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Article: The mitochondrial thiolase ACAT1 regulates monocyte/macrophage type I interferon

Wu, Jing / Singh, Komudi / Shing, Vivian / Gupta, Anand K / Huffstutler, Rebecca D / Lee, Duck-Yeon / Sack, Michael N

bioRxiv : the preprint server for biology

2024

Abstract: Lipid-derived acetyl-CoA is shown to be the major carbon source for histone acetylation. However, there is no direct evidence demonstrating lipid metabolic pathway contribututions to this process. Mitochondrial acetyl-CoA acetyltransferase 1 (ACAT1) ... ...

Abstract	Lipid-derived acetyl-CoA is shown to be the major carbon source for histone acetylation. However, there is no direct evidence demonstrating lipid metabolic pathway contribututions to this process. Mitochondrial acetyl-CoA acetyltransferase 1 (ACAT1) catalyzes the final step of ß-oxidation, the aerobic process catabolizing fatty acids (FA) into acetyl-CoA. To investigate this in the context of immunometabolism, we generated macrophage cell line lacking ACAT1.
Language	English
Publishing date	2024-01-31
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.01.29.577773
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Article: Macrodomain Mac1 of SARS-CoV-2 Nonstructural Protein 3 Hydrolyzes Diverse ADP-ribosylated Substrates.

Chea, Chanbora / Lee, Duck-Yeon / Kato, Jiro / Ishiwata-Endo, Hiroko / Moss, Joel

bioRxiv : the preprint server for biology

2023

Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for a global pandemic that resulted in more than 6-million deaths worldwide. The virus encodes several non-structural proteins (Nsps) that contain elements capable of disrupting ... ...

Abstract	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for a global pandemic that resulted in more than 6-million deaths worldwide. The virus encodes several non-structural proteins (Nsps) that contain elements capable of disrupting cellular processes. Among these Nsp proteins, Nsp3 contains macrodomains, e.g., Mac1, Mac2, Mac3, with potential effects on host cells. Mac1 has been shown to increase SARS-CoV-2 virulence and disrupt ADP-ribosylation pathways in mammalian cells. ADP-ribosylation results from the transfer of the ADP-ribose moiety of NAD Importance: SARS-CoV-2, the virus responsible for COVID-19, encodes 3 macrodomain-containing proteins, e.g., Mac1, Mac2, Mac3, within non-structural proteins 3 (Nsp3). Mac1 was shown previously to hydrolyze ADP-ribose-phosphate. Inactivation of Mac1 reduced viral proliferation. Here we report that Mac1, but not Mac2 and Mac3, has multiple activities, i.e., Mac1 hydrolyzed. α-NAD
Language	English
Publishing date	2023-02-07
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.02.07.527501
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Article ; Online: Structural Relationships to Efficacy for Prazole-Derived Antivirals.

Nyenhuis, David A / Watanabe, Susan / Bernstein, Rebecca / Swenson, Rolf E / Raju, Natarajan / Sabbasani, Venkata R / Mushti, Chandrasekhar / Lee, Duck-Yeon / Carter, Carol / Tjandra, Nico

Advanced science (Weinheim, Baden-Wurttemberg, Germany)

2024 , Page(s) e2308312

Abstract: Here, an in vitro characterization of a family of prazole derivatives that covalently bind to the C73 site on Tsg101 and assay their ability to inhibit viral particle production is presented. Structurally, increased steric bulk on the 4-pyridyl of the ... ...

Abstract	Here, an in vitro characterization of a family of prazole derivatives that covalently bind to the C73 site on Tsg101 and assay their ability to inhibit viral particle production is presented. Structurally, increased steric bulk on the 4-pyridyl of the prazole expands the prazole site on the UEV domain toward the β-hairpin in the Ub-binding site and is coupled to increased inhibition of virus-like particle production in HIV-1. Increased bulk also increased toxicity, which is alleviated by increasing flexibility. Further, the formation of a novel secondary Tsg101 adduct for several of the tested compounds and the commercial drug lansoprazole. The secondary adduct involved the loss of the 4-pyridyl substituent to form an irreversible species, with implications for increasing the half-life of the active species or its specificity toward Tsg101 UEV. It is also determined that sulfide derivatives display effective viral inhibition, presumably through cellular sulfoxidation, allowing for delayed conversion within the cellular environment, and identify SARS-COV-2 as a target of prazole inhibition. These results open multiple avenues for the design of prazole derivatives for antiviral applications.
Language	English
Publishing date	2024-03-06
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2808093-2
ISSN	2198-3844 ; 2198-3844
ISSN (online)	2198-3844
ISSN	2198-3844
DOI	10.1002/advs.202308312
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Article ; Online: Macrodomain Mac1 of SARS-CoV-2 Nonstructural Protein 3 Hydrolyzes Diverse ADP-ribosylated Substrates

Chea, Chanbora / Lee, Duck-Yeon / Kato, Jiro / Ishiwata-Endo, Hiroko / Moss, Joel

bioRxiv

Abstract	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for a global pandemic that resulted in more than 6-million deaths worldwide. The virus encodes several non-structural proteins (Nsps) that contain elements capable of disrupting cellular processes. Among these Nsp proteins, Nsp3 contains macrodomains, e.g., Mac1, Mac2, Mac3, with potential effects on host cells. Mac1 has been shown to increase SARS-CoV-2 virulence and disrupt ADP-ribosylation pathways in mammalian cells. ADP-ribosylation results from the transfer of the ADP-ribose moiety of NAD+ to various acceptors, e.g., proteins, DNA, RNA, contributing on a cell9s biological processes. ADP-ribosylation is the mechanism of action of bacterial toxins, e.g., Pseudomonas toxins, diphtheria toxin that disrupt protein biosynthetic and signaling pathways. On the other hand, some viral macrodomains cleavage ADP-ribose-acceptor bond, generating free ADP-ribose. By this reaction, the macrodomain-containing proteins interfere ADP-ribose homeostasis in host cells. Here, we examined potential hydrolytic activities of SARS-CoV-2 Mac1, 2, and 3 on substrates containing ADP-ribose. Mac1 cleaved alpha-NAD+, but not beta-NAD+, consistent with stereospecificity at the C-1-bond. In contrast to ARH1 and ARH3, Mac1 did not require Mg2+ for optimal activity. Mac1 also hydrolyzed O-acetyl-ADP-ribose and ADP-ribose-1-phosphate, but not Mac2 and Mac3. However, Mac1 did not cleave alpha-ADP-ribose-(arginine) and ADP-ribose-(serine)-histone H3 peptide, suggesting that Mac1 hydrolyzes ADP-ribose attached to O- and N-linked functional groups, with specificity at the catalytic site in the ADP-ribose moiety. We conclude that SARS-CoV-2 Mac1 may exert anti-viral activity by reversing host-mediated ADP-ribosylation. New insights on Nsp3 activities may shed light on potential SARS-CoV-2 therapeutic targets.
Keywords	covid19
Language	English
Publishing date	2023-02-07
Publisher	Cold Spring Harbor Laboratory
Document type	Article ; Online
DOI	10.1101/2023.02.07.527501
Database	COVID19

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Article ; Online: ARH Family of ADP-Ribose-Acceptor Hydrolases.

Ishiwata-Endo, Hiroko / Kato, Jiro / Yamashita, Sachiko / Chea, Chanbora / Koike, Kazushige / Lee, Duck-Yeon / Moss, Joel

Cells

2022 Volume 11, Issue 23

Abstract: The ARH family of ADP-ribose-acceptor hydrolases consists of three 39-kDa members (ARH1-3), with similarities in amino acid sequence. ARH1 was identified based on its ability to cleave ADP-ribosyl-arginine synthesized by cholera toxin. Mammalian ADP- ... ...

Abstract	The ARH family of ADP-ribose-acceptor hydrolases consists of three 39-kDa members (ARH1-3), with similarities in amino acid sequence. ARH1 was identified based on its ability to cleave ADP-ribosyl-arginine synthesized by cholera toxin. Mammalian ADP-ribosyltransferases (ARTCs) mimicked the toxin reaction, with ARTC1 catalyzing the synthesis of ADP-ribosyl-arginine. ADP-ribosylation of arginine was stereospecific, with β-NAD
Language	English
Publishing date	2022-11-30
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells11233853
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Article ; Online: Humanin selectively prevents the activation of pro-apoptotic protein BID by sequestering it into fibers.

Morris, Daniel L / Johnson, Sabrina / Bleck, Christopher K E / Lee, Duck-Yeon / Tjandra, Nico

The Journal of biological chemistry

2020 Volume 295, Issue 52, Page(s) 18226–18238

Abstract: Members of the B-cell lymphoma (BCL-2) protein family regulate mitochondrial outer membrane permeabilization (MOMP), a phenomenon in which mitochondria become porous and release death-propagating complexes during the early stages of apoptosis. Pro- ... ...

Abstract	Members of the B-cell lymphoma (BCL-2) protein family regulate mitochondrial outer membrane permeabilization (MOMP), a phenomenon in which mitochondria become porous and release death-propagating complexes during the early stages of apoptosis. Pro-apoptotic BCL-2 proteins oligomerize at the mitochondrial outer membrane during MOMP, inducing pore formation. Of current interest are endogenous factors that can inhibit pro-apoptotic BCL-2 mitochondrial outer membrane translocation and oligomerization. A mitochondrial-derived peptide, Humanin (HN), was reported being expressed from an alternate ORF in the mitochondrial genome and inhibiting apoptosis through interactions with the pro-apoptotic BCL-2 proteins. Specifically, it is known to complex with BAX and BID. We recently reported the fibrillation of HN and BAX into β-sheets. Here, we detail the fibrillation between HN and BID. These fibers were characterized using several spectroscopic techniques, protease fragmentation with mass analysis, and EM. Enhanced fibrillation rates were detected with rising temperatures or pH values and the presence of a detergent. BID fibers are similar to those produced using BAX; however, the structures differ in final conformations of the BCL-2 proteins. BID fibers display both types of secondary structure in the fiber, whereas BAX was converted entirely to β-sheets. The data show that two distinct segments of BID are incorporated into the fiber structure, whereas other portions of BID remain solvent-exposed and retain helical structure. Similar analyses show that anti-apoptotic BCL-x
MeSH term(s)	Amino Acid Sequence ; BH3 Interacting Domain Death Agonist Protein/chemistry ; BH3 Interacting Domain Death Agonist Protein/metabolism ; Humans ; Intracellular Signaling Peptides and Proteins/genetics ; Intracellular Signaling Peptides and Proteins/metabolism ; Mitochondrial Membranes/metabolism ; Mutation ; Protein Conformation ; Proto-Oncogene Proteins c-bcl-2/chemistry ; Proto-Oncogene Proteins c-bcl-2/metabolism ; bcl-2-Associated X Protein/chemistry ; bcl-2-Associated X Protein/metabolism ; bcl-X Protein/chemistry ; bcl-X Protein/metabolism
Chemical Substances	BAX protein, human ; BCL2 protein, human ; BCL2L1 protein, human ; BH3 Interacting Domain Death Agonist Protein ; BID protein, human ; Intracellular Signaling Peptides and Proteins ; Proto-Oncogene Proteins c-bcl-2 ; bcl-2-Associated X Protein ; bcl-X Protein ; humanin
Language	English
Publishing date	2020-10-26
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	2997-x
ISSN	1083-351X ; 0021-9258
ISSN (online)	1083-351X
ISSN	0021-9258
DOI	10.1074/jbc.RA120.013023
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Article ; Online: Isoquercetin for thromboinflammation in sickle cell disease: a randomized double-blind placebo-controlled trial.

Lizarralde-Iragorri, Maria A / Parachalil Gopalan, Bindu / Merriweather, Brenda / Brooks, Jennifer / Hill, Mai / Lovins, Dianna / Pierre-Charles, Ruth / Cullinane, Ann / Dulau-Florea, Alina / Lee, Duck-Yeon / Villasmil, Rafael / Jeffries, Neal / Shet, Arun S

Blood advances

2023 Volume 8, Issue 1, Page(s) 172–182

Abstract: Abstract: Data from a small trial in patients with cancer suggest that isoquercetin (IQ) treatment lowered thrombosis biomarkers and prevented clinical thrombosis, but, to our knowledge, no studies of IQ have been conducted to target thromboinflammation ...

Abstract	Abstract: Data from a small trial in patients with cancer suggest that isoquercetin (IQ) treatment lowered thrombosis biomarkers and prevented clinical thrombosis, but, to our knowledge, no studies of IQ have been conducted to target thromboinflammation in adults with sickle cell disease (SCD). We conducted a randomized, double-blind, placebo-controlled trial in adults with steady-state SCD (hemoglobin SS [HbSS], HbSβ0thal, HbSβ+thal, or HbSC). The primary outcome was the change in plasma soluble P-selectin (sP-selectin) after treatment compared with baseline, analyzed in the intention-to-treat population. Between November 2019 and July 2022, 46 patients (aged 40 ± 11 years, 56% female, 75% under hydroxyurea treatment) were randomized to receive IQ (n = 23) or placebo (n = 23). IQ was well tolerated and all the adverse events (AEs; n = 21) or serious AEs (n = 14) recorded were not attributable to the study drug. The mean posttreatment change for sP-selectin showed no significant difference between the treatment groups (IQ, 0.10 ± 6.53 vs placebo, 0.74 ± 4.54; P = .64). In patients treated with IQ, whole-blood coagulation (P = .03) and collagen-induced platelet aggregation (P = .03) were significantly reduced from the baseline. Inducible mononuclear cell tissue factor gene expression and plasma protein disulfide isomerase reductase activity were also significantly inhibited (P = .003 and P = .02, respectively). Short-term fixed-dose IQ in patients with SCD was safe with no off-target bleeding and was associated with changes from the baseline in the appropriate direction for several biomarkers of thromboinflammation. The trial was registered at www.clinicaltrials.gov as #NCT04514510.
MeSH term(s)	Adult ; Female ; Humans ; Male ; Anemia, Sickle Cell/complications ; Anemia, Sickle Cell/drug therapy ; Biomarkers ; Inflammation/drug therapy ; Inflammation/etiology ; Selectins ; Thromboinflammation ; Thrombosis/drug therapy ; Thrombosis/etiology ; Double-Blind Method
Chemical Substances	Biomarkers ; isoquercitrin (0YX10VRV6J) ; Selectins
Language	English
Publishing date	2023-12-29
Publishing country	United States
Document type	Journal Article ; Randomized Controlled Trial ; Research Support, N.I.H., Intramural
ZDB-ID	2915908-8
ISSN	2473-9537 ; 2473-9529
ISSN (online)	2473-9537
ISSN	2473-9529
DOI	10.1182/bloodadvances.2023011542
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Article ; Online: Bax expression is optimal at low oxygen tension and constant agitation.

He, Yi / Chen, Yong / Morris, Daniel L / Lee, Duck-Yeon / Tjandra, Nico

Protein expression and purification

2019 Volume 165, Page(s) 105501

Abstract: Bax is a pro-apoptosis protein that translocates from the cytosol to the mitochondria membrane upon initiation of programed cell death. Bax subsequently disrupts the mitochondria membrane, resulting in the release of cytochrome C which activates the ... ...

Abstract	Bax is a pro-apoptosis protein that translocates from the cytosol to the mitochondria membrane upon initiation of programed cell death. Bax subsequently disrupts the mitochondria membrane, resulting in the release of cytochrome C which activates the downstream caspases. The structure of inactive Bax has been solved, but despite intensive investigation, the mechanism by which it regulates apoptosis is not established. The low yield of Bax expression in E. coli hampers efforts to elucidate the mechanism. Thus, we undertook a systematic study aimed at improving the yield of Bax. Bacteria were grown in a computer-controlled fermenter and expression was induced by addition of Isopropyl ß-d-1-thiogalactopyranoside (IPTG). The Bax expression level decreased continuously when the dissolved oxygen level was kept at 30%, which is non-limiting for E. coli. Alternatively, when oxygen input was decreased with constant agitation and air flow (or k
MeSH term(s)	Bioreactors ; Chromatography, Affinity ; Chromatography, High Pressure Liquid ; Escherichia coli/metabolism ; Fatty Acids, Volatile/metabolism ; Fermentation ; Gene Expression ; Glycerol/chemistry ; Hydrogen-Ion Concentration ; Oxygen/metabolism ; Proteomics/methods ; Transfection ; bcl-2-Associated X Protein/genetics ; bcl-2-Associated X Protein/metabolism
Chemical Substances	BAX protein, human ; Fatty Acids, Volatile ; bcl-2-Associated X Protein ; Glycerol (PDC6A3C0OX) ; Oxygen (S88TT14065)
Language	English
Publishing date	2019-09-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	1055455-5
ISSN	1096-0279 ; 1046-5928
ISSN (online)	1096-0279
ISSN	1046-5928
DOI	10.1016/j.pep.2019.105501
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Article ; Online: MitoRACE: evaluating mitochondrial function in vivo and in single cells with subcellular resolution using multiphoton NADH autofluorescence.

Willingham, T Bradley / Zhang, Yingfan / Andreoni, Alessio / Knutson, Jay R / Lee, Duck-Yeon / Glancy, Brian

The Journal of physiology

2019 Volume 597, Issue 22, Page(s) 5411–5428

Abstract: Key points: We developed a novel metabolic imaging approach that provides direct measures of the rate of mitochondrial energy conversion with single-cell and subcellular resolution by evaluating NADH autofluorescence kinetics during the mitochondrial ... ...

Abstract	Key points: We developed a novel metabolic imaging approach that provides direct measures of the rate of mitochondrial energy conversion with single-cell and subcellular resolution by evaluating NADH autofluorescence kinetics during the mitochondrial redox after cyanide experiment (mitoRACE). Measures of mitochondrial NADH flux by mitoRACE are sensitive to physiological and pharmacological perturbations in vivo. Metabolic imaging with mitoRACE provides a highly adaptable platform for evaluating mitochondrial function in vivo and in single cells with potential for broad applications in the study of energy metabolism. Abstract: Mitochondria play a critical role in numerous cell types and diseases, and structure and function of mitochondria can vary greatly among cells or within different regions of the same cell. However, there are currently limited methodologies that provide direct assessments of mitochondrial function in vivo, and contemporary measures of mitochondrial energy conversion lack the spatial resolution necessary to address cellular and subcellular heterogeneity. Here, we describe a novel metabolic imaging approach that provides direct measures of mitochondrial energy conversion with single-cell and subcellular resolution by evaluating NADH autofluorescence kinetics during the mitochondrial redox after cyanide experiment (mitoRACE). MitoRACE measures the rate of NADH flux through the steady-state mitochondrial NADH pool by rapidly inhibiting mitochondrial energetic flux, resulting in an immediate, linear increase in NADH fluorescence proportional to the steady-state NADH flux rate, thereby providing a direct measure of mitochondrial NADH flux. The experiments presented here demonstrate the sensitivity of this technique to detect physiological and pharmacological changes in mitochondrial flux within tissues of living animals and reveal the unique capability of this technique to evaluate mitochondrial function with single-cell and subcellular resolution in different cell types in vivo and in cell culture. Furthermore, we highlight the potential applications of mitoRACE by showing that within single neurons, mitochondria in neurites have higher energetic flux rates than mitochondria in the cell body. Metabolic imaging with mitoRACE provides a highly adaptable platform for evaluating mitochondrial function in vivo and in single cells, with potential for broad applications in the study of energy metabolism.
MeSH term(s)	Animals ; Cyanides/metabolism ; Energy Metabolism/physiology ; Fluorescence ; Kinetics ; Male ; Mice, Inbred C57BL ; Mitochondria/metabolism ; NAD/metabolism ; Oxidation-Reduction
Chemical Substances	Cyanides ; NAD (0U46U6E8UK)
Language	English
Publishing date	2019-10-10
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Intramural
ZDB-ID	3115-x
ISSN	1469-7793 ; 0022-3751
ISSN (online)	1469-7793
ISSN	0022-3751
DOI	10.1113/JP278611
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Article ; Online: The ARH and Macrodomain Families of α-ADP-ribose-acceptor Hydrolases Catalyze α-NAD

Stevens, Linda A / Kato, Jiro / Kasamatsu, Atsushi / Oda, Hirotake / Lee, Duck-Yeon / Moss, Joel

ACS chemical biology

2019 Volume 14, Issue 12, Page(s) 2576–2584

Abstract: ADP-ribosyltransferases transfer ADP-ribose from β- ... ...

Abstract	ADP-ribosyltransferases transfer ADP-ribose from β-NAD
MeSH term(s)	ADP-Ribosylation ; Adenosine Diphosphate Ribose/metabolism ; Animals ; Catalysis ; Cells, Cultured ; Humans ; Hydrolysis ; Mice ; NAD/metabolism
Chemical Substances	NAD (0U46U6E8UK) ; Adenosine Diphosphate Ribose (20762-30-5)
Language	English
Publishing date	2019-11-06
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Intramural
ISSN	1554-8937
ISSN (online)	1554-8937
DOI	10.1021/acschembio.9b00429
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