects on gene expression have been intensively studied over the last two decades. Recently, renewed interest in non-histone protein methylation has gained momentum for its role in regulating important cellular processes and the activity of many proteins, including transcription factors, enzymes, and structural complexes. The extensive and dynamic role that protein methylation plays within the cell also highlights its potential for bioengineering applications. Indeed, while synthetic histone protein methylation has been extensively used to engineer gene expression, engineering of non-histone protein methylation has not been fully explored yet. Here, we report the latest findings, highlighting how non-histone protein methylation is fundamental for certain cellular functions and is implicated in disease, and review recent efforts in the engineering of protein methylation.
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Affiliation(s)
- Roberto Di Blasi
- Department of Chemical Engineering, Faculty of Engineering, Imperial College London, London, U.K
- Imperial College Centre for Synthetic Biology, Imperial College London, London, U.K
| | - Oleg Blyuss
- School of Physics, Astronomy and Mathematics, University of Hertfordshire, Hatfield, U.K
- Department of Paediatrics and Paediatric Infectious Diseases, Sechenov First Moscow State Medical University, Moscow, Russia
- Department of Applied Mathematics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - John F Timms
- Department of Women's Cancer, EGA Institute for Women's Health, University College London, London, U.K
| | - Daniel Conole
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London, U.K
| | - Francesca Ceroni
- Department of Chemical Engineering, Faculty of Engineering, Imperial College London, London, U.K
- Imperial College Centre for Synthetic Biology, Imperial College London, London, U.K
| | - Harry J Whitwell
- Department of Applied Mathematics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
- National Phenome Centre and Imperial Clinical Phenotyping Centre, Department of Metabolism, Digestion and Reproduction, IRDB Building, Imperial College London, Hammersmith Campus, London, W12 0NN, U.K
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Sir Alexander Fleming Building, Imperial College London, Hammersmith Campus, London, SW7 2AZ, U.K
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31
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Lukinović V, Casanova AG, Roth GS, Chuffart F, Reynoird N. Lysine Methyltransferases Signaling: Histones are Just the Tip of the Iceberg. Curr Protein Pept Sci 2021; 21:655-674. [PMID: 31894745 DOI: 10.2174/1871527319666200102101608] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/15/2019] [Accepted: 11/27/2019] [Indexed: 12/28/2022]
Abstract
Protein lysine methylation is a functionally diverse post-translational modification involved in various major cellular processes. Lysine methylation can modulate proteins activity, stability, localization, and/or interaction, resulting in specific downstream signaling and biological outcomes. Lysine methylation is a dynamic and fine-tuned process, deregulation of which often leads to human pathologies. In particular, the lysine methylome and its associated signaling network can be linked to carcinogenesis and cancer progression. Histone modifications and chromatin regulation is a major aspect of lysine methylation importance, but increasing evidence suggests that a high relevance and impact of non-histone lysine methylation signaling has emerged in recent years. In this review, we draw an updated picture of the current scientific knowledge regarding non-histone lysine methylation signaling and its implication in physiological and pathological processes. We aim to demonstrate the significance of lysine methylation as a major and yet underestimated posttranslational modification, and to raise the importance of this modification in both epigenetic and cellular signaling by focusing on the observed activities of SET- and 7β-strandcontaining human lysine methyltransferases. Recent evidence suggests that what has been observed so far regarding lysine methylation's implication in human pathologies is only the tip of the iceberg. Therefore, the exploration of the "methylome network" raises the possibility to use these enzymes and their substrates as promising new therapeutic targets for the development of future epigenetic and methyllysine signaling cancer treatments.
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Affiliation(s)
- Valentina Lukinović
- Institute for Advanced Biosciences, INSERM U1209 - CNRS UMR5309 - Universite Grenoble Alpes, Grenoble Cedex, France
| | - Alexandre G Casanova
- Institute for Advanced Biosciences, INSERM U1209 - CNRS UMR5309 - Universite Grenoble Alpes, Grenoble Cedex, France
| | - Gael S Roth
- Institute for Advanced Biosciences, INSERM U1209 - CNRS UMR5309 - Universite Grenoble Alpes, Grenoble Cedex, France
| | - Florent Chuffart
- Institute for Advanced Biosciences, INSERM U1209 - CNRS UMR5309 - Universite Grenoble Alpes, Grenoble Cedex, France
| | - Nicolas Reynoird
- Institute for Advanced Biosciences, INSERM U1209 - CNRS UMR5309 - Universite Grenoble Alpes, Grenoble Cedex, France
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32
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Jethmalani Y, Green EM. Using Yeast to Define the Regulatory Role of Protein Lysine Methylation. Curr Protein Pept Sci 2021; 21:690-698. [PMID: 31642774 DOI: 10.2174/1389203720666191023150727] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/18/2019] [Accepted: 09/27/2019] [Indexed: 12/31/2022]
Abstract
The post-translational modifications (PTM) of proteins are crucial for cells to survive under diverse environmental conditions and to respond to stimuli. PTMs are known to govern a broad array of cellular processes including signal transduction and chromatin regulation. The PTM lysine methylation has been extensively studied within the context of chromatin and the epigenetic regulation of the genome. However, it has also emerged as a critical regulator of non-histone proteins important for signal transduction pathways. While the number of known non-histone protein methylation events is increasing, the molecular functions of many of these modifications are not yet known. Proteomic studies of the model system Saccharomyces cerevisiae suggest lysine methylation may regulate a diversity of pathways including transcription, RNA processing, translation, and signal transduction cascades. However, there has still been relatively little investigation of lysine methylation as a broad cellular regulator beyond chromatin and transcription. Here, we outline our current state of understanding of non-histone protein methylation in yeast and propose ways in which the yeast system can be leveraged to develop a much more complete picture of molecular mechanisms through which lysine methylation regulates cellular functions.
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Affiliation(s)
- Yogita Jethmalani
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, United States
| | - Erin M Green
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD, United States
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Xiao S, Wang Y, Ma Y, Liu J, Tang C, Deng A, Fang C. Dimethylation of eEF1A at Lysine 55 Plays a Key Role in the Regulation of eEF1A2 on Malignant Cell Functions of Acute Myeloid Leukemia. Technol Cancer Res Treat 2020; 19:1533033820914295. [PMID: 32347192 PMCID: PMC7225831 DOI: 10.1177/1533033820914295] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE This study aimed to explore whether eukaryotic translation elongation factor 1 alpha 2 affected cell proliferation, migration, and apoptosis via regulating the dimethylation of eukaryotic translation elongation factor 1 alpha at lysine 55 in acute myeloid leukemia. METHODS The expressions of eukaryotic translation elongation factor 1 alpha 2 and dimethylation of eukaryotic translation elongation factor 1 alpha at lysine 55 in acute myeloid leukemia cell lines and human normal bone marrow mononuclear cells (as control) were assessed. Control CRISPR-Cas9 lentivirus, eukaryotic translation elongation factor 1 alpha 2 knockout CRISPR-Cas9 lentivirus, vector plasmid, eukaryotic translation elongation factor 1 alpha 2 wild type overexpression plasmid, and eukaryotic translation elongation factor 1 alpha 2 with a K55R substitution overexpression plasmid were transfected into AML-193 and Kasumi-1 cells combined or alone, and were accordingly divided into 4 groups (Sgcontrol + vector group, SgeEF1A2 + vector group, SgeEF1A2 + eEF1A2WT group, and SgeEFIA2 + eEF1A2K55R group). RESULTS Eukaryotic translation elongation factor 1 alpha 2 and dimethylation of eukaryotic translation elongation factor 1 alpha at lysine 55 expressions were higher in AML-193, Kasumi-1, and KG-1 cell lines compared to the control. In AML-193 and Kasumi-1 cells, the knockout and compensated experiments revealed that eukaryotic translation elongation factor 1 alpha 2 promoted cell proliferation and migration but repressed apoptosis. Additionally, the knockout of eukaryotic translation elongation factor 1 alpha 2 decreased dimethylation of eukaryotic translation elongation factor 1 alpha at lysine 55 expression, meanwhile, eukaryotic translation elongation factor 1 alpha 2 wild type overexpression enhanced while eukaryotic translation elongation factor 1 alpha 2 with a K55R substitution overexpression did not influence the dimethylation of eukaryotic translation elongation factor 1 alpha at lysine 55 expression. Furthermore, eukaryotic translation elongation factor 1 alpha 2 wild type overexpression promoted cell proliferation, enhanced migration, and decreased apoptosis, but eukaryotic translation elongation factor 1 alpha 2 with a K55R substitution overexpression did not influence these cellular functions in AML-193 and Kasumi-1 cells, suggesting the implication of dimethylation of eukaryotic translation elongation factor 1 alpha at lysine 55 in eukaryotic translation elongation factor 1 alpha 2 mediated oncogenesis of acute myeloid leukemia. CONCLUSION Eukaryotic translation elongation factor 1 alpha 2 and its dimethylated product may serve as therapeutic targets, and these findings may provide support for exploring novel strategies in acute myeloid leukemia treatment.
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Affiliation(s)
- Shan Xiao
- Department of Pharmacy, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Yanping Wang
- Department of Pediatrics, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Yuwen Ma
- Department of Pharmacy, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Jue Liu
- Department of Pharmacy, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Can'e Tang
- Key Laboratory of Cancer Proteomics of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, People's Republic of China
| | - Aiping Deng
- Department of Pharmacy, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
| | - Chunxiang Fang
- Department of Pharmacy, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China
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Zoabi M, Zhang L, Li TM, Elias JE, Carlson SM, Gozani O. Methyltransferase-like 21C (METTL21C) methylates alanine tRNA synthetase at Lys-943 in muscle tissue. J Biol Chem 2020; 295:11822-11832. [PMID: 32611769 DOI: 10.1074/jbc.ra120.014505] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/26/2020] [Indexed: 12/24/2022] Open
Abstract
Protein-lysine methylation is a common posttranslational modification (PTM) throughout the human proteome that plays important roles in diverse biological processes. In humans, there are >100 known and candidate protein lysine methyltransferases (PKMTs), many of which are linked to human diseases. Methyltransferase-like protein 21C (METTL21C) is a PKMT implicated in muscle biology that has been reported to methylate valosin-containing protein/p97 (VCP) and heat shock 70-kDa protein 8 (HSPA8). However, a clear in vitro methyltransferase activity for METTL21C remains yet to be demonstrated, and whether it is an active enzyme that directly methylates substrate(s) in vivo is unclear. Here, we used an unbiased biochemistry-based screening assay coupled to MS, which identified alanine tRNA synthetase 1 (AARS1) as a direct substrate of METTL21C. We found that METTL21C catalyzes methylation of Lys-943 of AARS1 (AARS1-K943me) both in vitro and in vivo In vitro METTL21C-mediated AARS1 methylation was independent of ATP or tRNA molecules. Unlike for AARS1, and in conflict with previous reports, we did not detect METTL21C methylation of VCP and HSPA8. AARS1-K943 methylation in HEK293T cells depends upon METTL21C levels. Finally, METTL2C was almost exclusively expressed in muscle tissue, and, accordingly, we detected METTL21C-catalyzed methylation of AARS1 in mouse skeletal muscle tissue. These results reveal that AARS1 is a bona fide in vitro substrate of METTL21C and suggest a role for the METTL21C-AARS1 axis in the regulation of protein synthesis in muscle tissue. Moreover, our study describes a straightforward protocol for elucidating the physiological substrates of poorly characterized or uncharacterized PKMTs.
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Affiliation(s)
- Muhammad Zoabi
- Department of Biology, Stanford University, Stanford, California, USA
| | - Lichao Zhang
- Chan Zuckerberg Biohub, Stanford University, Stanford, California, USA
| | - Tie-Mei Li
- Department of Biology, Stanford University, Stanford, California, USA
| | - Josh E Elias
- Chan Zuckerberg Biohub, Stanford University, Stanford, California, USA
| | - Scott M Carlson
- Department of Biology, Stanford University, Stanford, California, USA
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, California, USA
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Nieman DC, Groen AJ, Pugachev A, Simonson AJ, Polley K, James K, El-Khodor BF, Varadharaj S, Hernández-Armenta C. Proteomics-Based Detection of Immune Dysfunction in an Elite Adventure Athlete Trekking Across the Antarctica. Proteomes 2020; 8:proteomes8010004. [PMID: 32138228 PMCID: PMC7151708 DOI: 10.3390/proteomes8010004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 02/29/2020] [Accepted: 03/01/2020] [Indexed: 12/31/2022] Open
Abstract
Proteomics monitoring of an elite adventure athlete (age 33 years) was conducted over a 28-week period that culminated in the successful, solo, unassisted, and unsupported two month trek across the Antarctica (1500 km). Training distress was monitored weekly using a 19-item, validated training distress scale (TDS). Weekly dried blood spot (DBS) specimens were collected via fingerprick blood drops onto standard blood spot cards. DBS proteins were measured with nano-electrospray ionization liquid chromatography tandem mass spectrometry (nanoLC-MS/MS) in data-independent acquisition (DIA) mode, and 712 proteins were identified and quantified. The 28-week period was divided into time segments based on TDS scores, and a contrast analysis between weeks five and eight (low TDS) and between weeks 20 and 23 (high TDS, last month of Antarctica trek) showed that 31 proteins (n = 20 immune related) were upregulated and 35 (n = 17 immune related) were downregulated. Protein-protein interaction (PPI) networks supported a dichotomous immune response. Gene ontology (GO) biological process terms for the upregulated immune proteins showed an increase in regulation of the immune system process, especially inflammation, complement activation, and leukocyte mediated immunity. At the same time, GO terms for the downregulated immune-related proteins indicated a decrease in several aspects of the overall immune system process including neutrophil degranulation and the antimicrobial humoral response. These proteomics data support a dysfunctional immune response in an elite adventure athlete during a sustained period of mental and physical distress while trekking solo across the Antarctica.
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Affiliation(s)
- David C. Nieman
- North Carolina Research Campus, Appalachian State University, Kannapolis, NC 28081, USA;
- Correspondence: ; Tel.: +1-828-773-0056
| | - Arnoud J. Groen
- ProteiQ Biosciences GmbH, 10967 Berlin, Germany; (A.J.G.); (A.P.); (C.H.-A.)
| | - Artyom Pugachev
- ProteiQ Biosciences GmbH, 10967 Berlin, Germany; (A.J.G.); (A.P.); (C.H.-A.)
| | - Andrew J. Simonson
- North Carolina Research Campus, Appalachian State University, Kannapolis, NC 28081, USA;
| | - Kristine Polley
- Standard Process Nutrition Innovation, Kannapolis, NC 28081, USA; (K.P.); (K.J.); (B.F.E.-K.); (S.V.)
| | - Karma James
- Standard Process Nutrition Innovation, Kannapolis, NC 28081, USA; (K.P.); (K.J.); (B.F.E.-K.); (S.V.)
| | - Bassem F. El-Khodor
- Standard Process Nutrition Innovation, Kannapolis, NC 28081, USA; (K.P.); (K.J.); (B.F.E.-K.); (S.V.)
| | - Saradhadevi Varadharaj
- Standard Process Nutrition Innovation, Kannapolis, NC 28081, USA; (K.P.); (K.J.); (B.F.E.-K.); (S.V.)
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Liang Q, Geng Q, Jiang L, Liang M, Li L, Zhang C, Wang W. Protein methylome analysis in Arabidopsis reveals regulation in RNA-related processes. J Proteomics 2020; 213:103601. [PMID: 31809900 DOI: 10.1016/j.jprot.2019.103601] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 10/23/2019] [Accepted: 11/25/2019] [Indexed: 01/09/2023]
Abstract
Protein methylation has been proposed as an important post-translational modification, which occurs predominantly on lysine and arginine residues. Recent discoveries have revealed that protein methylation is also present on non-histones besides histones, and plays critical roles in regulating protein stability and function. However, proteome-wide identification of methylated proteins in plants remains unexplored. Here, we present the first global survey of monomethyl arginine, symmetric and asymmetric dimethyl arginine, and monomethyl, dimethyl, trimethyl lysine modifications in the proteomes of 10-day-old Arabidopsis seedlings through a combination of immunoaffinity purification and mass spectrometry analysis. In total, we identified 617 methylation sites which mapped to 412 proteins, with 263 proteins harboring 381 lysine methylation sites and 149 proteins harboring 236 arginine methylation sites. Among them, 607 methylation sites on 408 proteins were novel findings. Motif analysis revealed that glycine preferentially flanked methylated arginine residues, whereas aspartate and glutamate enriched around mono- and dimethylated lysine sites. Methylated proteins were involved in a variety of metabolic processes, showing significant enrichment in RNA-related metabolic pathways including spliceosome, RNA transport, and ribosome. Our data provide a global view of methylated non-histone proteins in Arabidopsis, laying foundations for elucidating the biological function of protein methylation in plants. SIGNIFICANCE: Protein methylation has emerged as a common and important modification both in eukaryotes and prokaryotes. The identification of methylated sites/peptides is fundamental for further functional analysis of protein methylation. This study was the first proteome-scale identification of lysine and arginine methylation in plants. We found that methylation occurred widely on non-histone proteins in Arabidopsis and was involved in diverse biological functions. The results provide foundations for the investigation of the protein methylome in Arabidopsis and provide powerful resources for the functional analysis of protein methylation in plants.
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Affiliation(s)
- Qiuju Liang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qinghe Geng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ling Jiang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Meng Liang
- Jingjie PTM BioLab (Hangzhou) Co.Ltd, Hangzhou 310018, China
| | - Linhan Li
- Jingjie PTM BioLab (Hangzhou) Co.Ltd, Hangzhou 310018, China
| | - Chunyi Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Weixuan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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Global characterization of proteome and lysine methylome features in EZH2 wild-type and mutant lymphoma cell lines. J Proteomics 2020; 213:103614. [DOI: 10.1016/j.jprot.2019.103614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/29/2019] [Accepted: 12/13/2019] [Indexed: 01/14/2023]
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38
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White JT, Cato T, Deramchi N, Gabunilas J, Roy KR, Wang C, Chanfreau GF, Clarke SG. Protein Methylation and Translation: Role of Lysine Modification on the Function of Yeast Elongation Factor 1A. Biochemistry 2019; 58:4997-5010. [PMID: 31738538 DOI: 10.1021/acs.biochem.9b00818] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To date, 12 protein lysine methyltransferases that modify translational elongation factors and ribosomal proteins (Efm1-7 and Rkm 1-5) have been identified in the yeast Saccharomyces cerevisiae. Of these 12, five (Efm1 and Efm4-7) appear to be specific to elongation factor 1A (EF1A), the protein responsible for bringing aminoacyl-tRNAs to the ribosome. In S. cerevisiae, the functional implications of lysine methylation in translation are mostly unknown. In this work, we assessed the physiological impact of disrupting EF1A methylation in a strain where four of the most conserved methylated lysine sites are mutated to arginine residues and in strains lacking either four or five of the Efm lysine methyltransferases specific to EF1A. We found that loss of EF1A methylation was not lethal but resulted in reduced growth rates, particularly under caffeine and rapamycin stress conditions, suggesting EF1A interacts with the TORC1 pathway, as well as altered sensitivities to ribosomal inhibitors. We also detected reduced cellular levels of the EF1A protein, which surprisingly was not reflected in its stability in vivo. We present evidence that these Efm methyltransferases appear to be largely devoted to the modification of EF1A, finding no evidence of the methylation of other substrates in the yeast cell. This work starts to illuminate why one protein can need five different methyltransferases for its functions and highlights the resilience of yeast to alterations in their posttranslational modifications.
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Affiliation(s)
- Jonelle T White
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Tieranee Cato
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Neil Deramchi
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Jason Gabunilas
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Kevin R Roy
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Charles Wang
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Guillaume F Chanfreau
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
| | - Steven G Clarke
- Department of Chemistry and Biochemistry and Molecular Biology Institute , University of California, Los Angeles , Los Angeles , California 90095 , United States
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Taneera J, Dhaiban S, Mohammed AK, Mukhopadhyay D, Aljaibeji H, Sulaiman N, Fadista J, Salehi A. GNAS gene is an important regulator of insulin secretory capacity in pancreatic β-cells. Gene 2019; 715:144028. [PMID: 31374326 DOI: 10.1016/j.gene.2019.144028] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/27/2019] [Accepted: 07/30/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Type 2 diabetes (T2D) is a complex polygenic disease with unclear mechanism. In an attempt to identify novel genes involved in β-cell function, we harness a bioinformatics method called Loss-of-function tool (LoFtool) gene score. METHODS RNA-sequencing data from human islets were used to cross-reference genes within the 1st quartile of most intolerant LoFtool score with the 100th most expressed genes in human islets. Out of these genes, GNAS and EEF1A1 genes were selected for further investigation in diabetic islets, metabolic tissues along with their correlation with diabetic phenotypes. The influence of GNAS and EEF1A1 on insulin secretion and β-cell function were validated in INS-1 cells. RESULTS A comparatively higher expression level of GNAS and EEF1A1 was observed in human islets than fat, liver and muscle tissues. Furthermore, diabetic islets displayed a reduced expression of GNAS, but not of EEF1A, compared to non-diabetic islets. The expression of GNAS was positively correlated with insulin secretory index, GLP1R, GIPR and inversely correlated with HbA1c. Diabetic human islets displayed a reduced cAMP generation and insulin secretory capacity in response to glucose. Moreover, siRNA silencing of GNAS in INS-1 cells reduced insulin secretion, insulin content, and cAMP production. In addition, the expression of Insulin, PDX1, and MAFA was significantly down-regulated in GNAS-silenced cells. However, cell viability and apoptosis rate were unaffected. CONCLUSION LoFtool is a powerful tool to identify genes associated with pancreatic islets dysfunction. GNAS is a crucial gene for the β-cell insulin secretory capacity.
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Affiliation(s)
- Jalal Taneera
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates.
| | - Sarah Dhaiban
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Abdul Khader Mohammed
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Debasmita Mukhopadhyay
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Hayat Aljaibeji
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Nabil Sulaiman
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Joao Fadista
- Department of Epidemiology Research, Statens Serum Institute, Copenhagen, Denmark; Lund University Diabetes Centre (LUDC), Department of Clinical Sciences, Lund University, Malmö, Sweden
| | - Albert Salehi
- Lund University Diabetes Centre (LUDC), Department of Clinical Sciences, Lund University, Malmö, Sweden
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40
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Yu X, Meng X, Liu Y, Wang X, Wang TJ, Zhang A, Li N, Qi X, Liu B, Xu ZY. The chromatin remodeler ZmCHB101 impacts alternative splicing contexts in response to osmotic stress. PLANT CELL REPORTS 2019; 38:131-145. [PMID: 30443733 DOI: 10.1007/s00299-018-2354-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 11/07/2018] [Indexed: 05/16/2023]
Abstract
Maize SWI3-type chromatin remodeler impacts alternative splicing contexts in response to osmotic stress by altering nucleosome density and affecting transcriptional elongation rate. Alternative splicing (AS) is commonly found in higher eukaryotes and is an important posttranscriptional regulatory mechanism to generate transcript diversity. AS has been widely accepted as playing essential roles in different biological processes including growth, development, signal transduction and responses to biotic and abiotic stresses in plants. However, whether and how chromatin remodeling complex functions in AS in plant under osmotic stress remains unknown. Here, we show that a maize SWI3D protein, ZmCHB101, impacts AS contexts in response to osmotic stress. Genome-wide analysis of mRNA contexts in response to osmotic stress using ZmCHB101-RNAi lines reveals that ZmCHB101 impacts alternative splicing contexts of a subset of osmotic stress-responsive genes. Intriguingly, ZmCHB101-mediated regulation of gene expression and AS is largely uncoupled, pointing to diverse molecular functions of ZmCHB101 in transcriptional and posttranscriptional regulation. We further found ZmCHB101 impacts the alternative splicing contexts by influencing alteration of chromatin and histone modification status as well as transcriptional elongation rates mediated by RNA polymerase II. Taken together, our findings suggest a novel insight of how plant chromatin remodeling complex impacts AS under osmotic stress .
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Affiliation(s)
- Xiaoming Yu
- School of Agronomy, Jilin Agricultural Science and Technology University, Jilin, 132301, People's Republic of China
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Xinchao Meng
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Xutong Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China
- Department of Agronomy, Purdue University, West Lafayette, USA
| | - Tian-Jing Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Ai Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Xin Qi
- Department of Agronomy, Jilin Agricultural University, Changchun, 130118, People's Republic of China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China.
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, People's Republic of China.
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Liu S, Hausmann S, Carlson SM, Fuentes ME, Francis JW, Pillai R, Lofgren SM, Hulea L, Tandoc K, Lu J, Li A, Nguyen ND, Caporicci M, Kim MP, Maitra A, Wang H, Wistuba II, Porco JA, Bassik MC, Elias JE, Song J, Topisirovic I, Van Rechem C, Mazur PK, Gozani O. METTL13 Methylation of eEF1A Increases Translational Output to Promote Tumorigenesis. Cell 2019; 176:491-504.e21. [PMID: 30612740 PMCID: PMC6499081 DOI: 10.1016/j.cell.2018.11.038] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 10/18/2018] [Accepted: 11/21/2018] [Indexed: 12/25/2022]
Abstract
Increased protein synthesis plays an etiologic role in diverse cancers. Here, we demonstrate that METTL13 (methyltransferase-like 13) dimethylation of eEF1A (eukaryotic elongation factor 1A) lysine 55 (eEF1AK55me2) is utilized by Ras-driven cancers to increase translational output and promote tumorigenesis in vivo. METTL13-catalyzed eEF1A methylation increases eEF1A's intrinsic GTPase activity in vitro and protein production in cells. METTL13 and eEF1AK55me2 levels are upregulated in cancer and negatively correlate with pancreatic and lung cancer patient survival. METTL13 deletion and eEF1AK55me2 loss dramatically reduce Ras-driven neoplastic growth in mouse models and in patient-derived xenografts (PDXs) from primary pancreatic and lung tumors. Finally, METTL13 depletion renders PDX tumors hypersensitive to drugs that target growth-signaling pathways. Together, our work uncovers a mechanism by which lethal cancers become dependent on the METTL13-eEF1AK55me2 axis to meet their elevated protein synthesis requirement and suggests that METTL13 inhibition may constitute a targetable vulnerability of tumors driven by aberrant Ras signaling.
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Affiliation(s)
- Shuo Liu
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Simone Hausmann
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Mary Esmeralda Fuentes
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Renjitha Pillai
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Shane Michael Lofgren
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Laura Hulea
- Lady Davis Institute and Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3T 1E2, Canada
| | - Kristofferson Tandoc
- Lady Davis Institute and Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3T 1E2, Canada
| | - Jiuwei Lu
- Department of Biochemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Ami Li
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nicholas Dang Nguyen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Marcello Caporicci
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael Paul Kim
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Anirban Maitra
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Huamin Wang
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ignacio Ivan Wistuba
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Michael Cory Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Joshua Eric Elias
- Deparment of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, Riverside, CA 92521, USA
| | - Ivan Topisirovic
- Lady Davis Institute and Gerald Bronfman Department of Oncology, McGill University, Montreal, QC H3T 1E2, Canada
| | - Capucine Van Rechem
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Pawel Karol Mazur
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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Sohtome Y, Sodeoka M. Development of Chaetocin and
S
‐Adenosylmethionine Analogues as Tools for Studying Protein Methylation. CHEM REC 2018; 18:1660-1671. [DOI: 10.1002/tcr.201800118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/25/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Yoshihiro Sohtome
- Synthetic Organic Chemistry LaboratoryRIKEN Cluster for Pioneering Research 2-1 Hirosawa, Wako Saitama Japan
- RIKEN Center for Sustainable Resource Science
- AMED-CREST, Japan Agency for Medical Research and Development
| | - Mikiko Sodeoka
- Synthetic Organic Chemistry LaboratoryRIKEN Cluster for Pioneering Research 2-1 Hirosawa, Wako Saitama Japan
- RIKEN Center for Sustainable Resource Science
- AMED-CREST, Japan Agency for Medical Research and Development
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Serre NBC, Alban C, Bourguignon J, Ravanel S. An outlook on lysine methylation of non-histone proteins in plants. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:4569-4581. [PMID: 29931361 DOI: 10.1093/jxb/ery231] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Protein methylation is a very diverse, widespread, and important post-translational modification affecting all aspects of cellular biology in eukaryotes. Methylation on the side-chain of lysine residues in histones has received considerable attention due to its major role in determining chromatin structure and the epigenetic regulation of gene expression. Over the last 20 years, lysine methylation of non-histone proteins has been recognized as a very common modification that contributes to the fine-tuned regulation of protein function. In plants, our knowledge in this field is much more fragmentary than in yeast and animal cells. In this review, we describe the plant enzymes involved in the methylation of non-histone substrates, and we consider historical and recent advances in the identification of non-histone lysine-methylated proteins in photosynthetic organisms. Finally, we discuss our current knowledge about the role of protein lysine methylation in regulating molecular and cellular functions in plants, and consider challenges for future research.
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Affiliation(s)
- Nelson B C Serre
- Univ. Grenoble Alpes, INRA, CEA, CNRS, BIG, PCV, Grenoble, France
| | - Claude Alban
- Univ. Grenoble Alpes, INRA, CEA, CNRS, BIG, PCV, Grenoble, France
| | | | - Stéphane Ravanel
- Univ. Grenoble Alpes, INRA, CEA, CNRS, BIG, PCV, Grenoble, France
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44
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Jakobsson ME, Małecki JM, Halabelian L, Nilges BS, Pinto R, Kudithipudi S, Munk S, Davydova E, Zuhairi FR, Arrowsmith CH, Jeltsch A, Leidel SA, Olsen JV, Falnes PØ. The dual methyltransferase METTL13 targets N terminus and Lys55 of eEF1A and modulates codon-specific translation rates. Nat Commun 2018; 9:3411. [PMID: 30143613 PMCID: PMC6109062 DOI: 10.1038/s41467-018-05646-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 07/16/2018] [Indexed: 11/09/2022] Open
Abstract
Eukaryotic elongation factor 1 alpha (eEF1A) delivers aminoacyl-tRNA to the ribosome and thereby plays a key role in protein synthesis. Human eEF1A is subject to extensive post-translational methylation, but several of the responsible enzymes remain unknown. Using a wide range of experimental approaches, we here show that human methyltransferase (MTase)-like protein 13 (METTL13) contains two distinct MTase domains targeting the N terminus and Lys55 of eEF1A, respectively. Our biochemical and structural analyses provide detailed mechanistic insights into recognition of the eEF1A N terminus by METTL13. Moreover, through ribosome profiling, we demonstrate that loss of METTL13 function alters translation dynamics and results in changed translation rates of specific codons. In summary, we here unravel the function of a human MTase, showing that it methylates eEF1A and modulates mRNA translation in a codon-specific manner. Eukaryotic elongation factor 1 alpha (eEF1A) is subject to extensive post-translational methylation but not all responsible enzymes are known. Here, the authors identify METTL13 as an eEF1A methyltransferase with dual specificity, which is involved in the codon-specific modulation of mRNA translation.
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Affiliation(s)
- Magnus E Jakobsson
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316, Oslo, Norway. .,Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research (NNF-CPR), University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.
| | - Jędrzej M Małecki
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316, Oslo, Norway
| | - Levon Halabelian
- Structural Genomics Consortium, and Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - Benedikt S Nilges
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149, Muenster, Germany.,Cells-in-Motion Cluster of Excellence, University of Muenster, 48149, Muenster, Germany
| | - Rita Pinto
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316, Oslo, Norway
| | - Srikanth Kudithipudi
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Stephanie Munk
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research (NNF-CPR), University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Erna Davydova
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316, Oslo, Norway
| | - Fawzi R Zuhairi
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316, Oslo, Norway
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, and Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Sebastian A Leidel
- Max Planck Research Group for RNA Biology, Max Planck Institute for Molecular Biomedicine, 48149, Muenster, Germany.,Cells-in-Motion Cluster of Excellence, University of Muenster, 48149, Muenster, Germany
| | - Jesper V Olsen
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research (NNF-CPR), University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark.
| | - Pål Ø Falnes
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316, Oslo, Norway.
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45
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Chen F, Xue Y, Pan N, Bhatti MZ, Niu T, Chen J. New contribution to the morphology and molecular mechanism of Euplotes encysticus encystment. Sci Rep 2018; 8:12795. [PMID: 30143743 PMCID: PMC6109176 DOI: 10.1038/s41598-018-31160-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 08/13/2018] [Indexed: 11/30/2022] Open
Abstract
Ciliated protists are a large group of single-cell eukaryotes, leading to the resting cysts in unfavorable environmental condition. However, the underlying molecular mechanism of encystment in the free-living ciliates is poorly understood. Here we show that the resting cysts are better than the vegetative cells of Euplotes encysticus in adverse survivor with respect to energy metabolism. Therefore scale identification of encystment-related proteins in Euplotes encysticus was investigated by iTRAQ analysis. We analyzed a total of 130 proteins, in which 19 proteins involving 12 upregulated and 7 downregulated proteins were associated with encystment in the resting cysts in comparison with the vegetative cells. Moreover, direct fluorescent labeling analysis showed that the vegetative cells treated with shRNA-β-tubulin recombinant E. coli accumulated a large number of granular materials, and dramatic cell morphology changes. Importantly, the cell membrane rupture phenomenon was observed after three weeks of shRNA-β-tubulin interference as compared to the control group. These results revealed that different proteins might play an important role in the process of the vegetative cells into the resting cysts. These results will help to reveal the morphological changes and molecular mechanism of resting cyst formation of ciliates.
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Affiliation(s)
- Fenfen Chen
- School of Life Sciences, East China Normal University, Shanghai, 200241, P. R. China
| | - Yanyan Xue
- School of Life Sciences, East China Normal University, Shanghai, 200241, P. R. China
| | - Nan Pan
- School of Life Sciences, East China Normal University, Shanghai, 200241, P. R. China
| | - Muhammad Zeeshan Bhatti
- Institute of Biomedical Sciences, School of Life Sciences, East China Normal University, Shanghai, 200241, P. R. China
- Department of Molecular Medicine, National University of Medical Sciences, Rawalpindi, Pakistan
| | - Tao Niu
- School of Life Sciences, East China Normal University, Shanghai, 200241, P. R. China
| | - Jiwu Chen
- School of Life Sciences, East China Normal University, Shanghai, 200241, P. R. China.
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Clarke SG. The ribosome: A hot spot for the identification of new types of protein methyltransferases. J Biol Chem 2018; 293:10438-10446. [PMID: 29743234 DOI: 10.1074/jbc.aw118.003235] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Cellular physiology depends on the alteration of protein structures by covalent modification reactions. Using a combination of bioinformatic, genetic, biochemical, and mass spectrometric approaches, it has been possible to probe ribosomal proteins from the yeast Saccharomyces cerevisiae for post-translationally methylated amino acid residues and for the enzymes that catalyze these modifications. These efforts have resulted in the identification and characterization of the first protein histidine methyltransferase, the first N-terminal protein methyltransferase, two unusual types of protein arginine methyltransferases, and a new type of cysteine methylation. Two of these enzymes may modify their substrates during ribosomal assembly because the final methylated histidine and arginine residues are buried deep within the ribosome with contacts only with RNA. Two of these modifications occur broadly in eukaryotes, including humans, whereas the others demonstrate a more limited phylogenetic range. Analysis of strains where the methyltransferase genes are deleted has given insight into the physiological roles of these modifications. These reactions described here add diversity to the modifications that generate the typical methylated lysine and arginine residues previously described in histones and other proteins.
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Affiliation(s)
- Steven G Clarke
- From the Department of Chemistry and Biochemistry and the Molecular Biology Institute, UCLA, Los Angeles, California 90095
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