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Article ; Online: Discovery of a small protein-encoding cis-regulatory overlapping gene of the tumor suppressor gene Scribble in humans.

Nomura, Yuhta / Dohmae, Naoshi

Communications biology

2021 Volume 4, Issue 1, Page(s) 1098

Abstract: Intensive gene annotation has revealed many functional and regulatory elements in the human genome. Although eukaryotic protein-coding genes are generally transcribed into monocistronic mRNAs, recent studies have discovered additional short open reading ... ...

Abstract	Intensive gene annotation has revealed many functional and regulatory elements in the human genome. Although eukaryotic protein-coding genes are generally transcribed into monocistronic mRNAs, recent studies have discovered additional short open reading frames (sORFs) in mRNAs. Here, we performed proteogenomic data mining for hidden proteins categorized into sORF-encoded polypeptides (SEPs) in human cancers. We identified a new SEP-encoding overlapping sORF (oORF) on the cell polarity determinant Scribble (SCRIB) that is considered a proto-oncogene with tumor suppressor function in Hippo-YAP/TAZ, MAPK/ERK, and PI3K/Akt/mTOR signaling. Reanalysis of clinical human proteomic data revealed translational dysregulation of both SCRIB and its oORF, oSCRIB, during carcinogenesis. Biochemical analyses suggested that the translatable oSCRIB constitutively limits the capacity of eukaryotic ribosomes to translate the downstream SCRIB. These findings provide a new example of cis-regulatory oORFs that function as a ribosomal roadblock and potentially serve as a fail-safe mechanism to normal cells for non-excessive downstream gene expression, which is hijacked in cancer.
MeSH term(s)	Cell Line, Tumor ; Humans ; Membrane Proteins/genetics ; Membrane Proteins/metabolism ; Open Reading Frames/genetics ; Tumor Suppressor Proteins/genetics ; Tumor Suppressor Proteins/metabolism
Chemical Substances	Membrane Proteins ; SCRIB protein, human ; Tumor Suppressor Proteins
Language	English
Publishing date	2021-09-17
Publishing country	England
Document type	Journal Article
ISSN	2399-3642
ISSN (online)	2399-3642
DOI	10.1038/s42003-021-02619-8
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Structural basis for antiepileptic drugs and botulinum neurotoxin recognition of SV2A.

Yamagata, Atsushi / Ito, Kaori / Suzuki, Takehiro / Dohmae, Naoshi / Terada, Tohru / Shirouzu, Mikako

Nature communications

2024 Volume 15, Issue 1, Page(s) 3027

Abstract: More than one percent of people have epilepsy worldwide. Levetiracetam (LEV) is a successful new-generation antiepileptic drug (AED), and its derivative, brivaracetam (BRV), shows improved efficacy. Synaptic vesicle glycoprotein 2a (SV2A), a putative ... ...

Abstract	More than one percent of people have epilepsy worldwide. Levetiracetam (LEV) is a successful new-generation antiepileptic drug (AED), and its derivative, brivaracetam (BRV), shows improved efficacy. Synaptic vesicle glycoprotein 2a (SV2A), a putative membrane transporter in the synaptic vesicles (SVs), has been identified as a target of LEV and BRV. SV2A also serves as a receptor for botulinum neurotoxin (BoNT), which is the most toxic protein and has paradoxically emerged as a potent reagent for therapeutic and cosmetic applications. Nevertheless, no structural analysis on AEDs and BoNT recognition by full-length SV2A has been available. Here we describe the cryo-electron microscopy structures of the full-length SV2A in complex with the BoNT receptor-binding domain, BoNT/A2 H
MeSH term(s)	Humans ; Anticonvulsants/metabolism ; Cryoelectron Microscopy ; Levetiracetam/therapeutic use ; Epilepsy/drug therapy ; Botulinum Toxins ; Membrane Glycoproteins/metabolism ; Nerve Tissue Proteins/metabolism
Chemical Substances	Anticonvulsants ; Levetiracetam (44YRR34555) ; Botulinum Toxins (EC 3.4.24.69) ; SV2A protein, human (148845-93-6) ; Membrane Glycoproteins ; Nerve Tissue Proteins
Language	English
Publishing date	2024-04-18
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-47322-4
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Article ; Online: C‐mannosylation regulates stabilization of RAMP1 protein and RAMP1‐mediated cell migration

Mizuta, Hayato / Takakusaki, Ayane / Suzuki, Takehiro / Otake, Keisuke / Dohmae, Naoshi / Simizu, Siro

The FEBS Journal. 2023 Jan., v. 290, no. 1 p.196-208

2023

Abstract: C‐mannosylation is a unique type of protein glycosylation via C‐C linkage between an α‐mannose and a tryptophan residue. This modification has been identified in about 30 proteins and regulates several functions, such as protein secretion and ... ...

Abstract	C‐mannosylation is a unique type of protein glycosylation via C‐C linkage between an α‐mannose and a tryptophan residue. This modification has been identified in about 30 proteins and regulates several functions, such as protein secretion and intracellular localization, as well as protein stability. About half of C‐mannosylated proteins are categorized as proteins containing thrombospondin type 1 repeat domain or type I cytokine receptors. To evaluate whether C‐mannosylation broadly affects protein functions regardless of protein domain or family, we have sought to identify other types of C‐mannosylated protein and analyse their functions. In this study, we focused on receptor activity modifying protein 1, which neither contains thrombospondin type 1 repeat domain nor belongs to the type I cytokine receptors. Our mass spectrometry analysis demonstrated that RAMP1 is C‐mannosylated at Trp⁵⁶. It has been shown that RAMP1 transports to the plasma membrane after dimerization with calcitonin receptor‐like receptor and is important for ligand‐dependent downstream signalling activation. Our results showed that C‐mannosylation has no effect on this transport activity. On the other hand, C‐mannosylation did enhance protein stability and cell migration activity. Our data may provide new insight into both C‐mannosylation research and novel RAMP1 analysis.
Keywords	calcitonin ; cell movement ; cytokines ; dimerization ; glycosylation ; mass spectrometry ; plasma membrane ; protein domains ; protein secretion ; tryptophan
Language	English
Dates of publication	2023-01
Size	p. 196-208.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.16592
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Destabilization of vitelline membrane outer layer protein 1 homolog (VMO1) by C‐mannosylation

Yoshimoto, Satoshi / Suzuki, Takehiro / Ōtani, Naoki / Takahashi, Daisuke / Toshima, Kazunobu / Dohmae, Naoshi / Simizu, Siro

FEBS Open Bio 2023 Mar., v. 13, no. 3, p. 490-499

2023 , Page(s) 490–499

Abstract: C‐mannosylation is a rare type of protein glycosylation whereby a single mannose is added to the first tryptophan in the consensus sequence Trp‐Xaa‐Xaa‐Trp/Cys (in which Xaa represents any amino acid). Its consensus sequence is mainly found in proteins ... ...

Abstract	C‐mannosylation is a rare type of protein glycosylation whereby a single mannose is added to the first tryptophan in the consensus sequence Trp‐Xaa‐Xaa‐Trp/Cys (in which Xaa represents any amino acid). Its consensus sequence is mainly found in proteins containing a thrombospondin type‐1 repeat (TSR1) domain and in type I cytokine receptors. In these proteins, C‐mannosylation affects protein secretion, intracellular localization, and protein stability; however, the role of C‐mannosylation in proteins that are not type I cytokine receptors and/or do not contain a TSR1 domain is less well explored. In this study, we focused on human vitelline membrane outer layer protein 1 homolog (VMO1). VMO1, which possesses two putative C‐mannosylation sites, is a 21‐kDa secreted protein that does not contain a TSR1 domain and is not a type I cytokine receptor. Mass spectrometry analyses revealed that VMO1 is C‐mannosylated at Trp¹⁰⁵ but not at Trp⁴⁴. Although C‐mannosylation does not affect the extracellular secretion of VMO1, it destabilizes the intracellular VMO1. In addition, a structural comparison between VMO1 and C‐mannosylated VMO1 showed that the modification of the mannose changes the conformation of three loops in VMO1. Taken together, our results demonstrate the first example of C‐mannosylation for protein destabilization of VMO1.
Keywords	consensus sequence ; cytokine receptors ; cytokines ; glycosylation ; humans ; mannose ; mass spectrometry ; protein secretion ; tryptophan ; vitelline membrane
Language	English
Dates of publication	2023-03
Size	p. 490-499
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2651702-4
ISSN	2211-5463
ISSN	2211-5463
DOI	10.1002/2211-5463.13561
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Article: Clathrin adapters AP-1 and GGA2 support expression of epidermal growth factor receptor for cell growth.

Uemura, Takefumi / Suzuki, Takehiro / Dohmae, Naoshi / Waguri, Satoshi

Oncogenesis

2021 Volume 10, Issue 11, Page(s) 80

Abstract: The role of Golgi/endosome-localized clathrin adapters in the maintenance of steady-state cell surface epidermal growth factor receptor (EGFR) is not well known. Here, we show that EGFR associates preferentially with both AP-1 and GGA2 in vitro. AP-1 ... ...

Abstract	The role of Golgi/endosome-localized clathrin adapters in the maintenance of steady-state cell surface epidermal growth factor receptor (EGFR) is not well known. Here, we show that EGFR associates preferentially with both AP-1 and GGA2 in vitro. AP-1 depletion caused a reduction in the EGFR protein by promoting its lysosomal degradation. Triple immunofluorescence microscopy and proximity ligation assays demonstrated that the interaction of EGFR with AP-1 or GGA2 occurred more frequently in Rab11-positive recycling endosomes than in Rab5-positive early endosomes. Biochemical recycling assay revealed that the depletion of AP-1 or GGA2 significantly suppressed EGFR recycling to the plasma membrane regardless of the EGF stimulation. Depletion of AP-1 or GGA2 also reduced cell contents of other tyrosine kinases, MET and ErbB4, and therefore, suppressed the growth of H1975 cancer cells in culture and xenograft model. Moreover, AP-1 was expressed in endosomes at higher levels in some cancer tissues. Collectively, these results suggest that AP-1 and GGA2 function in recycling endosomes to retrieve endocytosed EGFR, thereby sustaining its cell surface expression and, consequently, cancer cell growth.
Language	English
Publishing date	2021-11-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	2674437-5
ISSN	2157-9024
ISSN	2157-9024
DOI	10.1038/s41389-021-00367-2
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Article ; Online: Destabilization of vitelline membrane outer layer protein 1 homolog (VMO1) by C-mannosylation.

Yoshimoto, Satoshi / Suzuki, Takehiro / Otani, Naoki / Takahashi, Daisuke / Toshima, Kazunobu / Dohmae, Naoshi / Simizu, Siro

FEBS open bio

2023 Volume 13, Issue 3, Page(s) 490–499

Abstract: C-mannosylation is a rare type of protein glycosylation whereby a single mannose is added to the first tryptophan in the consensus sequence Trp-Xaa-Xaa-Trp/Cys (in which Xaa represents any amino acid). Its consensus sequence is mainly found in proteins ... ...

Abstract	C-mannosylation is a rare type of protein glycosylation whereby a single mannose is added to the first tryptophan in the consensus sequence Trp-Xaa-Xaa-Trp/Cys (in which Xaa represents any amino acid). Its consensus sequence is mainly found in proteins containing a thrombospondin type-1 repeat (TSR1) domain and in type I cytokine receptors. In these proteins, C-mannosylation affects protein secretion, intracellular localization, and protein stability; however, the role of C-mannosylation in proteins that are not type I cytokine receptors and/or do not contain a TSR1 domain is less well explored. In this study, we focused on human vitelline membrane outer layer protein 1 homolog (VMO1). VMO1, which possesses two putative C-mannosylation sites, is a 21-kDa secreted protein that does not contain a TSR1 domain and is not a type I cytokine receptor. Mass spectrometry analyses revealed that VMO1 is C-mannosylated at Trp
MeSH term(s)	Humans ; Glycosylation ; Mannose/metabolism ; Vitelline Membrane/metabolism ; Protein Transport ; Receptors, Cytokine/metabolism
Chemical Substances	Mannose (PHA4727WTP) ; Receptors, Cytokine
Language	English
Publishing date	2023-01-30
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2651702-4
ISSN	2211-5463 ; 2211-5463
ISSN (online)	2211-5463
ISSN	2211-5463
DOI	10.1002/2211-5463.13561
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Article ; Online: Methyl vinyl ketone and its analogs covalently modify PI3K and alter physiological functions by inhibiting PI3K signaling.

Morimoto, Atsushi / Takasugi, Nobumasa / Pan, Yuexuan / Kubota, Sho / Dohmae, Naoshi / Abiko, Yumi / Uchida, Koji / Kumagai, Yoshito / Uehara, Takashi

The Journal of biological chemistry

2024 Volume 300, Issue 3, Page(s) 105679

Abstract: Reactive carbonyl species (RCS), which are abundant in the environment and are produced in vivo under stress, covalently bind to nucleophilic residues such as Cys in proteins. Disruption of protein function by RCS exposure is predicted to play a role in ... ...

Abstract	Reactive carbonyl species (RCS), which are abundant in the environment and are produced in vivo under stress, covalently bind to nucleophilic residues such as Cys in proteins. Disruption of protein function by RCS exposure is predicted to play a role in the development of various diseases such as cancer and metabolic disorders, but most studies on RCS have been limited to simple cytotoxicity validation, leaving their target proteins and resulting physiological changes unknown. In this study, we focused on methyl vinyl ketone (MVK), which is one of the main RCS found in cigarette smoke and exhaust gas. We found that MVK suppressed PI3K-Akt signaling, which regulates processes involved in cellular homeostasis, including cell proliferation, autophagy, and glucose metabolism. Interestingly, MVK inhibits the interaction between the epidermal growth factor receptor and PI3K. Cys656 in the SH2 domain of the PI3K p85 subunit, which is the covalently binding site of MVK, is important for this interaction. Suppression of PI3K-Akt signaling by MVK reversed epidermal growth factor-induced negative regulation of autophagy and attenuated glucose uptake. Furthermore, we analyzed the effects of the 23 RCS compounds with structures similar to MVK and showed that their analogs also suppressed PI3K-Akt signaling in a manner that correlated with their similarities to MVK. Our study demonstrates the mechanism of MVK and its analogs in suppressing PI3K-Akt signaling and modulating physiological functions, providing a model for future studies analyzing environmental reactive species.
MeSH term(s)	Butanones/pharmacology ; Phosphatidylinositol 3-Kinases/metabolism ; Proto-Oncogene Proteins c-akt/antagonists & inhibitors ; Proto-Oncogene Proteins c-akt/metabolism ; Signal Transduction ; Humans ; Cell Line, Tumor ; Protein Kinase Inhibitors/chemistry ; Protein Kinase Inhibitors/pharmacology
Chemical Substances	3-buten-2-one (AR7642I1MP) ; Butanones ; Phosphatidylinositol 3-Kinases (EC 2.7.1.-) ; Proto-Oncogene Proteins c-akt (EC 2.7.11.1) ; N-(2-(methylamino)ethyl)-5-isoquinolinesulfonamide (84478-11-5) ; Protein Kinase Inhibitors
Language	English
Publishing date	2024-01-24
Publishing country	United States
Document type	Journal Article
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1016/j.jbc.2024.105679
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Article ; Online: Rationalizing the Influence of the Binding Affinity on the Activity of Phosphoserine Phosphatases.

Chiba, Yoko / Ooka, Hideshi / Wintzer, Marie E / Tsunematsu, Nao / Nogawa, Toshihiko / Suzuki, Takehiro / Dohmae, Naoshi / Nakamura, Ryuhei

Angewandte Chemie (International ed. in English)

2024 Volume 63, Issue 13, Page(s) e202318635

Abstract: The Sabatier principle states that catalytic activity can be maximized when the substrate binding affinity is neither too strong nor too weak. Recent studies have shown that the activity of several hydrolases is maximized at intermediate values of the ... ...

Abstract	The Sabatier principle states that catalytic activity can be maximized when the substrate binding affinity is neither too strong nor too weak. Recent studies have shown that the activity of several hydrolases is maximized at intermediate values of the binding affinity (Michaelis-Menten constant: K
MeSH term(s)	Phosphoserine ; Phylogeny ; Phosphoric Monoester Hydrolases
Chemical Substances	phosphoserine phosphatase (EC 3.1.3.3) ; Phosphoserine (17885-08-4) ; Phosphoric Monoester Hydrolases (EC 3.1.3.2)
Language	English
Publishing date	2024-02-26
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2011836-3
ISSN	1521-3773 ; 1433-7851
ISSN (online)	1521-3773
ISSN	1433-7851
DOI	10.1002/anie.202318635
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Article ; Online: Discovery of a Plant 14-3-3 Inhibitor Possessing Isoform Selectivity and In Planta Activity.

Nishiyama, Kotaro / Aihara, Yusuke / Suzuki, Takehiro / Takahashi, Koji / Kinoshita, Toshinori / Dohmae, Naoshi / Sato, Ayato / Hagihara, Shinya

Angewandte Chemie (International ed. in English)

2024 , Page(s) e202400218

Abstract: Synthetic modulators for plant 14-3-3s are promising chemical tools both for understanding the 14-3-3-related signaling pathways and controlling plant physiology. Here, we describe a novel small-molecule inhibitor for 14-3-3 proteins ofArabidopsis ... ...

Abstract	Synthetic modulators for plant 14-3-3s are promising chemical tools both for understanding the 14-3-3-related signaling pathways and controlling plant physiology. Here, we describe a novel small-molecule inhibitor for 14-3-3 proteins ofArabidopsis thaliana. The inhibitor was identified from unexpected products in DMSO stock solution of an in-house chemical library. Mass spectroscopy, mutant-based analyses, fluorescence polarization assays, and thermal shift assaysrevealed that the inhibitor covalently binds to an allosteric site of 14-3-3 with isoform selectivity. Moreover, infiltration of the inhibitor to Arabidopsis leaves suppressed the stomatal aperture. The inhibitor should provide a new insight into the design of potent and isoform-selective 14-3-3 modulators.
Language	English
Publishing date	2024-04-24
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2011836-3
ISSN	1521-3773 ; 1433-7851
ISSN (online)	1521-3773
ISSN	1433-7851
DOI	10.1002/anie.202400218
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Article ; Online: Involvement of LH3 and GLT25D1 for glucosyl-galactosyl-hydroxylation on non-collagen-like domain of FGL1.

Mori, Kento / Suzuki, Takehiro / Miura, Kazuki / Dohmae, Naoshi / Simizu, Siro

Biochemical and biophysical research communications

2021 Volume 560, Page(s) 93–98

Abstract: Glucosyl-galactosyl-hydroxylation (GGH) is one type of post-translational modification, which is mainly observed in collagen-like domain-containing proteins. Using LC-MS/MS analysis, we found a GGH-like modification at Lys65 of fibrinogen-like protein 1 ( ...

Abstract	Glucosyl-galactosyl-hydroxylation (GGH) is one type of post-translational modification, which is mainly observed in collagen-like domain-containing proteins. Using LC-MS/MS analysis, we found a GGH-like modification at Lys65 of fibrinogen-like protein 1 (FGL1), although it does not contain a collagen-like domain. To identify the glycosyltransferases responsible for this modification, we established LH3/GLT25D1-knockout FGL1-overexpressing HT1080 cell lines. The result showed that knockout of LH3 or GLT25D1 significantly inhibited the glycosylation. Furthermore, deficiency of GGH by point mutation of the FGL1 protein or knockout of the GGH-related glycosyltransferase reduced FGL1 protein levels. Taken together, these data indicate that Lys65 of FGL1 is glucosyl-galactosyl-hydroxylated by LH3 and GLT25D1. Our results provide novel insights to regulate various FGL1 functions.
MeSH term(s)	Cell Line, Tumor ; Fibrinogen/chemistry ; Fibrinogen/metabolism ; Galactosyltransferases/metabolism ; Glycosylation ; Humans ; Lysine/metabolism ; Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase/metabolism ; Protein Domains ; Protein Processing, Post-Translational ; Protein Stability
Chemical Substances	FGL1 protein, human ; Fibrinogen (9001-32-5) ; PLOD3 protein, human (EC 1.14.11.-) ; Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase (EC 1.14.11.4) ; Galactosyltransferases (EC 2.4.1.-) ; COLGALT1 protein, human (EC 2.4.1.50) ; Lysine (K3Z4F929H6)
Language	English
Publishing date	2021-05-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	205723-2
ISSN	1090-2104 ; 0006-291X ; 0006-291X
ISSN (online)	1090-2104 ; 0006-291X
ISSN	0006-291X
DOI	10.1016/j.bbrc.2021.04.128
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