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Onodera W, Asahi T, Sawamura N. Rapid evolution of mammalian APLP1 as a synaptic adhesion molecule. Sci Rep 2021; 11:11305. [PMID: 34050225 PMCID: PMC8163877 DOI: 10.1038/s41598-021-90737-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/17/2021] [Indexed: 01/10/2023] Open
Abstract
Amyloid precursor protein (APP) family members are involved in essential neuronal development including neurite outgrowth, neuronal migration and maturation of synapse and neuromuscular junction. Among the APP gene family members, amyloid precursor-like protein 1 (APLP1) is selectively expressed in neurons and has specialized functions during synaptogenesis. Although a potential role for APLP1 in neuronal evolution has been indicated, its precise evolutionary and functional contributions are unknown. This study shows the molecular evolution of the vertebrate APP family based on phylogenetic analysis, while contrasting the evolutionary differences within the APP family. Phylogenetic analysis showed 15 times higher substitution rate that is driven by positive selection at the stem branch of the mammalian APLP1, resulting in dissimilar protein sequences compared to APP/APLP2. Docking simulation identified one positively selected site in APLP1 that alters the heparin-binding site, which could affect its function, and dimerization rate. Furthermore, the evolutionary rate covariation between the mammalian APP family and synaptic adhesion molecules (SAMs) was confirmed, indicating that only APLP1 has evolved to gain synaptic adhesion property. Overall, our results suggest that the enhanced synaptogenesis property of APLP1 as one of the SAMs may have played a role in mammalian brain evolution.
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Affiliation(s)
- Wataru Onodera
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo, 162-8480, Japan
| | - Toru Asahi
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo, 162-8480, Japan.,Research Organization for Nano & Life Innovation, Waseda University, #03C309, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo, 162-8480, Japan
| | - Naoya Sawamura
- Research Organization for Nano & Life Innovation, Waseda University, #03C309, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo, 162-8480, Japan. .,Green Computing Systems Research Organization, Waseda University, Shinjuku, Japan.
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Ovens AJ, Scott JW, Langendorf CG, Kemp BE, Oakhill JS, Smiles WJ. Post-Translational Modifications of the Energy Guardian AMP-Activated Protein Kinase. Int J Mol Sci 2021; 22:ijms22031229. [PMID: 33513781 PMCID: PMC7866021 DOI: 10.3390/ijms22031229] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 01/20/2021] [Accepted: 01/22/2021] [Indexed: 01/13/2023] Open
Abstract
Physical exercise elicits physiological metabolic perturbations such as energetic and oxidative stress; however, a diverse range of cellular processes are stimulated in response to combat these challenges and maintain cellular energy homeostasis. AMP-activated protein kinase (AMPK) is a highly conserved enzyme that acts as a metabolic fuel sensor and is central to this adaptive response to exercise. The complexity of AMPK’s role in modulating a range of cellular signalling cascades is well documented, yet aside from its well-characterised regulation by activation loop phosphorylation, AMPK is further subject to a multitude of additional regulatory stimuli. Therefore, in this review we comprehensively outline current knowledge around the post-translational modifications of AMPK, including novel phosphorylation sites, as well as underappreciated roles for ubiquitination, sumoylation, acetylation, methylation and oxidation. We provide insight into the physiological ramifications of these AMPK modifications, which not only affect its activity, but also subcellular localisation, nutrient interactions and protein stability. Lastly, we highlight the current knowledge gaps in this area of AMPK research and provide perspectives on how the field can apply greater rigour to the characterisation of novel AMPK regulatory modifications.
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Affiliation(s)
- Ashley J. Ovens
- Metabolic Signalling Laboratory, St Vincent’s Institute of Medical Research, School of Medicine, University of Melbourne, Fitzroy, VIC 3065, Australia; (A.J.O.); (J.S.O.)
- Mary MacKillop Institute for Health Research, Australian Catholic University, Fitzroy, VIC 3000, Australia; (J.W.S.); (B.E.K.)
| | - John W. Scott
- Mary MacKillop Institute for Health Research, Australian Catholic University, Fitzroy, VIC 3000, Australia; (J.W.S.); (B.E.K.)
- Protein Chemistry & Metabolism, St Vincent’s Institute of Medical Research, School of Medicine, University of Melbourne, Fitzroy, VIC 3065, Australia;
- The Florey Institute of Neuroscience and Mental Health, Parkville, VIC 3052, Australia
| | - Christopher G. Langendorf
- Protein Chemistry & Metabolism, St Vincent’s Institute of Medical Research, School of Medicine, University of Melbourne, Fitzroy, VIC 3065, Australia;
| | - Bruce E. Kemp
- Mary MacKillop Institute for Health Research, Australian Catholic University, Fitzroy, VIC 3000, Australia; (J.W.S.); (B.E.K.)
- Protein Chemistry & Metabolism, St Vincent’s Institute of Medical Research, School of Medicine, University of Melbourne, Fitzroy, VIC 3065, Australia;
| | - Jonathan S. Oakhill
- Metabolic Signalling Laboratory, St Vincent’s Institute of Medical Research, School of Medicine, University of Melbourne, Fitzroy, VIC 3065, Australia; (A.J.O.); (J.S.O.)
- Mary MacKillop Institute for Health Research, Australian Catholic University, Fitzroy, VIC 3000, Australia; (J.W.S.); (B.E.K.)
| | - William J. Smiles
- Metabolic Signalling Laboratory, St Vincent’s Institute of Medical Research, School of Medicine, University of Melbourne, Fitzroy, VIC 3065, Australia; (A.J.O.); (J.S.O.)
- Correspondence:
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Furihata H, Yamanaka S, Honda T, Miyauchi Y, Asano A, Shibata N, Tanokura M, Sawasaki T, Miyakawa T. Structural bases of IMiD selectivity that emerges by 5-hydroxythalidomide. Nat Commun 2020; 11:4578. [PMID: 32929090 PMCID: PMC7490372 DOI: 10.1038/s41467-020-18488-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 08/25/2020] [Indexed: 01/31/2023] Open
Abstract
Thalidomide and its derivatives exert not only therapeutic effects as immunomodulatory drugs (IMiDs) but also adverse effects such as teratogenicity, which are due in part to different C2H2 zinc-finger (ZF) transcription factors, IKZF1 (or IKZF3) and SALL4, respectively. Here, we report the structural bases for the SALL4-specific proteasomal degradation induced by 5-hydroxythalidomide, a primary thalidomide metabolite generated by the enzymatic activity of cytochrome P450 isozymes, through the interaction with cereblon (CRBN). The crystal structure of the metabolite-mediated human SALL4-CRBN complex and mutagenesis studies elucidate the complex formation enhanced by the interaction between CRBN and an additional hydroxy group of (S)-5-hydroxythalidomide and the variation in the second residue of β-hairpin structure that underlies the C2H2 ZF-type neo-morphic substrate (neosubstrate) selectivity of 5-hydroxythalidomide. These findings deepen our understanding of the pharmaceutical action of IMiDs and provide structural evidence that the glue-type E3 ligase modulators cause altered neosubstrate specificities through their metabolism.
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Affiliation(s)
- Hirotake Furihata
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Satoshi Yamanaka
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan
| | - Toshiaki Honda
- Department of Nanopharmaceutical Sciences and Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Aichi, 466-8555, Japan
| | - Yumiko Miyauchi
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Atsuko Asano
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Norio Shibata
- Department of Nanopharmaceutical Sciences and Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso-cho, Showa-ku, Aichi, 466-8555, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
| | - Tatsuya Sawasaki
- Proteo-Science Center, Ehime University, 3 Bunkyo-cho, Matsuyama, Ehime, 790-8577, Japan.
| | - Takuya Miyakawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
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Onodera W, Asahi T, Sawamura N. Data for positive selection test and co-evolutionary analysis on mammalian cereblon. Data Brief 2019; 26:104499. [PMID: 31667262 PMCID: PMC6811870 DOI: 10.1016/j.dib.2019.104499] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 09/03/2019] [Accepted: 09/04/2019] [Indexed: 12/04/2022] Open
Abstract
Cereblon (CRBN) is a substrate recognition subunit of the CRL4 E3 ubiquitin ligase complex, directly binding to specific substrates for poly-ubiquitination followed by proteasome-dependent degradation of proteins. Cellular CRBN is responsible for energy metabolism, ion-channel activation, and cellular stress response through binding to proteins related to the respective pathways. As CRBN binds to various proteins, the selective pressure at the interacting surface is expected to result in functional divergence. Here, we present two mammalian CRBN datasets of molecular evolutionary analyses. (1) The multiple sequence alignment data shows that positive selection occurred, determined with a dN/dS calculation. (2) Data on co-evolutionary analysis between vertebrate CRBN and related proteins are represented by calculating the correlation coefficient based on the comparison of phylogenetic trees. Co-evolutionary analysis shows the similarity of evolutionary traits of two proteins. Further molecular, functional interpretation of these analyses is explained in ‘Positive selection of Cereblon modified function including its E3 Ubiquitin Ligase activity and binding efficiency with AMPK’ (W. Onodera, T. Asahi, N. Sawamura, Positive selection of cereblon modified function including its E3 ubiquitin ligase activity and binding efficiency with AMPK. Mol Phylogenet Evol. (2019) 135:78-85. [1]).
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Affiliation(s)
- Wataru Onodera
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo, 162-8480, Japan
| | - Toru Asahi
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo, 162-8480, Japan.,Research Organization for Nano & Life Innovation, Waseda University, Japan
| | - Naoya Sawamura
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo, 162-8480, Japan.,Research Organization for Nano & Life Innovation, Waseda University, Japan
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