1
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Liu J, Huang J, Lu J, Ouyang R, Xu W, Zhang J, Chen-Xiao K, Wu C, Shang D, Go VLWB, Guo J, Xiao GG. Obg-like ATPase 1 exacerbated gemcitabine drug resistance of pancreatic cancer. iScience 2024; 27:110027. [PMID: 38883822 PMCID: PMC11177196 DOI: 10.1016/j.isci.2024.110027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 04/01/2024] [Accepted: 05/16/2024] [Indexed: 06/18/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly malignant disease with a poor prognosis due to inefficient diagnosis and tenacious drug resistance. Obg-like ATPase 1 (OLA1) is overexpressed in many malignant tumors. The molecular mechanism of OLA1 underlying gemcitabine (GEM)-induced drug resistance was investigated in this study. An enhanced expression of OLA1 was observed in a GEM acquired resistant pancreatic cancer cell lines and in patients with pancreatic cancer. Overexpressed OLA1 showed poor overall survival rates in patients with pancreatic cancer. Dysregulation of the OLA1 reduced expression of CD44+/CD133+, and improved the sensitivity of pancreatic cancer cells to GEM. OLA1 highly expression facilitated the formation of the OLA1/Sonic Hedgehog (SHH)/Hedgehog-interacting protein (HHIP) complex in nuclei, resulting in the inhibition of negative feedback of Hedgehog signaling induced by HHIP. This study suggests that OLA1 may be developed as an innovative drug target for an effective therapy of pancreatic cancer.
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Affiliation(s)
- Jianzhou Liu
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, China
- Institute of clinical medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jing Huang
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, China
| | - Jun Lu
- Department of General Surgery, Peking University Third Hospital, Beijing 100191, China
| | - Runze Ouyang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Wenchao Xu
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jianlu Zhang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Kevin Chen-Xiao
- Department of Nutritional Sciences and Toxicology, University of California Berkeley, San Francisco, CA, USA
| | - Chengjun Wu
- School of Biomedical Engineering, Dalian University of Technology, Dalian, China
| | - Dong Shang
- Department of General Surgery, Clinical Laboratory of Integrative Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Vay Liang W Bill Go
- The UCLA Agi Hirshberg Center for Pancreatic Diseases, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Junchao Guo
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Gary Guishan Xiao
- State Key Laboratory of Fine Chemicals, Department of Pharmaceutical Sciences, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, China
- The UCLA Agi Hirshberg Center for Pancreatic Diseases, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Functional Genomics and Proteomics Laboratory, Osteoporosis Research Center, Creighton University Medical Center, Omaha, NE, USA
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2
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Yoshino Y, Ogoh H, Iichi Y, Sasaki T, Yoshida T, Ichimura S, Nakayama M, Xi W, Fujita H, Kikuchi M, Fang Z, Li X, Abe T, Futakuchi M, Nakamura Y, Watanabe T, Chiba N. Knockout of Brca1-interacting factor Ola1 in female mice induces tumors with estrogen suppressible centrosome amplification. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167138. [PMID: 38537683 DOI: 10.1016/j.bbadis.2024.167138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 03/06/2024] [Accepted: 03/18/2024] [Indexed: 04/08/2024]
Abstract
Obg-like ATPase 1 (OLA1) is a binding protein of Breast cancer gene 1 (BRCA1), germline pathogenic variants of which cause hereditary breast cancer. Cancer-associated variants of BRCA1 and OLA1 are deficient in the regulation of centrosome number. Although OLA1 might function as a tumor suppressor, the relevance of OLA1 deficiency to carcinogenesis is unclear. Here, we generated Ola1 knockout mice. Aged female Ola1+/- mice developed lymphoproliferative diseases, including malignant lymphoma. The lymphoma tissues had low expression of Ola1 and an increase in the number of cells with centrosome amplification. Interestingly, the proportion of cells with centrosome amplification in normal spleen from Ola1+/- mice was higher in male mice than in female mice. In human cells, estrogen stimulation attenuated centrosome amplification induced by OLA1 knockdown. Previous reports indicate that prominent centrosome amplification causes cell death but does not promote tumorigenesis. Thus, in the current study, the mild centrosome amplification observed under estrogen stimulation in Ola1+/- female mice is likely more tumorigenic than the prominent centrosome amplification observed in Ola1+/- male mice. Our findings provide a possible sex-dependent mechanism of the tumor suppressor function of OLA1.
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Affiliation(s)
- Yuki Yoshino
- Department of Cancer Biology, Institute of Aging, Development, and Cancer, Tohoku University, 4-1 Seiryomachi, Aoba-ku, Sendai 980-8575, Japan; Laboratory of Cancer Biology, Graduate School of Life Sciences, Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan; Department of Cancer Biology, Tohoku University Graduate School of Medicine, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan
| | - Honami Ogoh
- Department of Biological Science, Graduate School of Humanities and Sciences, Nara Women's University, Kitauoya-Nishimachi, Nara, 630-8506, Japan
| | - Yudai Iichi
- Department of Cancer Biology, Institute of Aging, Development, and Cancer, Tohoku University, 4-1 Seiryomachi, Aoba-ku, Sendai 980-8575, Japan; Laboratory of Cancer Biology, Graduate School of Life Sciences, Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan
| | - Tomohiro Sasaki
- Department of Cancer Biology, Institute of Aging, Development, and Cancer, Tohoku University, 4-1 Seiryomachi, Aoba-ku, Sendai 980-8575, Japan; Laboratory of Cancer Biology, Graduate School of Life Sciences, Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan
| | - Takahiro Yoshida
- Department of Cancer Biology, Institute of Aging, Development, and Cancer, Tohoku University, 4-1 Seiryomachi, Aoba-ku, Sendai 980-8575, Japan; Laboratory of Cancer Biology, Graduate School of Life Sciences, Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan
| | - Shiori Ichimura
- Department of Cancer Biology, Institute of Aging, Development, and Cancer, Tohoku University, 4-1 Seiryomachi, Aoba-ku, Sendai 980-8575, Japan; Laboratory of Cancer Biology, Graduate School of Life Sciences, Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan
| | - Masahiro Nakayama
- Department of Molecular Immunology, Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan; Laboratory of Molecular Immunology, Graduate School of Life Sciences, Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan
| | - Wu Xi
- Department of Cancer Biology, Institute of Aging, Development, and Cancer, Tohoku University, 4-1 Seiryomachi, Aoba-ku, Sendai 980-8575, Japan; Laboratory of Cancer Biology, Graduate School of Life Sciences, Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan
| | - Hiroki Fujita
- Department of Cancer Biology, Institute of Aging, Development, and Cancer, Tohoku University, 4-1 Seiryomachi, Aoba-ku, Sendai 980-8575, Japan; Laboratory of Cancer Biology, Graduate School of Life Sciences, Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan
| | - Megumi Kikuchi
- Department of Cancer Biology, Institute of Aging, Development, and Cancer, Tohoku University, 4-1 Seiryomachi, Aoba-ku, Sendai 980-8575, Japan; Laboratory of Cancer Biology, Graduate School of Life Sciences, Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan
| | - Zhenzhou Fang
- Department of Cancer Biology, Institute of Aging, Development, and Cancer, Tohoku University, 4-1 Seiryomachi, Aoba-ku, Sendai 980-8575, Japan; Department of Cancer Biology, Tohoku University Graduate School of Medicine, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan
| | - Xingming Li
- Department of Cancer Biology, Institute of Aging, Development, and Cancer, Tohoku University, 4-1 Seiryomachi, Aoba-ku, Sendai 980-8575, Japan; Laboratory of Cancer Biology, Graduate School of Life Sciences, Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan
| | - Takaya Abe
- Laboratory for Animal Resources and Genetic Engineering, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Mitsuru Futakuchi
- Department of Pathology, Yamagata University Faculty of Medicine, 2-2-2 Iida-Nishi, Yamagata 990-9585, Japan
| | - Yasuhiro Nakamura
- Division of Pathology, Faculty of Medicine, Tohoku Medical and Pharmaceutical University, 1-15-1 Fukumuro, Miyagino-ku, Sendai 983-8536, Japan
| | - Toshio Watanabe
- Department of Biological Science, Graduate School of Humanities and Sciences, Nara Women's University, Kitauoya-Nishimachi, Nara, 630-8506, Japan
| | - Natsuko Chiba
- Department of Cancer Biology, Institute of Aging, Development, and Cancer, Tohoku University, 4-1 Seiryomachi, Aoba-ku, Sendai 980-8575, Japan; Laboratory of Cancer Biology, Graduate School of Life Sciences, Tohoku University, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan; Department of Cancer Biology, Tohoku University Graduate School of Medicine, 4-1 Seiryomachi Aoba-ku, Sendai 980-8575, Japan.
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3
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Komlosi K, Glocker C, Hsu-Rehder HH, Alter S, Kopp J, Hotz A, Zimmer AD, Hausser I, Sandhoff R, Oji V, Fischer J. Autosomal Dominant Lamellar Ichthyosis Due to a Missense Variant in the Gene NKPD1. J Invest Dermatol 2024:S0022-202X(24)00303-8. [PMID: 38642798 DOI: 10.1016/j.jid.2024.03.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/23/2024] [Accepted: 03/08/2024] [Indexed: 04/22/2024]
Abstract
The identification of monogenic causes for cornification disorders has enhanced our understanding of epidermal differentiation and skin barrier function. Autosomal dominant lamellar ichthyosis is a rare condition, and ASPRV1 was the only gene linked to autosomal dominant lamellar ichthyosis to date. We identified a heterozygous variant (ENST00000686631.1:c.1372G>T, p.[Val458Phe]) in the NKPD1 gene in 7 individuals from a 4-generation German pedigree with generalized lamellar ichthyosis by whole-exome sequencing. Segregation analysis confirmed its presence in affected individuals, resulting in a logarithm of the odds score of 3.31. NKPD1 encodes the NKPD1 protein, implicated in the plasma membrane; its role in human disease is as yet unknown. Skin histology showed moderate acanthosis and compact orthohyperkeratosis, and the ultrastructure differed clearly from that in ASPRV1-autosomal dominant lamellar ichthyosis. Although NKPD1 mRNA expression increased during keratinocyte differentiation, stratum corneum ceramides exhibited no significant changes. However, affected individuals showed an elevated ratio of protein-bound ceramides to omega-esterified ceramides. This highlights NKPD1's role in autosomal dominant lamellar ichthyosis, impacting ceramide metabolism and skin lipid barrier formation, as demonstrated through functional characterization.
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Affiliation(s)
- Katalin Komlosi
- Institute of Human Genetics, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Cornification Disorders, Freiburg Center for Rare Diseases, Medical Center, University of Freiburg, Freiburg, Germany
| | - Cristina Glocker
- Institute of Human Genetics, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Cornification Disorders, Freiburg Center for Rare Diseases, Medical Center, University of Freiburg, Freiburg, Germany
| | - Hao-Hsiang Hsu-Rehder
- Institute of Human Genetics, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Cornification Disorders, Freiburg Center for Rare Diseases, Medical Center, University of Freiburg, Freiburg, Germany
| | - Svenja Alter
- Institute of Human Genetics, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Cornification Disorders, Freiburg Center for Rare Diseases, Medical Center, University of Freiburg, Freiburg, Germany
| | - Julia Kopp
- Institute of Human Genetics, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Cornification Disorders, Freiburg Center for Rare Diseases, Medical Center, University of Freiburg, Freiburg, Germany
| | - Alrun Hotz
- Institute of Human Genetics, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Cornification Disorders, Freiburg Center for Rare Diseases, Medical Center, University of Freiburg, Freiburg, Germany
| | - Andreas David Zimmer
- Institute of Human Genetics, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Cornification Disorders, Freiburg Center for Rare Diseases, Medical Center, University of Freiburg, Freiburg, Germany
| | - Ingrid Hausser
- Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Roger Sandhoff
- Lipid Pathobiochemistry Group, German Cancer Research Center, Heidelberg, Germany
| | - Vinzenz Oji
- Department of Dermatology, University Hospital Münster, Münster, Germany
| | - Judith Fischer
- Institute of Human Genetics, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Center for Cornification Disorders, Freiburg Center for Rare Diseases, Medical Center, University of Freiburg, Freiburg, Germany.
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4
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Chen P, Huang R, Hazbun TR. Unlocking the Mysteries of Alpha-N-Terminal Methylation and its Diverse Regulatory Functions. J Biol Chem 2023:104843. [PMID: 37209820 PMCID: PMC10293735 DOI: 10.1016/j.jbc.2023.104843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/22/2023] Open
Abstract
Protein post-translation modifications (PTMs) are a critical regulatory mechanism of protein function. Protein α-N-terminal (Nα) methylation is a conserved PTM across prokaryotes and eukaryotes. Studies of the Nα methyltransferases responsible for Να methylation and their substrate proteins have shown that the PTM involves diverse biological processes, including protein synthesis and degradation, cell division, DNA damage response, and transcription regulation. This review provides an overview of the progress toward the regulatory function of Να methyltransferases and their substrate landscape. More than 200 proteins in humans and 45 in yeast are potential substrates for protein Nα methylation based on the canonical recognition motif, XP[KR]. Based on recent evidence for a less stringent motif requirement, the number of substrates might be increased, but further validation is needed to solidify this concept. A comparison of the motif in substrate orthologs in selected eukaryotic species indicates intriguing gain and loss of the motif across the evolutionary landscape. We discuss the state of knowledge in the field that has provided insights into the regulation of protein Να methyltransferases and their role in cellular physiology and disease. We also outline the current research tools that are key to understanding Να methylation. Finally, challenges are identified and discussed that would aid in unlocking a system-level view of the roles of Να methylation in diverse cellular pathways.
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Affiliation(s)
- Panyue Chen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Rong Huang
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States; Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States
| | - Tony R Hazbun
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States; Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana 47907, United States.
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5
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The Role of the Universally Conserved ATPase YchF/Ola1 in Translation Regulation during Cellular Stress. Microorganisms 2021; 10:microorganisms10010014. [PMID: 35056463 PMCID: PMC8779481 DOI: 10.3390/microorganisms10010014] [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: 11/27/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 11/17/2022] Open
Abstract
The ability to respond to metabolic or environmental changes is an essential feature in all cells and involves both transcriptional and translational regulators that adjust the metabolic activity to fluctuating conditions. While transcriptional regulation has been studied in detail, the important role of the ribosome as an additional player in regulating gene expression is only beginning to emerge. Ribosome-interacting proteins are central to this translational regulation and include universally conserved ribosome interacting proteins, such as the ATPase YchF (Ola1 in eukaryotes). In both eukaryotes and bacteria, the cellular concentrations of YchF/Ola1 determine the ability to cope with different stress conditions and are linked to several pathologies in humans. The available data indicate that YchF/Ola1 regulates the stress response via controlling non-canonical translation initiation and via protein degradation. Although the molecular mechanisms appear to be different between bacteria and eukaryotes, increased non-canonical translation initiation is a common consequence of YchF/Ola1 regulated translational control in E. coli and H. sapiens. In this review, we summarize recent insights into the role of the universally conserved ATPase YchF/Ola1 in adapting translation to unfavourable conditions.
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6
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Landwehr V, Milanov M, Angebauer L, Hong J, Jüngert G, Hiersemenzel A, Siebler A, Schmit F, Öztürk Y, Dannenmaier S, Drepper F, Warscheid B, Koch HG. The Universally Conserved ATPase YchF Regulates Translation of Leaderless mRNA in Response to Stress Conditions. Front Mol Biosci 2021; 8:643696. [PMID: 34026826 PMCID: PMC8138138 DOI: 10.3389/fmolb.2021.643696] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/13/2021] [Indexed: 12/14/2022] Open
Abstract
The universally conserved P-loop GTPases control diverse cellular processes, like signal transduction, ribosome assembly, cell motility, and intracellular transport and translation. YchF belongs to the Obg-family of P-loop GTPases and is one of the least characterized member of this family. It is unique because it preferentially hydrolyses ATP rather than GTP, but its physiological role is largely unknown. Studies in different organisms including humans suggest a possible role of YchF in regulating the cellular adaptation to stress conditions. In the current study, we explored the role of YchF in the model organism Escherichia coli. By western blot and promoter fusion experiments, we demonstrate that YchF levels decrease during stress conditions or when cells enter stationary phase. The decline in YchF levels trigger increased stress resistance and cells lacking YchF are resistant to multiple stress conditions, like oxidative stress, replication stress, or translational stress. By in vivo site directed cross-linking we demonstrate that YchF interacts with the translation initiation factor 3 (IF3) and with multiple ribosomal proteins at the surface of the small ribosomal subunit. The absence of YchF enhances the anti-association activity of IF3, stimulates the translation of leaderless mRNAs, and increases the resistance against the endoribonuclease MazF, which generates leaderless mRNAs during stress conditions. In summary, our data identify YchF as a stress-responsive regulator of leaderless mRNA translation.
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Affiliation(s)
- Victoria Landwehr
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Martin Milanov
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Larissa Angebauer
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Jiang Hong
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
- Faculty of Biology, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Gabriela Jüngert
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Anna Hiersemenzel
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Ariane Siebler
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Fränk Schmit
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Yavuz Öztürk
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Stefan Dannenmaier
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Friedel Drepper
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Bettina Warscheid
- Spemann Graduate School of Biology and Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
- Biochemistry and Functional Proteomics, Institute of Biology II, Faculty of Biology, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
- Signalling Research Centers BIOSS and CIBSS, University Freiburg, Freiburg, Germany
| | - Hans-Georg Koch
- Institute for Biochemistry and Molecular Biology, Zentrum für Biochemie und Molekulare Medizin, Faculty of Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
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7
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Liu Y, Makarova KS, Huang WC, Wolf YI, Nikolskaya AN, Zhang X, Cai M, Zhang CJ, Xu W, Luo Z, Cheng L, Koonin EV, Li M. Expanded diversity of Asgard archaea and their relationships with eukaryotes. Nature 2021; 593:553-557. [PMID: 33911286 PMCID: PMC11165668 DOI: 10.1038/s41586-021-03494-3] [Citation(s) in RCA: 116] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 03/26/2021] [Indexed: 01/21/2023]
Abstract
Asgard is a recently discovered superphylum of archaea that appears to include the closest archaeal relatives of eukaryotes1-5. Debate continues as to whether the archaeal ancestor of eukaryotes belongs within the Asgard superphylum or whether this ancestor is a sister group to all other archaea (that is, a two-domain versus a three-domain tree of life)6-8. Here we present a comparative analysis of 162 complete or nearly complete genomes of Asgard archaea, including 75 metagenome-assembled genomes that-to our knowledge-have not previously been reported. Our results substantially expand the phylogenetic diversity of Asgard and lead us to propose six additional phyla that include a deep branch that we have provisionally named Wukongarchaeota. Our phylogenomic analysis does not resolve unequivocally the evolutionary relationship between eukaryotes and Asgard archaea, but instead-depending on the choice of species and conserved genes used to build the phylogeny-supports either the origin of eukaryotes from within Asgard (as a sister group to the expanded Heimdallarchaeota-Wukongarchaeota branch) or a deeper branch for the eukaryote ancestor within archaea. Our comprehensive protein domain analysis using the 162 Asgard genomes results in a major expansion of the set of eukaryotic signature proteins. The Asgard eukaryotic signature proteins show variable phyletic distributions and domain architectures, which is suggestive of dynamic evolution through horizontal gene transfer, gene loss, gene duplication and domain shuffling. The phylogenomics of the Asgard archaea points to the accumulation of the components of the mobile archaeal 'eukaryome' in the archaeal ancestor of eukaryotes (within or outside Asgard) through extensive horizontal gene transfer.
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Affiliation(s)
- Yang Liu
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, P. R. China
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Wen-Cong Huang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, P. R. China
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Anastasia N Nikolskaya
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Xinxu Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, P. R. China
| | - Mingwei Cai
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, P. R. China
| | - Cui-Jing Zhang
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, P. R. China
| | - Wei Xu
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, P. R. China
| | - Zhuhua Luo
- Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, Ministry of Natural Resources, Xiamen, P. R. China
| | - Lei Cheng
- Key Laboratory of Development and Application of Rural Renewable Energy, Biogas Institute of Ministry of Agriculture, Chengdu, P. R. China
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
| | - Meng Li
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, P. R. China.
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8
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Thakor N, Kothe U, Wieden HJ, Patel TR. Proceedings of the 14th annual RiboWest conference: perspectives and outcome. Biochem Cell Biol 2020; 98:vii-ix. [PMID: 31934779 DOI: 10.1139/bcb-2019-0187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The RiboWest Conference brings together RNA researchers in Canada with the 2-fold goals of fostering internationally competitive RNA research and of training the next generation of scientists. The 14th Annual RiboWest conference (RiboWest 2018) was held at the University of Lethbridge (Lethbridge, Alberta) from June 10th to 13th, 2018. This meeting was focused on all major aspects of RNA research, ranging from understanding the cellular role of RNA, studying RNA interactions and structures, and employing them as a therapeutic tool. The invited keynote speakers (5) provided insights into the wide-range of RNA-based research. One of the unique features of this conference was that the majority of the oral presentations were given by the trainees (undergraduate/graduate students and postdoctoral researchers). Hosted by the Alberta RNA Research and Training Institute (ARRTI) at the University of Lethbridge as the leading center of RNA research in Western Canada, the RiboWest 2018 was well attended by researchers from across the country (>110 attendees in total). This conference proceedings editorial presents the overview of the conference, and briefly introduces articles published in this special issue of Biochemistry and Cell Biology.
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Affiliation(s)
- Nehal Thakor
- Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry & Biochemistry, University of Lethbridge, 4401 University Drive West, T1K 3M4, Lethbridge, Alberta, Canada.,Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry & Biochemistry, University of Lethbridge, 4401 University Drive West, T1K 3M4, Lethbridge, Alberta, Canada
| | - Ute Kothe
- Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry & Biochemistry, University of Lethbridge, 4401 University Drive West, T1K 3M4, Lethbridge, Alberta, Canada.,Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry & Biochemistry, University of Lethbridge, 4401 University Drive West, T1K 3M4, Lethbridge, Alberta, Canada
| | - Hans-Joachim Wieden
- Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry & Biochemistry, University of Lethbridge, 4401 University Drive West, T1K 3M4, Lethbridge, Alberta, Canada.,Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry & Biochemistry, University of Lethbridge, 4401 University Drive West, T1K 3M4, Lethbridge, Alberta, Canada
| | - Trushar R Patel
- Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry & Biochemistry, University of Lethbridge, 4401 University Drive West, T1K 3M4, Lethbridge, Alberta, Canada.,Alberta RNA Research and Training Institute (ARRTI), Department of Chemistry & Biochemistry, University of Lethbridge, 4401 University Drive West, T1K 3M4, Lethbridge, Alberta, Canada
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Jia K, Huang G, Wu W, Shrestha R, Wu B, Xiong Y, Li P. In vivo methylation of OLA1 revealed by activity-based target profiling of NTMT1. Chem Sci 2019; 10:8094-8099. [PMID: 31857877 PMCID: PMC6889141 DOI: 10.1039/c9sc02550b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 08/08/2019] [Indexed: 01/11/2023] Open
Abstract
Target profiling of NTMT1 by Hey-SAM revealed that OLA1 undergoes N-terminal methylation catalyzed by NTMT1 in vivo.
N-Terminal methyltransferase 1 (NTMT1) catalyzes the N-terminal methylation of proteins with a specific N-terminal motif after methionine removal. Aberrant N-terminal methylation has been implicated in several cancers and developmental diseases. Together with motif sequence and signal peptide analyses, activity-based substrate profiling of NTMT1 utilizing (E)-hex-2-en-5-ynyl-S-adenosyl-l-methionine (Hey-SAM) revealed 72 potential targets, which include several previously confirmed ones and many unknowns. Target validation using normal and NTMT1 knock-out (KO) HEK293FT cells generated by CRISPR-Cas9 demonstrated that Obg-like ATPase 1 (OLA1), a protein involved in many critical cellular functions, is methylated in vivo by NTMT1. Additionally, Hey-SAM synthesis achieved ≥98% yield for SAH conversion.
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Affiliation(s)
- Kaimin Jia
- Department of Chemistry , Kansas State University , Manhattan , Kansas 66506 , USA .
| | - Gaochao Huang
- Department of Chemistry , Kansas State University , Manhattan , Kansas 66506 , USA .
| | - Wei Wu
- Department of Chemistry , Kansas State University , Manhattan , Kansas 66506 , USA .
| | - Ruben Shrestha
- Department of Chemistry , Kansas State University , Manhattan , Kansas 66506 , USA .
| | - Bingbing Wu
- Department of Chemistry , Kansas State University , Manhattan , Kansas 66506 , USA .
| | - Yulan Xiong
- Department of Anatomy and Physiology , Kansas State University , Manhattan , Kansas 66506 , USA
| | - Ping Li
- Department of Chemistry , Kansas State University , Manhattan , Kansas 66506 , USA .
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