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Gu Z, Wang Y, Fang Z, Wang T, Gao S, Yang Q, Zhang Y, Wang Y, Wang L, Fan L, Cao F. Plasma metabolomics identifies S-adenosylmethionine as a biomarker and potential therapeutic target for vascular aging in older adult males. J Pharm Biomed Anal 2024; 243:116097. [PMID: 38489960 DOI: 10.1016/j.jpba.2024.116097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/04/2024] [Accepted: 03/06/2024] [Indexed: 03/17/2024]
Abstract
Brachial-ankle pulse wave velocity (baPWV) is a noninvasive index of vascular aging. However, the metabolic profile underlying vascular aging has not yet been fully elucidated. The current study aimed to identify circulating markers of vascular aging as assessed by baPWV and to elucidate its mechanism from a metabolomic perspective in older adults. A total of 60 and 61 Chinese male participants aged ≥80 years were recruited to the metabolome and validation cohorts, respectively. The baPWV of participants was measured using an automatic waveform analyzer. Plasma metabolic profile was investigated using ultra-performance liquid chromatography coupled with triple quadrupole linear ion trap tandem mass spectrometry. Orthogonal partial least squares (OPLS) regression modeling established the association between metabolic profile and baPWV to determine important metabolites predictive of vascular aging. Additionally, an enzyme-linked immunosorbent assay was employed to validate the metabolites in plasma and culture media of vascular smooth muscle cells in vitro. OPLS modeling identified 14 and 22 metabolites inversely and positively associated with baPWV, respectively. These 36 biomarkers were significantly enriched in seven metabolite sets, especially in cysteine and methionine metabolism (p <0.05). Notably, among metabolites involved in cysteine and methionine metabolism, S-adenosylmethionine (SAM) level was inversely related to baPWV, with a significant correlation coefficient in the OPLS model (p <0.05). Furthermore, the relationship between SAM and vascular aging was reconfirmed in an independent cohort and at the cellular level in vitro. SAM was independently associated with baPWV after adjustments for clinical covariates (β = -0.448, p <0.001) in the validation cohort. In summary, plasma metabolomics identified an inverse correlation between SAM and baPWV in older males. SAM has the potential to be a novel biomarker and therapeutic target for vascular aging.
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Affiliation(s)
- Zhenghui Gu
- Chinese PLA Medical School & Department of Cardiology, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing 100853, China
| | - Yujia Wang
- Chinese PLA Medical School & Department of Cardiology, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing 100853, China
| | - Zhiyi Fang
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Tianhu Wang
- Chinese PLA Medical School & Department of Cardiology, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing 100853, China
| | - Shan Gao
- Chinese PLA Medical School & Department of Cardiology, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing 100853, China
| | - Qian Yang
- Chinese PLA Medical School & Department of Cardiology, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing 100853, China
| | - Yingjie Zhang
- Chinese PLA Medical School & Department of Cardiology, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing 100853, China
| | - Yabin Wang
- Chinese PLA Medical School & Department of Cardiology, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing 100853, China
| | - Linghuan Wang
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Li Fan
- Chinese PLA Medical School & Department of Cardiology, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing 100853, China.
| | - Feng Cao
- Chinese PLA Medical School & Department of Cardiology, The Second Medical Center and National Clinical Research Center for Geriatric Diseases, Chinese PLA General Hospital, Beijing 100853, China.
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2
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Xiao Y, Han C, Li X, Zhu X, Li S, Jiang N, Yu C, Liu Y, Liu F. S-Adenosylmethionine (SAM) diet promotes innate immunity via histone H3K4me3 complex. Int Immunopharmacol 2024; 131:111837. [PMID: 38471365 DOI: 10.1016/j.intimp.2024.111837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/27/2024] [Accepted: 03/08/2024] [Indexed: 03/14/2024]
Abstract
S-adenosylmethionine (SAM) was a methyl donor for modifying histones, which had crucial roles in lipid accumulation, tissue injury, and immune responses. SAM fluctuation might be linked to variations in histone methylation. However, the underlying molecular mechanisms of whether the SAM diet influenced the immune response via histone modification remained obscure. In this study, we utilized the Caenorhabditis elegans as a model to investigate the role of SAM diet in innate immunity. We found that 50 μM SAM increased resistance to Gram-negative pathogen Pseudomonas aeruginosa PA14 by reducing the bacterial burden in the intestine. Furthermore, through the genetic screening in C. elegans, we found that SAM functioned in germline to enhance innate immunity via an H3K4 methyltransferase complex to upregulate the immune response genes, including irg-1 and T24B8.5. Intriguingly, SAM also protected mice from P. aeruginosa PA14 infection by reducing the bacterial burden in lung. These findings provided insight into the mechanisms of molecular connections among SAM diet, histone modifications and innate immunity.
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Affiliation(s)
- Yi Xiao
- Guizhou Provincial College-based Key Lab for Tumor Prevention and Treatment with Distinctive Medicines, Zunyi Medical University, Zunyi, Guizhou 563000, China; College of Basic Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, China; Institute of Life Sciences, Zunyi Medical University, Zunyi, Guizhou 563000, China.
| | - Chao Han
- Guizhou Provincial College-based Key Lab for Tumor Prevention and Treatment with Distinctive Medicines, Zunyi Medical University, Zunyi, Guizhou 563000, China; College of Basic Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, China; Institute of Life Sciences, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Xiaocong Li
- Guizhou Provincial College-based Key Lab for Tumor Prevention and Treatment with Distinctive Medicines, Zunyi Medical University, Zunyi, Guizhou 563000, China; College of Basic Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, China; Institute of Life Sciences, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Xinting Zhu
- Guizhou Provincial College-based Key Lab for Tumor Prevention and Treatment with Distinctive Medicines, Zunyi Medical University, Zunyi, Guizhou 563000, China; College of Basic Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Sanhua Li
- Guizhou Provincial College-based Key Lab for Tumor Prevention and Treatment with Distinctive Medicines, Zunyi Medical University, Zunyi, Guizhou 563000, China; College of Basic Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, China; Institute of Life Sciences, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Nian Jiang
- Guizhou Provincial College-based Key Lab for Tumor Prevention and Treatment with Distinctive Medicines, Zunyi Medical University, Zunyi, Guizhou 563000, China; College of Basic Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, China; Institute of Life Sciences, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Changyan Yu
- Guizhou Provincial College-based Key Lab for Tumor Prevention and Treatment with Distinctive Medicines, Zunyi Medical University, Zunyi, Guizhou 563000, China; College of Basic Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, China; Institute of Life Sciences, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Yun Liu
- Guizhou Provincial College-based Key Lab for Tumor Prevention and Treatment with Distinctive Medicines, Zunyi Medical University, Zunyi, Guizhou 563000, China; College of Basic Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, China; Institute of Life Sciences, Zunyi Medical University, Zunyi, Guizhou 563000, China.
| | - Fang Liu
- Guizhou Provincial College-based Key Lab for Tumor Prevention and Treatment with Distinctive Medicines, Zunyi Medical University, Zunyi, Guizhou 563000, China; College of Basic Medicine, Zunyi Medical University, Zunyi, Guizhou 563000, China.
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3
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Kachalkin MN, Ryazanova TK, Sokolova IV. Quantitative determination of ademetionine in tablets utilizing ATR-FTIR and partial least squares methods approaches. J Pharm Biomed Anal 2024; 241:115991. [PMID: 38301577 DOI: 10.1016/j.jpba.2024.115991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/08/2024] [Accepted: 01/17/2024] [Indexed: 02/03/2024]
Abstract
In this study there were utilized a combination of Fourier transform infrared spectroscopy in attenuated total reflection mode (ATR-FTIR) and partial least squares (PLS) regression method to develop quantitative models for determining the concentration of ademetionine in commercial tablets. The established and validated models were specifically designed for a commercial product containing ademetionine 1,4-butandiesulfonate. The coefficient of determination for the developed model was 0.999. Relative standard deviation (RSD) does not exceed 1.6% for repeatability and intermediate accuracy, which meets the international ICH and AOAC requirements for the method performance. The validation results effectively confirmed that this method is suitable and meets the current requirements for analytical methods in drug quality control. Consequently, this approach can be used for routine ademetionine analysis in pharmaceutical products and has the potential to be applied to other active pharmaceutical ingredients (APIs) in drug quality control.
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Affiliation(s)
- M N Kachalkin
- Scientific and educational center "Pharmacy", Federal State Budgetary Educational Institution of Higher Education «Samara State Medical University» of the Ministry of Healthcare of the Russian Federation, st. Chapaevskaya, 89, Samara 443099, Russian Federation
| | - T K Ryazanova
- Scientific and educational center "Pharmacy", Federal State Budgetary Educational Institution of Higher Education «Samara State Medical University» of the Ministry of Healthcare of the Russian Federation, st. Chapaevskaya, 89, Samara 443099, Russian Federation.
| | - I V Sokolova
- Scientific and educational center "Pharmacy", Federal State Budgetary Educational Institution of Higher Education «Samara State Medical University» of the Ministry of Healthcare of the Russian Federation, st. Chapaevskaya, 89, Samara 443099, Russian Federation
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Pushpakumar S, Singh M, Sen U, Tyagi N, Tyagi SC. The role of the mitochondrial trans-sulfuration in cerebro-cardio renal dysfunction during trisomy down syndrome. Mol Cell Biochem 2024; 479:825-829. [PMID: 37198322 DOI: 10.1007/s11010-023-04761-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 05/05/2023] [Indexed: 05/19/2023]
Abstract
One in 700 children is born with the down syndrome (DS). In DS, there is an extra copy of X chromosome 21 (trisomy). Interestingly, the chromosome 21 also contains an extra copy of the cystathionine beta synthase (CBS) gene. The CBS activity is known to contribute in mitochondrial sulfur metabolism via trans-sulfuration pathway. We hypothesize that due to an extra copy of the CBS gene there is hyper trans-sulfuration in DS. We believe that understanding the mechanism of hyper trans-sulfuration during DS will be important in improving the quality of DS patients and towards developing new treatment strategies. We know that folic acid "1-carbon" metabolism (FOCM) cycle transfers the "1-carbon" methyl group to DNA (H3K4) via conversion of s-adenosyl methionine (SAM) to s-adenosyl homocysteine (SAH) by DNMTs (the gene writers). The demethylation reaction is carried out by ten-eleven translocation methylcytosine dioxygenases (TETs; the gene erasers) through epigenetics thus turning the genes off/on and opening the chromatin by altering the acetylation/HDAC ratio. The S-adenosyl homocysteine hydrolase (SAHH) hydrolyzes SAH to homocysteine (Hcy) and adenosine. The Hcy is converted to cystathionine, cysteine and hydrogen sulfide (H2S) via CBS/cystathioneγ lyase (CSE)/3-mercaptopyruvate sulfurtransferase (3MST) pathways. Adenosine by deaminase is converted to inosine and then to uric acid. All these molecules remain high in DS patients. H2S is a potent inhibitor of mitochondrial complexes I-IV, and regulated by UCP1. Therefore, decreased UCP1 levels and ATP production can ensue in DS subjects. Interestingly, children born with DS show elevated levels of CBS/CSE/3MST/Superoxide dismutase (SOD)/cystathionine/cysteine/H2S. We opine that increased levels of epigenetic gene writers (DNMTs) and decreased in gene erasers (TETs) activity cause folic acid exhaustion, leading to an increase in trans-sulphuration by CBS/CSE/3MST/SOD pathways. Thus, it is important to determine whether SIRT3 (inhibitor of HDAC3) can decrease the trans-sulfuration activity in DS patients. Since there is an increase in H3K4 and HDAC3 via epigenetics in DS, we propose that sirtuin-3 (Sirt3) may decrease H3K4 and HDAC3 and hence may be able to decrease the trans-sulfuration in DS. It would be worth to determine whether the lactobacillus, a folic acid producing probiotic, mitigates hyper-trans-sulphuration pathway in DS subjects. Further, as we know that in DS patients the folic acid is exhausted due to increase in CBS, Hcy and re-methylation. In this context, we suggest that folic acid producing probiotics such as lactobacillus might be able to improve re-methylation process and hence may help decrease the trans-sulfuration pathway in the DS patients.
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Affiliation(s)
- Sathnur Pushpakumar
- Department of Physiology, University of Louisville, Louisville, Kentucky, 40202, USA
| | - Mahavir Singh
- Department of Physiology, University of Louisville, Louisville, Kentucky, 40202, USA.
- School of Medicine, University of Louisville, Louisville, Kentucky, USA.
| | | | - N Tyagi
- Department of Physiology, University of Louisville, Louisville, Kentucky, 40202, USA
| | - Suresh C Tyagi
- Department of Physiology, University of Louisville, Louisville, Kentucky, 40202, USA
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Antón-Fernández A, Cuadros R, Peinado-Cahuchola R, Hernández F, Avila J. Role of folate receptor α in the partial rejuvenation of dentate gyrus cells: Improvement of cognitive function in 21-month-old aged mice. Sci Rep 2024; 14:6915. [PMID: 38519576 PMCID: PMC10960019 DOI: 10.1038/s41598-024-57095-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 03/14/2024] [Indexed: 03/25/2024] Open
Abstract
Neuronal aging may be, in part, related to a change in DNA methylation. Thus, methyl donors, like folate and methionine, may play a role in cognitive changes associated to neuronal aging. To test the role of these metabolites, we performed stereotaxic microinjection of these molecules into the dentate gyrus (DG) of aged mice (an average age of 21 month). Folate, but not S-Adenosyl-Methionine (SAM), enhances cognition in aged mice. In the presence of folate, we observed partial rejuvenation of DG cells, characterized by the expression of juvenile genes or reorganization of extracellular matrix. Here, we have also tried to identify the mechanism independent of DNA methylation, that involve folate effects on cognition. Our analyses indicated that folate binds to folate receptor α (FRα) and, upon folate binding, FRα is transported to cell nucleus, where it is acting as transcription factor for expressing genes like SOX2 or GluN2B. In this work, we report that a FRα binding peptide also replicates the folate effect on cognition, in aged mice. Our data suggest that such effect is not sex-dependent. Thus, we propose the use of this peptide to improve cognition since it lacks of folate-mediated side effects. The use of synthetic FRα binding peptides emerge as a future strategy for the study of brain rejuvenation.
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Affiliation(s)
- A Antón-Fernández
- Centro de Biología Molecular Severo Ochoa, CSIC/UAM, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - R Cuadros
- Centro de Biología Molecular Severo Ochoa, CSIC/UAM, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
- Center for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - R Peinado-Cahuchola
- Centro de Biología Molecular Severo Ochoa, CSIC/UAM, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - F Hernández
- Centro de Biología Molecular Severo Ochoa, CSIC/UAM, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain
| | - Jesús Avila
- Centro de Biología Molecular Severo Ochoa, CSIC/UAM, Universidad Autónoma de Madrid, Cantoblanco, 28049, Madrid, Spain.
- Center for Networked Biomedical Research on Neurodegenerative Diseases (CIBERNED), Madrid, Spain.
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6
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Liu GY, Jouandin P, Bahng RE, Perrimon N, Sabatini DM. An evolutionary mechanism to assimilate new nutrient sensors into the mTORC1 pathway. Nat Commun 2024; 15:2517. [PMID: 38514639 PMCID: PMC10957897 DOI: 10.1038/s41467-024-46680-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 03/06/2024] [Indexed: 03/23/2024] Open
Abstract
Animals sense and respond to nutrient availability in their environments, a task coordinated in part by the mTOR complex 1 (mTORC1) pathway. mTORC1 regulates growth in response to nutrients and, in mammals, senses specific amino acids through specialized sensors that bind the GATOR1/2 signaling hub. Given that animals can occupy diverse niches, we hypothesized that the pathway might evolve distinct sensors in different metazoan phyla. Whether such customization occurs, and how the mTORC1 pathway might capture new inputs, is unknown. Here, we identify the Drosophila melanogaster protein Unmet expectations (CG11596) as a species-restricted methionine sensor that directly binds the fly GATOR2 complex in a fashion antagonized by S-adenosylmethionine (SAM). We find that in Dipterans GATOR2 rapidly evolved the capacity to bind Unmet and to thereby repurpose a previously independent methyltransferase as a SAM sensor. Thus, the modular architecture of the mTORC1 pathway allows it to co-opt preexisting enzymes to expand its nutrient sensing capabilities, revealing a mechanism for conferring evolvability on an otherwise conserved system.
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Affiliation(s)
- Grace Y Liu
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 455 Main Street, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research and Massachusetts Institute of Technology, Department of Biology, 77 Massachusetts Avenue, Cambridge, MA, USA.
| | - Patrick Jouandin
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Institut de Recherche en Cancérologie de Montpellier, Inserm U1194-UM-ICM, Campus Val d'Aurelle, Montpellier, Cedex 5, France
| | - Raymond E Bahng
- Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology, Department of Biology, 455 Main Street, Cambridge, MA, USA
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research and Massachusetts Institute of Technology, Department of Biology, 77 Massachusetts Avenue, Cambridge, MA, USA
| | - Norbert Perrimon
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
| | - David M Sabatini
- Institute of Organic Chemistry and Biochemistry, Flemingovo n. 2, 166 10 Praha 6, Prague, Czech Republic.
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Corbeski I, Vargas-Rosales PA, Bedi RK, Deng J, Coelho D, Braud E, Iannazzo L, Li Y, Huang D, Ethève-Quelquejeu M, Cui Q, Caflisch A. The catalytic mechanism of the RNA methyltransferase METTL3. eLife 2024; 12:RP92537. [PMID: 38470714 PMCID: PMC10932547 DOI: 10.7554/elife.92537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024] Open
Abstract
The complex of methyltransferase-like proteins 3 and 14 (METTL3-14) is the major enzyme that deposits N6-methyladenosine (m6A) modifications on messenger RNA (mRNA) in humans. METTL3-14 plays key roles in various biological processes through its methyltransferase (MTase) activity. However, little is known about its substrate recognition and methyl transfer mechanism from its cofactor and methyl donor S-adenosylmethionine (SAM). Here, we study the MTase mechanism of METTL3-14 by a combined experimental and multiscale simulation approach using bisubstrate analogues (BAs), conjugates of a SAM-like moiety connected to the N6-atom of adenosine. Molecular dynamics simulations based on crystal structures of METTL3-14 with BAs suggest that the Y406 side chain of METTL3 is involved in the recruitment of adenosine and release of m6A. A crystal structure with a BA representing the transition state of methyl transfer shows a direct involvement of the METTL3 side chains E481 and K513 in adenosine binding which is supported by mutational analysis. Quantum mechanics/molecular mechanics (QM/MM) free energy calculations indicate that methyl transfer occurs without prior deprotonation of adenosine-N6. Furthermore, the QM/MM calculations provide further support for the role of electrostatic contributions of E481 and K513 to catalysis. The multidisciplinary approach used here sheds light on the (co)substrate binding mechanism, catalytic step, and (co)product release, and suggests that the latter step is rate-limiting for METTL3. The atomistic information on the substrate binding and methyl transfer reaction of METTL3 can be useful for understanding the mechanisms of other RNA MTases and for the design of transition state analogues as their inhibitors.
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Affiliation(s)
- Ivan Corbeski
- Department of Biochemistry, University of ZurichZurichSwitzerland
| | | | - Rajiv Kumar Bedi
- Department of Biochemistry, University of ZurichZurichSwitzerland
| | - Jiahua Deng
- Department of Chemistry, Boston UniversityBostonUnited States
| | - Dylan Coelho
- Université Paris Cité, CNRS, Laboratoire de Chimie et Biochimie Pharmacologiques et ToxicologiquesParisFrance
| | - Emmanuelle Braud
- Université Paris Cité, CNRS, Laboratoire de Chimie et Biochimie Pharmacologiques et ToxicologiquesParisFrance
| | - Laura Iannazzo
- Université Paris Cité, CNRS, Laboratoire de Chimie et Biochimie Pharmacologiques et ToxicologiquesParisFrance
| | - Yaozong Li
- Department of Biochemistry, University of ZurichZurichSwitzerland
| | - Danzhi Huang
- Department of Biochemistry, University of ZurichZurichSwitzerland
| | - Mélanie Ethève-Quelquejeu
- Université Paris Cité, CNRS, Laboratoire de Chimie et Biochimie Pharmacologiques et ToxicologiquesParisFrance
| | - Qiang Cui
- Department of Chemistry, Boston UniversityBostonUnited States
- Department of Physics, Boston UniversityBostonUnited States
- Department of Biomedical Engineering, Boston UniversityBostonUnited States
| | - Amedeo Caflisch
- Department of Biochemistry, University of ZurichZurichSwitzerland
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Zhang Y, Shen Z, Jiao R. Segment anything model for medical image segmentation: Current applications and future directions. Comput Biol Med 2024; 171:108238. [PMID: 38422961 DOI: 10.1016/j.compbiomed.2024.108238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 02/06/2024] [Accepted: 02/25/2024] [Indexed: 03/02/2024]
Abstract
Due to the inherent flexibility of prompting, foundation models have emerged as the predominant force in the fields of natural language processing and computer vision. The recent introduction of the Segment Anything Model (SAM) signifies a noteworthy expansion of the prompt-driven paradigm into the domain of image segmentation, thereby introducing a plethora of previously unexplored capabilities. However, the viability of its application to medical image segmentation remains uncertain, given the substantial distinctions between natural and medical images. In this work, we provide a comprehensive overview of recent endeavors aimed at extending the efficacy of SAM to medical image segmentation tasks, encompassing both empirical benchmarking and methodological adaptations. Additionally, we explore potential avenues for future research directions in SAM's role within medical image segmentation. While direct application of SAM to medical image segmentation does not yield satisfactory performance on multi-modal and multi-target medical datasets so far, numerous insights gleaned from these efforts serve as valuable guidance for shaping the trajectory of foundational models in the realm of medical image analysis. To support ongoing research endeavors, we maintain an active repository that contains an up-to-date paper list and a succinct summary of open-source projects at https://github.com/YichiZhang98/SAM4MIS.
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Affiliation(s)
- Yichi Zhang
- School of Data Science, Fudan University, Shanghai, China.
| | - Zhenrong Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Rushi Jiao
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China
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9
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Hu ZC, Tao YC, Pan JC, Zheng CM, Wang YS, Xue YP, Liu ZQ, Zheng YG. Breeding of Saccharomyces cerevisiae with a High-Throughput Screening Strategy for Improvement of S-Adenosyl-L-Methionine Production. Appl Biochem Biotechnol 2024; 196:1450-1463. [PMID: 37418127 DOI: 10.1007/s12010-023-04622-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2023] [Indexed: 07/08/2023]
Abstract
S-adenosyl-l-methionine (SAM), a vital physiologically active substance in living organisms, is produced by fermentation over Saccharomyces cerevisiae. The main limitation in SAM production was the low biosynthesis ability of SAM in S. cerevisiae. The aim of this work is to breed an SAM-overproducing mutant through UV mutagenesis coupled with high-throughput selection. Firstly, a high-throughput screening method by rapid identification of positive colonies was conducted. White colonies on YND medium were selected as positive strains. Then, nystatin/sinefungin was chosen as a resistant agent in directed mutagenesis. After several cycles of mutagenesis, a stable mutant 616-19-5 was successfully obtained and exhibited higher SAM production (0.41 g/L vs 1.39 g/L). Furthermore, the transcript levels of the genes SAM2, ADO1, and CHO2 involved in SAM biosynthesis increased, while ergosterol biosynthesis genes in mutant 616-19-5 significantly decreased. Finally, building on the above work, S. cerevisiae 616-19-5 could produce 10.92 ± 0.2 g/L SAM in a 5-L fermenter after 96 h of fermentation, showing a 2.02-fold increase in the product yield compared with the parent strain. Paving the way of breeding SAM-overproducing strain has improved the good basis for SAM industrial production.
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Affiliation(s)
- Zhong-Ce Hu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
| | - Yun-Chao Tao
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
| | - Jun-Chao Pan
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
| | - Chui-Mu Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
| | - Yuan-Shan Wang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
| | - Ya-Ping Xue
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
| | - Zhi-Qiang Liu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China.
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China.
| | - Yu-Guo Zheng
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
- The National and Local Joint Engineering Research Center for Biomanufacturing of Chiral Chemicals, Zhejiang University of Technology, 18 Chaowang Road, Hangzhou, 310014, People's Republic of China
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10
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Waraky A, Östlund A, Nilsson T, Weichenhan D, Lutsik P, Bähr M, Hey J, Tunali G, Adamsson J, Jacobsson S, Morsy MHA, Li S, Fogelstrand L, Plass C, Palmqvist L. Aberrant MNX1 expression associated with t(7;12)(q36;p13) pediatric acute myeloid leukemia induces the disease through altering histone methylation. Haematologica 2024; 109:725-739. [PMID: 37317878 PMCID: PMC10905087 DOI: 10.3324/haematol.2022.282255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 06/05/2023] [Indexed: 06/16/2023] Open
Abstract
Certain subtypes of acute myeloid leukemia (AML) in children have inferior outcome, such as AML with translocation t(7;12)(q36;p13) leading to an MNX1::ETV6 fusion along with high expression of MNX1. We have identified the transforming event in this AML and possible ways of treatment. Retroviral expression of MNX1 was able to induce AML in mice, with similar gene expression and pathway enrichment to t(7;12) AML patient data. Importantly, this leukemia was only induced in immune incompetent mice using fetal but not adult hematopoietic stem and progenitor cells. The restriction in transforming capacity to cells from fetal liver is in alignment with t(7;12)(q36;p13) AML being mostly seen in infants. Expression of MNX1 led to increased histone 3 lysine 4 mono-, di- and trimethylation, reduction in H3K27me3, accompanied with changes in genome-wide chromatin accessibility and genome expression, likely mediated through MNX1 interaction with the methionine cycle and methyltransferases. MNX1 expression increased DNA damage, depletion of the Lin-/Sca1+/c-Kit+ population and skewing toward the myeloid lineage. These effects, together with leukemia development, were prevented by pre-treatment with the S-adenosylmethionine analog Sinefungin. In conclusion, we have shown the importance of MNX1 in development of AML with t(7;12), supporting a rationale for targeting MNX1 and downstream pathways.
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Affiliation(s)
- Ahmed Waraky
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, and; Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg
| | - Anders Östlund
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg
| | - Tina Nilsson
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg
| | - Pavlo Lutsik
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg
| | - Marion Bähr
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg
| | - Joschka Hey
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg
| | - Gürcan Tunali
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg
| | - Jenni Adamsson
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg
| | - Susanna Jacobsson
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg
| | | | - Susann Li
- Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg
| | - Linda Fogelstrand
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, and; Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg
| | - Lars Palmqvist
- Department of Laboratory Medicine, Institute of Biomedicine, University of Gothenburg, and; Department of Clinical Chemistry, Sahlgrenska University Hospital, Gothenburg.
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11
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Leclerc D, Christensen KE, Reagan AM, Keser V, Luan Y, Malysheva OV, Wasek B, Bottiglieri T, Caudill MA, Howell GR, Rozen R. Folate Deficiency and/or the Genetic Variant Mthfr 677C >T Can Drive Hepatic Fibrosis or Steatosis in Mice, in a Sex-Specific Manner. Mol Nutr Food Res 2024; 68:e2300355. [PMID: 38327171 DOI: 10.1002/mnfr.202300355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 11/24/2023] [Indexed: 02/09/2024]
Abstract
SCOPE Disturbances in one-carbon metabolism contribute to nonalcoholic fatty liver disease (NAFLD) which encompasses steatosis, steatohepatitis, fibrosis, and cirrhosis. The goal is to examine impact of folate deficiency and the Mthfr677C >T variant on NAFLD. METHODS AND RESULTS This study uses the new Mthfr677C >T mouse model for the human MTHFR677C >T variant. Mthfr677CC and Mthfr677TT mice were fed control diet (CD) or folate-deficient (FD) diets for 4 months. FD and Mthfr677TT alter choline/methyl metabolites in liver and/or plasma (decreased S-adenosylmethionine (SAM):S-adenosylhomocysteine (SAH) ratio, methyltetrahydrofolate, and betaine; increased homocysteine [Hcy]). FD, with contribution from Mthfr677TT, provokes fibrosis in males. Studies of normal livers reveal alterations in plasma markers and gene expression that suggest an underlying predisposition to fibrosis induced by FD and/or Mthfr677TT in males. These changes are absent or reverse in females, consistent with the sex disparity of fibrosis. Sex-based differences in methylation potential, betaine, sphingomyelin, and trimethylamine-N-oxide (TMAO) levels may prevent fibrogenesis in females. In contrast, Mthfr677TT alters choline metabolism, dysregulates expression of lipid metabolism genes, and promotes steatosis in females. CONCLUSION This study suggests that folate deficiency predisposes males to fibrosis, which is exacerbated by Mthfr677TT, whereas Mthfr677TT predisposes females to steatosis, and reveal novel contributory mechanisms for these NAFLD-related disorders.
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Affiliation(s)
- Daniel Leclerc
- Departments of Human Genetics and Pediatrics, McGill University, Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - Karen E Christensen
- Departments of Human Genetics and Pediatrics, McGill University, Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | | | - Vafa Keser
- Departments of Human Genetics and Pediatrics, McGill University, Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - Yan Luan
- Departments of Human Genetics and Pediatrics, McGill University, Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - Olga V Malysheva
- Division of Nutritional Sciences and Genomics, Cornell University, Ithaca, NY, USA
| | - Brandi Wasek
- Center of Metabolomics, Institute of Metabolic Disease, Baylor Scott & White Research Institute, Dallas, TX, USA
| | - Teodoro Bottiglieri
- Center of Metabolomics, Institute of Metabolic Disease, Baylor Scott & White Research Institute, Dallas, TX, USA
| | - Marie A Caudill
- Division of Nutritional Sciences and Genomics, Cornell University, Ithaca, NY, USA
| | | | - Rima Rozen
- Departments of Human Genetics and Pediatrics, McGill University, Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
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12
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Kubiak X, Polsinelli I, Chavas LMG, Fyfe CD, Guillot A, Fradale L, Brewee C, Grimaldi S, Gerbaud G, Thureau A, Legrand P, Berteau O, Benjdia A. Structural and mechanistic basis for RiPP epimerization by a radical SAM enzyme. Nat Chem Biol 2024; 20:382-391. [PMID: 38158457 DOI: 10.1038/s41589-023-01493-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/30/2023] [Indexed: 01/03/2024]
Abstract
D-Amino acid residues, found in countless peptides and natural products including ribosomally synthesized and post-translationally modified peptides (RiPPs), are critical for the bioactivity of several antibiotics and toxins. Recently, radical S-adenosyl-L-methionine (SAM) enzymes have emerged as the only biocatalysts capable of installing direct and irreversible epimerization in RiPPs. However, the mechanism underpinning this biochemical process is ill-understood and the structural basis for this post-translational modification remains unknown. Here we report an atomic-resolution crystal structure of a RiPP-modifying radical SAM enzyme in complex with its substrate properly positioned in the active site. Crystallographic snapshots, size-exclusion chromatography-small-angle x-ray scattering, electron paramagnetic resonance spectroscopy and biochemical analyses reveal how epimerizations are installed in RiPPs and support an unprecedented enzyme mechanism for peptide epimerization. Collectively, our study brings unique perspectives on how radical SAM enzymes interact with RiPPs and catalyze post-translational modifications in natural products.
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Affiliation(s)
- Xavier Kubiak
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | - Ivan Polsinelli
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | | | - Cameron D Fyfe
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | - Alain Guillot
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | - Laura Fradale
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | - Clémence Brewee
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France
| | | | | | - Aurélien Thureau
- Synchrotron SOLEIL, HelioBio Group, L'Orme des Merisiers, Saint-Aubin, France
| | - Pierre Legrand
- Synchrotron SOLEIL, HelioBio Group, L'Orme des Merisiers, Saint-Aubin, France
| | - Olivier Berteau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France.
| | - Alhosna Benjdia
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, ChemSyBio, Jouy-en-Josas, France.
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13
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Liu Z, Li X, Wang T, Zhang H, Li X, Xu J, Zhang Y, Zhao Z, Yang P, Zhou C, Ge Q, Zhao L. SAH and SAM/SAH ratio associate with acute kidney injury in critically ill patients: A case-control study. Clin Chim Acta 2024; 553:117726. [PMID: 38110027 DOI: 10.1016/j.cca.2023.117726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/12/2023] [Accepted: 12/15/2023] [Indexed: 12/20/2023]
Abstract
BACKGROUND Acute kidney injury (AKI) is a serious clinical emergency with an acute onset, rapid progression and poor prognosis, which has high morbidity and mortality in hospitalized patients. DNA methylation plays an important role in the occurrence and progression of kidney disease, and aberrant methylation and certain altered methylation-related metabolites have been reported in AKI patients. However, the specific alterations of methylation-related metabolites in the AKI patients were not investigated clearly. METHOD In this study, 61 AKI and 61 matched non-AKI inpatients were recruited after propensity score matching the age and hypertension. And 11 methylation-related metabolites in the plasma and urine of the two groups were quantified by using UHPLC-MS/MS method. RESULTS Certain methylation-relate intermediates were up-regulated in the plasma (choline, trimethylamine N-oxide (TMAO), trimethyl lysine (TML), S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH)) and down-regulated in the urine of AKI inpatients (choline, betaine, TMAO, dimethylglycine (DMG), SAM and taurine). The correlation analysis revealed a relatively strong correlation between plasma SAH, SAM/SAH ratio and renal function index (serum creatinine (SCr) and estimated glomerular filtration rate (eGFR), r = 0.523-0.616), and the correlation of urinary intermediates with renal function index was weaker than that in the plasma. Furthermore, receiver operating characteristic (ROC) analysis showed that plasma SAH and urinary SAM/SAH ratio represented the best distinguishing efficiency with AUC 0.844 and 0.794, respectively. Moreover, the findings of binary regression analysis demonstrated plasma choline, TMAO, TML, SAM and SAH were the risk markers of AKI (up-regulation in plasma, OR > 1), urinary choline, betaine, TMAO, DMG and SAM were protective markers of AKI (down-regulation in urine, OR < 1), and SAM/SAH ratio was a protective marker in plasma and urine (down-regulation in both two biofluids, OR = 0.510, 0.383-0.678 in plasma, OR = 0.904, 0.854-0.968 in urine), indicating the increased risk of AKI when combined with the alteration of plasma and urinary levels. CONCLUSION The comprehensive analysis of plasma and urine samples from AKI inpatients offers a more extensive assessment of methylated metabolic alterations, suggesting a close relationship between AKI stress and altered methylation ability. The plasma level of SAH and SAM/SAH ratio and urinary SAM/SAH ratio both showed a strong correlation with renal function (SCr and eGFR) and good accuracy for distinguishing AKI in the two biomatrices, which exhibited promising prospects in predicting renal function decline and providing further information for the pathogenesis of AKI.
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Affiliation(s)
- Zhini Liu
- Department of Pharmacy, Peking University Third Hospital, Beijing 100191, China; School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu Province 211198, China; Therapeutic Drug Monitoring and Clinical Toxicology Center of Peking University, Beijing 100191, China
| | - Xiaona Li
- Department of Pharmacy, Peking University Third Hospital, Beijing 100191, China; Therapeutic Drug Monitoring and Clinical Toxicology Center of Peking University, Beijing 100191, China; NMPA Key Laboratory for Research and Evaluation of Generic Drugs, Beijing 100191, China.
| | - Tiehua Wang
- Department of Intensive Care Unit, Peking University Third Hospital, Beijing, China
| | - Hua Zhang
- Research Center of Clinical Epidemiology, Peking University Third Hospital, Beijing, China
| | - Xiaoxiao Li
- Department of Pharmacy, Peking University Third Hospital, Beijing 100191, China
| | - Jiamin Xu
- Department of Pharmacy, Peking University Third Hospital, Beijing 100191, China; Therapeutic Drug Monitoring and Clinical Toxicology Center of Peking University, Beijing 100191, China; NMPA Key Laboratory for Research and Evaluation of Generic Drugs, Beijing 100191, China
| | - Yuanyuan Zhang
- Department of Pharmacy, Peking University Third Hospital, Beijing 100191, China; Therapeutic Drug Monitoring and Clinical Toxicology Center of Peking University, Beijing 100191, China; NMPA Key Laboratory for Research and Evaluation of Generic Drugs, Beijing 100191, China
| | - Zhiling Zhao
- Department of Intensive Care Unit, Peking University Third Hospital, Beijing, China
| | - Ping Yang
- Department of Pharmacy, Peking University Third Hospital, Beijing 100191, China; Therapeutic Drug Monitoring and Clinical Toxicology Center of Peking University, Beijing 100191, China; NMPA Key Laboratory for Research and Evaluation of Generic Drugs, Beijing 100191, China
| | - Congya Zhou
- Department of Pharmacy, Peking University Third Hospital, Beijing 100191, China; Therapeutic Drug Monitoring and Clinical Toxicology Center of Peking University, Beijing 100191, China; NMPA Key Laboratory for Research and Evaluation of Generic Drugs, Beijing 100191, China
| | - Qinggang Ge
- Department of Intensive Care Unit, Peking University Third Hospital, Beijing, China.
| | - Libo Zhao
- Department of Pharmacy, Peking University Third Hospital, Beijing 100191, China; Therapeutic Drug Monitoring and Clinical Toxicology Center of Peking University, Beijing 100191, China; NMPA Key Laboratory for Research and Evaluation of Generic Drugs, Beijing 100191, China.
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14
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Li L, Atkinson N, Crews KR, Molinelli AR. Determination of Thiopurine S-Methyltransferase (TPMT) Activity in Human Erythrocytes by Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS). Methods Mol Biol 2024; 2737:465-472. [PMID: 38036847 DOI: 10.1007/978-1-0716-3541-4_43] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Abstract
Thiopurine methyltransferase (TPMT) is a cytosolic enzyme involved in the metabolism of thiopurine medications that are used in the treatment of multiple malignant and nonmalignant immunologic conditions. Polymorphisms in the TPMT gene associated with low enzyme activity can produce pronounced pharmacologic effects during therapy. The determination of TPMT erythrocyte activity is a valuable adjunct test to genotyping for the assignment of TPMT phenotype, especially in the presence of indeterminate genotypes. We present a method for the determination TPMT activity in human erythrocytes whereby we utilize LC-MS/MS to measure the amount of 6-methylmercaptopurine formed in red blood cell (RBC) lysates using 6-mercaptopurine as substrate and S-adenosylmethionine (SAM) as methyl donor. This method has been successfully implemented and proven to be reliable for use in human specimens.
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Affiliation(s)
- Lie Li
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Natalya Atkinson
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kristine R Crews
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Alejandro R Molinelli
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.
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15
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Moon JD, Yusko K, Nassimos L, Wu J. Imaging S-Adenosyl Methionine Dynamics in Living Cells Using an RNA-Based Fluorescent Sensor. Methods Mol Biol 2024; 2774:259-267. [PMID: 38441770 DOI: 10.1007/978-1-0716-3718-0_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
S-Adenosyl methionine (SAM) is a critical metabolite involved in numerous cellular processes, including DNA methylation and gene expression regulation. Understanding the spatiotemporal dynamics of SAM within living cells is essential for deciphering its roles in maintaining cell homeostasis and in disease development. Here, we describe a protocol based on a recently reported SAM sensor exploiting a fluorogenic RNA and an RNA three-way junction for visualizing SAM dynamics in cultured mammalian cells.
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Affiliation(s)
- Jared D Moon
- Department of Psychiatry, Columbia University, New York, NY, USA.
- Research Foundation for Mental Hygiene, Menands, NY, USA.
- New York State Psychiatric Institute, New York, NY, USA.
| | - Kevin Yusko
- Department of Chemistry, Binghamton University, Binghamton, NY, USA
| | - Lindsey Nassimos
- Department of Chemistry, Binghamton University, Binghamton, NY, USA
| | - Jiahui Wu
- Department of Chemistry, Binghamton University, Binghamton, NY, USA.
- Department of Chemistry, University of Massachusetts, Amherst, MA, USA.
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16
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Wang Z, Wang Q, Chen C, Zhao X, Wang H, Xu L, Fu Y, Huang G, Li M, Xu J, Zhang Q, Wang B, Xu G, Wang L, Zou X, Wang S. NNMT enriches for AQP5 + cancer stem cells to drive malignant progression in early gastric cardia adenocarcinoma. Gut 2023; 73:63-77. [PMID: 36977555 DOI: 10.1136/gutjnl-2022-328408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 03/15/2023] [Indexed: 03/30/2023]
Abstract
OBJECTIVE Early gastric cardia adenocarcinoma (EGCA) is a highly heterogeneous cancer, and the understanding of its classification and malignant progression is limited. This study explored the cellular and molecular heterogeneity in EGCA using single-cell RNA sequencing (scRNA-seq). DESIGN scRNA-seq was conducted on 95 551 cells from endoscopic biopsies of low-grade intraepithelial neoplasia, well/moderately/poorly differentiated EGCA and their paired adjacent nonmalignant biopsy samples. Large-scale clinical samples and functional experiments were employed. RESULTS Integrative analysis of epithelial cells revealed that chief cells, parietal cells and enteroendocrine cells were rarely detected in the malignant epithelial subpopulation, whereas gland and pit mucous cells and AQP5+ stem cells were predominant during malignant progression. Pseudotime and functional enrichment analyses showed that the WNT and NF-κB signalling pathways were activated during the transition. Cluster analysis of heterogeneous malignant cells revealed that NNMT-mediated nicotinamide metabolism was enriched in gastric mucin phenotype cell population, which was associated with tumour initiation and inflammation-induced angiogenesis. Furthermore, the expression level of NNMT was gradually increased during the malignant progression and associated with poor prognosis in cardia adenocarcinoma. Mechanistically, NNMT catalysed the conversion of nicotinamide to 1-methyl nicotinamide via depleting S-adenosyl methionine, which led to a reduction in H3K27 trimethylation (H3K27me3) and then activated the WNT signalling pathway to maintain the stemness of AQP5+ stem cells during EGCA malignant progression. CONCLUSION Our study extends the understanding of the heterogeneity of EGCA and identifies a functional NNMT+/AQP5+ population that may drive malignant progression in EGCA and could be used for early diagnosis and therapy.
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Affiliation(s)
- Zhangding Wang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, People's Republic of China
| | - Qiang Wang
- Department of Hepatobiliary Surgery, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, People's Republic of China
| | - Chen Chen
- Medical School of Nanjing University, Nanjing, Jiangsu Province, People's Republic of China
| | - Xiaoya Zhao
- Medical School of Nanjing University, Nanjing, Jiangsu Province, People's Republic of China
| | - Honggang Wang
- Department of Gastroenterology, The Affiliated Huaian No. 1 People's Hospital of Nanjing Medical University, Huai'an, Jiangsu Province, People's Republic of China
| | - Lei Xu
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, People's Republic of China
| | - Yao Fu
- Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, People's Republic of China
| | - Guang Huang
- Center for Global Health, Key Lab of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Mengmeng Li
- Medical School of Nanjing University, Nanjing, Jiangsu Province, People's Republic of China
| | - Jiawen Xu
- Medical School of Nanjing University, Nanjing, Jiangsu Province, People's Republic of China
| | - Qianyi Zhang
- Medical School of Nanjing University, Nanjing, Jiangsu Province, People's Republic of China
| | - Bo Wang
- Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, People's Republic of China
| | - Guifang Xu
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, People's Republic of China
| | - Lei Wang
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, People's Republic of China
| | - Xiaoping Zou
- Department of Gastroenterology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, People's Republic of China
- Department of Gastroenterology, Affiliated Taikang Xianlin Drum Tower Hospital, Medical School of Nanjing University, Nanjing, Jiangsu Province, People's Republic of China
| | - Shouyu Wang
- Department of Hepatobiliary Surgery, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu Province, People's Republic of China
- Jiangsu Key Laboratory of Molecular Medicine, Medical School of Nanjing University, Nanjing, Jiangsu Province, People's Republic of China
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17
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Clément A, Clément P, Viot G, Menezo YJR. The importance of preconception Hcy testing: identification of a folate trap syndrome in a woman attending an assisted reproduction program. J Assist Reprod Genet 2023; 40:2879-2883. [PMID: 37819550 PMCID: PMC10656398 DOI: 10.1007/s10815-023-02964-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/02/2023] [Indexed: 10/13/2023] Open
Abstract
Methylation is a ubiquitous and permanent key biochemical process playing a major role in gametogenesis and embryogenesis in relation to epigenetics and imprinting. Methylation relies on a unique cofactor S-Adenosyl Methionine: SAM. Release of the methyl group onto target molecules is followed by liberation of S-Adenosyl Homocysteine (SAH), and then homocysteine (Hcy), both potent inhibitors of the methylation process. Defective recycling of homocysteine, leading to Hyperhomocysteinemia, is mainly due to reduced activity of MTHFR (Methylene TetraHydroFolate Reductase). However, we described here, in a woman attending an ART program, a rather rare syndrome: The Folate trap syndrome. Due to vitamin B12 deficiency (malabsorption), Hcy cannot be recycled to methionine by the methionine synthase. Transmethylation activity is weak and leads to Hhcy (Hyperhomocysteinhemia). Her Hhcy, over 16µM, was resistant to 5MTHF (5 Methyltetrahydrofolate) associated with a support of the one carbon cycle, a classical efficient treatment for elevated homocysteine. Treatment with Methylcobalamine (associated with adenosyl Cobalamine) allowed a Hcy drop down to 10 µM. Knowing the pleiotropic negative impact of Hcy on gametes, embryos and pregnancy in general, we strongly recommend a Hcy dosage in both members of couples seeking treatment for pregnancy.
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Affiliation(s)
- Arthur Clément
- Laboratoire Clement, Genetics and IVF, 17 Avenue d'Eylau, 75016, Paris, France
| | - Patrice Clément
- Laboratoire Clement, Genetics and IVF, 17 Avenue d'Eylau, 75016, Paris, France
| | - Géraldine Viot
- Cabinet Médical de génétique Clinique, 74 Avenue Paul Doumer, 75116, Paris, France
| | - Yves J R Menezo
- Laboratoire Clement, Genetics and IVF, 17 Avenue d'Eylau, 75016, Paris, France.
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18
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Chen J, Cui X, Fang N, Wu Y, Yu S, Xiao D. Methionine-CBS axis promotes intracellular ROS levels by reprogramming serine metabolism. FASEB J 2023; 37:e23268. [PMID: 37889798 DOI: 10.1096/fj.202300804rrrr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 09/29/2023] [Accepted: 10/07/2023] [Indexed: 10/29/2023]
Abstract
As a non-essential amino acid, cysteine could be obtained through both exogenous uptake and endogenous de novo synthesis pathways. Research has demonstrated that restricting the uptake of cystine could result in a depletion of intracellular cysteine and glutathione, ultimately leading to an increase in intracellular reactive oxygen species (ROS) levels. However, the role of methionine in regulating intracellular ROS levels is currently unclear. Here, we want to explore the role of methionine in regulating intracellular ROS levels. We found that methionine restriction could lead to a decrease in intracellular ROS levels, while supplementation with SAM can restore these levels through flow cytometry. Mechanically, we found that the methionine-SAM axis relies on CBS when regulating intracellular ROS levels. Furthermore, we speculate and prove that the methionine-SAM-CBS axis alters the metabolism of serine, thereby reducing intracellular reductive power, therefore promoting intracellular ROS levels through changing metabolite levels and genetic methods. Finally, our study revealed that high expression of CBS in tumor cells could lead to increased intracellular ROS levels, ultimately resulting in faster proliferation rates. Together, our study confirmed that methionine plays a promoting role in the regulation of intracellular ROS levels.
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Affiliation(s)
- Jingyun Chen
- Cancer Center, The First Hospital of Jilin university, Changchun, China
| | - Xiangyan Cui
- Department of Otolaryngology-Head and Neck Surgery, The First Hospital of Jilin University, Changchun, China
| | - Ning Fang
- Department of Otolaryngology-Head and Neck Surgery, The First Hospital of Jilin University, Changchun, China
| | - Yu Wu
- Department of Otolaryngology-Head and Neck Surgery, The First Hospital of Jilin University, Changchun, China
| | - Shujian Yu
- Department of Otolaryngology-Head and Neck Surgery, The First Hospital of Jilin University, Changchun, China
| | - Dong Xiao
- Department of Otolaryngology-Head and Neck Surgery, The First Hospital of Jilin University, Changchun, China
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19
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Okuda T, Lenz AK, Seitz F, Vogel J, Höbartner C. A SAM analogue-utilizing ribozyme for site-specific RNA alkylation in living cells. Nat Chem 2023; 15:1523-1531. [PMID: 37667013 PMCID: PMC10624628 DOI: 10.1038/s41557-023-01320-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 08/08/2023] [Indexed: 09/06/2023]
Abstract
Post-transcriptional RNA modification methods are in high demand for site-specific RNA labelling and analysis of RNA functions. In vitro-selected ribozymes are attractive tools for RNA research and have the potential to overcome some of the limitations of chemoenzymatic approaches with repurposed methyltransferases. Here we report an alkyltransferase ribozyme that uses a synthetic, stabilized S-adenosylmethionine (SAM) analogue and catalyses the transfer of a propargyl group to a specific adenosine in the target RNA. Almost quantitative conversion was achieved within 1 h under a wide range of reaction conditions in vitro, including physiological magnesium ion concentrations. A genetically encoded version of the SAM analogue-utilizing ribozyme (SAMURI) was expressed in HEK293T cells, and intracellular propargylation of the target adenosine was confirmed by specific fluorescent labelling. SAMURI is a general tool for the site-specific installation of the smallest tag for azide-alkyne click chemistry, which can be further functionalized with fluorophores, affinity tags or other functional probes.
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Affiliation(s)
- Takumi Okuda
- Institute of Organic Chemistry, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Ann-Kathrin Lenz
- Institute of Organic Chemistry, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Florian Seitz
- Institute of Organic Chemistry, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Jörg Vogel
- Institute of Molecular Infection Biology (IMIB), Julius-Maximilians-Universität Würzburg, Würzburg, Germany
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany
| | - Claudia Höbartner
- Institute of Organic Chemistry, Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
- Center for Nanosystems Chemistry (CNC), Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
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20
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Ma L, Lv J, Zhang A. Depletion of S-adenosylmethionine induced by arsenic exposure is involved in liver injury of rat through perturbing histone H3K36 trimethylation dependent bile acid metabolism. Environ Pollut 2023; 334:122228. [PMID: 37481032 DOI: 10.1016/j.envpol.2023.122228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/22/2023] [Accepted: 07/18/2023] [Indexed: 07/24/2023]
Abstract
Long-term exposure to arsenic, a common environmental pollutant, can induce various types of liver injury, but the mechanism and treatment measures remain unclear. This study constructed a rat model of arsenic-induced liver injury, with methyl group donor S-adenosylmethionine (SAM) supplementation and Rosa roxburghii Tratt juice intervention, to explore the epigenetic mechanism and intervention method of arsenic-induced liver injury from the perspective of hepatic bile acid metabolism. The results showed that arsenic exposure induced the accumulation of total bile acids (TBA) in the liver and serum of rats, and the abnormalities in liver function and liver histopathology. Arsenic reduced histone H3K36 trimethylation (H3K36me3) in the liver via consuming methyl group donor SAM. The reduction of H3K36me3 was involved in arsenic-induced bile acid accumulation by inhibiting the transcription of negative feedback regulators Fxr and Fgfr4 for hepatic bile acid synthesis. SAM supplementation reversed arsenic-induced bile acid accumulation and liver injury by reactivating H3k36me3-dependent transcription of Fxr and Fgfr4. Moreover, this study found that Rosa roxburghii Tratt juice could rescue arsenic-induced SAM consumption, recover H3K36me3-dependent negative feedback regulation of hepatic bile acid synthesis, and alleviate arsenic-induced bile acid accumulation and liver injury. In conclusion, arsenic exposure perturbed H3K36me3-dependent hepatic bile acid metabolism via depleting SAM, thereby inducing hepatic bile acid accumulation and liver injury, which was ameliorated by the supporting effect of Rosa roxburghii Tratt juice on SAM. This study contributes to understanding the mechanism of arsenic-induced liver injury from the perspective of SAM-dependent epigenetics, providing new insight into its prevention and treatment.
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Affiliation(s)
- Lu Ma
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang, 550025, Guizhou, PR China.
| | - Jiaxin Lv
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang, 550025, Guizhou, PR China.
| | - Aihua Zhang
- The Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, Department of Toxicology, School of Public Health, Guizhou Medical University, Guiyang, 550025, Guizhou, PR China.
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21
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Subash Chandra Bose K, Shah MI, Krishna J, Sankaranarayanan M. Genome-scale metabolic model analysis of Pichia pastoris for enhancing the production of S-adenosyl-L-methionine. Bioprocess Biosyst Eng 2023; 46:1471-1482. [PMID: 37597025 DOI: 10.1007/s00449-023-02913-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 07/21/2023] [Indexed: 08/21/2023]
Abstract
Komagataella phaffii, formerly Pichia pastoris (P. pastoris), is a promising methylotrophic yeast used in industry to produce recombinant protein and valuable metabolites. In this study, a genome-scale metabolic model (GEMs) was reconstructed and used to assess P. pastoris' metabolic capabilities for the production of S-adenosyl-L-methionine (AdoMet or SAM or SAMe) from individual carbon sources along with the addition of L-methionine. In a model-driven P. pastoris strain, the well-established genome-scale metabolic model iAUKM can be implemented to predict high valuable metabolite production. The model, iAUKM, was created by merging the previously published iMT1026 model and the draught model generated using Raven toolbox from the KEGG database which covered 2309 enzymatic reactions associated with 1033 metabolic genes and 1750 metabolites. The highly curated model was successful in capturing P. pastoris growth on various carbon sources, as well as AdoMet production under various growth conditions. Many overexpression gene targets for increasing AdoMet accumulation in the cell have been predicted for various carbon sources. Inorganic phosphatase (IPP) was one of the predicted overexpression targets as revealed from simulations using iAUKM. When IPP gene was integrated into P. pastoris, we found that AdoMet accumulation increased by 16% and 14% using glucose and glycerol as carbon sources, respectively. Our in silico results shed light on the factors limiting AdoMet production, as well as key pathways for rationalized engineering to increase AdoMet yield.
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Affiliation(s)
| | - Mohd Imran Shah
- Department of Biotechnology, Anna University, Chennai, Tamil Nadu, India
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22
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Mazurowski MA, Dong H, Gu H, Yang J, Konz N, Zhang Y. Segment anything model for medical image analysis: An experimental study. Med Image Anal 2023; 89:102918. [PMID: 37595404 PMCID: PMC10528428 DOI: 10.1016/j.media.2023.102918] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 07/03/2023] [Accepted: 07/31/2023] [Indexed: 08/20/2023]
Abstract
Training segmentation models for medical images continues to be challenging due to the limited availability of data annotations. Segment Anything Model (SAM) is a foundation model trained on over 1 billion annotations, predominantly for natural images, that is intended to segment user-defined objects of interest in an interactive manner. While the model performance on natural images is impressive, medical image domains pose their own set of challenges. Here, we perform an extensive evaluation of SAM's ability to segment medical images on a collection of 19 medical imaging datasets from various modalities and anatomies. In our experiments, we generated point and box prompts for SAM using a standard method that simulates interactive segmentation. We report the following findings: (1) SAM's performance based on single prompts highly varies depending on the dataset and the task, from IoU=0.1135 for spine MRI to IoU=0.8650 for hip X-ray. (2) Segmentation performance appears to be better for well-circumscribed objects with prompts with less ambiguity such as the segmentation of organs in computed tomography and poorer in various other scenarios such as the segmentation of brain tumors. (3) SAM performs notably better with box prompts than with point prompts. (4) SAM outperforms similar methods RITM, SimpleClick, and FocalClick in almost all single-point prompt settings. (5) When multiple-point prompts are provided iteratively, SAM's performance generally improves only slightly while other methods' performance improves to the level that surpasses SAM's point-based performance. We also provide several illustrations for SAM's performance on all tested datasets, iterative segmentation, and SAM's behavior given prompt ambiguity. We conclude that SAM shows impressive zero-shot segmentation performance for certain medical imaging datasets, but moderate to poor performance for others. SAM has the potential to make a significant impact in automated medical image segmentation in medical imaging, but appropriate care needs to be applied when using it. Code for evaluation SAM is made publicly available at https://github.com/mazurowski-lab/segment-anything-medical-evaluation.
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Affiliation(s)
- Maciej A Mazurowski
- Department of Radiology, Duke University, Durham, NC, 27708, USA; Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA; Department of Computer Science, Duke University, Durham, NC, 27708, USA; Department of Biostatistics & Bioinformatics, Duke University, Durham, NC, 27708, USA
| | - Haoyu Dong
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA.
| | - Hanxue Gu
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA
| | - Jichen Yang
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA
| | - Nicholas Konz
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA
| | - Yixin Zhang
- Department of Electrical and Computer Engineering, Duke University, Durham, NC, 27708, USA
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23
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Abstract
Covering: from 2000 up to the very early part of 2023S-Adenosyl-L-methionine (SAM) is a naturally occurring trialkyl sulfonium molecule that is typically associated with biological methyltransfer reactions. However, SAM is also known to donate methylene, aminocarboxypropyl, adenosyl and amino moieties during natural product biosynthetic reactions. The reaction scope is further expanded as SAM itself can be modified prior to the group transfer such that a SAM-derived carboxymethyl or aminopropyl moiety can also be transferred. Moreover, the sulfonium cation in SAM has itself been found to be critical for several other enzymatic transformations. Thus, while many SAM-dependent enzymes are characterized by a methyltransferase fold, not all of them are necessarily methyltransferases. Furthermore, other SAM-dependent enzymes do not possess such a structural feature suggesting diversification along different evolutionary lineages. Despite the biological versatility of SAM, it nevertheless parallels the chemistry of sulfonium compounds used in organic synthesis. The question thus becomes how enzymes catalyze distinct transformations via subtle differences in their active sites. This review summarizes recent advances in the discovery of novel SAM utilizing enzymes that rely on Lewis acid/base chemistry as opposed to radical mechanisms of catalysis. The examples are categorized based on the presence of a methyltransferase fold and the role played by SAM within the context of known sulfonium chemistry.
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Affiliation(s)
- Yu-Hsuan Lee
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| | - Daan Ren
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| | - Byungsun Jeon
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
| | - Hung-Wen Liu
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, USA.
- Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy, University of Texas at Austin, Austin, TX 78712, USA
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24
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Zhang X, Meng W, Feng J, Gao X, Qin C, Feng P, Huang Y, Gao SJ. METTL16 controls Kaposi's sarcoma-associated herpesvirus replication by regulating S-adenosylmethionine cycle. Cell Death Dis 2023; 14:591. [PMID: 37673880 PMCID: PMC10482891 DOI: 10.1038/s41419-023-06121-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/22/2023] [Accepted: 08/29/2023] [Indexed: 09/08/2023]
Abstract
Oncogenic Kaposi's sarcoma-associated herpesvirus (KSHV) consists of latent and lytic replication phases, both of which are important for the development of KSHV-related cancers. As one of the most abundant RNA modifications, N6-methyladenosine (m6A) and its related complexes regulate KSHV life cycle. However, the role of METTL16, a newly discovered RNA methyltransferase, in KSHV life cycle remains unknown. In this study, we have identified a suppressive role of METTL16 in KSHV lytic replication. METTL16 knockdown increased while METTL16 overexpression reduced KSHV lytic replication. METTL16 binding to and writing of m6A on MAT2A transcript are essential for its splicing, maturation and expression. As a rate-limiting enzyme in the methionine-S-adenosylmethionine (SAM) cycle, MAT2A catalyzes the conversion of L-methionine to SAM required for the transmethylation of protein, DNA and RNA, transamination of polyamines, and transsulfuration of cystathionine. Consequently, knockdown or chemical inhibition of MAT2A reduced intracellular SAM level and enhanced KSHV lytic replication. In contrast, SAM treatment was sufficient to inhibit KSHV lytic replication and reverse the effect of the enhanced KSHV lytic program caused by METTL16 or MAT2A knockdown. Mechanistically, METTL16 or MAT2A knockdown increased while SAM treatment decreased the intracellular reactive oxygen species level by altering glutathione level, which is essential for efficient KSHV lytic replication. These findings demonstrate that METTL16 suppresses KSHV lytic replication by modulating the SAM cycle to maintain intracellular SAM level and redox homeostasis, thus illustrating the linkage of KSHV life cycle with specific m6A modifications, and cellular metabolic and oxidative conditions.
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Affiliation(s)
- Xinquan Zhang
- Cancer Virology Program, University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Wen Meng
- Cancer Virology Program, University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jian Feng
- Cancer Virology Program, University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Xinghong Gao
- Cancer Virology Program, University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Chao Qin
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Pinghui Feng
- Section of Infection and Immunity, Herman Ostrow School of Dentistry, Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yufei Huang
- Cancer Virology Program, University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Electrical and Computer Engineering, Swanson School of Engineering, Pittsburgh, PA, USA
| | - Shou-Jiang Gao
- Cancer Virology Program, University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA.
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
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25
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Mirzadeh Azad F, Struys EA, Wingert V, Hannibal L, Mills K, Jansen JH, Longley DB, Stunnenberg HG, Atlasi Y. Spic regulates one-carbon metabolism and histone methylation in ground-state pluripotency. Sci Adv 2023; 9:eadg7997. [PMID: 37595034 DOI: 10.1126/sciadv.adg7997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 07/20/2023] [Indexed: 08/20/2023]
Abstract
Understanding mechanisms of epigenetic regulation in embryonic stem cells (ESCs) is of fundamental importance for stem cell and developmental biology. Here, we identify Spic, a member of the ETS family of transcription factors (TFs), as a marker of ground state pluripotency. We show that Spic is rapidly induced in ground state ESCs and in response to extracellular signal-regulated kinase (ERK) inhibition. We find that SPIC binds to enhancer elements and stabilizes NANOG binding to chromatin, particularly at genes involved in choline/one-carbon (1C) metabolism such as Bhmt, Bhmt2, and Dmgdh. Gain-of-function and loss-of-function experiments revealed that Spic controls 1C metabolism and the flux of S-adenosyl methionine to S-adenosyl-L-homocysteine (SAM-to-SAH), thereby, modulating the levels of H3R17me2 and H3K4me3 histone marks in ESCs. Our findings highlight betaine-dependent 1C metabolism as a hallmark of ground state pluripotency primarily activated by SPIC. These findings underscore the role of uncharacterized auxiliary TFs in linking cellular metabolism to epigenetic regulation in ESCs.
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Affiliation(s)
- Fatemeh Mirzadeh Azad
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Eduard A Struys
- Department of Clinical Chemistry, Amsterdam University Medical Center, Amsterdam, Netherlands
| | - Victoria Wingert
- Laboratory of Clinical Biochemistry and Metabolism, Department of General Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Luciana Hannibal
- Laboratory of Clinical Biochemistry and Metabolism, Department of General Pediatrics, Adolescent Medicine and Neonatology, Faculty of Medicine, Medical Center, University of Freiburg, Freiburg, Germany
| | - Ken Mills
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Joop H Jansen
- Department of Laboratory Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, Netherlands
| | - Daniel B Longley
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen, Netherlands
- Princess Maxima Centre for Pediatric Oncology, Utrecht, Netherlands
| | - Yaser Atlasi
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, Belfast, UK
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26
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Liu F, Zhou H, Peng Y, Qiao Y, Wang P, Si C, Wang X, Gong J, Chen K, Song F. Plasma One-Carbon Metabolism-Related Micronutrients and the Risk of Breast Cancer: Involvement of DNA Methylation. Nutrients 2023; 15:3621. [PMID: 37630812 PMCID: PMC10458034 DOI: 10.3390/nu15163621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/05/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Findings of epidemiologic studies focusing on the association between one-carbon metabolism-related micronutrients and breast cancer risk, along with the involvement of DNA methylation, have been inconsistent and incomprehensive. We conducted a case-control study in China including 107 paired participants and comprehensively detected 12 plasma one-carbon metabolism-related micronutrients. Genomic DNA methylation was measured using an 850 K chip and differential methylation probes (DMPs) were identified. Multivariate logistic regression was performed to estimate the associations between plasma micronutrients and the odds of breast cancer. The mediation of selected DMPs in micronutrient breast cancer associations was examined using mediation analyses. An inverse association of plasma folate, methionine cycling-related micronutrients (methionine, S-adenosylmethionine, and S-adenosylhomocysteine), and all micronutrients in the choline metabolism and enzymatic factor groups, and a positive association of methionine cycling-related cysteine with breast cancer risk were observed. Nine micronutrients (methionine, cysteine, SAM, folate, choline, betaine, P5P, vitamins B2, and B12) were related to global or probe-specific methylation levels (p < 0.05). The selected DMPs mediated the micronutrient breast cancer associations with an average mediation proportion of 36.43%. This study depicted comprehensive associations between circulating one-carbon metabolism-related micronutrients and breast cancer risk mediated by DNA methylation.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Kexin Chen
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Major Diseases in the Population, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China; (F.L.); (H.Z.); (Y.P.); (Y.Q.); (P.W.); (C.S.); (X.W.); (J.G.)
| | - Fangfang Song
- Department of Epidemiology and Biostatistics, Key Laboratory of Molecular Cancer Epidemiology, Key Laboratory of Prevention and Control of Major Diseases in the Population, Ministry of Education, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China; (F.L.); (H.Z.); (Y.P.); (Y.Q.); (P.W.); (C.S.); (X.W.); (J.G.)
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27
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Centner FS, Schoettler JJ, Brohm K, Mindt S, Jäger E, Hahn B, Fuderer T, Lindner HA, Schneider-Lindner V, Krebs J, Neumaier M, Thiel M. S-Adenosylhomocysteine Is a Useful Metabolic Factor in the Early Prediction of Septic Disease Progression and Death in Critically Ill Patients: A Prospective Cohort Study. Int J Mol Sci 2023; 24:12600. [PMID: 37628779 PMCID: PMC10454796 DOI: 10.3390/ijms241612600] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 07/26/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
A common final pathway of pathogenetic mechanisms in septic organ dysfunction and death is a lack or non-utilization of oxygen. Plasma concentrations of lactate serve as surrogates for the oxygen-deficiency-induced imbalance between energy supply and demand. As S-adenosylhomocysteine (SAH) was shown to reflect tissue hypoxia, we compared the ability of SAH versus lactate to predict the progression of inflammatory and septic disease to septic organ dysfunction and death. Using univariate and multiple logistic regression, we found that SAH but not lactate, taken upon patients' inclusion in the study close to ICU admission, significantly and independently contributed to the prediction of disease progression and death. Due to the stronger increase in SAH in relation to S-adenosylmethionine (SAM), the ratio of SAM to SAH, representing methylation potential, was significantly decreased in patients with septic organ dysfunction and non-survivors compared with SIRS/sepsis patients (2.8 (IQR 2.3-3.9) vs. 8.8 (4.9-13.8); p = 0.003) or survivors (4.9 (2.8-9.5) vs. 8.9 (5.1-14.3); p = 0.026), respectively. Thus, SAH appears to be a better contributor to the prediction of septic organ dysfunction and death than lactate in critically ill patients. As SAH is a potent inhibitor of SAM-dependent methyltransferases involved in numerous vital biochemical processes, the impairment of the SAM-to-SAH ratio in severely critically ill septic patients and non-survivors warrants further studies on the pathogenetic role of SAH in septic multiple organ failure.
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Affiliation(s)
- Franz-Simon Centner
- Department of Anesthesiology, Surgical Intensive Care Medicine and Pain Medicine, Medical Faculty Mannheim, University Medical Center Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany; (F.-S.C.); (J.J.S.); (K.B.); (B.H.); (T.F.); (H.A.L.); (V.S.-L.); (J.K.)
| | - Jochen J. Schoettler
- Department of Anesthesiology, Surgical Intensive Care Medicine and Pain Medicine, Medical Faculty Mannheim, University Medical Center Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany; (F.-S.C.); (J.J.S.); (K.B.); (B.H.); (T.F.); (H.A.L.); (V.S.-L.); (J.K.)
| | - Kathrin Brohm
- Department of Anesthesiology, Surgical Intensive Care Medicine and Pain Medicine, Medical Faculty Mannheim, University Medical Center Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany; (F.-S.C.); (J.J.S.); (K.B.); (B.H.); (T.F.); (H.A.L.); (V.S.-L.); (J.K.)
- Merck KGaA (SQ-Animal Affairs), Frankfurterstrasse 250, 64293 Darmstadt, Germany
| | - Sonani Mindt
- Institute for Clinical Chemistry, Medical Faculty Mannheim, University Medical Center Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany; (S.M.); (E.J.); (M.N.)
- Institute for Laboratory and Transfusion Medicine, Hospital Passau, Innstrasse 76, 94032 Passau, Germany
| | - Evelyn Jäger
- Institute for Clinical Chemistry, Medical Faculty Mannheim, University Medical Center Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany; (S.M.); (E.J.); (M.N.)
| | - Bianka Hahn
- Department of Anesthesiology, Surgical Intensive Care Medicine and Pain Medicine, Medical Faculty Mannheim, University Medical Center Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany; (F.-S.C.); (J.J.S.); (K.B.); (B.H.); (T.F.); (H.A.L.); (V.S.-L.); (J.K.)
| | - Tanja Fuderer
- Department of Anesthesiology, Surgical Intensive Care Medicine and Pain Medicine, Medical Faculty Mannheim, University Medical Center Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany; (F.-S.C.); (J.J.S.); (K.B.); (B.H.); (T.F.); (H.A.L.); (V.S.-L.); (J.K.)
| | - Holger A. Lindner
- Department of Anesthesiology, Surgical Intensive Care Medicine and Pain Medicine, Medical Faculty Mannheim, University Medical Center Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany; (F.-S.C.); (J.J.S.); (K.B.); (B.H.); (T.F.); (H.A.L.); (V.S.-L.); (J.K.)
| | - Verena Schneider-Lindner
- Department of Anesthesiology, Surgical Intensive Care Medicine and Pain Medicine, Medical Faculty Mannheim, University Medical Center Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany; (F.-S.C.); (J.J.S.); (K.B.); (B.H.); (T.F.); (H.A.L.); (V.S.-L.); (J.K.)
| | - Joerg Krebs
- Department of Anesthesiology, Surgical Intensive Care Medicine and Pain Medicine, Medical Faculty Mannheim, University Medical Center Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany; (F.-S.C.); (J.J.S.); (K.B.); (B.H.); (T.F.); (H.A.L.); (V.S.-L.); (J.K.)
| | - Michael Neumaier
- Institute for Clinical Chemistry, Medical Faculty Mannheim, University Medical Center Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany; (S.M.); (E.J.); (M.N.)
| | - Manfred Thiel
- Department of Anesthesiology, Surgical Intensive Care Medicine and Pain Medicine, Medical Faculty Mannheim, University Medical Center Mannheim, University of Heidelberg, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany; (F.-S.C.); (J.J.S.); (K.B.); (B.H.); (T.F.); (H.A.L.); (V.S.-L.); (J.K.)
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Lee JM, Park MH, Park BS, Oh MK. Production of S-methyl-methionine using engineered Saccharomyces cerevisiae sake K6. J Ind Microbiol Biotechnol 2023; 50:kuad026. [PMID: 37653437 PMCID: PMC10495038 DOI: 10.1093/jimb/kuad026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/29/2023] [Indexed: 09/02/2023]
Abstract
S-methyl-methionine (SMM), also known as vitamin U, is an important food supplement produced by various plants. In this study, we attempted to produce it in an engineered microorganism, Saccharomyces cerevisiae, by introducing an MMT gene encoding a methionine S-methyltransferase from Arabidopsis thaliana. The S. cerevisiae sake K6 strain, which is a Generally Recognized as Safe (GRAS) strain, was chosen as the host because it produces a significant amount of S-adenosylmethionine (SAM), a precursor of SMM. To increase SMM production in the host, MHT1 and SAM4 genes encoding homocysteine S-methyltransferase were knocked out to prevent SMM degradation. Additionally, MMP1, which encodes S-methyl-methionine permease, was deleted to prevent SMM from being imported into the cell. Finally, ACS2 gene encoding acetyl-CoA synthase was overexpressed, and MLS1 gene encoding malate synthase was deleted to increase SAM availability. Using the engineered strain, 1.92 g/L of SMM was produced by fed-batch fermentation. ONE-SENTENCE SUMMARY Introducing a plant-derived MMT gene encoding methionine S-methyltransferase into engineered Saccharomyces cerevisiae sake K6 allowed microbial production of S-methyl-methionine (SMM).
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Affiliation(s)
- Jun-Min Lee
- Department of Chemical & Biological Engineering, Korea University, Seoul 136-763, Korea
| | - Min-Ho Park
- Department of Chemical & Biological Engineering, Korea University, Seoul 136-763, Korea
| | - Bu-Soo Park
- Department of Chemical & Biological Engineering, Korea University, Seoul 136-763, Korea
- Samyang Corp. 295 Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do 13488, Republic of Korea
| | - Min-Kyu Oh
- Department of Chemical & Biological Engineering, Korea University, Seoul 136-763, Korea
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Diakite B, Kassogue Y, Maiga M, Dolo G, Kassogue O, Holl JL, Joyce B, Wang J, Cisse K, Diarra F, Keita ML, Traore CB, Kamate B, Sissoko SB, Coulibaly B, Sissoko AS, Traore D, Sidibe FM, Bah S, Teguete I, Ly M, Nadifi S, Dehbi H, Kim K, Murphy R, Hou L. Lack of Association of C677T Methylenetetrahydrofolate Reductase Polymorphism with Breast Cancer Risk in Mali. Genet Res (Camb) 2023; 2023:4683831. [PMID: 36721432 PMCID: PMC9873441 DOI: 10.1155/2023/4683831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 12/22/2022] [Accepted: 01/06/2023] [Indexed: 01/19/2023] Open
Abstract
Methylenetetrahydrofolate reductase (MTHFR) plays a major role in the metabolism of folates and homocysteine, which in turn can affect gene expression and ultimately promote the development of breast cancer. Thus, mutations in the MTHFR gene could influence homocysteine, methionine, and S-adenosylmethionine levels and, indirectly, nucleotide levels. Imbalance in methionine and S-adenosylmethionine synthesis affects protein synthesis and methylation. These changes, which affect gene expression, may ultimately promote the development of breast cancer. We therefore hypothesized that such mutations could also play an important role in the occurrence and pathogenesis of breast cancer in a Malian population. In this study, we used the PCR-RFLP technique to identify the different genotypic profiles of the C677T MTHFR polymorphism in 127 breast cancer women and 160 healthy controls. The genotypic distribution of the C677T polymorphism in breast cancer cases was 88.2% for CC, 11.0% for CT, and 0.8% for TT. Healthy controls showed a similar distribution with 90.6% for CC, 8.8% for CT, and 0.6% for TT. We found no statistical association between the C677T polymorphism and breast cancer risk for the codominant models CT and TT (p > 0.05). The same trend was observed when the analysis was extended to other genetic models, including dominant (p = 0.50), recessive (p = 0.87), and additive (p = 0.50) models. The C677T polymorphism of MTHFR gene did not influence the risk of breast cancer in the Malian samples.
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Affiliation(s)
- Brehima Diakite
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Yaya Kassogue
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Mamoudou Maiga
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
- Institute for Global Health, Northwestern University, Chicago, IL 60611, USA
- Preventive Medicine Department, Northwestern University, Chicago, IL 60611, USA
| | - Guimogo Dolo
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Oumar Kassogue
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Jane L Holl
- Department of Neurology, University of Chicago, Chicago, IL 60637, USA
| | - Brian Joyce
- Institute for Global Health, Northwestern University, Chicago, IL 60611, USA
- Preventive Medicine Department, Northwestern University, Chicago, IL 60611, USA
| | - Jun Wang
- Preventive Medicine Department, Northwestern University, Chicago, IL 60611, USA
- Department of Neurology, University of Chicago, Chicago, IL 60637, USA
| | - Kadidiatou Cisse
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Fousseyni Diarra
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Mamadou L Keita
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Cheick B Traore
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bakarou Kamate
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Sidi B Sissoko
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Bourama Coulibaly
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Adama S Sissoko
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Drissa Traore
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Fatoumata M Sidibe
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Sekou Bah
- Faculty of Pharmacy, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Ibrahim Teguete
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Madani Ly
- Faculty of Medicine and Odontostomatology, University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | | | - Hind Dehbi
- Hassan II University Aïn Chock, Casablanca, Morocco
| | - Kyeezu Kim
- Institute for Global Health, Northwestern University, Chicago, IL 60611, USA
- Preventive Medicine Department, Northwestern University, Chicago, IL 60611, USA
| | - Robert Murphy
- Institute for Global Health, Northwestern University, Chicago, IL 60611, USA
| | - Lifang Hou
- Institute for Global Health, Northwestern University, Chicago, IL 60611, USA
- Preventive Medicine Department, Northwestern University, Chicago, IL 60611, USA
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Semchuchot W, Chotwiwatthanakun C, Santimanawong W, Kruangkum T, Thaijongrak P, Withyachumnarnkul B, Vanichviriyakit R. Sesquiterpenoid pathway in the mandibular organ of Penaeus monodon: Cloning, expression, characterization of PmJHAMT and its alteration response to eyestalk ablation. Gen Comp Endocrinol 2023; 331:114176. [PMID: 36410448 DOI: 10.1016/j.ygcen.2022.114176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 11/07/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022]
Abstract
Methyl farnesoate (MF), a crustacean equivalent of juvenile hormone (JH) of insects, is known to be produced from the mandibular organ (MO). This study reports transcriptome analysis of Penaeus monodon MO and identifies putative genes encoding enzymes in the sesquiterpenoid pathway. A total of 44,490,420 clean reads were obtained and utilized for subsequent analysis. De novo assembly created 31,201 transcripts and 31,167 unigenes. To archive the functional annotation, all unigenes were annotated with KOG, KEGG, and GO. Putative genes encoding enzymes and regulatory proteins involved in the sesquiterpenoid pathway were obtained from the MO transcriptome data based on the conserved domains and sequence homology. They included S-adenosylmethionine synthetase, farnesyl pyrophosphate synthase, short chain dependent dehydrogenase/reductase (SDR), NAD(P) + -dependent aldehyde dehydrogenase, S-adenosylmethionine-dependent methyltransferases or juvenile hormone acid-O-methyl transferase (JHAMT), farnesoic acid O-methyl transferase (FAMeT), juvenile hormone binding protein, cytochrome C/P-450 family 15 (CRYP15A1)/methylfarnesoate epoxidase (MFE), juvenile hormone epoxide hydrolase (JHEH), and juvenile hormone esterase (JHE). We first identified and characterized JHAMT orthologs inP. monodon(PmJHAMT). The complete cDNA sequence ofPmJHAMTconsisted of 1,221 nt encoded 271 amino acids with a conserved S-adenosyl methionine (SAM) binding domain. Phylogenetic analysis clusteredPmJHAMTinto the group JHAMT with the same clade of the crabPortunus trituberculausJHAMT. Moreover, the predicted three-dimensional structure of PmJHAMT showed remarkable similarity with the recent crystal structure ofthe Bombyx moriJHAMT homodimer. RT-PCR analysis revealed that PmJHAMT was exclusively expressed in MO and initially expressed at stage 3 postlarvae. In situ hybridization with a specific probe to PmJHAMT validated the specific expression of this gene in MO cells. Finally, we evaluated the regulation of MO by eyestalk inhibitory peptides. Diminishing MO inhibitory hormone through unilateral eyestalk ablation resulted in a significantly higher expression ofPmJHAMTin MO by quantitative PCR. This result indicated that the eyestalk inhibitory hormone inhibited MF synthesis byPmJHAMTgene suppression in the MO. This finding provides insight into the crustacean sesquiterpenoid pathway and improves our understanding of crustacean endocrinology.
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Affiliation(s)
- Wanita Semchuchot
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Department of Science, Faculty of Science and Technology, Prince of Songkla University, Pattani 94000, Thailand
| | - Charoonroj Chotwiwatthanakun
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Mahidol University, Nakhonsawan Campus, Nakhonsawan 60130, Thailand
| | - Wanida Santimanawong
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Thanapong Kruangkum
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok 10400, Thailand
| | - Prawporn Thaijongrak
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Boonsirm Withyachumnarnkul
- Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Faculty of Science and Industrial Technology, Prince of Songkla University, Hat Yai, Songkhla 90110, Thailand
| | - Rapeepun Vanichviriyakit
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok 10400, Thailand; Center of Excellence for Shrimp Molecular Biology and Biotechnology (Centex Shrimp), Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
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Wang L, Zhou C, Yu H, Hao L, Ju M, Feng W, Guo Z, Sun X, Fan Q, Xiao R. Vitamin D, Folic Acid and Vitamin B 12 Can Reverse Vitamin D Deficiency-Induced Learning and Memory Impairment by Altering 27-Hydroxycholesterol and S-Adenosylmethionine. Nutrients 2022; 15:nu15010132. [PMID: 36615790 PMCID: PMC9824694 DOI: 10.3390/nu15010132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/09/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
The cholesterol-oxidized metabolite 27-hydroxycholesterol (27-OHC) is synthesized by CYP27A1, which is a key factor in vitamin D and oxysterol metabolism. Both vitamin D and 27-OHC are considered to play important roles in Alzheimer’s disease (AD). The study aims to research the effects of co-supplementation of vitamin D, folic acid, and vitamin B12 on learning and memory ability in vitamin D-deficient mice, and to explore the underlying mechanism. In this study, C57BL/6J mice were fed a vitamin D-deficient diet for 13 weeks to establish a vitamin D-deficient mice model. The vitamin D-deficient mice were then orally gavaged with vitamin D (VD), folic acid (FA), and vitamin B12 (VB12) alone or together for eight weeks. Following the gavage, the learning and memory ability of the mice were evaluated by Morris Water Maze and Novel object recognition test. The CYP27A1-related gene and protein expressions in the liver and brain were determined by qRT-PCR. The serum level of 27-OHC was detected by HPLC-MS. Serum levels of 25(OH)D, homocysteine (Hcy), and S-Adenosylmethionine (SAM) were measured by ELISA. After feeding with the vitamin D-deficient diet, the mice performed longer latency to a platform (p < 0.001), lower average speed (p = 0.026) in the Morris Water Maze, a lower time discrimination index (p = 0.009) in Novel object recognition, and performances were reversed after vitamin D, folic acid and vitamin B12 supplementation alone or together (p < 0.05). The gene expressions of CYP27A1 in the liver and brain were upregulated in the vitamin D-deficiency (VDD) group compared with the control (CON) group (p = 0.015), while it was downregulated in VDD + VD and VDD + VD-FA/VB12 groups compared with the VDD group (p < 0.05), with a similar trend in the protein expression of CYP27A1. The serum levels of 27-OHC were higher in the VDD group, compared with CON, VDD + VD, and VDD + VD-FA/VB12 group (p < 0.05), and a similar trend was found in the brain. The serum 25(OH)D levels were significantly decreased in the vitamin D-deficiency group (p = 0.008), and increased in the vitamin D-supplemented group (p < 0.001). The serum levels of SAM were higher in the B vitamins-supplemented group, compared with CON and VDD groups (p < 0.05). This study suggests that CYP27A1 expression may be involved in the mechanism of learning and memory impairment induced by vitamin D deficiency. Co-supplementation with vitamin D, folic acid, and vitamin B12 significantly reverses this effect by affecting the expression of CYP27A1, which in turn regulates the metabolism of 27-OHC, 25(OH)D, and SAM.
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Affiliation(s)
- Lijing Wang
- Beijing Key Laboratory of Environmental Toxicology, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Cui Zhou
- Beijing Key Laboratory of Environmental Toxicology, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Huiyan Yu
- Beijing Key Laboratory of Environmental Toxicology, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Ling Hao
- Beijing Key Laboratory of Environmental Toxicology, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Mengwei Ju
- Beijing Key Laboratory of Environmental Toxicology, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Wenjing Feng
- Beijing Key Laboratory of Environmental Toxicology, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Zhiting Guo
- Beijing Key Laboratory of Environmental Toxicology, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Xuejing Sun
- Beijing Key Laboratory of Environmental Toxicology, School of Public Health, Capital Medical University, Beijing 100069, China
| | - Qiushi Fan
- Medical Nutrition, College of Allied Health Professions, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Rong Xiao
- Beijing Key Laboratory of Environmental Toxicology, School of Public Health, Capital Medical University, Beijing 100069, China
- Correspondence: ; Tel.: +86-010-83911512; Fax: +86-010-83911512
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32
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Peddinti G, Hotti H, Teeri TH, Rischer H. De novo transcriptome assembly of Conium maculatum L. to identify candidate genes for coniine biosynthesis. Sci Rep 2022; 12:17562. [PMID: 36266299 PMCID: PMC9584964 DOI: 10.1038/s41598-022-21728-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 09/30/2022] [Indexed: 01/13/2023] Open
Abstract
Poison hemlock (Conium maculatum L.) is a notorious weed containing the potent alkaloid coniine. Only some of the enzymes in the coniine biosynthesis have so far been characterized. Here, we utilize the next-generation RNA sequencing approach to report the first-ever transcriptome sequencing of five organs of poison hemlock: developing fruit, flower, root, leaf, and stem. Using a de novo assembly approach, we derived a transcriptome assembly containing 123,240 transcripts. The assembly is deemed high quality, representing over 88% of the near-universal ortholog genes of the Eudicots clade. Nearly 80% of the transcripts were functionally annotated using a combination of three approaches. The current study focuses on describing the coniine pathway by identifying in silico transcript candidates for polyketide reductase, L-alanine:5-keto-octanal aminotransferase, γ-coniceine reductase, and S-adenosyl-L-methionine:coniine methyltransferase. In vitro testing will be needed to confirm the assigned functions of the selected candidates.
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Affiliation(s)
- Gopal Peddinti
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, VTT, P.O. Box 1000, 02044, Espoo, Finland
| | - Hannu Hotti
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, VTT, P.O. Box 1000, 02044, Espoo, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, PO Box 56, 00014, Helsinki, Finland
| | - Teemu H Teeri
- Viikki Plant Science Centre, Department of Agricultural Sciences, University of Helsinki, PO Box 27, 00014, Helsinki, Finland
| | - Heiko Rischer
- VTT Technical Research Centre of Finland Ltd, Tietotie 2, VTT, P.O. Box 1000, 02044, Espoo, Finland.
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Kellum AH, Pallan PS, Nilforoushan A, Sturla SJ, Stone MP, Egli M. Conformation and Pairing Properties of an O6-Methyl-2'-deoxyguanosine-Directed Benzimidazole Nucleoside Analog in Duplex DNA. Chem Res Toxicol 2022; 35:1903-1913. [PMID: 35973057 PMCID: PMC9988402 DOI: 10.1021/acs.chemrestox.2c00165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
O6-Methyl-2'-deoxyguanosine (O6-MeG) is one of the most common DNA lesions and arises as a consequence of both xenobiotic carcinogens and endogenous methylation by S-adenosylmethionine. O6-MeG frequently causes G-to-A mutations during DNA replication due to the misincorporation of dTTP and continued DNA synthesis. Efforts to detect DNA adducts such as O6-MeG, and to understand their impacts on DNA structure and function, have motivated the creation of nucleoside analogs with altered base moieties to afford a more favorable interaction with the adduct as compared to the unmodified nucleotide. Such analogs directed at O6-MeG include benzimidazolinone and benzimidazole nucleotides, as well as their extended π surface analogs naphthimidazolinone and napthimidazole derivatives. These analogs form a more stable pair with O6-MeG than with G, most likely due to a combination of H-bonding and stacking. While extending the π surface of the analogs enhances their performance as adduct-directed probes, the precise origins of the increased affinity between the synthetic analogs and O6-MeG remain unclear. To better understand relevant conformational and pairing properties, we used X-ray crystallography and analyzed the structures of the DNA duplexes with naphthimidazolinone inserted opposite G or O6-MeG. The structures reveal a complex interaction of the analog found either in an anti orientation and stacked inside the duplex, either above or below G or O6-MeG, or in a syn orientation and paired opposite G with formation of a single H-bond. The experimental structural data are consistent with the stabilizing effect of the synthetic analog observed in UV melting experiments and calculations and moreover reveal that the origin of these observations appears to be superior stacking between O6-MeG and the extended π system of the synthetic probe.
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Affiliation(s)
- Andrew H Kellum
- Department of Chemistry, Vanderbilt University, College of Arts and Science, Nashville, Tennessee 37235, United States
| | - Pradeep S Pallan
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, United States
| | - Arman Nilforoushan
- Department of Health Sciences and Technology, ETH Zürich, Zurich 8092, Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zürich, Zurich 8092, Switzerland
| | - Michael P Stone
- Department of Chemistry, Vanderbilt University, College of Arts and Science, Nashville, Tennessee 37235, United States
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, United States
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, Tennessee 37232, United States
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Wu K, Moore JA, Miller MD, Chen Y, Lee C, Xu W, Peng Z, Duan Q, Phillips GN, Uribe RA, Xiao H. Expanding the eukaryotic genetic code with a biosynthesized 21st amino acid. Protein Sci 2022; 31:e4443. [PMID: 36173166 PMCID: PMC9601876 DOI: 10.1002/pro.4443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 08/18/2022] [Accepted: 08/24/2022] [Indexed: 01/31/2023]
Abstract
Genetic code expansion technology allows for the use of noncanonical amino acids (ncAAs) to create semisynthetic organisms for both biochemical and biomedical applications. However, exogenous feeding of chemically synthesized ncAAs at high concentrations is required to compensate for the inefficient cellular uptake and incorporation of these components into proteins, especially in the case of eukaryotic cells and multicellular organisms. To generate organisms capable of autonomously biosynthesizing an ncAA and incorporating it into proteins, we have engineered a metabolic pathway for the synthesis of O-methyltyrosine (OMeY). Specifically, we endowed organisms with a marformycins biosynthetic pathway-derived methyltransferase that efficiently converts tyrosine to OMeY in the presence of the co-factor S-adenosylmethionine. The resulting cells can produce and site-specifically incorporate OMeY into proteins at much higher levels than cells exogenously fed OMeY. To understand the structural basis for the substrate selectivity of the transferase, we solved the X-ray crystal structures of the ligand-free and tyrosine-bound enzymes. Most importantly, we have extended this OMeY biosynthetic system to both mammalian cells and the zebrafish model to enhance the utility of genetic code expansion. The creation of autonomous eukaryotes using a 21st amino acid will make genetic code expansion technology more applicable to multicellular organisms, providing valuable vertebrate models for biological and biomedical research.
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Affiliation(s)
- Kuan‐Lin Wu
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - Joshua A. Moore
- Department of BiosciencesRice UniversityHoustonTexasUSA
- Biochemistry and Cell Biology ProgramRice UniversityHoustonTexasUSA
| | | | - Yuda Chen
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - Catherine Lee
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - Weijun Xu
- Department of BiosciencesRice UniversityHoustonTexasUSA
| | - Zane Peng
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - Qinghui Duan
- Department of ChemistryRice UniversityHoustonTexasUSA
| | - George N. Phillips
- Department of ChemistryRice UniversityHoustonTexasUSA
- Department of BiosciencesRice UniversityHoustonTexasUSA
| | - Rosa A. Uribe
- Department of BiosciencesRice UniversityHoustonTexasUSA
- Biochemistry and Cell Biology ProgramRice UniversityHoustonTexasUSA
| | - Han Xiao
- Department of ChemistryRice UniversityHoustonTexasUSA
- Department of BiosciencesRice UniversityHoustonTexasUSA
- Department of BioengineeringRice UniversityHoustonTexasUSA
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Leong BJ, Folz JS, Bathe U, Clark DG, Fiehn O, Hanson AD. Fluoroacetate distribution, response to fluoridation, and synthesis in juvenile Gastrolobium bilobum plants. Phytochemistry 2022; 202:113356. [PMID: 35934105 DOI: 10.1016/j.phytochem.2022.113356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/23/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
Like angiosperms from several other families, the leguminous shrub Gastrolobium bilobum R.Br. produces and accumulates fluoroacetate, indicating that it performs the difficult chemistry needed to make a C-F bond. Bioinformatic analyses indicate that plants lack homologs of the only enzymes known to make a C-F bond, i.e., the Actinomycete flurorinases that form 5'-fluoro-5'-deoxyadenosine from S-adenosylmethionine and fluoride ion. To probe the origin of fluoroacetate in G. bilobum we first showed that fluoroacetate accumulates to millimolar levels in young leaves but not older leaves, stems or roots, that leaf fluoroacetate levels vary >20-fold between individual plants and are not markedly raised by sodium fluoride treatment. Young leaves were fed adenosine-13C-ribose, 13C-serine, or 13C-acetate to test plausible biosynthetic routes to fluoroacetate from S-adenosylmethionine, a C3-pyridoxal phosphate complex, or acetyl-CoA, respectively. Incorporation of 13C into expected metabolites confirmed that all three precursors were taken up and metabolized. Consistent with the bioinformatic evidence against an Actinomycete-type pathway, no adenosine-13C-ribose was converted to 13C-fluoroacetate; nor was the characteristic 4-fluorothreonine product of the Actinomycete pathway detected. Similarly, no 13C from acetate or serine was incorporated into fluoroacetate. While not fully excluding the hypothetical pathways that were tested, these negative labeling data imply that G. bilobum creates the C-F bond by an unprecedented biochemical reaction. Enzyme(s) that mediate such a reaction could be of great value in pharmaceutical and agrochemical manufacturing.
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Affiliation(s)
- Bryan J Leong
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
| | - Jacob S Folz
- West Coast Metabolomics Center, University of California Davis, Davis, CA, USA
| | - Ulschan Bathe
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA
| | - David G Clark
- Department of Environmental Horticulture, University of Florida, Gainesville, FL, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California Davis, Davis, CA, USA
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA.
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Arning E, Wasek B, Bottiglieri T. Quantification of Plasma S-adenosylmethionine and S-adenosylhomocysteine Using Liquid Chromatography-Electrospray-Tandem Mass Spectrometry. Methods Mol Biol 2022; 2546:35-43. [PMID: 36127576 DOI: 10.1007/978-1-0716-2565-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
We describe a simple stable isotope dilution method for accurate determination of S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH) in plasma as a clinical diagnostic test. Determination of SAM/SAH in plasma (20 μL) was performed by high-performance liquid chromatography coupled with electrospray positive ionization tandem mass spectrometry (HPLC-ESI-MS/MS). Calibrators (SAM and SAH) and internal standards (2H3-SAM and 2H4-SAH) were included in each analytical run for calibration. Sample preparation involved combining 20 μL sample with 180 μL of internal standard solution consisting of heavy-isotope-labeled internal standards in mobile phase A and filtering by ultracentrifugation through a 10 kd MW cutoff membrane. Sample filtrate (3 μL) was injected by a Shimadzu Nexera LC System interfaced with a 5500 QTRAP® (Sciex). Chromatographic separation was achieved on a 250 mm × 2.0 mm EZ-faast column from Phenomenex. Samples were eluted at a flow rate of 0.20 mL/min with a binary gradient with a total run time of 10 min. The source operated in positive ion mode at an ion spray voltage of +5000 V. SAM and SAH resolved by a gradient to 100% methanol with retention times of 5.8 and 5.5 min, respectively. HPLC chromatographic conditions did not produce complete separation of SAM and SAH, but they were completely discerned by their different fragmentation pattern in the mass spectrometer working in the MS-MS mode. The observed m/z values of the fragment ions were m/z 399→250 for SAM, m/z 385→136 for SAH, m/z 402→250 for 2H3-SAM, and m/z 203→46. The calibration curve was linear over the range of 12.5-5000 nmol/L for SAM and SAH.
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Affiliation(s)
- Erland Arning
- Institute of Metabolic Disease, Baylor Scott & White Research Institute, Dallas, TX, USA.
| | - Brandi Wasek
- Institute of Metabolic Disease, Baylor Scott & White Research Institute, Dallas, TX, USA
| | - Teodoro Bottiglieri
- Institute of Metabolic Disease, Baylor Scott & White Research Institute, Dallas, TX, USA
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Abstract
A subset of natural products, such as polyketides and nonribosomal peptides, is biosynthesized while tethered to a carrier peptide via a thioester linkage. Recently, we reported that the biosyntheses of 3-thiaglutamate and ammosamide, single amino acid-derived natural products, employ a very different type of carrier peptide to which the biosynthetic intermediates are bound via an amide linkage. During their biosyntheses, a peptide aminoacyl-transfer ribonucleic acid (tRNA) ligase (PEARL) first loads an amino acid to the C terminus of the carrier peptide for subsequent modification by other enzymes. Proteolytic removal of the modified C-terminal amino acid yields the mature product. We termed natural products that are biosynthesized using such pathways pearlins. To investigate the diversity of pearlins, in this study we experimentally characterized another PEARL-encoding biosynthetic gene cluster (BGC) from Tistrella mobilis (tmo). The enzymes encoded in the tmo BGC transformed cysteine into 3-thiahomoleucine both in vitro and in Escherichia coli. During this process, a cobalamin-dependent radical S-adenosylmethionine (SAM) enzyme catalyzes C-isopropylation. This work illustrates that the biosynthesis of amino acid-derived natural products on a carrier peptide is a widespread strategy in nature and expands the spectrum of thiahemiaminal analogs of amino acids that may serve a broader, currently unknown function.
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Affiliation(s)
- Yue Yu
- Department of Chemistry, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- HHMI, University of Illinois at Urbana–Champaign, Urbana, IL 61801
| | - Wilfred A. van der Donk
- Department of Chemistry, University of Illinois at Urbana–Champaign, Urbana, IL 61801
- HHMI, University of Illinois at Urbana–Champaign, Urbana, IL 61801
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Liu XH, Li BR, Ying ZM, Tang LJ, Wang F, Jiang JH. Small-Molecule-Mediated Split-Aptamer Assembly for Inducible CRISPR-dCas9 Transcription Activation. ACS Chem Biol 2022; 17:1769-1777. [PMID: 35700146 DOI: 10.1021/acschembio.2c00101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Inducible CRISPR-dCas9 transcription system has become a powerful tool for transcription regulation and sensing. Here, we develop a new concept of small-molecule-mediated split-aptamer assembly for inducible CRISPR-dCas9 transcription activation, allowing quantitative detection and imaging of S-adenosyl methionine (SAM) in live cells. This inducible transcription system is designed by integrating one fragment of a split SAM aptamer to guide RNA (gRNA) and the other to MS2 arrays. SAM-mediated reassembly of the split fragments recruits an MCP-fused transcription activator to the gRNA-dCas9 complex, activating the expression of a near-infrared fluorescent protein for imaging. We demonstrate that this inducible transcription system achieves quantitative detection of SAM with high sensitivity in live cells. Our system shows that methionine adenosyltransferase 1A (MAT1A) and MAT2A can both catalyze SAM production in live cells and the SAM levels in cancer cells can be increased via upregulation of MAT1A mRNA by epigenetic inhibitors. This split-aptamer assembly strategy could afford a new approach for controlling the CRISPR-dCas9 system, enabling conditional transcription regulation in response to endogenous metabolites in live cells.
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Affiliation(s)
- Xiao-Han Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Bang-Rui Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Zhan-Ming Ying
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Li-Juan Tang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Fenglin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
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Tang X, Zhang Y, Wang G, Zhang C, Wang F, Shi J, Zhang T, Ding J. Molecular mechanism of S-adenosylmethionine sensing by SAMTOR in mTORC1 signaling. Sci Adv 2022; 8:eabn3868. [PMID: 35776786 PMCID: PMC10883374 DOI: 10.1126/sciadv.abn3868] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The mechanistic target of rapamycin-mLST8-raptor complex (mTORC1) functions as a central regulator of cell growth and metabolism in response to changes in nutrient signals such as amino acids. SAMTOR is an S-adenosylmethionine (SAM) sensor, which regulates the mTORC1 activity through its interaction with the GTPase-activating protein activity toward Rags-1 (GATOR1)-KPTN, ITFG2, C12orf66 and SZT2-containing regulator (KICSTOR) complex. In this work, we report the crystal structures of Drosophila melanogaster SAMTOR in apo form and in complex with SAM. SAMTOR comprises an N-terminal helical domain and a C-terminal SAM-dependent methyltransferase (MTase) domain. The MTase domain contains the SAM-binding site and the potential GATOR1-KICSTOR-binding site. The helical domain functions as a molecular switch, which undergoes conformational change upon SAM binding and thereby modulates the interaction of SAMTOR with GATOR1-KICSTOR. The functional roles of the key residues and the helical domain are validated by functional assays. Our structural and functional data together reveal the molecular mechanism of the SAM sensing of SAMTOR and its functional role in mTORC1 signaling.
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Affiliation(s)
- Xin Tang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
| | - Yifan Zhang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Guanchao Wang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Chunxiao Zhang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Fang Wang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
| | - Jiawen Shi
- Institute of Geriatrics, Affiliated Nantong Hospital of Shanghai University, Sixth People's Hospital of Nantong, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Nantong 226011, China
| | - Tianlong Zhang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
- Institute of Geriatrics, Affiliated Nantong Hospital of Shanghai University, Sixth People's Hospital of Nantong, Shanghai Engineering Research Center of Organ Repair, School of Medicine, Shanghai University, Nantong 226011, China
| | - Jianping Ding
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, China
- School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, 1 Xiangshan Road, Hangzhou 310024, China
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Brown T, Cao M, Zheng YG. Synthesis and Activity of Triazole-Adenosine Analogs as Protein Arginine Methyltransferase 5 Inhibitors. Molecules 2022; 27:3779. [PMID: 35744905 PMCID: PMC9228412 DOI: 10.3390/molecules27123779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 11/17/2022] Open
Abstract
Protein arginine methyltransferase 5 (PRMT5) is an attractive molecular target in anticancer drug discovery due to its extensive involvement in transcriptional control, RNA processing, and other cellular pathways that are causally related to tumor initiation and progression. In recent years, various compounds have been screened or designed to target either the substrate- or cofactor-binding site of PRMT5. To expand the diversity of chemotypes for inhibitory binding to PRMT5 and other AdoMet-dependent methyltransferases, in this work, we designed a series of triazole-containing adenosine analogs aimed at targeting the cofactor-binding site of PRMT5. Triazole rings have commonly been utilized in drug discovery due to their ease of synthesis and functionalization as bioisosteres of amide bonds. Herein, we utilized the electronic properties of the triazole ring as a novel way to specifically target the cofactor-binding site of PRMT5. A total of about 30 compounds were synthesized using the modular alkyne-azide cycloaddition reaction. Biochemical tests showed that these compounds exhibited inhibitory activity of PRMT5 at varying degrees and several showed single micromolar potency, with clear selectivity for PRMT5 over PRMT1. Docking-based structural analysis showed that the triazole ring plays a key role in binding to the characteristic residue Phe327 in the active pocket of PRMT5, explaining the compounds' selectivity for this type-II enzyme. Overall, this work provides new structure-activity relationship information on the design of AdoMet analogs for selective inhibition of PRMT5. Further structural optimization work will further improve the potency of the top leads.
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Affiliation(s)
| | | | - Y. George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA; (T.B.); (M.C.)
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41
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Pagnier A, Balci B, Shepard EM, Yang H, Warui DM, Impano S, Booker SJ, Hoffman BM, Broderick WE, Broderick JB. [FeFe]-Hydrogenase: Defined Lysate-Free Maturation Reveals a Key Role for Lipoyl-H-Protein in DTMA Ligand Biosynthesis. Angew Chem Int Ed Engl 2022; 61:e202203413. [PMID: 35319808 PMCID: PMC9117470 DOI: 10.1002/anie.202203413] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Indexed: 11/09/2022]
Abstract
Maturation of [FeFe]-hydrogenase (HydA) involves synthesis of a CO, CN- , and dithiomethylamine (DTMA)-coordinated 2Fe subcluster that is inserted into HydA to make the active hydrogenase. This process requires three maturation enzymes: the radical S-adenosyl-l-methionine (SAM) enzymes HydE and HydG, and the GTPase HydF. In vitro maturation with purified maturation enzymes has been possible only when clarified cell lysate was added, with the lysate presumably providing essential components for DTMA synthesis and delivery. Here we report maturation of [FeFe]-hydrogenase using a fully defined system that includes components of the glycine cleavage system (GCS), but no cell lysate. Our results reveal for the first time an essential role for the aminomethyl-lipoyl-H-protein of the GCS in hydrogenase maturation and the synthesis of the DTMA ligand of the H-cluster. In addition, we show that ammonia is the source of the bridgehead nitrogen of DTMA.
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Affiliation(s)
- Adrien Pagnier
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Batuhan Balci
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Eric M Shepard
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Hao Yang
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - Douglas M Warui
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
| | - Stella Impano
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Squire J Booker
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Brian M Hoffman
- Department of Chemistry, Northwestern University, Evanston, IL 60208, USA
| | - William E Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Joan B Broderick
- Department of Chemistry & Biochemistry, Montana State University, Bozeman, MT 59717, USA
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Hsu JCC, Laurent-Rolle M, Pawlak JB, Xia H, Kunte A, Hee JS, Lim J, Harris LD, Wood JM, Evans GB, Shi PY, Grove TL, Almo SC, Cresswell P. Viperin triggers ribosome collision-dependent translation inhibition to restrict viral replication. Mol Cell 2022; 82:1631-1642.e6. [PMID: 35316659 PMCID: PMC9081181 DOI: 10.1016/j.molcel.2022.02.031] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 01/06/2022] [Accepted: 02/23/2022] [Indexed: 12/31/2022]
Abstract
Innate immune responses induce hundreds of interferon-stimulated genes (ISGs). Viperin, a member of the radical S-adenosyl methionine (SAM) superfamily of enzymes, is the product of one such ISG that restricts the replication of a broad spectrum of viruses. Here, we report a previously unknown antiviral mechanism in which viperin activates a ribosome collision-dependent pathway that inhibits both cellular and viral RNA translation. We found that the radical SAM activity of viperin is required for translation inhibition and that this is mediated by viperin's enzymatic product, 3'-deoxy-3',4'-didehydro-CTP (ddhCTP). Viperin triggers ribosome collisions and activates the MAPKKK ZAK pathway that in turn activates the GCN2 arm of the integrated stress response pathway to inhibit translation. The study illustrates the importance of translational repression in the antiviral response and identifies viperin as a translation regulator in innate immunity.
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Affiliation(s)
- Jack Chun-Chieh Hsu
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Maudry Laurent-Rolle
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06520, USA
| | - Joanna B Pawlak
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Amit Kunte
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jia Shee Hee
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jaechul Lim
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Lawrence D Harris
- The Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand; The Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1010, New Zealand
| | - James M Wood
- The Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand; The Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1010, New Zealand
| | - Gary B Evans
- The Ferrier Research Institute, Victoria University of Wellington, Wellington 6012, New Zealand; The Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland 1010, New Zealand
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA; Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX 77555, USA; Sealy Institute for Drug Discovery, Galveston, TX 77555, USA
| | - Tyler L Grove
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Peter Cresswell
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Cell Biology, Yale University School of Medicine, New Haven, CT 06520, USA.
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43
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Ahmed-Belkacem R, Hausdorff M, Delpal A, Sutto-Ortiz P, Colmant AMG, Touret F, Ogando NS, Snijder EJ, Canard B, Coutard B, Vasseur JJ, Decroly E, Debart F. Potent Inhibition of SARS-CoV-2 nsp14 N7-Methyltransferase by Sulfonamide-Based Bisubstrate Analogues. J Med Chem 2022; 65:6231-6249. [PMID: 35439007 PMCID: PMC9045040 DOI: 10.1021/acs.jmedchem.2c00120] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Indexed: 12/15/2022]
Abstract
Enzymes involved in RNA capping of SARS-CoV-2 are essential for the stability of viral RNA, translation of mRNAs, and virus evasion from innate immunity, making them attractive targets for antiviral agents. In this work, we focused on the design and synthesis of nucleoside-derived inhibitors against the SARS-CoV-2 nsp14 (N7-guanine)-methyltransferase (N7-MTase) that catalyzes the transfer of the methyl group from the S-adenosyl-l-methionine (SAM) cofactor to the N7-guanosine cap. Seven compounds out of 39 SAM analogues showed remarkable double-digit nanomolar inhibitory activity against the N7-MTase nsp14. Molecular docking supported the structure-activity relationships of these inhibitors and a bisubstrate-based mechanism of action. The three most potent inhibitors significantly stabilized nsp14 (ΔTm ≈ 11 °C), and the best inhibitor demonstrated high selectivity for nsp14 over human RNA N7-MTase.
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Affiliation(s)
| | - Marcel Hausdorff
- IBMM,
University of Montpellier, CNRS, ENSCM, 34293 Montpellier, cedex 5, France
| | - Adrien Delpal
- AFMB,
University of Aix-Marseille, CNRS, 13288 Marseille, cedex 9, France
| | | | - Agathe M. G. Colmant
- IHU
Méditerranée Infection, Unité Virus Emergents, University of Aix-Marseille, IRD 190, INSERM 1207, 13005 Marseille, France
| | - Franck Touret
- IHU
Méditerranée Infection, Unité Virus Emergents, University of Aix-Marseille, IRD 190, INSERM 1207, 13005 Marseille, France
| | - Natacha S. Ogando
- Department
of Medical Microbiology, Leiden University
Medical Center, 2333 ZA Leiden, The Netherlands
| | - Eric J. Snijder
- Department
of Medical Microbiology, Leiden University
Medical Center, 2333 ZA Leiden, The Netherlands
| | - Bruno Canard
- AFMB,
University of Aix-Marseille, CNRS, 13288 Marseille, cedex 9, France
| | - Bruno Coutard
- IHU
Méditerranée Infection, Unité Virus Emergents, University of Aix-Marseille, IRD 190, INSERM 1207, 13005 Marseille, France
| | - Jean-Jacques Vasseur
- IBMM,
University of Montpellier, CNRS, ENSCM, 34293 Montpellier, cedex 5, France
| | - Etienne Decroly
- AFMB,
University of Aix-Marseille, CNRS, 13288 Marseille, cedex 9, France
| | - Françoise Debart
- IBMM,
University of Montpellier, CNRS, ENSCM, 34293 Montpellier, cedex 5, France
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Skrypnyk RІ, Maslova GS, Skrypnyk IN. THE EFFECT OF S-ADEMETIONINE ON PLASMA CITRULLINE LEVEL DURING CHEMOTHERAPY-INDUCED OXIDATIVE STRESS IN PATIENTS WITH CHRONIC LYMPHOPROLIFERATIVE DISORDERS. Wiad Lek 2022; 75:1553-1557. [PMID: 35907233 DOI: 10.36740/wlek202206123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
OBJECTIVE The aim: To investigate the effect of S-ademetionine on plasma citrulline level in patients with chronic lymphoproliferative disorders (CLPD) during chemotherapy-induced oxidative stress. PATIENTS AND METHODS Materials and methods: 25 patients with CLPD were examined. Examinations were conducted twice: before chemotherapy (CT) and after 3 courses of CT. Several biochemical markers in the blood were determined: the activity of catalase, the level of plasma citrulline, the concentration of N-acetylneuraminic acid (NANA) and the concentration of substances that form a trimethine complex (TBARS) with 2-thiobarbituric acid. Patients were divided into groups: І (n=14) - patients who underwent only CT; ІІ (n=16) - patients who during CT received S-ademetionine, at a dose of 1000 mg/day intravenously for 10 days, then 500 mg twice a day for 20 days. ІІІ (n=20) -the control group of 20 practically healthy individuals. RESULTS Results: Patients in both groups with CLPD had pre-existed mucosal injury that was characterized by 1.25 (p=0.0025) and 1.26 times (р=0.006) higher blood NANA concentration compared to the control group. The conduction of CT was associated with enterocytes dysfunction, which was characterized by 1,66 times (p=0,0002) lower plasma citrulline level in patients of group I compared to the initial examination. The infusion of S-ademetionine attenuated intestinal dysfunction that was associated with 1,23 times (p=0,0005) higher blood citrulline level after the CT as compared to group I. CONCLUSION Conclusions: The infusion of S-ademetionine as adjuvant treatment in patients with CLPD provided effective prophylaxis of intestinal injury that was associated with higher blood citrulline level after the conduction of CT.
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Velayutham M, Guru A, Arasu MV, Al-Dhabi NA, Choi KC, Elumalai P, Harikrishnan R, Arshad A, Arockiaraj J. GR15 peptide of S-adenosylmethionine synthase (SAMe) from Arthrospira platensis demonstrated antioxidant mechanism against H 2O 2 induced oxidative stress in in-vitro MDCK cells and in-vivo zebrafish larvae model. J Biotechnol 2021; 342:79-91. [PMID: 34751134 DOI: 10.1016/j.jbiotec.2021.10.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/29/2021] [Accepted: 10/25/2021] [Indexed: 01/09/2023]
Abstract
GR15 is a short molecule or peptide composed of aliphatic amino acids and possesses to have antioxidant properties. The GR15, 1GGGAFSGKDPTKVDR15 was identified from the protein S-adenosylmethionine synthase (SAMe) expressed during the sulfur departed state of Arthrospira platensis (spirulina or cyanobacteria). The in-silico assessment and the structural features of GR15 showed its antioxidant potency. Real-time PCR analysis found the up-regulation of ApSAMe expression on day 15 against oxidative stress due to 10 mM H2O2 treatment in A. platensis (Ap). The antioxidant activity of GR15 was accessed by the cell-free antioxidant assays such as ABTS, SARS, HRAS and NO; the results showed dose-dependent antioxidant activity. The toxicity assay was performed in both in vitro and in vivo models, in which peptide does not exhibit any toxicity in MDCK cell and zebrafish embryos. The intercellular ROS reduction potential of GR15 peptide was also investigated in both in vitro and in vivo models including LDH assay, antioxidant enzymes (SOD and CAT), and fluorescent staining assay (DCFDA, Hochest and Acridine orange sting) was performed; the results showed that the GR15 peptide was effectively reduced the ROS level. Further, RT-PCR demonstrated that GR15 enhanced the antioxidant property and also up-regulated the antioxidant gene, thus reduced the ROS level in both in vitro and in vivo models. Based on the results obtained from this study, we propose that GR15 has the potential antioxidant ability; hence further research can be directed towards the therapeutic product or drug development against disease caused by oxidative stress.
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Affiliation(s)
- Manikandan Velayutham
- SRM Research Institute, SRM Institute of Science and Technology, Kattankulathur, Chennai 603 203, Tamil Nadu, India; Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur, Chennai 603 203, Tamil Nadu, India
| | - Ajay Guru
- SRM Research Institute, SRM Institute of Science and Technology, Kattankulathur, Chennai 603 203, Tamil Nadu, India; Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur, Chennai 603 203, Tamil Nadu, India
| | - Mariadhas Valan Arasu
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Naif Abdullah Al-Dhabi
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
| | - Ki Choon Choi
- Grassland and Forage Division, National Institute of Animal Science, RDA, Seonghwan-Eup, Cheonan-Si, Chungnam 330-801, Republic of Korea
| | - Preetham Elumalai
- Department of Fish Processing Technology (Biochemistry), School of Ocean Science and Technology, Kerala University of Fisheries and Ocean Studies, Panangad, Kochi 682 506, Kerala, India
| | - Ramasamy Harikrishnan
- Department of Zoology, Pachaiyappa's College for Men, Kanchipuram 631 501, Tamil Nadu, India
| | - Aziz Arshad
- International Institute of Aquaculture and Aquatic Sciences (I-AQUAS), Universiti Putra Malaysia, 71050 Port Dickson, Negeri Sembilan, Malaysia; Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Jesu Arockiaraj
- SRM Research Institute, SRM Institute of Science and Technology, Kattankulathur, Chennai 603 203, Tamil Nadu, India; Department of Biotechnology, College of Science and Humanities, SRM Institute of Science and Technology, Kattankulathur, Chennai 603 203, Tamil Nadu, India.
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Yan G, Li X, Yang J, Li Z, Hou J, Rao B, Hu Y, Ma L, Wang Y. Cost-Effective Production of ATP and S-Adenosylmethionine Using Engineered Multidomain Scaffold Proteins. Biomolecules 2021; 11:biom11111706. [PMID: 34827704 PMCID: PMC8616028 DOI: 10.3390/biom11111706] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/18/2021] [Accepted: 10/18/2021] [Indexed: 12/27/2022] Open
Abstract
Adenosine triphosphate (ATP) and S-adenosyl-L-methionine (SAM) are important intermediates that are widely present in living organisms. Large-scale preparation and application of ATP or SAM is limited by expensive raw materials. To lower the production costs for ATP/SAM, in this study we used strategies applying engineered multidomain scaffold proteins to synthesize ATP and SAM. An artificial scaffold protein containing CBM3 domain, IM proteins and CL-labeled proteins was assembled to form complex 1 for catalytic reactions to increase ATP production. The ATP synthesis system produced approximately 25 g/L of ATP with approximately 15 g/L of ADP and 5 g/L of AMP using 12.5 g/L of adenosine and 40 g/L of sodium hexametaphosphate reaction at 35 °C and a pH of 8.5 for 6 h. Based on the above ATP synthesis system, two CL-labeled methionine adenosyltransferases (CL9-MAT4 and CL9-MAT5) were applied to construct scaffold protein complex 2 to achieve SAM synthesis. Approximately 25 μg of MAT4 in a reaction system with 0.3 M MgCl2 catalyzed at 20 °C and a pH of 8 catalyzed 0.5 g/L of l-Met to produce approximately 0.9 g/L of SAM. Approximately 25 μg of MAT5 in a reaction system with 0.7 M MgCl2 catalyzed at 35 °C and a pH of 8 catalyzed 0.5 g/L of l-Met to produce approximately 1.2 g/L of SAM. Here, we showed that low-cost substrates can be efficiently converted into high-value additional ATP and SAM via multi-enzyme catalytic reactions by engineered multidomain scaffold proteins.
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Affiliation(s)
- Guangbo Yan
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China; (G.Y.); (X.L.); (J.Y.); (Z.L.); (J.H.); (L.M.)
| | - Xia Li
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China; (G.Y.); (X.L.); (J.Y.); (Z.L.); (J.H.); (L.M.)
| | - Jun Yang
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China; (G.Y.); (X.L.); (J.Y.); (Z.L.); (J.H.); (L.M.)
| | - Zhongchen Li
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China; (G.Y.); (X.L.); (J.Y.); (Z.L.); (J.H.); (L.M.)
| | - Jia Hou
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China; (G.Y.); (X.L.); (J.Y.); (Z.L.); (J.H.); (L.M.)
| | - Ben Rao
- National Biopesticide Engineering Technology Research Center, Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Biopesticide Branch of Hubei Innovation Centre of Agricultural Science and Technology, Wuhan 430064, China;
| | - Yong Hu
- Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei Key Laboratoy of Industrial Microbiology, National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Hubei Research Center of Food Fermentation Engineering and Technology, Hubei University of Technology, Wuhan 430062, China;
| | - Lixin Ma
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China; (G.Y.); (X.L.); (J.Y.); (Z.L.); (J.H.); (L.M.)
| | - Yaping Wang
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China; (G.Y.); (X.L.); (J.Y.); (Z.L.); (J.H.); (L.M.)
- Correspondence:
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Das A, Sanyal T, Bhattacharjee P, Bhattacharjee P. Depletion of S-adenosylmethionine pool and promoter hypermethylation of Arsenite methyltransferase in arsenic-induced skin lesion individuals: A case-control study from West Bengal, India. Environ Res 2021; 198:111184. [PMID: 33894237 DOI: 10.1016/j.envres.2021.111184] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/09/2021] [Accepted: 04/10/2021] [Indexed: 06/12/2023]
Abstract
Methylation of arsenic compounds in the human body occurs following a series of biochemical reactions in the presence of methyl donor S-adenosylmethionine (SAM) and catalyzed by arsenite methyltransferase (AS3MT). However, the extent and pattern of methylation differs among the arsenic exposed individuals leading to differential susceptibility. The mechanism for such inter-individual difference is enigmatic. In the present case-control study we recruited exposed individuals with and without arsenic induced skin lesion (WSL and WOSL), and an unexposed cohort, each having 120 individuals. Using ELISA, we observed a reduction in SAM levels (p < 0.05) in WSL compared to WOSL. Linear regression analysis revealed a negative correlation between urinary arsenic concentration and SAM concentration between the study groups. qRT-PCR revealed a significant down-regulation (p < 0.01) of key regulatory genes like MTHFR, MTR, MAT2A and MAT2B of SAM biogenesis pathway in WSL cohort. Methylation-specific PCR revealed significant promoter hypermethylation of AS3MT (WSL vs. WOSL: p < 0.01) which resulted in its subsequent transcriptional repression (WSL vs. WOSL: p < 0.001). Linear regression analysis also showed a negative correlation between SAM concentration and percentage of promoter methylation. Taken together, these results indicate that reduction in SAM biogenesis along with a higher utilization of SAM results in a decreased availability of methyl donor. These along with epigenetic down-regulation of AS3MT may be responsible for higher susceptibility in arsenic exposed individuals.
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Affiliation(s)
- Ankita Das
- Department of Environmental Science, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Tamalika Sanyal
- Department of Environmental Science, University of Calcutta and Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Pritha Bhattacharjee
- Department of Environmental Science, University of Calcutta and Department of Zoology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Pritha Bhattacharjee
- Department of Environmental Science, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, West Bengal, India.
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Abstract
Catechol O-methyltransferase (COMT) is an enzyme that transfers a methyl group to the catechol-derivative substrates using S-adenosyl-l-methionine (SAM) and Mg2+. We report the biochemical and structural analysis of COMT from Niastella koreensis (NkCOMT). NkCOMT showed the highest activity with Mg2+, although the enzyme also showed a significant level of activity with Cu2+ and Zn2+. NkCOMT structures complexed with SAH and Mg2+ elucidated how the enzyme stabilized the cosubstrate and the metal ion and revealed that the region near the SAM binding site undergoes conformational changes upon the binding of the cosubstrate and the metal ion. We also identified the catechol binding pocket of the enzyme and explained a broad substrate specificity of the bacterial enzyme and its ability to accommodate the catechol derivatives. In addition, we developed the NkCOMTE211R and NkCOMTE211K variants that showed both enhanced activities and regiospecificity for the production of the para-forms. Our study provides a structural basis for regiospecificity of NkCOMT, which is related with the conformational change upon binding of SAM and Mg2+.
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Affiliation(s)
- Seul Hoo Lee
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
- KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Bongsang Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
- KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea
- KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
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Sahid S, Roy C, Paul S, Datta R. Rice lectin protein r40c1 imparts drought tolerance by modulating S-adenosylmethionine synthase 2, stress-associated protein 8 and chromatin-associated proteins. J Exp Bot 2020; 71:7331-7346. [PMID: 32853345 DOI: 10.1093/jxb/eraa400] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 08/25/2020] [Indexed: 06/11/2023]
Abstract
Lectin proteins play an important role in biotic and abiotic stress responses in plants. Although the rice lectin protein Osr40c1 has been reported to be regulated by drought stress, the mechanism of its drought tolerance activity has not been studied so far. In this study, it is shown that expression of the Osr40c1 gene correlates with the drought tolerance potential of various rice cultivars. Transgenic rice plants overexpressing Osr40c1 were significantly more tolerant to drought stress than the wild-type plants. Furthermore, ectopic expression of the Osr40c1 gene in tobacco yielded a similar result. Interestingly, the protein displayed a nucleo-cytoplasmic localization and was found to interact with a number of drought-responsive proteins such as S-adenosylmethionine synthase 2 (OsSAM2), stress-associated protein 8 (OsSAP8), DNA-binding protein MNB1B (OsMNB1B), and histone 4 (OsH4). Silencing of each of these protein partners led to drought sensitivity in otherwise tolerant Osr40c1-expressing transgenic tobacco lines indicating that these partners were crucial for the Osr40c1-mediated drought tolerance in planta. Moreover, the association of Osr40c1 with these partners occurred specifically under drought stress forming a multi-protein complex. Together, our findings delineate a novel role of Osr40c1 in imparting drought tolerance by regulating OsMNB1B, OsSAM2, and OsH4 proteins, which presumably enables OsSAP8 to induce downstream gene expression.
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Affiliation(s)
- Salman Sahid
- Department of Botany, University of Calcutta, Kolkata, West Bengal, India
- Department of Botany, Dr A. P. J. Abdul Kalam Government College, New Town, Kolkata, West Bengal, India
| | - Chandan Roy
- Department of Botany, University of Calcutta, Kolkata, West Bengal, India
| | - Soumitra Paul
- Department of Botany, University of Calcutta, Kolkata, West Bengal, India
| | - Riddhi Datta
- Department of Botany, Dr A. P. J. Abdul Kalam Government College, New Town, Kolkata, West Bengal, India
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Mhamdi A. Here, There, and Everywhere: Plastid- and Nuclear-Localized WHIRLY1 Regulates Salicylic Acid Homeostasis during Developmental Senescence. Plant Physiol 2020; 184:1620-1621. [PMID: 33277328 PMCID: PMC7723119 DOI: 10.1104/pp.20.01475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Affiliation(s)
- Amna Mhamdi
- Department of Plant Biotechnology and Bioinformatics, Center for Plant Systems Biology, Ghent University, 9052 Ghent, Belgium
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