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Chen Y, Anderson MT, Payne N, Santori FR, Ivanova NB. Nuclear Receptors and the Hidden Language of the Metabolome. Cells 2024; 13:1284. [PMID: 39120315 PMCID: PMC11311682 DOI: 10.3390/cells13151284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/16/2024] [Accepted: 07/22/2024] [Indexed: 08/10/2024] Open
Abstract
Nuclear hormone receptors (NHRs) are a family of ligand-regulated transcription factors that control key aspects of development and physiology. The regulation of NHRs by ligands derived from metabolism or diet makes them excellent pharmacological targets, and the mechanistic understanding of how NHRs interact with their ligands to regulate downstream gene networks, along with the identification of ligands for orphan NHRs, could enable innovative approaches for cellular engineering, disease modeling and regenerative medicine. We review recent discoveries in the identification of physiologic ligands for NHRs. We propose new models of ligand-receptor co-evolution, the emergence of hormonal function and models of regulation of NHR specificity and activity via one-ligand and two-ligand models as well as feedback loops. Lastly, we discuss limitations on the processes for the identification of physiologic NHR ligands and emerging new methodologies that could be used to identify the natural ligands for the remaining 17 orphan NHRs in the human genome.
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Affiliation(s)
- Yujie Chen
- Center for Molecular Medicine, University of Georgia, Athens, GA 30602, USA; (Y.C.); (M.T.A.); (N.P.)
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Matthew Tom Anderson
- Center for Molecular Medicine, University of Georgia, Athens, GA 30602, USA; (Y.C.); (M.T.A.); (N.P.)
| | - Nathaniel Payne
- Center for Molecular Medicine, University of Georgia, Athens, GA 30602, USA; (Y.C.); (M.T.A.); (N.P.)
| | - Fabio R. Santori
- Center for Molecular Medicine, University of Georgia, Athens, GA 30602, USA; (Y.C.); (M.T.A.); (N.P.)
| | - Natalia B. Ivanova
- Center for Molecular Medicine, University of Georgia, Athens, GA 30602, USA; (Y.C.); (M.T.A.); (N.P.)
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
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2
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Kundu B, Iyer MR. A patent review on aldehyde dehydrogenase inhibitors: an overview of small molecule inhibitors from the last decade. Expert Opin Ther Pat 2023; 33:651-668. [PMID: 38037334 DOI: 10.1080/13543776.2023.2287515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 11/21/2023] [Indexed: 12/02/2023]
Abstract
INTRODUCTION Physiological and pathophysiological effects arising from detoxification of aldehydes in humans implicate the enzyme aldehyde dehydrogenase (ALDH) gene family comprising of 19 isoforms. The main function of this enzyme family is to metabolize reactive aldehydes to carboxylic acids. Dysregulation of ALDH activity has been associated with various diseases. Extensive research has since gone into studying ALHD isozymes, their structural biology and developing small-molecule inhibitors. Novel chemical strategies to enhance the selectivity of ALDH inhibitors have now appeared. AREAS COVERED A comprehensive review of patent literature related to aldehyde dehydrogenase inhibitors in the last decade and half (2007-2022) is provided. EXPERT OPINION Aldehyde dehydrogenase (ALDH) is an important enzyme that metabolizes reactive exogenous and endogenous aldehydes in the body through NAD(P)±dependent oxidation. Hence this family of enzymes possess important physiological as well as toxicological roles in human body. Significant efforts in the field have led to potent inhibitors with approved clinical agents for alcohol use disorder therapy. Further clinical translation of novel compounds targeting ALDH inhibition will validate the promised therapeutic potential in treating many human diseases.The scientific/patent literature has been searched on SciFinder-n, Reaxys, PubMed, Espacenet and Google Patents. The search terms used were 'ALDH inhibitors', 'Aldehyde Dehydrogenase Inhibitors'.
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Affiliation(s)
- Biswajit Kundu
- Section on Medicinal Chemistry, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, MD, USA
| | - Malliga R Iyer
- Section on Medicinal Chemistry, National Institute on Alcohol Abuse and Alcoholism, National Institutes of Health, Rockville, MD, USA
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3
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Bozzo M, Bellitto D, Amaroli A, Ferrando S, Schubert M, Candiani S. Retinoic Acid and POU Genes in Developing Amphioxus: A Focus on Neural Development. Cells 2023; 12:cells12040614. [PMID: 36831281 PMCID: PMC9953854 DOI: 10.3390/cells12040614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/27/2023] [Accepted: 02/07/2023] [Indexed: 02/16/2023] Open
Abstract
POU genes are a family of evolutionarily conserved transcription factors with key functions in cell type specification and neurogenesis. In vitro experiments have indicated that the expression of some POU genes is controlled by the intercellular signaling molecule retinoic acid (RA). In this work, we aimed to characterize the roles of RA signaling in the regulation of POU genes in vivo. To do so, we studied POU genes during the development of the cephalochordate amphioxus, an animal model crucial for understanding the evolutionary origins of vertebrates. The expression patterns of amphioxus POU genes were assessed at different developmental stages by chromogenic in situ hybridization and hybridization chain reaction. Expression was further assessed in embryos subjected to pharmacological manipulation of endogenous RA signaling activity. In addition to a detailed description of the effects of these treatments on amphioxus POU gene expression, our survey included the first description of Pou2 and Pou6 expression in amphioxus embryos. We found that Pit-1, Pou2, Pou3l, and Pou6 expression are not affected by alterations of endogenous RA signaling levels. In contrast, our experiments indicated that Brn1/2/4 and Pou4 expression are regulated by RA signaling in the endoderm and the nerve cord, respectively. The effects of the treatments on Pou4 expression in the nerve cord revealed that, in developing amphioxus, RA signaling plays a dual role by (1) providing anteroposterior patterning information to neural cells and (2) specifying neural cell types. This finding is coherent with a terminal selector function of Pou4 for GABAergic neurons in amphioxus and represents the first description of RA-induced changes in POU gene expression in vivo.
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Affiliation(s)
- Matteo Bozzo
- Dipartimento di Scienze della Terra dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy
- Correspondence: (M.B.); (S.C.); Tel.: +39-0103358043 (M.B.); +39-0103358051 (S.C.)
| | - Deianira Bellitto
- Dipartimento di Scienze della Terra dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy
| | - Andrea Amaroli
- Dipartimento di Scienze della Terra dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy
| | - Sara Ferrando
- Dipartimento di Scienze della Terra dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy
| | - Michael Schubert
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer (LBDV), Institut de la Mer de Villefranche, Sorbonne Université, CNRS, 06230 Villefranche-sur-Mer, France
| | - Simona Candiani
- Dipartimento di Scienze della Terra dell’Ambiente e della Vita (DISTAV), Università degli Studi di Genova, 16132 Genoa, Italy
- Correspondence: (M.B.); (S.C.); Tel.: +39-0103358043 (M.B.); +39-0103358051 (S.C.)
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4
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Hinojosa JC, Dapporto L, Pitteloud C, Koubínová D, Hernández-Roldán J, Vicente JC, Alvarez N, Vila R. Hybridization fuelled diversification in Spialia butterflies. Mol Ecol 2022; 31:2951-2967. [PMID: 35263484 PMCID: PMC9310813 DOI: 10.1111/mec.16426] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 01/17/2022] [Accepted: 02/28/2022] [Indexed: 12/02/2022]
Abstract
The importance of hybridization and introgression is well documented in the evolution of plants but, in insects, their role is not fully understood. Given the fact that insects are the most diverse group of organisms, assessing the impact of reticulation events on their evolution may be key to comprehend the emergence of such remarkable diversity. Here, we used an insect model, the Spialia butterflies, to gather genomic evidence of hybridization as a promoter of novel diversity. By using double‐digest RADseq (ddRADseq), we explored the phylogenetic relationships between Spialia orbifer, S. rosae and S. sertorius, and documented two independent events of interspecific gene flow. Our data support that the Iberian endemism S. rosae probably received genetic material from S. orbifer in both mitochondrial and nuclear DNA, which could have contributed to a shift in the ecological preferences of S. rosae. We also show that admixture between S. sertorius and S. orbifer probably occurred in Italy. As a result, the admixed Sicilian populations of S. orbifer are differentiated from the rest of populations both genetically and morphologically, and display signatures of reproductive character displacement in the male genitalia. Additionally, our analyses indicated that genetic material from S. orbifer is present in S. sertorius along the Italian Peninsula. Our findings add to the view that hybridization is a pervasive phenomenon in nature and in butterflies in particular, with important consequences for evolution due to the emergence of novel phenotypes.
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Affiliation(s)
- Joan C Hinojosa
- Institut de Biologia Evolutiva (CSIC-UPF), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
| | - Leonardo Dapporto
- ZEN lab, Biology Department, Università degli Studi di Firenze, 50019, Sesto Fiorentino, Italy
| | - Camille Pitteloud
- Geneva Natural History Museum, Route de Malagnou 1, 1208, Geneva, Switzerland
| | - Darina Koubínová
- Laboratory of Evolutionary Genetics, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, 2000, Neuchâtel, Switzerland
| | - Juan Hernández-Roldán
- Departamento de Biología, Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Calle Darwin 2, 28049, Madrid, Spain
| | - Juan Carlos Vicente
- Asociación Española para la Protección de las Mariposas y su Medio (ZERYNTHIA), Madrid, Spain
| | - Nadir Alvarez
- Geneva Natural History Museum, Route de Malagnou 1, 1208, Geneva, Switzerland.,Department of Genetics and Evolution, University of Geneva, Boulevard d'Ivoy 4, 1205, Geneva, Switzerland
| | - Roger Vila
- Institut de Biologia Evolutiva (CSIC-UPF), Passeig Marítim de la Barceloneta 37-49, 08003, Barcelona, Spain
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Li J, Garavaglia S, Ye Z, Moretti A, Belyaeva OV, Beiser A, Ibrahim M, Wilk A, McClellan S, Klyuyeva AV, Goggans KR, Kedishvili NY, Salter EA, Wierzbicki A, Migaud ME, Mullett SJ, Yates NA, Camacho CJ, Rizzi M, Sobol RW. A specific inhibitor of ALDH1A3 regulates retinoic acid biosynthesis in glioma stem cells. Commun Biol 2021; 4:1420. [PMID: 34934174 PMCID: PMC8692581 DOI: 10.1038/s42003-021-02949-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 12/07/2021] [Indexed: 01/31/2023] Open
Abstract
Elevated aldehyde dehydrogenase (ALDH) activity correlates with poor outcome for many solid tumors as ALDHs may regulate cell proliferation and chemoresistance of cancer stem cells (CSCs). Accordingly, potent, and selective inhibitors of key ALDH enzymes may represent a novel CSC-directed treatment paradigm for ALDH+ cancer types. Of the many ALDH isoforms, we and others have implicated the elevated expression of ALDH1A3 in mesenchymal glioma stem cells (MES GSCs) as a target for the development of novel therapeutics. To this end, our structure of human ALDH1A3 combined with in silico modeling identifies a selective, active-site inhibitor of ALDH1A3. The lead compound, MCI-INI-3, is a selective competitive inhibitor of human ALDH1A3 and shows poor inhibitory effect on the structurally related isoform ALDH1A1. Mass spectrometry-based cellular thermal shift analysis reveals that ALDH1A3 is the primary binding protein for MCI-INI-3 in MES GSC lysates. The inhibitory effect of MCI-INI-3 on retinoic acid biosynthesis is comparable with that of ALDH1A3 knockout, suggesting that effective inhibition of ALDH1A3 is achieved with MCI-INI-3. Further development is warranted to characterize the role of ALDH1A3 and retinoic acid biosynthesis in glioma stem cell growth and differentiation.
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Affiliation(s)
- Jianfeng Li
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Silvia Garavaglia
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100, Novara, Italy
| | - Zhaofeng Ye
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
- School of Medicine, Tsinghua University, Beijing, China
| | - Andrea Moretti
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100, Novara, Italy
- Structural Plant Biology Laboratory, Department of Botany and Plant Biology, University of Geneva, 1211, Geneva, Switzerland
| | - Olga V Belyaeva
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 720 20th Street South, Kaul 440B, Birmingham, AL, 35294, USA
| | - Alison Beiser
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Md Ibrahim
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Anna Wilk
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Steve McClellan
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
| | - Alla V Klyuyeva
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 720 20th Street South, Kaul 440B, Birmingham, AL, 35294, USA
| | - Kelli R Goggans
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 720 20th Street South, Kaul 440B, Birmingham, AL, 35294, USA
| | - Natalia Y Kedishvili
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Schools of Medicine and Dentistry, 720 20th Street South, Kaul 440B, Birmingham, AL, 35294, USA
| | - E Alan Salter
- Department of Chemistry, University of South Alabama, 6040 USA South Drive, Mobile, AL, 36688, USA
| | - Andrzej Wierzbicki
- Department of Chemistry, University of South Alabama, 6040 USA South Drive, Mobile, AL, 36688, USA
| | - Marie E Migaud
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA
| | - Steven J Mullett
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Nathan A Yates
- Department of Cell Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Carlos J Camacho
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Menico Rizzi
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Largo Donegani 2, 28100, Novara, Italy.
| | - Robert W Sobol
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, 36604, USA.
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, 36604, USA.
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6
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Study of ALDH from Thermus thermophilus-Expression, Purification and Characterisation of the Non-Substrate Specific, Thermophilic Enzyme Displaying Both Dehydrogenase and Esterase Activity. Cells 2021; 10:cells10123535. [PMID: 34944041 PMCID: PMC8699947 DOI: 10.3390/cells10123535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/10/2021] [Accepted: 12/11/2021] [Indexed: 01/16/2023] Open
Abstract
Aldehyde dehydrogenases (ALDH), found in all kingdoms of life, form a superfamily of enzymes that primarily catalyse the oxidation of aldehydes to form carboxylic acid products, while utilising the cofactor NAD(P)+. Some superfamily members can also act as esterases using p-nitrophenyl esters as substrates. The ALDHTt from Thermus thermophilus was recombinantly expressed in E. coli and purified to obtain high yields (approximately 15–20 mg/L) and purity utilising an efficient heat treatment step coupled with IMAC and gel filtration chromatography. The use of the heat treatment step proved critical, in its absence decreased yield of 40% was observed. Characterisation of the thermophilic ALDHTt led to optimum enzymatic working conditions of 50 °C, and a pH of 8. ALDHTt possesses dual enzymatic activity, with the ability to act as a dehydrogenase and an esterase. ALDHTt possesses broad substrate specificity, displaying activity for a range of aldehydes, most notably hexanal and the synthetic dialdehyde, terephthalaldehyde. Interestingly, para-substituted benzaldehydes could be processed efficiently, but ortho-substitution resulted in no catalytic activity. Similarly, ALDHTt displayed activity for two different esterase substrates, p-nitrophenyl acetate and p-nitrophenyl butyrate, but with activities of 22.9% and 8.9%, respectively, compared to the activity towards hexanal.
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Shortall K, Djeghader A, Magner E, Soulimane T. Insights into Aldehyde Dehydrogenase Enzymes: A Structural Perspective. Front Mol Biosci 2021; 8:659550. [PMID: 34055881 PMCID: PMC8160307 DOI: 10.3389/fmolb.2021.659550] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 04/28/2021] [Indexed: 12/30/2022] Open
Abstract
Aldehyde dehydrogenases engage in many cellular functions, however their dysfunction resulting in accumulation of their substrates can be cytotoxic. ALDHs are responsible for the NAD(P)-dependent oxidation of aldehydes to carboxylic acids, participating in detoxification, biosynthesis, antioxidant and regulatory functions. Severe diseases, including alcohol intolerance, cancer, cardiovascular and neurological diseases, were linked to dysfunctional ALDH enzymes, relating back to key enzyme structure. An in-depth understanding of the ALDH structure-function relationship and mechanism of action is key to the understanding of associated diseases. Principal structural features 1) cofactor binding domain, 2) active site and 3) oligomerization mechanism proved critical in maintaining ALDH normal activity. Emerging research based on the combination of structural, functional and biophysical studies of bacterial and eukaryotic ALDHs contributed to the appreciation of diversity within the superfamily. Herewith, we discuss these studies and provide our interpretation for a global understanding of ALDH structure and its purpose–including correct function and role in disease. Our analysis provides a synopsis of a common structure-function relationship to bridge the gap between the highly studied human ALDHs and lesser so prokaryotic models.
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Affiliation(s)
- Kim Shortall
- Department of Chemical Sciences, Bernal Institute, University of Limerick, Limerick, Ireland
| | - Ahmed Djeghader
- Department of Chemical Sciences, Bernal Institute, University of Limerick, Limerick, Ireland
| | - Edmond Magner
- Department of Chemical Sciences, Bernal Institute, University of Limerick, Limerick, Ireland
| | - Tewfik Soulimane
- Department of Chemical Sciences, Bernal Institute, University of Limerick, Limerick, Ireland
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8
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Campos JC, Chen CH, Ferreira JCB. Comment on: "Aldehyde dehydrogenases contribute to skeletal muscle homeostasis in healthy, aging, and Duchenne muscular dystrophy patients" by Etienne et al. J Cachexia Sarcopenia Muscle 2020; 11:1858-1859. [PMID: 32729226 PMCID: PMC7749548 DOI: 10.1002/jcsm.12609] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Juliane C Campos
- University of Sao Paulo, Institute of Biomedical Sciences, Sao Paulo, Brazil
| | - Che-Hong Chen
- Department of Chemical and Systems Biology, School of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Julio C B Ferreira
- University of Sao Paulo, Institute of Biomedical Sciences, Sao Paulo, Brazil.,Department of Chemical and Systems Biology, School of Medicine, Stanford University, Stanford, CA, 94305, USA
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Etienne J, Joanne P, Catelain C, Riveron S, Bayer AC, Lafable J, Punzon I, Blot S, Agbulut O, Vilquin JT. Aldehyde dehydrogenases contribute to skeletal muscle homeostasis in healthy, aging, and Duchenne muscular dystrophy patients. J Cachexia Sarcopenia Muscle 2020; 11:1047-1069. [PMID: 32157826 PMCID: PMC7432589 DOI: 10.1002/jcsm.12557] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 12/12/2019] [Accepted: 01/30/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Aldehyde dehydrogenases (ALDHs) are key players in cell survival, protection, and differentiation via the metabolism and detoxification of aldehydes. ALDH activity is also a marker of stem cells. The skeletal muscle contains populations of ALDH-positive cells amenable to use in cell therapy, whose distribution, persistence in aging, and modifications in myopathic context have not been investigated yet. METHODS The Aldefluor® (ALDEF) reagent was used to assess the ALDH activity of muscle cell populations, whose phenotypic characterizations were deepened by flow cytometry. The nature of ALDH isoenzymes expressed by the muscle cell populations was identified in complementary ways by flow cytometry, immunohistology, and real-time PCR ex vivo and in vitro. These populations were compared in healthy, aging, or Duchenne muscular dystrophy (DMD) patients, healthy non-human primates, and Golden Retriever dogs (healthy vs. muscular dystrophic model, Golden retriever muscular dystrophy [GRMD]). RESULTS ALDEF+ cells persisted through muscle aging in humans and were equally represented in several anatomical localizations in healthy non-human primates. ALDEF+ cells were increased in dystrophic individuals in humans (nine patients with DMD vs. five controls: 14.9 ± 1.63% vs. 3.6 ± 0.39%, P = 0.0002) and dogs (three GRMD dogs vs. three controls: 10.9 ± 2.54% vs. 3.7 ± 0.45%, P = 0.049). In DMD patients, such increase was due to the adipogenic ALDEF+ /CD34+ populations (11.74 ± 1.5 vs. 2.8 ± 0.4, P = 0.0003), while in GRMD dogs, it was due to the myogenic ALDEF+ /CD34- cells (3.6 ± 0.6% vs. 1.03 ± 0.23%, P = 0.0165). Phenotypic characterization associated the ALDEF+ /CD34- cells with CD9, CD36, CD49a, CD49c, CD49f, CD106, CD146, and CD184, some being associated with myogenic capacities. Cytological and histological analyses distinguished several ALDH isoenzymes (ALDH1A1, 1A2, 1A3, 1B1, 1L1, 2, 3A1, 3A2, 3B1, 3B2, 4A1, 7A1, 8A1, and 9A1) expressed by different cell populations in the skeletal muscle tissue belonging to multinucleated fibres, or myogenic, endothelial, interstitial, and neural lineages, designing them as potential new markers of cell type or of metabolic activity. Important modifications were noted in isoenzyme expression between healthy and DMD muscle tissues. The level of gene expression of some isoenzymes (ALDH1A1, 1A3, 1B1, 2, 3A2, 7A1, 8A1, and 9A1) suggested their specific involvement in muscle stability or regeneration in situ or in vitro. CONCLUSIONS This study unveils the importance of the ALDH family of isoenzymes in the skeletal muscle physiology and homeostasis, suggesting their roles in tissue remodelling in the context of muscular dystrophies.
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Affiliation(s)
- Jessy Etienne
- Sorbonne Université, INSERM, AIM, Centre de Recherche en Myologie, UMRS 974, AP-HP, Hôpital Pitié Salpêtrière, Paris, France.,Department of Bioengineering and QB3 Institute, University of California, Berkeley, CA, USA
| | - Pierre Joanne
- Sorbonne Université, CNRS, INSERM, Institut de Biologie Paris-Seine, IBPS, UMR 8256 Biological Adaptation and Ageing, Paris, France
| | - Cyril Catelain
- Sorbonne Université, INSERM, AIM, Centre de Recherche en Myologie, UMRS 974, AP-HP, Hôpital Pitié Salpêtrière, Paris, France
| | - Stéphanie Riveron
- Sorbonne Université, INSERM, AIM, Centre de Recherche en Myologie, UMRS 974, AP-HP, Hôpital Pitié Salpêtrière, Paris, France
| | - Alexandra Clarissa Bayer
- Sorbonne Université, INSERM, AIM, Centre de Recherche en Myologie, UMRS 974, AP-HP, Hôpital Pitié Salpêtrière, Paris, France
| | - Jérémy Lafable
- Sorbonne Université, INSERM, AIM, Centre de Recherche en Myologie, UMRS 974, AP-HP, Hôpital Pitié Salpêtrière, Paris, France
| | - Isabel Punzon
- Université Paris-Est Créteil, INSERM, Institut Mondor de Recherche Biomédicale, IMRB, École Nationale Vétérinaire d'Alfort, ENVA, U955-E10, Maisons-Alfort, France
| | - Stéphane Blot
- Université Paris-Est Créteil, INSERM, Institut Mondor de Recherche Biomédicale, IMRB, École Nationale Vétérinaire d'Alfort, ENVA, U955-E10, Maisons-Alfort, France
| | - Onnik Agbulut
- Sorbonne Université, CNRS, INSERM, Institut de Biologie Paris-Seine, IBPS, UMR 8256 Biological Adaptation and Ageing, Paris, France
| | - Jean-Thomas Vilquin
- Sorbonne Université, INSERM, AIM, Centre de Recherche en Myologie, UMRS 974, AP-HP, Hôpital Pitié Salpêtrière, Paris, France
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10
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Quattrini L, Gelardi ELM, Coviello V, Sartini S, Ferraris DM, Mori M, Nakano I, Garavaglia S, La Motta C. Imidazo[1,2- a]pyridine Derivatives as Aldehyde Dehydrogenase Inhibitors: Novel Chemotypes to Target Glioblastoma Stem Cells. J Med Chem 2020; 63:4603-4616. [PMID: 32223240 DOI: 10.1021/acs.jmedchem.9b01910] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Glioblastoma multiforme (GBM) is the deadliest form of brain tumor. It is known for its ability to escape the therapeutic options available to date thanks to the presence of a subset of cells endowed with stem-like properties and ability to resist to cytotoxic treatments. As the cytosolic enzyme aldehyde dehydrogenase 1A3 turns out to be overexpressed in these kinds of cells, playing a key role for their vitality, treatments targeting this enzyme may represent a successful strategy to fight GBM. In this work, we describe a novel class of imidazo[1,2-a]pyridine derivatives as aldehyde dehydrogenase 1A3 inhibitors, reporting the evidence of their significance as novel drug candidates for the treatment of GBM. Besides showing an interesting functional profile, in terms of activity against the target enzyme and selectivity toward highly homologous isoenzymes, representative examples of the series also showed a nanomolar to picomolar efficacy against patient-derived GBM stem-like cells, thus proving the concept that targeting aldehyde dehydrogenase might represent a novel and promising way to combat GBM by striking its ability to divide immortally.
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Affiliation(s)
- Luca Quattrini
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | | | - Vito Coviello
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Stefania Sartini
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
| | - Davide Maria Ferraris
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy
| | - Mattia Mori
- Department of Biotechnology, Chemistry and Pharmacy "Department of Excellence 2018-2022", University of Siena, via Aldo Moro 2, 53100 Siena, Italy
| | - Ichiro Nakano
- Department of Neurosurgery, University of Alabama at Birmingham, WTI 401, 1824 Sixth Avenue South, Birmingham, Alabama 35233, United States
| | - Silvia Garavaglia
- Department of Pharmaceutical Sciences, University of Piemonte Orientale, Via Bovio 6, 28100 Novara, Italy
| | - Concettina La Motta
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
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11
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Wang Y, Li PY, Zhang Y, Cao HY, Wang YJ, Li CY, Wang P, Su HN, Chen Y, Chen XL, Zhang YZ. 3,6-Anhydro-L-Galactose Dehydrogenase VvAHGD is a Member of a New Aldehyde Dehydrogenase Family and Catalyzes by a Novel Mechanism with Conformational Switch of Two Catalytic Residues Cysteine 282 and Glutamate 248. J Mol Biol 2020; 432:2186-2203. [PMID: 32087198 DOI: 10.1016/j.jmb.2020.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/05/2020] [Accepted: 02/06/2020] [Indexed: 12/26/2022]
Abstract
3,6-anhydro-α-L-galactose (L-AHG) is one of the main monosaccharide constituents of red macroalgae. In the recently discovered bacterial L-AHG catabolic pathway, L-AHG is first oxidized by a NAD(P)+-dependent dehydrogenase (AHGD), which is a key step of this pathway. However, the catalytic mechanism(s) of AHGDs is still unclear. Here, we identified and characterized an AHGD from marine bacterium Vibrio variabilis JCM 19239 (VvAHGD). The NADP+-dependent VvAHGD could efficiently oxidize L-AHG. Phylogenetic analysis suggested that VvAHGD and its homologs represent a new aldehyde dehydrogenase (ALDH) family with different substrate preferences from reported ALDH families, named the L-AHGDH family. To explain the catalytic mechanism of VvAHGD, we solved the structures of VvAHGD in the apo form and complex with NADP+ and modeled its structure with L-AHG. Based on structural, mutational, and biochemical analyses, the cofactor channel and the substrate channel of VvAHGD are identified, and the key residues involved in the binding of NADP+ and L-AHG and the catalysis are revealed. VvAHGD performs catalysis by controlling the consecutive connection and interruption of the cofactor channel and the substrate channel via the conformational changes of its two catalytic residues Cys282 and Glu248. Comparative analyses of structures and enzyme kinetics revealed that differences in the substrate channels (in shape, size, electrostatic surface, and residue composition) lead to the different substrate preferences of VvAHGD from other ALDHs. This study on VvAHGD sheds light on the diversified catalytic mechanisms and evolution of NAD(P)+-dependent ALDHs.
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Affiliation(s)
- Yue Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Ping-Yi Li
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Yi Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Hai-Yan Cao
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Yan-Jun Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Chun-Yang Li
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China
| | - Peng Wang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China
| | - Hai-Nan Su
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China
| | - Yin Chen
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China; School of Life Sciences, University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Xiu-Lan Chen
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Yu-Zhong Zhang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, 266237, China; College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
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12
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Pequerul R, Vera J, Giménez-Dejoz J, Crespo I, Coines J, Porté S, Rovira C, Parés X, Farrés J. Structural and kinetic features of aldehyde dehydrogenase 1A (ALDH1A) subfamily members, cancer stem cell markers active in retinoic acid biosynthesis. Arch Biochem Biophys 2020; 681:108256. [PMID: 31923393 DOI: 10.1016/j.abb.2020.108256] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 01/01/2020] [Accepted: 01/02/2020] [Indexed: 11/30/2022]
Abstract
Aldehyde dehydrogenases catalyze the NAD(P)+-dependent oxidation of aldehydes to their corresponding carboxylic acids. The three-dimensional structures of the human ALDH1A enzymes were recently obtained, while a complete kinetic characterization of them, under the same experimental conditions, is lacking. We show that the three enzymes, ALDH1A1, ALDH1A2 and ALDH1A3, have similar topologies, although with decreasing volumes in their substrate-binding pockets. The activity with aliphatic and retinoid aldehydes was characterized side-by-side, using an improved HPLC-based method for retinaldehyde. Hexanal was the most efficient substrate. ALDH1A1 displayed lower Km values with hexanal, trans-2-hexenal and citral, compared to ALDH1A2 and ALDH1A3. ALDH1A2 was the best enzyme for the lipid peroxidation product, 4-hydroxy-2-nonenal, in terms of kcat/Km. The catalytic efficiency towards all-trans and 9-cis-retinaldehyde was in general lower than for alkanals and alkenals. ALDH1A2 and ALDH1A3 showed higher catalytic efficiency for all-trans-retinaldehyde. The lower specificity of ALDH1A3 for 9-cis-retinaldehyde against the all-trans- isomer might be related to the smaller volume of its substrate-binding pocket. Magnesium inhibited ALDH1A1 and ALDH1A2, while it activated ALDH1A3, which is consistent with cofactor dissociation being the rate-limiting step for ALDH1A1 and ALDH1A2, and deacylation for ALDH1A3, with hexanal as a substrate. We mutated both ALDH1A1 (L114P) and ALDH1A2 (N475G, A476V, L477V, N478S) to mimic their counterpart substrate-binding pockets. ALDH1A1 specificity for citral was traced to residue 114 and to residues 458 to 461. Regarding retinaldehyde, the mutants did not show significant differences with their respective wild-type forms, suggesting that the mutated residues are not critical for retinoid specificity.
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Affiliation(s)
- Raquel Pequerul
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193, Bellaterra, Barcelona, Spain
| | - Javier Vera
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193, Bellaterra, Barcelona, Spain
| | - Joan Giménez-Dejoz
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193, Bellaterra, Barcelona, Spain
| | - Isidro Crespo
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193, Bellaterra, Barcelona, Spain
| | - Joan Coines
- Department of Inorganic and Organic Chemistry, Universitat de Barcelona, E-08028, Barcelona, Spain
| | - Sergio Porté
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193, Bellaterra, Barcelona, Spain
| | - Carme Rovira
- Department of Inorganic and Organic Chemistry, Universitat de Barcelona, E-08028, Barcelona, Spain
| | - Xavier Parés
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193, Bellaterra, Barcelona, Spain
| | - Jaume Farrés
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, E-08193, Bellaterra, Barcelona, Spain.
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13
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Elkashty OA, Ashry R, Tran SD. Head and neck cancer management and cancer stem cells implication. Saudi Dent J 2019; 31:395-416. [PMID: 31700218 PMCID: PMC6823822 DOI: 10.1016/j.sdentj.2019.05.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 05/27/2019] [Indexed: 12/20/2022] Open
Abstract
Head and neck squamous cell carcinomas (HNSCCs) arise in the mucosal linings of the upper aerodigestive tract and are heterogeneous in nature. Risk factors for HNSCCs are smoking, excessive alcohol consumption, and the human papilloma virus. Conventional treatments are surgery, radiotherapy, chemotherapy, or a combined modality; however, no international standard mode of therapy exists. In contrast to the conventional model of clonal evolution in tumor development, there is a newly proposed theory based on the activity of cancer stem cells (CSCs) as the model for carcinogenesis. This “CSC hypothesis” may explain the high mortality rate, low response to treatments, and tendency to develop multiple tumors for HNSCC patients. We review current knowledge on HNSCC etiology and treatment, with a focus on CSCs, including their origins, identifications, and effects on therapeutic options.
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Key Words
- ABC, ATP-binding cassette transporters
- ATC, amplifying transitory cell
- Antineoplastic agents
- BMI-1, B cell-specific Moloney murine leukemia virus integration site 1
- Cancer stem cells
- Cancer treatment
- Carcinoma
- EGFR, epidermal growth factor receptor
- HIFs, hypoxia-inducible factors
- Head and neck cancer
- MDR1, Multidrug Resistance Protein 1
- NF-κB, nuclear factor kappa-light-chain-enhancer of activated B cells
- PI3K, phosphatidylinositol-4,5-bisphosphate 3-kinase
- Squamous cell
- TKIs, tyrosine kinase inhibitors
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Affiliation(s)
- Osama A Elkashty
- McGill Craniofacial Tissue Engineering and Stem Cells Laboratory, Faculty of Dentistry, McGill University, Montreal, QC, Canada.,Oral Pathology Department, Faculty of Dentistry, Mansoura University, Mansoura, Egypt
| | - Ramy Ashry
- Oral Pathology Department, Faculty of Dentistry, Mansoura University, Mansoura, Egypt
| | - Simon D Tran
- McGill Craniofacial Tissue Engineering and Stem Cells Laboratory, Faculty of Dentistry, McGill University, Montreal, QC, Canada
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14
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Miles JA, Machattou P, Nevin-Jones D, Webb ME, Millard A, Scanlan DJ, Taylor PC. Identification of a cyanobacterial aldehyde dehydrogenase that produces retinoic acid in vitro. Biochem Biophys Res Commun 2019; 510:27-34. [DOI: 10.1016/j.bbrc.2018.12.171] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 12/27/2018] [Indexed: 11/15/2022]
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15
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Srinivasan K, Buys EM. Insights into the role of bacteria in vitamin A biosynthesis: Future research opportunities. Crit Rev Food Sci Nutr 2019; 59:3211-3226. [PMID: 30638045 DOI: 10.1080/10408398.2018.1546670] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Significant efforts have been made to address the hidden hunger challenges due to iron, zinc, iodine, and vitamin A since the beginning of the 21st century. Prioritizing the vitamin A deficiency (VAD) disorders, many countries are looking for viable alternative strategies such as biofortification. One of the leading causes of VAD is the poor bioconversion of β-carotene into retinoids. This review is focused on the opportunities of bacterial biosynthesis of retinoids, in particular, through the gut microbiota. The proposed hypothesis starts with the premise that an animal can able to store and timely convert carotenoids into retinoids in the liver and intestinal tissues. This theory is experimental with many scientific insights. The syntrophic metabolism, potential crosstalk of bile acids, lipocalins and lipopolysaccharides of gut microbiota are reported to contribute significantly to the retinoid biosynthesis. The gut bacteria respond to these kinds of factors by genetic restructuring driven mainly by events like horizontal gene transfer. A phylogenetic analysis of β-carotene 15, 15'-mono (di) oxygenase enzymes among a selected group of prokaryotes and eukaryotes was carried out to validate the hypotheses. Shedding light on the probiotic strategies through non-genetically modified organism such as gut bacteria capable of synthesizing vitamin A would address the VAD disorders.
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Affiliation(s)
- K Srinivasan
- Department of Consumer and Food Sciences, University of Pretoria, Hatfield Campus, Pretoria, South Africa
| | - Elna M Buys
- Department of Consumer and Food Sciences, University of Pretoria, Hatfield Campus, Pretoria, South Africa
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16
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Hayes K, Noor M, Djeghader A, Armshaw P, Pembroke T, Tofail S, Soulimane T. The quaternary structure of Thermus thermophilus aldehyde dehydrogenase is stabilized by an evolutionary distinct C-terminal arm extension. Sci Rep 2018; 8:13327. [PMID: 30190503 PMCID: PMC6127216 DOI: 10.1038/s41598-018-31724-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 08/22/2018] [Indexed: 12/04/2022] Open
Abstract
Aldehyde dehydrogenases (ALDH) form a superfamily of dimeric or tetrameric enzymes that catalyze the oxidation of a broad range of aldehydes into their corresponding carboxylic acids with the concomitant reduction of the cofactor NAD(P) into NAD(P)H. Despite their varied polypeptide chain length and oligomerisation states, ALDHs possess a conserved architecture of three domains: the catalytic domain, NAD(P)+ binding domain, and the oligomerization domain. Here, we describe the structure and function of the ALDH from Thermus thermophilus (ALDHTt) which exhibits non-canonical features of both dimeric and tetrameric ALDH and a previously uncharacterized C-terminal arm extension forming novel interactions with the N-terminus in the quaternary structure. This unusual tail also interacts closely with the substrate entry tunnel in each monomer providing further mechanistic detail for the recent discovery of tail-mediated activity regulation in ALDH. However, due to the novel distal extension of the tail of ALDHTt and stabilizing termini-interactions, the current model of tail-mediated substrate access is not apparent in ALDHTt. The discovery of such a long tail in a deeply and early branching phylum such as Deinococcus-Thermus indicates that ALDHTt may be an ancestral or primordial metabolic model of study. This structure provides invaluable evidence of how metabolic regulation has evolved and provides a link to early enzyme regulatory adaptations.
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Affiliation(s)
- Kevin Hayes
- Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland.,Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Mohamed Noor
- Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland.,Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Ahmed Djeghader
- Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland.,Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Patricia Armshaw
- Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland.,Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Tony Pembroke
- Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland.,Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Syed Tofail
- Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland.,Physics Department, University of Limerick, Limerick, V94 T9PX, Ireland
| | - Tewfik Soulimane
- Department of Chemical Sciences, University of Limerick, Limerick, V94 T9PX, Ireland. .,Bernal Institute, University of Limerick, Limerick, V94 T9PX, Ireland.
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17
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Grace CS, Mikkola HKA, Dou DR, Calvanese V, Ronn RE, Purton LE. Protagonist or antagonist? The complex roles of retinoids in the regulation of hematopoietic stem cells and their specification from pluripotent stem cells. Exp Hematol 2018; 65:1-16. [PMID: 29981365 DOI: 10.1016/j.exphem.2018.06.287] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 06/24/2018] [Accepted: 06/26/2018] [Indexed: 10/28/2022]
Abstract
Hematopoietic stem cells (HSCs) are multipotent cells responsible for the maintenance of the hematopoietic system throughout life. Dysregulation of the balance in HSC self-renewal, death, and differentiation can have serious consequences such as myelodysplastic syndromes or leukemia. All-trans retinoic acid (ATRA), the biologically active metabolite of vitamin A/RA, has been shown to have pleiotropic effects on hematopoietic cells, enhancing HSC self-renewal while also increasing differentiation of more mature progenitors. Furthermore, ATRA has been shown to have key roles in regulating the specification and formation of hematopoietic cells from pluripotent stem cells including embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). Here, we summarize the known roles of vitamin A and RA receptors in the regulation of hematopoiesis from HSCs, ES, and iPSCs.
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Affiliation(s)
- Clea S Grace
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia; The University of Melbourne, Department of Medicine at St. Vincent's Hospital, Fitzroy, Victoria, Australia
| | - Hanna K A Mikkola
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA; Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
| | - Diana R Dou
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA; Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
| | - Vincenzo Calvanese
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA, USA; Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
| | - Roger E Ronn
- Medical Research Council Centre for Inflammation Research, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
| | - Louise E Purton
- St. Vincent's Institute of Medical Research, Fitzroy, Victoria, Australia; The University of Melbourne, Department of Medicine at St. Vincent's Hospital, Fitzroy, Victoria, Australia.
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18
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Zieger E, Garbarino G, Robert NSM, Yu JK, Croce JC, Candiani S, Schubert M. Retinoic acid signaling and neurogenic niche regulation in the developing peripheral nervous system of the cephalochordate amphioxus. Cell Mol Life Sci 2018; 75:2407-2429. [PMID: 29387904 PMCID: PMC11105557 DOI: 10.1007/s00018-017-2734-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 12/19/2017] [Indexed: 10/18/2022]
Abstract
The retinoic acid (RA) signaling pathway regulates axial patterning and neurogenesis in the developing central nervous system (CNS) of chordates, but little is known about its roles during peripheral nervous system (PNS) formation and about how these roles might have evolved. This study assesses the requirement of RA signaling for establishing a functional PNS in the cephalochordate amphioxus, the best available stand-in for the ancestral chordate condition. Pharmacological manipulation of RA signaling levels during embryogenesis reduces the ability of amphioxus larvae to respond to sensory stimulation and alters the number and distribution of ectodermal sensory neurons (ESNs) in a stage- and context-dependent manner. Using gene expression assays combined with immunohistochemistry, we show that this is because RA signaling specifically acts on a small population of soxb1c-expressing ESN progenitors, which form a neurogenic niche in the trunk ectoderm, to modulate ESN production during elongation of the larval body. Our findings reveal an important role for RA signaling in regulating neurogenic niche activity in the larval amphioxus PNS. Although only few studies have addressed this issue so far, comparable RA signaling functions have been reported for neurogenic niches in the CNS and in certain neurogenic placode derivatives of vertebrates. Accordingly, the here-described mechanism is likely a conserved feature of chordate embryonic and adult neural development.
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Affiliation(s)
- Elisabeth Zieger
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, Sorbonne Universités, UPMC Université Paris 06, CNRS, 181 Chemin du Lazaret, 06230, Villefranche-sur-Mer, France
| | - Greta Garbarino
- Department of Earth, Environment and Life Sciences (Dipartimento di Scienze della Terra dell'Ambiente e della Vita, DISTAV), University of Genoa, Viale Benedetto XV 5, 16132, Genoa, Italy
| | - Nicolas S M Robert
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, Sorbonne Universités, UPMC Université Paris 06, CNRS, 181 Chemin du Lazaret, 06230, Villefranche-sur-Mer, France
| | - Jr-Kai Yu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Jenifer C Croce
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, Sorbonne Universités, UPMC Université Paris 06, CNRS, 181 Chemin du Lazaret, 06230, Villefranche-sur-Mer, France
| | - Simona Candiani
- Department of Earth, Environment and Life Sciences (Dipartimento di Scienze della Terra dell'Ambiente e della Vita, DISTAV), University of Genoa, Viale Benedetto XV 5, 16132, Genoa, Italy
| | - Michael Schubert
- Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, Sorbonne Universités, UPMC Université Paris 06, CNRS, 181 Chemin du Lazaret, 06230, Villefranche-sur-Mer, France.
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19
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Blanchoud S, Rutherford K, Zondag L, Gemmell NJ, Wilson MJ. De novo draft assembly of the Botrylloides leachii genome provides further insight into tunicate evolution. Sci Rep 2018; 8:5518. [PMID: 29615780 PMCID: PMC5882950 DOI: 10.1038/s41598-018-23749-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 03/20/2018] [Indexed: 01/17/2023] Open
Abstract
Tunicates are marine invertebrates that compose the closest phylogenetic group to the vertebrates. These chordates present a particularly diverse range of regenerative abilities and life-history strategies. Consequently, tunicates provide an extraordinary perspective into the emergence and diversity of these traits. Here we describe the genome sequencing, annotation and analysis of the Stolidobranchian Botrylloides leachii. We have produced a high-quality 159 Mb assembly, 82% of the predicted 194 Mb genome. Analysing genome size, gene number, repetitive elements, orthologs clustering and gene ontology terms show that B. leachii has a genomic architecture similar to that of most solitary tunicates, while other recently sequenced colonial ascidians have undergone genome expansion. In addition, ortholog clustering has identified groups of candidate genes for the study of colonialism and whole-body regeneration. By analysing the structure and composition of conserved gene linkages, we observed examples of cluster breaks and gene dispersions, suggesting that several lineage-specific genome rearrangements occurred during tunicate evolution. We also found lineage-specific gene gain and loss within conserved cell-signalling pathways. Such examples of genetic changes within conserved cell-signalling pathways commonly associated with regeneration and development that may underlie some of the diverse regenerative abilities observed in tunicates. Overall, these results provide a novel resource for the study of tunicates and of colonial ascidians.
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Affiliation(s)
- Simon Blanchoud
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.,Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Kim Rutherford
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Lisa Zondag
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Neil J Gemmell
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
| | - Megan J Wilson
- Department of Anatomy, School of Biomedical Sciences, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand.
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20
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Jung K, Hong SH, Ngo HPT, Ho TH, Ahn YJ, Oh DK, Kang LW. Crystal structures of an atypical aldehyde dehydrogenase having bidirectional oxidizing and reducing activities. Int J Biol Macromol 2017; 105:816-824. [PMID: 28732729 DOI: 10.1016/j.ijbiomac.2017.07.112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 07/17/2017] [Accepted: 07/17/2017] [Indexed: 11/15/2022]
Abstract
Aldehyde dehydrogenases (ALDHs) are NAD(P)+-dependent oxidoreductases that catalyze the oxidation of a variety of aldehydes to their acid forms. In this study, we determined the crystal structures of ALDH from Bacillus cereus (BcALDH), alone, and in complex with NAD+ and NADP+. This enzyme can oxidize all-trans-retinal to all-trans-retinoic acid using either NAD+ or NADP+ with equal efficiency, and atypically, as a minor activity, can reduce all-trans-retinal to all-trans-retinol using NADPH. BcALDH accommodated the additional 2'-phosphate of NADP+ by expanding the cofactor-binding pocket and upshifting the AMP moiety in NADP+. The nicotinamide moiety in NAD+ and NADP+ had direct interactions with the conserved catalytic residues (Cys300 and Glu266) and caused concerted conformational changes. We superimposed the structure of retinoic acid bound to human ALDH1A3 onto the BcALDH structure and speculated a model of the substrate all-trans-retinal bound to BcALDH. We also proposed a plausible mechanism for the minor reducing activity of BcALDH. These BcALDH structures will be useful in understanding cofactor specificity and the catalytic mechanism of an atypical bacterial BcALDH and should help the development of a new biocatalyst to produce retinoic acid and related high-end products.
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Affiliation(s)
- Kyoungho Jung
- Department of Biological Sciences, Konkuk University, Seoul 143-701, South Korea
| | - Seung-Hye Hong
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, South Korea
| | - Ho-Phuong-Thuy Ngo
- Department of Biological Sciences, Konkuk University, Seoul 143-701, South Korea
| | - Thien-Hoang Ho
- Department of Biological Sciences, Konkuk University, Seoul 143-701, South Korea
| | - Yeh-Jin Ahn
- Department of Life Science, Sangmyung University, Seoul 110-743, South Korea
| | - Deok-Kun Oh
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 143-701, South Korea.
| | - Lin-Woo Kang
- Department of Biological Sciences, Konkuk University, Seoul 143-701, South Korea.
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21
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Babkova P, Sebestova E, Brezovsky J, Chaloupkova R, Damborsky J. Ancestral Haloalkane Dehalogenases Show Robustness and Unique Substrate Specificity. Chembiochem 2017; 18:1448-1456. [PMID: 28419658 DOI: 10.1002/cbic.201700197] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Indexed: 11/08/2022]
Abstract
Ancestral sequence reconstruction (ASR) represents a powerful approach for empirical testing structure-function relationships of diverse proteins. We employed ASR to predict sequences of five ancestral haloalkane dehalogenases (HLDs) from the HLD-II subfamily. Genes encoding the inferred ancestral sequences were synthesized and expressed in Escherichia coli, and the resurrected ancestral enzymes (AncHLD1-5) were experimentally characterized. Strikingly, the ancestral HLDs exhibited significantly enhanced thermodynamic stability compared to extant enzymes (ΔTm up to 24 °C), as well as higher specific activities with preference for short multi-substituted halogenated substrates. Moreover, multivariate statistical analysis revealed a shift in the substrate specificity profiles of AncHLD1 and AncHLD2. This is extremely difficult to achieve by rational protein engineering. The study highlights that ASR is an efficient approach for the development of novel biocatalysts and robust templates for directed evolution.
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Affiliation(s)
- Petra Babkova
- Loschmidt Laboratories, Department of Experimental Biology and, Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Eva Sebestova
- Loschmidt Laboratories, Department of Experimental Biology and, Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic
| | - Jan Brezovsky
- Loschmidt Laboratories, Department of Experimental Biology and, Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Radka Chaloupkova
- Loschmidt Laboratories, Department of Experimental Biology and, Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and, Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 625 00, Brno, Czech Republic.,International Clinical Research Center, St. Anne's University Hospital, Pekarska 53, 656 91, Brno, Czech Republic
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22
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Missihoun TD, Kotchoni SO, Bartels D. Active Sites of Reduced Epidermal Fluorescence1 (REF1) Isoforms Contain Amino Acid Substitutions That Are Different between Monocots and Dicots. PLoS One 2016; 11:e0165867. [PMID: 27798665 PMCID: PMC5087895 DOI: 10.1371/journal.pone.0165867] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 10/19/2016] [Indexed: 11/22/2022] Open
Abstract
Plant aldehyde dehydrogenases (ALDHs) play important roles in cell wall biosynthesis, growth, development, and tolerance to biotic and abiotic stresses. The Reduced Epidermal Fluorescence1 is encoded by the subfamily 2C of ALDHs and was shown to oxidise coniferaldehyde and sinapaldehyde to ferulic acid and sinapic acid in the phenylpropanoid pathway, respectively. This knowledge has been gained from works in the dicotyledon model species Arabidopsis thaliana then used to functionally annotate ALDH2C isoforms in other species, based on the orthology principle. However, the extent to which the ALDH isoforms differ between monocotyledons and dicotyledons has rarely been accessed side-by-side. In this study, we used a phylogenetic approach to address this question. We have analysed the ALDH genes in Brachypodium distachyon, alongside those of other sequenced monocotyledon and dicotyledon species to examine traits supporting either a convergent or divergent evolution of the ALDH2C/REF1-type proteins. We found that B. distachyon, like other grasses, contains more ALDH2C/REF1 isoforms than A. thaliana and other dicotyledon species. Some amino acid residues in ALDH2C/REF1 isoforms were found as being conserved in dicotyledons but substituted by non-equivalent residues in monocotyledons. One example of those substitutions concerns a conserved phenylalanine and a conserved tyrosine in monocotyledons and dicotyledons, respectively. Protein structure modelling suggests that the presence of tyrosine would widen the substrate-binding pocket in the dicotyledons, and thereby influence substrate specificity. We discussed the importance of these findings as new hints to investigate why ferulic acid contents and cell wall digestibility differ between the dicotyledon and monocotyledon species.
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Affiliation(s)
- Tagnon D. Missihoun
- Department of Biology, Rutgers University, Camden, New Jersey, United States of America
- * E-mail: (SOK); (TDM)
| | - Simeon O. Kotchoni
- Department of Biology, Rutgers University, Camden, New Jersey, United States of America
- Center for Computational and Integrative Biology, Rutgers University, Camden, New Jersey, United States of America
- * E-mail: (SOK); (TDM)
| | - Dorothea Bartels
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Bonn, Germany
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23
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Campos JC, Bozi LHM, Bechara LRG, Lima VM, Ferreira JCB. Mitochondrial Quality Control in Cardiac Diseases. Front Physiol 2016; 7:479. [PMID: 27818636 PMCID: PMC5073139 DOI: 10.3389/fphys.2016.00479] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/05/2016] [Indexed: 01/08/2023] Open
Abstract
Disruption of mitochondrial homeostasis is a hallmark of cardiac diseases. Therefore, maintenance of mitochondrial integrity through different surveillance mechanisms is critical for cardiomyocyte survival. In this review, we discuss the most recent findings on the central role of mitochondrial quality control processes including regulation of mitochondrial redox balance, aldehyde metabolism, proteostasis, dynamics, and clearance in cardiac diseases, highlighting their potential as therapeutic targets.
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Affiliation(s)
- Juliane C Campos
- Department of Anatomy, Institute of Biomedical Sciences, University of Sao Paulo Sao Paulo, Brazil
| | - Luiz H M Bozi
- Department of Anatomy, Institute of Biomedical Sciences, University of Sao Paulo Sao Paulo, Brazil
| | - Luiz R G Bechara
- Department of Anatomy, Institute of Biomedical Sciences, University of Sao Paulo Sao Paulo, Brazil
| | - Vanessa M Lima
- Department of Anatomy, Institute of Biomedical Sciences, University of Sao Paulo Sao Paulo, Brazil
| | - Julio C B Ferreira
- Department of Anatomy, Institute of Biomedical Sciences, University of Sao Paulo Sao Paulo, Brazil
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24
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Crystal structure of human aldehyde dehydrogenase 1A3 complexed with NAD + and retinoic acid. Sci Rep 2016; 6:35710. [PMID: 27759097 PMCID: PMC5069622 DOI: 10.1038/srep35710] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/27/2016] [Indexed: 01/02/2023] Open
Abstract
The aldehyde dehydrogenase family 1 member A3 (ALDH1A3) catalyzes the oxidation of retinal to the pleiotropic factor retinoic acid using NAD+. The level of ALDHs enzymatic activity has been used as a cancer stem cell marker and seems to correlate with tumour aggressiveness. Elevated ALDH1A3 expression in mesenchymal glioma stem cells highlights the potential of this isozyme as a prognosis marker and drug target. Here we report the first crystal structure of human ALDH1A3 complexed with NAD+ and the product all-trans retinoic acid (REA). The tetrameric ALDH1A3 folds into a three domain-based architecture highly conserved along the ALDHs family. The structural analysis revealed two different and coupled conformations for NAD+ and REA that we propose to represent two snapshots along the catalytic cycle. Indeed, the isoprenic moiety of REA points either toward the active site cysteine, or moves away adopting the product release conformation. Although ALDH1A3 shares high sequence identity with other members of the ALDH1A family, our structural analysis revealed few peculiar residues in the 1A3 isozyme active site. Our data provide information into the ALDH1As catalytic process and can be used for the structure-based design of selective inhibitors of potential medical interest.
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Genome-Wide Identification and Functional Classification of Tomato (Solanum lycopersicum) Aldehyde Dehydrogenase (ALDH) Gene Superfamily. PLoS One 2016; 11:e0164798. [PMID: 27755582 PMCID: PMC5068750 DOI: 10.1371/journal.pone.0164798] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/30/2016] [Indexed: 11/25/2022] Open
Abstract
Aldehyde dehydrogenases (ALDHs) is a protein superfamily that catalyzes the oxidation of aldehyde molecules into their corresponding non-toxic carboxylic acids, and responding to different environmental stresses, offering promising genetic approaches for improving plant adaptation. The aim of the current study is the functional analysis for systematic identification of S. lycopersicum ALDH gene superfamily. We performed genome-based ALDH genes identification and functional classification, phylogenetic relationship, structure and catalytic domains analysis, and microarray based gene expression. Twenty nine unique tomato ALDH sequences encoding 11 ALDH families were identified, including a unique member of the family 19 ALDH. Phylogenetic analysis revealed 13 groups, with a conserved relationship among ALDH families. Functional structure analysis of ALDH2 showed a catalytic mechanism involving Cys-Glu couple. However, the analysis of ALDH3 showed no functional gene duplication or potential neo-functionalities. Gene expression analysis reveals that particular ALDH genes might respond to wounding stress increasing the expression as ALDH2B7. Overall, this study reveals the complexity of S. lycopersicum ALDH gene superfamily and offers new insights into the structure-functional features and evolution of ALDH gene families in vascular plants. The functional characterization of ALDHs is valuable and promoting molecular breeding in tomato for the improvement of stress tolerance and signaling.
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Alternative Biotransformation of Retinal to Retinoic Acid or Retinol by an Aldehyde Dehydrogenase from Bacillus cereus. Appl Environ Microbiol 2016; 82:3940-3946. [PMID: 27107124 DOI: 10.1128/aem.00848-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 04/17/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED A novel bacterial aldehyde dehydrogenase (ALDH) that converts retinal to retinoic acid was first identified in Bacillus cereus The amino acid sequence of ALDH from B. cereus (BcALDH) was more closely related to mammalian ALDHs than to bacterial ALDHs. This enzyme converted not only small aldehydes to carboxylic acids but also the large aldehyde all-trans-retinal to all-trans-retinoic acid with NAD(P)(+) We newly found that BcALDH and human ALDH (ALDH1A1) could reduce all-trans-retinal to all-trans-retinol with NADPH. The catalytic residues in BcALDH were Glu266 and Cys300, and the cofactor-binding residues were Glu194 and Glu457. The E266A and C300A variants showed no oxidation activity. The E194S and E457V variants showed 15- and 7.5-fold higher catalytic efficiency (kcat/Km) for the reduction of all-trans-retinal than the wild-type enzyme, respectively. The wild-type, E194S variant, and E457V variant enzymes with NAD(+) converted 400 μM all-trans-retinal to 210 μM all-trans-retinoic acid at the same amount for 240 min, while with NADPH, they converted 400 μM all-trans-retinal to 20, 90, and 40 μM all-trans-retinol, respectively. These results indicate that BcALDH and its variants are efficient biocatalysts not only in the conversion of retinal to retinoic acid but also in its conversion to retinol with a cofactor switch and that retinol production can be increased by the variant enzymes. Therefore, BcALDH is a novel bacterial enzyme for the alternative production of retinoic acid and retinol. IMPORTANCE Although mammalian ALDHs have catalyzed the conversion of retinal to retinoic acid with NAD(P)(+) as a cofactor, a bacterial ALDH involved in the conversion is first characterized. The biotransformation of all-trans-retinal to all-trans-retinoic acid by BcALDH and human ALDH was altered to the biotransformation to all-trans-retinol by a cofactor switch using NADPH. Moreover, the production of all-trans-retinal to all-trans-retinol was changed by mutations at positions 194 and 457 in BcALDH. The alternative biotransformation of retinoids was first performed in the present study. These results will contribute to the biotechnological production of retinoids, including retinoic acid and retinol.
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27
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Chakraborty M, Fry JD. Evidence that Environmental Heterogeneity Maintains a Detoxifying Enzyme Polymorphism in Drosophila melanogaster. Curr Biol 2015; 26:219-223. [PMID: 26748852 DOI: 10.1016/j.cub.2015.11.049] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/09/2015] [Accepted: 11/11/2015] [Indexed: 11/28/2022]
Abstract
Environmental heterogeneity is thought to be an important process maintaining genetic variation in populations [1-4]: if alternative alleles are favored in different environments, a stable polymorphism can be maintained [1, 5, 6]. This situation has been hypothesized to occur in genes encoding multi-substrate enzymes [7], in which changes that increase activity with one substrate typically decrease activity with others [8-10], but examples of polymorphisms maintained by this mechanism are rare. Here, we present evidence that a polymorphism in an enzyme gene in Drosophila melanogaster is maintained by such a trade-off. The mitochondrially localized aldehyde dehydrogenase in D. melanogaster has two important functions: detoxifying acetaldehyde derived from dietary ethanol [11] and detoxifying larger aldehydes produced as byproducts of oxidative phosphorylation [12]. A derived variant of the enzyme, Leu479Phe, is present in moderate frequencies in most temperate populations but is rare in more ethanol-averse tropical populations. Using purified recombinant protein, we show that the Leu-Phe substitution increases turnover rate of acetaldehyde but decreases turnover rate of larger aldehydes. Furthermore, using transgenic fly lines, we show that the substitution increases lifetime fitness on medium supplemented with an ecologically relevant ethanol concentration but decreases fitness on medium lacking ethanol. The strong, opposing selection pressures, coupled with documented highly variable ethanol concentrations in breeding sites of temperate populations, implicate an essential role for environmental heterogeneity in maintaining the polymorphism.
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Affiliation(s)
- Mahul Chakraborty
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - James D Fry
- Department of Biology, University of Rochester, Rochester, NY 14627, USA.
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28
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Cancer stem cells in laryngeal cancer: what we know. Eur Arch Otorhinolaryngol 2015; 273:3487-3495. [DOI: 10.1007/s00405-015-3837-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Accepted: 11/12/2015] [Indexed: 02/06/2023]
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29
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Chakraborty M, Fry JD. Parallel functional changes in independent testis-specific duplicates of Aldehyde dehydrogenase in Drosophila. Mol Biol Evol 2015; 32:1029-38. [PMID: 25564519 DOI: 10.1093/molbev/msu407] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A large proportion of duplicates, originating from ubiquitously expressed genes, acquire testis-biased expression. Identifying the underlying cause of this observation requires determining whether the duplicates have altered functions relative to the parental genes. Typically, statistical methods are used to test for positive selection, signature of which in protein sequence of duplicates implies functional divergence. When assumptions are violated, however, such tests can lead to false inference of positive selection. More convincing evidence for naturally selected functional changes would be the occurrence of structural changes with similar functional consequences in independent duplicates of the same gene. We investigated two testis-specific duplicates of the broadly expressed enzyme gene Aldehyde dehydrogenase (Aldh) that arose in different Drosophila lineages. The duplicates show a typical pattern of accelerated amino acid substitutions relative to their broadly expressed paralogs, with statistical evidence for positive selection in both cases. Importantly, in both duplicates, width of the entrance to the substrate binding site, known a priori to influence substrate specificity, and otherwise conserved throughout the genus Drosophila, has been reduced, resulting in narrowing of the entrance. Protein structure modeling suggests that the reduction of the size of the enzyme's substrate entry channel, which is likely to shift substrate specificity toward smaller aldehydes, is accounted for by the positively selected parallel substitutions in one duplicate but not the other. Evolution of the testis-specific duplicates was accompanied by reduction in expression of the ancestral Aldh in males, supporting the hypothesis that the duplicates may have helped resolve intralocus sexual conflict over Aldh function.
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Affiliation(s)
- Mahul Chakraborty
- Department of Ecology and Evolutionary Biology, University of California, Irvine
| | - James D Fry
- Department of Biology, University of Rochester
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30
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Carter CJ, Rand C, Mohammad I, Lepp A, Vesprini N, Wiebe O, Carlone R, Spencer GE. Expression of a retinoic acid receptor (RAR)-like protein in the embryonic and adult nervous system of a protostome species. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2014; 324:51-67. [DOI: 10.1002/jez.b.22604] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 10/18/2014] [Indexed: 01/08/2023]
Affiliation(s)
| | - Christopher Rand
- Department of Biological Sciences; Brock University; Ontario Canada
| | - Imtiaz Mohammad
- Department of Biological Sciences; Brock University; Ontario Canada
| | - Amanda Lepp
- Department of Biological Sciences; Brock University; Ontario Canada
| | | | - Olivia Wiebe
- Department of Biological Sciences; Brock University; Ontario Canada
| | - Robert Carlone
- Department of Biological Sciences; Brock University; Ontario Canada
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31
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André A, Ruivo R, Gesto M, Castro LFC, Santos MM. Retinoid metabolism in invertebrates: when evolution meets endocrine disruption. Gen Comp Endocrinol 2014; 208:134-45. [PMID: 25132059 DOI: 10.1016/j.ygcen.2014.08.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 07/20/2014] [Accepted: 08/07/2014] [Indexed: 02/07/2023]
Abstract
Recent genomic and biochemical evidence in invertebrate species pushes back the origin of the retinoid metabolic and signaling modules to the last common ancestor of all bilaterians. However, the evolution of retinoid pathways are far from fully understood. In the majority of non-chordate invertebrate lineages, the ongoing functional characterization of retinoid-related genes (metabolism and signaling pathways), as well as the characterization of the endogenous retinoid content (precursors and active retinoids), is still incomplete. Despite limited, the available data supports the presence of biologically active retinoid pathways in invertebrates. Yet, the mechanisms controlling the spatial and temporal distribution of retinoids as well as their physiological significance share similarities and differences with vertebrates. For instance, retinol storage in the form of retinyl esters, a key feature for the maintenance of retinoid homeostatic balance in vertebrates, was only recently demonstrated in some mollusk species, suggesting that such ability is older than previously anticipated. In contrast, the enzymatic repertoire involved in this process is probably unlike that of vertebrates. The suggested ancestry of active retinoid pathways implies that many more metazoan species might be potential targets for endocrine disrupting chemicals. Here, we review the current knowledge about the occurrence and functionality of retinoid metabolic and signaling pathways in invertebrate lineages, paying special attention to the evolutionary origin of retinoid storage mechanisms. Additionally, we summarize existing information on the endocrine disruption of invertebrate retinoid modules by environmental chemicals. Research priorities in the field are highlighted.
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Affiliation(s)
- A André
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal; ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
| | - R Ruivo
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal.
| | - M Gesto
- Laboratorio de Fisioloxía Animal, Facultade de Bioloxía, Universidade de Vigo, 36310 Vigo, Spain.
| | - L Filipe C Castro
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal; FCUP - Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal.
| | - M M Santos
- CIMAR/CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal; FCUP - Department of Biology, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal.
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32
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Belyaeva OV, Chang C, Berlett MC, Kedishvili NY. Evolutionary origins of retinoid active short-chain dehydrogenases/reductases of SDR16C family. Chem Biol Interact 2014; 234:135-43. [PMID: 25451586 DOI: 10.1016/j.cbi.2014.10.026] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 10/09/2014] [Accepted: 10/17/2014] [Indexed: 12/11/2022]
Abstract
Vertebrate enzymes that belong to the 16C family of short-chain dehydrogenases/reductases (SDR16C) were shown to play an essential role in the control of retinoic acid (RA) levels during development. To trace the evolution of enzymatic function of SDR16C family, and to examine the origins of the pathway for RA biosynthesis from vitamin A, we identified putative SDR16C enzymes through the extensive search of available genome sequencing data in a subset of species representing major metazoan phyla. The phylogenetic analysis revealed that enzymes from protostome, non-chordate deuterostome and invertebrate chordate species are found in three clades of SDR16C family containing retinoid active enzymes, which are retinol dehydrogenase 10 (RDH10), retinol dehydrogenases E2 (RDHE2) and RDHE2-similar, and dehydrogenase reductase (SDR family) member 3 (DHRS3). For the initial functional analysis, we cloned RDH10- and RDHE2-related enzymes from the early developmental stages of a non-chordate deuterostome, green sea urchin Lytechinus variegatus, and an invertebrate chordate, sea squirt Ciona intestinalis. In situ hybridization revealed that these proteins are expressed in a pattern relevant to development, while assays performed on proteins expressed in mammalian cell culture showed that they possess retinol-oxidizing activity as their vertebrate homologs. The existence of invertebrate homologs of DHRS3 was inferred from the analysis of phylogeny and cofactor-binding residues characteristic of preference for NADP(H). The presence of invertebrate homologs in the DHRS3 group of SDR16C is interesting in light of the complex mutually activating interaction, which we have recently described for human RDH10 and DHRS3 enzymes. Further functional analysis of these homologs will establish whether this interaction evolved to control retinoid homeostasis only in vertebrates, or is also conserved in pre-vertebrates.
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Affiliation(s)
- Olga V Belyaeva
- Department of Biochemistry and Molecular Genetics, University of Alabama - Birmingham, Birmingham, AL 35294, USA.
| | - Chenbei Chang
- Department of Cell, Developmental and Integrative Biology, University of Alabama - Birmingham, Birmingham, AL 35294, USA
| | - Michael C Berlett
- Department of Biochemistry and Molecular Genetics, University of Alabama - Birmingham, Birmingham, AL 35294, USA
| | - Natalia Y Kedishvili
- Department of Biochemistry and Molecular Genetics, University of Alabama - Birmingham, Birmingham, AL 35294, USA
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33
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Koop D, Chen J, Theodosiou M, Carvalho JE, Alvarez S, de Lera AR, Holland LZ, Schubert M. Roles of retinoic acid and Tbx1/10 in pharyngeal segmentation: amphioxus and the ancestral chordate condition. EvoDevo 2014; 5:36. [PMID: 25664163 PMCID: PMC4320481 DOI: 10.1186/2041-9139-5-36] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 08/27/2014] [Indexed: 12/16/2022] Open
Abstract
Background Although chordates descend from a segmented ancestor, the evolution of head segmentation has been very controversial for over 150 years. Chordates generally possess a segmented pharynx, but even though anatomical evidence and gene expression analyses suggest homologies between the pharyngeal apparatus of invertebrate chordates, such as the cephalochordate amphioxus, and vertebrates, these homologies remain contested. We, therefore, decided to study the evolution of the chordate head by examining the molecular mechanisms underlying pharyngeal morphogenesis in amphioxus, an animal lacking definitive neural crest. Results Focusing on the role of retinoic acid (RA) in post-gastrulation pharyngeal morphogenesis, we found that during gastrulation, RA signaling in the endoderm is required for defining pharyngeal and non-pharyngeal domains and that this process involves active degradation of RA anteriorly in the embryo. Subsequent extension of the pharyngeal territory depends on the creation of a low RA environment and is coupled to body elongation. RA further functions in pharyngeal segmentation in a regulatory network involving the mutual inhibition of RA- and Tbx1/10-dependent signaling. Conclusions These results indicate that the involvement of RA signaling and its interactions with Tbx1/10 in head segmentation preceded the evolution of neural crest and were thus likely present in the ancestral chordate. Furthermore, developmental comparisons between different deuterostome models suggest that the genetic mechanisms for pharyngeal segmentation are evolutionary ancient and very likely predate the origin of chordates. Electronic supplementary material The online version of this article (doi:10.1186/2041-9139-5-36) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Demian Koop
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0202 USA
| | - Jie Chen
- Institut de Génomique Fonctionnelle de Lyon (CNRS UMR 5242, UCBL, ENS, INRA 1288), Ecole Normale Supérieure de Lyon, 69364 Lyon, Cedex 07, France
| | - Maria Theodosiou
- Institut de Génomique Fonctionnelle de Lyon (CNRS UMR 5242, UCBL, ENS, INRA 1288), Ecole Normale Supérieure de Lyon, 69364 Lyon, Cedex 07, France
| | - João E Carvalho
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR 7009, Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, 06230 Villefranche-sur-Mer, France ; CNRS, UMR 7009, Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, 06230 Villefranche-sur-Mer, France
| | - Susana Alvarez
- Departamento de Química Orgánica, Universidade de Vigo, 33610 Vigo, Spain
| | - Angel R de Lera
- Departamento de Química Orgánica, Universidade de Vigo, 33610 Vigo, Spain
| | - Linda Z Holland
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92093-0202 USA
| | - Michael Schubert
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR 7009, Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, 06230 Villefranche-sur-Mer, France ; CNRS, UMR 7009, Laboratoire de Biologie du Développement de Villefranche-sur-Mer, Observatoire Océanologique de Villefranche-sur-Mer, 06230 Villefranche-sur-Mer, France
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34
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Signaling through retinoic acid receptors in cardiac development: Doing the right things at the right times. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1849:94-111. [PMID: 25134739 DOI: 10.1016/j.bbagrm.2014.08.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 06/19/2014] [Accepted: 08/04/2014] [Indexed: 11/23/2022]
Abstract
Retinoic acid (RA) is a terpenoid that is synthesized from vitamin A/retinol (ROL) and binds to the nuclear receptors retinoic acid receptor (RAR)/retinoid X receptor (RXR) to control multiple developmental processes in vertebrates. The available clinical and experimental data provide uncontested evidence for the pleiotropic roles of RA signaling in development of multiple embryonic structures and organs such eyes, central nervous system, gonads, lungs and heart. The development of any of these above-mentioned embryonic organ systems can be effectively utilized to showcase the many strategies utilized by RA signaling. However, it is very likely that the strategies employed to transfer RA signals during cardiac development comprise the majority of the relevant and sophisticated ways through which retinoid signals can be conveyed in a complex biological system. Here, we provide the reader with arguments indicating that RA signaling is exquisitely regulated according to specific phases of cardiac development and that RA signaling itself is one of the major regulators of the timing of cardiac morphogenesis and differentiation. We will focus on the role of signaling by RA receptors (RARs) in early phases of heart development. This article is part of a Special Issue entitled: Nuclear receptors in animal development.
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Oliveira SHP, Ferraz FAN, Honorato RV, Xavier-Neto J, Sobreira TJP, de Oliveira PSL. KVFinder: steered identification of protein cavities as a PyMOL plugin. BMC Bioinformatics 2014; 15:197. [PMID: 24938294 PMCID: PMC4071799 DOI: 10.1186/1471-2105-15-197] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 06/09/2014] [Indexed: 01/25/2023] Open
Abstract
Background The characterization of protein binding sites is a major challenge in computational biology. Proteins interact with a wide variety of molecules and understanding of such complex interactions is essential to gain deeper knowledge of protein function. Shape complementarity is known to be important in determining protein-ligand interactions. Furthermore, these protein structural features have been shown to be useful in assisting medicinal chemists during lead discovery and optimization. Results We developed KVFinder, a highly versatile and easy-to-use tool for cavity prospection and spatial characterization. KVFinder is a geometry-based method that has an innovative customization of the search space. This feature provides the possibility of cavity segmentation, which alongside with the large set of customizable parameters, allows detailed cavity analyses. Although the main focus of KVFinder is the steered prospection of cavities, we tested it against a benchmark dataset of 198 known drug targets in order to validate our software and compare it with some of the largely accepted methods. Using the one click mode, we performed better than most of the other methods, staying behind only of hybrid prospection methods. When using just one of KVFinder’s customizable features, we were able to outperform all other compared methods. KVFinder is also user friendly, as it is available as a PyMOL plugin, or command-line version. Conclusion KVFinder presents novel usability features, granting full customizable and highly detailed cavity prospection on proteins, alongside with a friendly graphical interface. KVFinder is freely available on http://lnbio.cnpem.br/bioinformatics/main/software/.
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Affiliation(s)
| | | | | | | | | | - Paulo S L de Oliveira
- National Laboratory of Biosciences, P,O, Box 6192, CEP 13083-970 Campinas, SP, Brazil.
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Zhou L, Ishizaki H, Spitzer M, Taylor KL, Temperley ND, Johnson SL, Brear P, Gautier P, Zeng Z, Mitchell A, Narayan V, McNeil EM, Melton DW, Smith TK, Tyers M, Westwood NJ, Patton EE. ALDH2 mediates 5-nitrofuran activity in multiple species. ACTA ACUST UNITED AC 2014; 19:883-92. [PMID: 22840776 PMCID: PMC3684953 DOI: 10.1016/j.chembiol.2012.05.017] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 05/10/2012] [Accepted: 05/14/2012] [Indexed: 01/23/2023]
Abstract
Understanding how drugs work in vivo is critical for drug design and for maximizing the potential of currently available drugs. 5-nitrofurans are a class of prodrugs widely used to treat bacterial and trypanosome infections, but despite relative specificity, 5-nitrofurans often cause serious toxic side effects in people. Here, we use yeast and zebrafish, as well as human in vitro systems, to assess the biological activity of 5-nitrofurans, and we identify a conserved interaction between aldehyde dehydrogenase (ALDH) 2 and 5-nitrofurans across these species. In addition, we show that the activity of nifurtimox, a 5-nitrofuran anti-trypanosome prodrug, is dependent on zebrafish Aldh2 and is a substrate for human ALDH2. This study reveals a conserved and biologically relevant ALDH2-5-nitrofuran interaction that may have important implications for managing the toxicity of 5-nitrofuran treatment.
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Affiliation(s)
- Linna Zhou
- School of Chemistry and Biomedical Sciences Research Complex, University of St. Andrews and EaStCHEM, St. Andrews, Fife, Scotland KY16 9ST, UK
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Millard A, Scanlan DJ, Gallagher C, Marsh A, Taylor PC. Unexpected evolutionary proximity of eukaryotic and cyanobacterial enzymes responsible for biosynthesis of retinoic acid and its oxidation. MOLECULAR BIOSYSTEMS 2014; 10:380-3. [DOI: 10.1039/c3mb70447e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Blum N, Begemann G. The roles of endogenous retinoid signaling in organ and appendage regeneration. Cell Mol Life Sci 2013; 70:3907-27. [PMID: 23479131 PMCID: PMC11113817 DOI: 10.1007/s00018-013-1303-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 01/29/2013] [Accepted: 02/14/2013] [Indexed: 12/20/2022]
Abstract
The ability to regenerate injured or lost body parts has been an age-old ambition of medical science. In contrast to humans, teleost fish and urodele amphibians can regrow almost any part of the body with seeming effortlessness. Retinoic acid is a molecule that has long been associated with these impressive regenerative capacities. The discovery 30 years ago that addition of retinoic acid to regenerating amphibian limbs causes "super-regeneration" initiated investigations into the presumptive roles of retinoic acid in regeneration of appendages and other organs. However, the evidence favoring or dismissing a role for endogenous retinoids in regeneration processes remained sparse and ambiguous. Now, the availability of genetic tools to manipulate and visualize the retinoic acid signaling pathway has opened up new routes to dissect its roles in regeneration. Here, we review the current understanding on endogenous functions of retinoic acid in regeneration and discuss key questions to be addressed in future research.
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Affiliation(s)
- Nicola Blum
- Developmental Biology, University of Bayreuth, 95440 Bayreuth, Germany
| | - Gerrit Begemann
- Developmental Biology, University of Bayreuth, 95440 Bayreuth, Germany
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Duester G. Retinoid signaling in control of progenitor cell differentiation during mouse development. Semin Cell Dev Biol 2013; 24:694-700. [PMID: 23973941 DOI: 10.1016/j.semcdb.2013.08.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 07/25/2013] [Accepted: 08/10/2013] [Indexed: 02/01/2023]
Abstract
The vitamin A metabolite retinoic acid (RA) serves as a ligand for nuclear RA receptors that control differentiation of progenitor cells important for vertebrate development. Genetic studies in mouse embryos deficient for RA-generating enzymes have been invaluable for deciphering RA function. RA first begins to act during early organogenesis when RA generated in trunk mesoderm begins to function as a diffusible signal controlling progenitor cell differentiation. In neuroectoderm, RA functions as an instructive signal to stimulate neuronal differentiation of progenitor cells in the hindbrain and spinal cord. RA is not required for early neuronal differentiation of the forebrain, but at later stages RA stimulates neuronal differentiation in forebrain basal ganglia. RA also acts as a permissive signal for differentiation by repressing fibroblast growth factor (FGF) signaling in differentiated cells as they emerge from progenitor populations in the caudal progenitor zone and second heart field. In addition, RA signaling stimulates differentiation of spermatogonial germ cells and induces meiosis in male but not female gonads. A more complete understanding of the normal functions of RA signaling during development will guide efforts to use RA as a differentiation agent for therapeutic purposes.
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Affiliation(s)
- Gregg Duester
- Sanford-Burnham Medical Research Institute, Development and Aging Program, 10901 North Torrey Pines Road, La Jolla, CA 92037, USA.
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Cañestro C, Albalat R, Irimia M, Garcia-Fernàndez J. Impact of gene gains, losses and duplication modes on the origin and diversification of vertebrates. Semin Cell Dev Biol 2013; 24:83-94. [DOI: 10.1016/j.semcdb.2012.12.008] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 12/25/2012] [Indexed: 02/06/2023]
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Voordeckers K, Brown CA, Vanneste K, van der Zande E, Voet A, Maere S, Verstrepen KJ. Reconstruction of ancestral metabolic enzymes reveals molecular mechanisms underlying evolutionary innovation through gene duplication. PLoS Biol 2012; 10:e1001446. [PMID: 23239941 PMCID: PMC3519909 DOI: 10.1371/journal.pbio.1001446] [Citation(s) in RCA: 138] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 10/30/2012] [Indexed: 11/24/2022] Open
Abstract
Gene duplications are believed to facilitate evolutionary innovation. However, the mechanisms shaping the fate of duplicated genes remain heavily debated because the molecular processes and evolutionary forces involved are difficult to reconstruct. Here, we study a large family of fungal glucosidase genes that underwent several duplication events. We reconstruct all key ancestral enzymes and show that the very first preduplication enzyme was primarily active on maltose-like substrates, with trace activity for isomaltose-like sugars. Structural analysis and activity measurements on resurrected and present-day enzymes suggest that both activities cannot be fully optimized in a single enzyme. However, gene duplications repeatedly spawned daughter genes in which mutations optimized either isomaltase or maltase activity. Interestingly, similar shifts in enzyme activity were reached multiple times via different evolutionary routes. Together, our results provide a detailed picture of the molecular mechanisms that drove divergence of these duplicated enzymes and show that whereas the classic models of dosage, sub-, and neofunctionalization are helpful to conceptualize the implications of gene duplication, the three mechanisms co-occur and intertwine.
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Affiliation(s)
- Karin Voordeckers
- VIB Laboratory for Systems Biology, Leuven, Belgium
- CMPG Laboratory for Genetics and Genomics, KU Leuven, Leuven, Belgium
| | - Chris A. Brown
- VIB Laboratory for Systems Biology, Leuven, Belgium
- CMPG Laboratory for Genetics and Genomics, KU Leuven, Leuven, Belgium
- Fathom Information Design, Boston, Massachusetts, United States of America
- Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Kevin Vanneste
- VIB Department of Plant Systems Biology, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Elisa van der Zande
- VIB Laboratory for Systems Biology, Leuven, Belgium
- CMPG Laboratory for Genetics and Genomics, KU Leuven, Leuven, Belgium
| | - Arnout Voet
- Laboratory for Molecular en Structural Biology, KU Leuven, Leuven, Belgium
| | - Steven Maere
- VIB Department of Plant Systems Biology, Gent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
| | - Kevin J. Verstrepen
- VIB Laboratory for Systems Biology, Leuven, Belgium
- CMPG Laboratory for Genetics and Genomics, KU Leuven, Leuven, Belgium
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Cloning and molecular evolution of the aldehyde dehydrogenase 2 gene (Aldh2) in bats (Chiroptera). Biochem Genet 2012; 51:7-19. [PMID: 23053874 DOI: 10.1007/s10528-012-9540-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 06/25/2012] [Indexed: 10/27/2022]
Abstract
Old World fruit bats (Pteropodidae) and New World fruit bats (Phyllostomidae) ingest significant quantities of ethanol while foraging. Mitochondrial aldehyde dehydrogenase (ALDH2, encoded by the Aldh2 gene) plays an important role in ethanol metabolism. To test whether the Aldh2 gene has undergone adaptive evolution in frugivorous and nectarivorous bats in relation to ethanol elimination, we sequenced part of the coding region of the gene (1,143 bp, ~73 % coverage) in 14 bat species, including three Old World fruit bats and two New World fruit bats. Our results showed that the Aldh2 coding sequences are highly conserved across all bat species we examined, and no evidence of positive selection was detected in the ancestral branches leading to Old World fruit bats and New World fruit bats. Further research is needed to determine whether other genes involved in ethanol metabolism have been the targets of positive selection in frugivorous and nectarivorous bats.
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Tanaka M, Onimaru K. Acquisition of the paired fins: a view from the sequential evolution of the lateral plate mesoderm. Evol Dev 2012; 14:412-20. [DOI: 10.1111/j.1525-142x.2012.00561.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Krishnamurthy S, Nör J. Head and neck cancer stem cells. J Dent Res 2012; 91:334-40. [PMID: 21933937 PMCID: PMC3310753 DOI: 10.1177/0022034511423393] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 08/12/2011] [Accepted: 08/16/2011] [Indexed: 12/13/2022] Open
Abstract
Most cancers contain a small sub-population of cells that are endowed with self-renewal, multipotency, and a unique potential for tumor initiation. These properties are considered hallmarks of cancer stem cells. Here, we provide an overview of the field of cancer stem cells with a focus on head and neck cancers. Cancer stem cells are located in the invasive fronts of head and neck squamous cell carcinomas (HNSCC) close to blood vessels (perivascular niche). Endothelial cell-initiated signaling events are critical for the survival and self-renewal of these stem cells. Markers such as aldehyde dehydrogenase (ALDH), CD133, and CD44 have been successfully used to identify highly tumorigenic cancer stem cells in HNSCC. This review briefly describes the orosphere assay, a method for in vitro culture of undifferentiated head and neck cancer stem cells under low attachment conditions. Notably, recent evidence suggests that cancer stem cells are exquisitely resistant to conventional therapy and are the "drivers" of local recurrence and metastatic spread. The emerging understanding of the role of cancer stem cells in the pathobiology of head and neck squamous cell carcinomas might have a profound impact on the treatment paradigms for this malignancy.
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Affiliation(s)
- S. Krishnamurthy
- Department of Cariology, Restorative Sciences and Endodontics, University of Michigan School of Dentistry, 1011 N. University, Rm. 2309, Ann Arbor, MI 48109-1078, USA
| | - J.E. Nör
- Department of Cariology, Restorative Sciences and Endodontics, University of Michigan School of Dentistry, 1011 N. University, Rm. 2309, Ann Arbor, MI 48109-1078, USA
- Department of Biomedical Engineering, University of Michigan College of Engineering
- Department of Otolaryngology, University of Michigan School of Medicine
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Holland LZ, Onai T. Early development of cephalochordates (amphioxus). WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2011; 1:167-83. [PMID: 23801434 DOI: 10.1002/wdev.11] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The Phylum Chordata includes three groups--Vertebrata, Tunicata, and Cephalochordata. In cephalochordates, commonly called amphioxus or lancelets, which are basal in the Chordata, the eggs are small and relatively non-yolky. As in vertebrates, cleavage is indeterminate with cell fates determined gradually as development proceeds. The oocytes are attached to the ovarian follicle at the animal pole, where the oocyte nucleus is located. The cytoplasm at the opposite side of the egg, the vegetal pole, contains the future germ plasm or pole plasm, which includes determinants of the germline. After fertilization, additional asymmetries are established by movements of the egg and sperm nuclei, resulting in a concentration of mitochondria at one side of the animal hemisphere. This may be related to establishment of the dorsal/ventral axis. Patterning along the embryonic axes is mediated by secreted signaling proteins. Dorsal identity is specified by Nodal/Vg1 signaling, while during the gastrula stage, opposition between Nodal/Vg1 and BMP signaling establishes dorsal/anterior (i.e., head) and ventral/posterior (i.e., trunk/tail) identities, respectively. Wnt/β-catenin signaling specifies posterior identity while retinoic acid signaling specifies positions along the anterior/posterior axis. These signals are further modulated by a number of secreted antagonists. This fundamental patterning mechanism is conserved, with some modifications, in vertebrates.
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Affiliation(s)
- Linda Z Holland
- Marine Biology Research Division, Scripps Institution of Oceanography, La Jolla, CA, USA.
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Jackson B, Brocker C, Thompson DC, Black W, Vasiliou K, Nebert DW, Vasiliou V. Update on the aldehyde dehydrogenase gene (ALDH) superfamily. Hum Genomics 2011; 5:283-303. [PMID: 21712190 PMCID: PMC3392178 DOI: 10.1186/1479-7364-5-4-283] [Citation(s) in RCA: 244] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Members of the aldehyde dehydrogenase gene (ALDH) superfamily play an important role in the enzymic detoxification of endogenous and exogenous aldehydes and in the formation of molecules that are important in cellular processes, like retinoic acid, betaine and gamma-aminobutyric acid. ALDHs exhibit additional, non-enzymic functions, including the capacity to bind to some hormones and other small molecules and to diminish the effects of ultraviolet irradiation in the cornea. Mutations in ALDH genes leading to defective aldehyde metabolism are the molecular basis of several diseases, including gamma-hydroxybutyric aciduria, pyridoxine-dependent seizures, Sjögren-Larsson syndrome and type II hyperprolinaemia. Interestingly, several ALDH enzymes appear to be markers for normal and cancer stem cells. The superfamily is evolutionarily ancient and is represented within Archaea, Eubacteria and Eukarya taxa. Recent improvements in DNA and protein sequencing have led to the identification of many new ALDH family members. To date, the human genome contains 19 known ALDH genes, as well as many pseudogenes. Whole-genome sequencing allows for comparison of the entire complement of ALDH family members among organisms. This paper provides an update of ALDH genes in several recently sequenced vertebrates and aims to clarify the associated records found in the National Center for Biotechnology Information (NCBI) gene database. It also highlights where and when likely gene-duplication and gene-loss events have occurred. This information should be useful to future studies that might wish to compare the role of ALDH members among species and how the gene superfamily as a whole has changed throughout evolution.
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Affiliation(s)
- Brian Jackson
- Molecular Toxicology and Environmental Health Sciences Program, Department of Pharmaceutical Sciences, University of Colorado Anschutz Medical Center, Aurora, USA
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