1
|
Moreira FA, Escobar JFB, Giordani C, Caseli L. Langmuir monolayers provide an effective strategy for studying molecular recognition of nucleobases using alkylated nucleotides. Colloids Surf B Biointerfaces 2024; 244:114129. [PMID: 39121572 DOI: 10.1016/j.colsurfb.2024.114129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/18/2024] [Accepted: 07/27/2024] [Indexed: 08/12/2024]
Abstract
Molecular Recognition in nucleotides is crucial for medicine, underpinning precise interactions in genetic replication and therapy. Alkylated nucleotides, in particular, play a key role in modifying DNA to inhibit cancer cell growth. In this study, we focused on an alkylated nucleotide, PNM2 (3',4',6'-O-tristearoyl uridine or uridine tri-stearate), to investigate the interaction between adenine molecules in the aqueous subphase and PNM2 Langmuir monolayers. Utilizing techniques such as tensiometry, Brewster angle microscopy, infrared spectroscopy, surface potential measurements, and dilatational surface rheology, we found compelling evidence of molecular Recognition between the polar head of the insoluble amphiphile (uridine) in the monolayer and adenine in the aqueous subphase, attributed to hydrogen bonding. These interactions significantly influenced the physicochemical properties of the air-water interface, including monolayer expansion upon molecular recognition, decreased dilatational modulus, increased tensiometric stability of the monolayer when compressed to relevant surface pressures, and decreased surface potential. These findings are noteworthy for drug development, providing crucial insights into the mechanisms of nucleotide interactions.
Collapse
Affiliation(s)
- Felipe Almeida Moreira
- Department of Chemistry, Federal University of Sao Paulo, Rua São Nicolau, 210, Diadema, SP 09913-030, Brazil
| | - Jhon Fernando Berrio Escobar
- Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia, Calle 70 No. 52-21, Medellìn 050010, Colombia
| | - Cristiano Giordani
- Instituto de Física, Universidad de Antioquia, Calle 70 No. 52-21, Medellìn 050010, Colombia; Grupo Productos Naturales Marinos, Facultad de Ciencias Farmacéuticas y Alimentarias, Universidad de Antioquia, Calle 70 No. 52-21, Medellín 050010, Colombia.
| | - Luciano Caseli
- Department of Chemistry, Federal University of Sao Paulo, Rua São Nicolau, 210, Diadema, SP 09913-030, Brazil.
| |
Collapse
|
2
|
Pelletier D, Blier PU, Vézina F, Dufresne F, Paquin F, Christen F, Guillemette M. Under pressure-exploring partner changes, physiological responses and telomere dynamics in northern gannets across varying breeding conditions. PeerJ 2023; 11:e16457. [PMID: 38054014 PMCID: PMC10695113 DOI: 10.7717/peerj.16457] [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: 04/13/2023] [Accepted: 10/23/2023] [Indexed: 12/07/2023] Open
Abstract
Background Life history theory predicts trade-offs between reproduction and survival in species like the northern gannet (Morus bassanus). During breeding, demanding foraging conditions lead them to expand their foraging range and diversify their diet, increasing the risk of reproductive failure. Changing partners may enhance breeding success but lead to more physiological costs. Methods To investigate the physiological costs of reproduction upon partner changes, we measured and compared 21 biomarkers related to telomere dynamics, oxidative stress, inflammation, hematology, nutritional status, and muscle damage. We used a longitudinal approach with gannets (n = 38) over three contrasting years (2017, 2018 and 2019). Results Our results suggest that annual breeding conditions exert a greater influence on physiological changes than partnership status. Individuals that changed partner experienced greater short-term stress than retained partners. This transient increase in stress was marked by short-term increases in oxidative lipid damage, lower antioxidant capacity, signs of inflammation, and greater weight loss than individuals that retained partners. During favorable conditions, individuals that changed mates had stabilized telomere length, decreased antioxidant capacity, glucose concentration, and muscle damage, along with increased oxygen transport capacity. Conversely, unfavorable breeding conditions led to increased telomere attrition, stabilized antioxidant capacity, decreased inflammation susceptibility, diminished oxygen transport capacity, and increased muscle damage. In the cases where partners were retained, distinct physiological changes were observed depending on the year's conditions, yet the telomere dynamics remained consistent across both partnership status categories. During the favorable year, there was an increase in unsaturated fatty acids and oxygen transport capacity in the blood, coupled with a reduction in inflammation potential and protein catabolism. In contrast, during the unfavorable year in the retained mates, we observed an increase in oxidative DNA damage, antioxidant capacity, weight loss, but a decrease in inflammation susceptibility as observed in changed mates. Discussion Our study shows that behavioral flexibility such as mate switching can help seabirds cope with the challenges of food scarcity during reproduction, but these coping strategies may have a negative impact on physiological status at the individual level. In addition, the marked reduction in telomere length observed during harsh conditions, coupled with the stabilization of telomere length in favorable conditions, highlights the long-term physiological impact of annual breeding conditions on seabirds. These findings underscore the effect on their potential survival and fitness, emphasizing that the influence of annual breeding conditions is greater than that of partnership status.
Collapse
Affiliation(s)
- David Pelletier
- Department of Biology, Université du Québec à Rimouski, Rimouski, Québec, Canada
- Department of Biology, Cégep de Rimouski, Rimouski, Québec, Canada
| | - Pierre U. Blier
- Department of Biology, Université du Québec à Rimouski, Rimouski, Québec, Canada
| | - François Vézina
- Department of Biology, Université du Québec à Rimouski, Rimouski, Québec, Canada
| | - France Dufresne
- Department of Biology, Université du Québec à Rimouski, Rimouski, Québec, Canada
| | - Frédérique Paquin
- Department of Biology, Université du Québec à Rimouski, Rimouski, Québec, Canada
| | - Felix Christen
- Department of Biology, Université du Québec à Rimouski, Rimouski, Québec, Canada
| | - Magella Guillemette
- Department of Biology, Université du Québec à Rimouski, Rimouski, Québec, Canada
| |
Collapse
|
3
|
Hou X, Xu H, Deng Z, Yan Y, Yuan Z, Liu X, Su Z, Yang S, Zhang Y, Rao Y. Discovery of the Biosynthetic Pathway of Beticolin 1 Reveals a Novel Non‐heme Iron‐dependent Oxygenase for Anthraquinone Ring Cleavage. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202208772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Xiaodong Hou
- Jiangnan University Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology CHINA
| | - Huibin Xu
- Jiangnan University Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology CHINA
| | - Zhiwei Deng
- Jiangnan University Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology CHINA
| | - Yijun Yan
- Kunming Institute of Botany Chinese Academy of Sciences State Key laboratory of Phytochemistry and Plant Resources in West China CHINA
| | - Zhenbo Yuan
- Jiangnan University Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology CHINA
| | - Xuanzhong Liu
- Jiangnan University Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology CHINA
| | - Zengping Su
- Jiangnan University Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology CHINA
| | - Sai Yang
- Jiangnan University Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology CHINA
| | - Yan Zhang
- Jiangnan University School of Life Sciences and Health Engineering CHINA
| | - Yijian Rao
- Jiangnan University School of Biotechnology Lihu Avenue 1800 214122 Wuxi CHINA
| |
Collapse
|
4
|
Hou X, Xu H, Deng Z, Yan Y, Yuan Z, Liu X, Su Z, Yang S, Zhang Y, Rao Y. Discovery of the Biosynthetic Pathway of Beticolin 1 Reveals a Novel Non-heme Iron-dependent Oxygenase for Anthraquinone Ring Cleavage. Angew Chem Int Ed Engl 2022; 61:e202208772. [PMID: 35862137 DOI: 10.1002/anie.202208772] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Indexed: 11/11/2022]
Abstract
This study used light-mediated comparative transcriptomics to identify the biosynthetic gene cluster of beticolin 1 in Cercospora. It contains an anthraquinone moiety and an unusual halogenated xanthone moiety connected by a bicyclo[3.2.2]nonane. During elucidation of the biosynthetic pathway of beticolin 1, a novel non-heme iron oxygenase BTG13 responsible for anthraquinone ring cleavage was discovered. More importantly, the discovery of non-heme iron oxygenase BTG13 is well supported by experimental evidence: (i) crystal structure and the inductively coupled plasma mass spectrometry revealed that its reactive site is built by an atypical iron ion coordination, where the iron ion is uncommonly coordinated by four histidine residues, an unusual carboxylated-lysine (Kcx377) and water; (ii) Kcx377 is mediated by His58 and Thr299 to modulate the catalytic activity of BTG13. Therefore, we believed this study updates our knowledge of metalloenzymes.
Collapse
Affiliation(s)
- Xiaodong Hou
- Jiangnan University, Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, CHINA
| | - Huibin Xu
- Jiangnan University, Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, CHINA
| | - Zhiwei Deng
- Jiangnan University, Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, CHINA
| | - Yijun Yan
- Kunming Institute of Botany Chinese Academy of Sciences, State Key laboratory of Phytochemistry and Plant Resources in West China, CHINA
| | - Zhenbo Yuan
- Jiangnan University, Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, CHINA
| | - Xuanzhong Liu
- Jiangnan University, Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, CHINA
| | - Zengping Su
- Jiangnan University, Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, CHINA
| | - Sai Yang
- Jiangnan University, Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, CHINA
| | - Yan Zhang
- Jiangnan University, School of Life Sciences and Health Engineering, CHINA
| | - Yijian Rao
- Jiangnan University, School of Biotechnology, Lihu Avenue 1800, 214122, Wuxi, CHINA
| |
Collapse
|
5
|
Csizi KS, Eckert L, Brunken C, Hofstetter TB, Reiher M. The Apparently Unreactive Substrate Facilitates the Electron Transfer for Dioxygen Activation in Rieske Dioxygenases. Chemistry 2022; 28:e202103937. [PMID: 35072969 PMCID: PMC9306888 DOI: 10.1002/chem.202103937] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Indexed: 12/29/2022]
Abstract
Rieske dioxygenases belong to the non‐heme iron family of oxygenases and catalyze important cis‐dihydroxylation as well as O‐/N‐dealkylation and oxidative cyclization reactions for a wide range of substrates. The lack of substrate coordination at the non‐heme ferrous iron center, however, makes it particularly challenging to delineate the role of the substrate for productive O2
activation. Here, we studied the role of the substrate in the key elementary reaction leading to O2
activation from a theoretical perspective by systematically considering (i) the 6‐coordinate to 5‐coordinate conversion of the non‐heme FeII upon abstraction of a water ligand, (ii) binding of O2
, and (iii) transfer of an electron from the Rieske cluster. We systematically evaluated the spin‐state‐dependent reaction energies and structural effects at the active site for all combinations of the three elementary processes in the presence and absence of substrate using naphthalene dioxygenase as a prototypical Rieske dioxygenase. We find that reaction energies for the generation of a coordination vacancy at the non‐heme FeII
center through thermoneutral H2O reorientation and exothermic O2
binding prior to Rieske cluster oxidation are largely insensitive to the presence of naphthalene and do not lead to formation of any of the known reactive Fe‐oxygen species. By contrast, the role of the substrate becomes evident after Rieske cluster oxidation and exclusively for the 6‐coordinate non‐heme FeII
sites in that the additional electron is found at the substrate instead of at the iron and oxygen atoms. Our results imply an allosteric control of the substrate on Rieske dioxygenase reactivity to happen prior to changes at the non‐heme FeII
in agreement with a strategy that avoids unproductive O2
activation.
Collapse
Affiliation(s)
- Katja-Sophia Csizi
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland.,ETH Zürich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Lina Eckert
- ETH Zürich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Christoph Brunken
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland.,ETH Zürich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| | - Thomas B Hofstetter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, 8600, Dübendorf, Switzerland
| | - Markus Reiher
- ETH Zürich, Laboratory for Physical Chemistry, Vladimir-Prelog-Weg 2, 8093, Zürich, Switzerland
| |
Collapse
|
6
|
Solomon EI, DeWeese DE, Babicz JT. Mechanisms of O 2 Activation by Mononuclear Non-Heme Iron Enzymes. Biochemistry 2021; 60:3497-3506. [PMID: 34266238 PMCID: PMC8768060 DOI: 10.1021/acs.biochem.1c00370] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Two major subclasses of mononuclear non-heme ferrous enzymes use two electron-donating organic cofactors (α-ketoglutarate or pterin) to activate O2 to form FeIV═O intermediates that further react with their substrates through hydrogen atom abstraction or electrophilic aromatic substitution. New spectroscopic methodologies have been developed, enabling the study of the active sites in these enzymes and their oxygen intermediates. Coupled to electronic structure calculations, the results of these spectroscopies provide fundamental insight into mechanism. This Perspective summarizes the results of these studies in elucidating the mechanism of dioxygen activation to form the FeIV═O intermediate and the geometric and electronic structure of this intermediate that enables its high reactivity and selectivity in product formation.
Collapse
Affiliation(s)
- Edward I. Solomon
- Department of Chemistry, Stanford University, 333 Campus Dr. Stanford, CA, 94305, United States,SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, United States
| | - Dory E. DeWeese
- Department of Chemistry, Stanford University, 333 Campus Dr. Stanford, CA, 94305, United States
| | - Jeffrey T. Babicz
- Department of Chemistry, Stanford University, 333 Campus Dr. Stanford, CA, 94305, United States
| |
Collapse
|
7
|
A combination of Class-I fumarases and metabolites (α-ketoglutarate and fumarate) signal the DNA damage response in Escherichia coli. Proc Natl Acad Sci U S A 2021; 118:2026595118. [PMID: 34083440 DOI: 10.1073/pnas.2026595118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Class-II fumarases (fumarate hydratase, FH) are dual-targeted enzymes occurring in the mitochondria and cytosol of all eukaryotes. They are essential components in the DNA damage response (DDR) and, more specifically, protect cells from DNA double-strand breaks. Similarly, the gram-positive bacterium Bacillus subtilis class-II fumarase, in addition to its role in the tricarboxylic acid cycle, participates in the DDR. Escherichia coli harbors three fumarase genes: class-I fumA and fumB and class-II fumC Notably, class-I fumarases show no sequence similarity to class-II fumarases and are of different evolutionary origin. Strikingly, here we show that E. coli fumarase functions are distributed between class-I fumarases, which participate in the DDR, and the class-II fumarase, which participates in respiration. In E. coli, we discover that the signaling molecule, alpha-ketoglutarate (α-KG), has a function, complementing DNA damage sensitivity of fum-null mutants. Excitingly, we identify the E. coli α-KG-dependent DNA repair enzyme AlkB as the target of this interplay of metabolite signaling. In addition to α-KG, fumarate (fumaric acid) is shown to affect DNA damage repair on two different levels, first by directly inhibiting the DNA damage repair enzyme AlkB demethylase activity, both in vitro and in vivo (countering α-KG). The second is a more global effect on transcription, because fum-null mutants exhibit a decrease in transcription of key DNA damage repair genes. Together, these results show evolutionary adaptable metabolic signaling of the DDR, in which fumarases and different metabolites are recruited regardless of the evolutionary enzyme class performing the function.
Collapse
|
8
|
Costanzo A, Ambrosini R, Parolini M, Caprioli M, Secomandi S, Rubolini D, Fusani L, Canoine V. Telomere shortening is associated with corticosterone stress response in adult barn swallows. Curr Zool 2021; 68:93-101. [PMID: 35169632 PMCID: PMC8836332 DOI: 10.1093/cz/zoab020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 03/03/2021] [Indexed: 12/19/2022] Open
Abstract
When vertebrates face stressful events, the hypothalamic–pituitary–adrenal (HPA) axis is activated, generating a rapid increase in circulating glucocorticoid (GC) stress hormones followed by a return to baseline levels. However, repeated activation of HPA axis may lead to increase in oxidative stress. One target of oxidative stress is telomeres, nucleoprotein complexes at the end of chromosomes that shorten at each cell division. The susceptibility of telomeres to oxidizing molecules has led to the hypothesis that increased GC levels boost telomere shortening, but studies on this link are scanty. We studied if, in barn swallows Hirundo rustica, changes in adult erythrocyte telomere length between 2 consecutive breeding seasons are related to corticosterone (CORT) (the main avian GC) stress response induced by a standard capture-restraint protocol. Within-individual telomere length did not significantly change between consecutive breeding seasons. Second-year individuals showed the highest increase in circulating CORT concentrations following restraint. Moreover, we found a decline in female stress response along the breeding season. In addition, telomere shortening covaried with the stress response: a delayed activation of the negative feedback loop terminating the stress response was associated with greater telomere attrition. Hence, among-individual variation in stress response may affect telomere dynamics.
Collapse
Affiliation(s)
- Alessandra Costanzo
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Roberto Ambrosini
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Marco Parolini
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Manuela Caprioli
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Simona Secomandi
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Diego Rubolini
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Leonida Fusani
- Department of Behavioral and Cognitive Biology, University of Vienna, Althanstr. 14, 1090 Vienna, Austria
- Konrad Lorenz Institute of Ethology, University of Veterinary Medicine Vienna, Savoyenstr. 1a, 1160 Vienna, Austria
| | - Virginie Canoine
- Department of Behavioral and Cognitive Biology, University of Vienna, Althanstr. 14, 1090 Vienna, Austria
| |
Collapse
|
9
|
Jermacz Ł, Kletkiewicz H, Krzyżyńska K, Klimiuk M, Kobak J. Does global warming intensify cost of antipredator reaction? A case study of freshwater amphipods. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 742:140474. [PMID: 32623164 DOI: 10.1016/j.scitotenv.2020.140474] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 06/18/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
Global warming is a worldwide phenomenon affecting the functioning of diverse ecosystems, including fresh waters. Temperature increase affects physiology and behaviour of ectotherms due to growing energetic demands necessary to sustain increased metabolic rate. Anti-predator responses may resemble temperature-induced changes in organisms, suggesting synergism between these factors. To check how temperature shapes physiological and behavioural responses of ectotherms to predation risk, we exposed amphipods: Dikerogammarus villosus and Gammarus jazdzewskii to fish kairomones at 10, 17 or 24 °C. Animals were placed in tanks where temperature was gradually adjusted to the desired test temperature and acclimated under such conditions for 3 subsequent days. Then they were exposed to the predator cue (the Eurasian perch kairomone) for 35 min to test their acute responses. We measured metabolic rate (as respiration), antioxidant defence (CAT: catalase activity, TAS: total antioxidant status), oxidative molecules (TOS: total oxidative status), oxidative damage (TBARS: thiobarbituric acid reactive substances) and behaviour (locomotor activity). Amphipods increased respiration with raising temperature and when exposed to predation risk (all temperatures). Only G. jazdzewskii exhibited increased TOS when exposed to 24 °C or to predation risk at all temperatures. Antioxidant defence increased with raising temperature (CAT, TAS) and decreased under predation risk (CAT). Cellular damage increased in G. jazdzewskii under predation risk at 10 and 24 °C, but raised temperature itself did not generate any damage. Amphipods reduced locomotor activity at 24 °C. Thus, at elevated temperatures, amphipods minimized their cellular damage at the cost of increased antioxidant defence and lower locomotor activity (potentially disadvantageous under higher energetic demands). Under predation risk, the performance of antioxidant systems was reduced, probably due to energy allocation into anti-predatory mechanisms, leading to increased cellular damage at suboptimum temperatures. Thus, negative consequences of elevated temperature for organisms may be amplified by changes in behaviour (compromising food acquisition) and non-consumptive predator effects.
Collapse
Affiliation(s)
- Łukasz Jermacz
- Nicolaus Copernicus University, Faculty of Biological and Veterinary Sciences, Department of Ecology and Biogeography, Lwowska 1, 87-100 Toruń, Poland.
| | - Hanna Kletkiewicz
- Nicolaus Copernicus University, Faculty of Biological and Veterinary Sciences, Department of Animal Physiology, Lwowska 1, 87-100 Toruń, Poland
| | - Katarzyna Krzyżyńska
- Nicolaus Copernicus University, Faculty of Biological and Veterinary Sciences, Department of Ecology and Biogeography, Lwowska 1, 87-100 Toruń, Poland
| | - Maciej Klimiuk
- Nicolaus Copernicus University, Faculty of Biological and Veterinary Sciences, Department of Animal Physiology, Lwowska 1, 87-100 Toruń, Poland
| | - Jarosław Kobak
- Nicolaus Copernicus University, Faculty of Biological and Veterinary Sciences, Department of Invertebrate Zoology and Parasitology, Lwowska 1, 87-100 Toruń, Poland
| |
Collapse
|
10
|
Van Deuren V, Plessers S, Robben J. Structural determinants of nucleobase modification recognition in the AlkB family of dioxygenases. DNA Repair (Amst) 2020; 96:102995. [PMID: 33069898 DOI: 10.1016/j.dnarep.2020.102995] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 09/30/2020] [Indexed: 01/29/2023]
Abstract
Iron-dependent dioxygenases of the AlkB protein family found in most organisms throughout the tree of life play a major role in oxidative dealkylation processes. Many of these enzymes have attracted the attention of researchers across different fields and have been subjected to thorough biochemical characterization because of their link to human health and disease. For example, several mammalian AlkB homologues are involved in the direct reversal of alkylation damage in DNA, while others have been shown to play a regulatory role in epigenetic or epitranscriptomic nucleic acid methylation or in post-translational modifications such as acetylation of actin filaments. These studies show that that divergence in amino acid sequence and structure leads to different characteristics and substrate specificities. In this review, we aim to summarize current insights in the structural features involved in the substrate selection of AlkB homologues, with focus on nucleic acid interactions.
Collapse
Affiliation(s)
- V Van Deuren
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, B-3001, Heverlee, Belgium
| | - S Plessers
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, B-3001, Heverlee, Belgium
| | - J Robben
- Department of Chemistry, KU Leuven, Celestijnenlaan 200G, B-3001, Heverlee, Belgium.
| |
Collapse
|
11
|
Jermacz Ł, Nowakowska A, Kletkiewicz H, Kobak J. Experimental evidence for the adaptive response of aquatic invertebrates to chronic predation risk. Oecologia 2020; 192:341-350. [PMID: 31919694 PMCID: PMC7002334 DOI: 10.1007/s00442-020-04594-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 01/02/2020] [Indexed: 12/29/2022]
Abstract
As acute stress induced by predation risk can generate significant oxidative damage, prey organisms are forced to balance their defence reaction and the cost of activating the cellular defence system. Stress tolerance differs significantly among species; therefore predator pressure indirectly shapes the community structure. To test adaptation abilities of amphipod crustaceans (Dikerogammarus villosus and Gammarus jazdzewskii) we exposed them to acute (35 min.) and chronic (1 or 7 days) predation risk (the Eurasian perch). We measured respiration (related to metabolic rate), cellular defence systems (antioxidant enzyme (catalase) activity and heat shock protein (Hsp70) concentration), and the level of oxidative damage (thiobarbituric acid reactive substances (TBARS) concentration). Both amphipods increased their respiration rate in the presence of predation cues, irrespective of the duration of their pre-exposure to danger. This increase in D. villosus was initiated more quickly (immediately vs. after 10 min. of the test) and lasted for a longer time (20 vs. 10 min.) than in G. jazdzewskii. However, only G. jazdzewskii after a short exposure to predation risk exhibited an increase in its catalase activity, Hsp70 concentration and oxidative damage. No changes in these parameters were exhibited by D. villosus or after a chronic exposure of G. jazdzewskii to predation cues. Our results show that prey organisms are able to reconfigure their physiology to maintain increased metabolic rate under prolonged predator pressure and, at the same time, reduce oxidative damage as well as costs related to anti-oxidant defence.
Collapse
Affiliation(s)
- Łukasz Jermacz
- Department of Invertebrate Zoology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland. .,Department of Ecology and Biogeography, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland.
| | - Anna Nowakowska
- Department of Animal Physiology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
| | - Hanna Kletkiewicz
- Department of Animal Physiology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
| | - Jarosław Kobak
- Department of Invertebrate Zoology, Faculty of Biology and Environmental Protection, Nicolaus Copernicus University, Lwowska 1, 87-100, Toruń, Poland
| |
Collapse
|
12
|
Casin KM, Fallica J, Mackowski N, Veenema RJ, Chan A, St Paul A, Zhu G, Bedja D, Biswal S, Kohr MJ. S-Nitrosoglutathione Reductase Is Essential for Protecting the Female Heart From Ischemia-Reperfusion Injury. Circ Res 2019; 123:1232-1243. [PMID: 30571462 DOI: 10.1161/circresaha.118.313956] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
RATIONALE Protein S-nitros(yl)ation (SNO) has been implicated as an essential mediator of nitric oxide-dependent cardioprotection. Compared with males, female hearts exhibit higher baseline levels of protein SNO and associated with this, reduced susceptibility to myocardial ischemia-reperfusion injury. Female hearts also exhibit enhanced S-nitrosoglutathione reductase (GSNO-R) activity, which would typically favor decreased SNO levels as GSNO-R mediates SNO catabolism. OBJECTIVE Because female hearts exhibit higher SNO levels, we hypothesized that GSNO-R is an essential component of sex-dependent cardioprotection in females. METHODS AND RESULTS Male and female wild-type mouse hearts were subjected to ex vivo ischemia-reperfusion injury with or without GSNO-R inhibition (N6022). Control female hearts exhibited enhanced functional recovery and decreased infarct size versus control males. Interestingly, GSNO-R inhibition reversed this sex disparity, significantly reducing injury in male hearts, and exacerbating injury in females. Similar results were obtained with male and female GSNO-R-/- hearts using ex vivo and in vivo models of ischemia-reperfusion injury. Assessment of SNO levels using SNO-resin assisted capture revealed an increase in total SNO levels with GSNO-R inhibition in males, whereas total SNO levels remained unchanged in females. However, we found that although GSNO-R inhibition significantly increased SNO at the cardioprotective Cys39 residue of nicotinamide adenine dinucleotide (NADH) dehydrogenase subunit 3 in males, SNO-NADH dehydrogenase subunit 3 levels were surprisingly reduced in N6022-treated female hearts. Because GSNO-R also acts as a formaldehyde dehydrogenase, we examined postischemic formaldehyde levels and found that they were nearly 2-fold higher in N6022-treated female hearts compared with nontreated hearts. Importantly, the mitochondrial aldehyde dehydrogenase 2 activator, Alda-1, rescued the phenotype in GSNO-R-/- female hearts, significantly reducing infarct size. CONCLUSIONS These striking findings point to GSNO-R as a critical sex-dependent mediator of myocardial protein SNO and formaldehyde levels and further suggest that different therapeutic strategies may be required to combat ischemic heart disease in males and females.
Collapse
Affiliation(s)
- Kevin M Casin
- From the Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD (K.M.C., J.F., N.M., R.J.V., A.C., A.S.P., S.B., M.J.K.)
| | - Jonathan Fallica
- From the Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD (K.M.C., J.F., N.M., R.J.V., A.C., A.S.P., S.B., M.J.K.)
| | - Nathan Mackowski
- From the Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD (K.M.C., J.F., N.M., R.J.V., A.C., A.S.P., S.B., M.J.K.)
| | - Ryne J Veenema
- From the Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD (K.M.C., J.F., N.M., R.J.V., A.C., A.S.P., S.B., M.J.K.)
| | - Ashley Chan
- From the Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD (K.M.C., J.F., N.M., R.J.V., A.C., A.S.P., S.B., M.J.K.)
| | - Amanda St Paul
- From the Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD (K.M.C., J.F., N.M., R.J.V., A.C., A.S.P., S.B., M.J.K.)
| | - Guangshuo Zhu
- Cardiology Division, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD (G.Z., D.B.)
| | - Djahida Bedja
- Cardiology Division, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD (G.Z., D.B.)
| | - Shyam Biswal
- From the Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD (K.M.C., J.F., N.M., R.J.V., A.C., A.S.P., S.B., M.J.K.)
| | - Mark J Kohr
- From the Department of Environmental Health and Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD (K.M.C., J.F., N.M., R.J.V., A.C., A.S.P., S.B., M.J.K.)
| |
Collapse
|
13
|
Identification of Flavin Mononucleotide as a Cell‐Active Artificial
N
6
‐Methyladenosine RNA Demethylase. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201900901] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
|
14
|
Xie LJ, Yang XT, Wang RL, Cheng HP, Li ZY, Liu L, Mao L, Wang M, Cheng L. Identification of Flavin Mononucleotide as a Cell-Active Artificial N 6 -Methyladenosine RNA Demethylase. Angew Chem Int Ed Engl 2019; 58:5028-5032. [PMID: 30756480 DOI: 10.1002/anie.201900901] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Indexed: 01/05/2023]
Abstract
N6 -Methyladenosine (m6 A) represents a common and highly dynamic modification in eukaryotic RNA that affects various cellular pathways. Natural dioxygenases such as FTO and ALKBH5 are enzymes that demethylate m6 A residues in mRNA. Herein, the first identification of a small-molecule modulator that functions as an artificial m6 A demethylase is reported. Flavin mononucleotide (FMN), the metabolite produced by riboflavin kinase, mediates substantial photochemical demethylation of m6 A residues of RNA in live cells. This study provides a new perspective to the understanding of demethylation of m6 A residues in mRNA and sheds light on the development of powerful small molecules as RNA demethylases and new probes for use in RNA biology.
Collapse
Affiliation(s)
- Li-Jun Xie
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Ti Yang
- BNLMS, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Rui-Li Wang
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hou-Ping Cheng
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi-Yan Li
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Li Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lanqun Mao
- BNLMS, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ming Wang
- BNLMS, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liang Cheng
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Molecular Recognition and Function, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.,Key Lab of Functional Molecular Engineering of Guangdong Province, South China University of Technology), Guangzhou, 510640, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
15
|
Devereaux ZJ, Zhu Y, Rodgers MT. Relative glycosidic bond stabilities of naturally occurring methylguanosines: 7-methylation is intrinsically activating. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2019; 25:16-29. [PMID: 30189754 DOI: 10.1177/1469066718798097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The frequency and diversity of posttranscriptional modifications add an additional layer of chemical complexity beyond canonical nucleic acid sequence. Methylations are particularly frequently occurring and often highly conserved throughout the kingdoms of life. However, the intricate functions of these modified nucleic acid constituents are often not fully understood. Systematic foundational research that reduces systems to their minimum constituents may aid in unraveling the complexities of nucleic acid biochemistry. Here, we examine the relative intrinsic N-glycosidic bond stabilities of guanosine and five naturally occurring methylguanosines (O2'-, 1-, 7-, N2,N2-di-, and N2,N2,O2'-trimethylguanosine) probed by energy-resolved collision-induced dissociation tandem mass spectrometry and complemented with quantum chemical calculations. Apparent glycosidic bond stability is generally found to increase with increasing methyl substitution (canonical < mono- < di- < trimethylated). Many biochemical transformations, including base excision repair mechanisms, involve protonation and/or noncovalent interactions to increase nucleobase leaving-group ability. The protonated gas-phase methylguanosines require less activation energy for glycosidic bond cleavage than their sodium cationized forms. However, methylation at the N7 position intrinsically weakens the glycosidic bond of 7-methylguanosine more significantly than subsequent cationization, and thus 7-methylguanosine is suggested to be under perpetually activated conditions. N7 methylation also alters the nucleoside geometric preferences relative to the other systems, including the nucleobase orientation in the neutral form, sugar puckering in the protonated form, and the preferred protonation and sodium cation binding sites. All of the methylated guanosines examined here are predicted to have proton affinities and gas-phase basicities that exceed that of canonical guanosine. Additionally, the proton affinity and gas-phase basicity trends exhibit a roughly inverse correlation with the apparent glycosidic bond stabilities.
Collapse
Affiliation(s)
| | - Y Zhu
- Department of Chemistry, Wayne State University, Detroit, USA
| | - M T Rodgers
- Department of Chemistry, Wayne State University, Detroit, USA
| |
Collapse
|
16
|
Kako K, Kim JD, Fukamizu A. Emerging impacts of biological methylation on genetic information. J Biochem 2019; 165:9-18. [PMID: 30219914 DOI: 10.1093/jb/mvy075] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 09/13/2018] [Indexed: 12/13/2022] Open
Abstract
The central dogma of molecular biology explains the fundamental flow of genetic information for life. Although genome sequence (DNA) itself is a static chemical signature, it includes multiple layers of information composed of mRNA, tRNA, rRNA and small RNAs, all of which are involved in protein synthesis and is passing from parents to offspring via DNA. Methylation is a biologically important modification, because DNA, RNAs and proteins, components of the central dogma, are methylated by a set of methyltransferases. Recent works focused on understanding a variety of biological methylation have shed light on new regulation of cellular functions. In this review, we briefly discuss some of those recent findings of methylation, including DNA, RNAs and proteins.
Collapse
Affiliation(s)
- Koichiro Kako
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan.,Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan
| | - Jun-Dal Kim
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan
| | - Akiyoshi Fukamizu
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan.,International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, Japan
| |
Collapse
|
17
|
Lindstedt BA, Finton MD, Porcellato D, Brandal LT. High frequency of hybrid Escherichia coli strains with combined Intestinal Pathogenic Escherichia coli (IPEC) and Extraintestinal Pathogenic Escherichia coli (ExPEC) virulence factors isolated from human faecal samples. BMC Infect Dis 2018; 18:544. [PMID: 30497396 PMCID: PMC6267907 DOI: 10.1186/s12879-018-3449-2] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 10/16/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Classification of pathogenic Escherichia coli (E. coli) has traditionally relied on detecting specific virulence associated genes (VAGs) or combinations thereof. For E. coli isolated from faecal samples, the presence of specific genes associated with different intestinal pathogenic pathovars will determine their classification and further course of action. However, the E. coli genome is not a static entity, and hybrid strains are emerging that cross the pathovar definitions. Hybrid strains may show gene contents previously associated with several distinct pathovars making the correct diagnostic classification difficult. We extended the analysis of routinely submitted faecal isolates to include known virulence associated genes that are usually not examined in faecal isolates to detect the frequency of possible hybrid strains. METHODS From September 2012 to February 2013, 168 faecal isolates of E. coli routinely submitted to the Norwegian Institute of Public Health (NIPH) from clinical microbiological laboratories throughout Norway were analysed for 33 VAGs using multiplex-PCR, including factors associated with extraintestinal pathogenic E. coli (ExPEC) strains. The strains were further typed by Multiple Locus Variable-Number Tandem-Repeat Analysis (MLVA), and the phylogenetic grouping was determined. One isolate from the study was selected for whole genome sequencing (WGS) with a combination of Oxford Nanopore's MinION and Illumina's MiSeq. RESULTS The analysis showed a surprisingly high number of strains carrying ExPEC associated VAGs and strains carrying a combination of both intestinal pathogenic E. coli (IPEC) and ExPEC VAGs. In particular, 93.5% (101/108) of isolates classified as belonging to an IPEC pathovar additionally carried ExPEC VAGs. WGS analysis of a selected hybrid strain revealed that it could, with present classification criteria, be classified as belonging to all of the Enteropathogenic Escherichia coli (EPEC), Uropathogenic Escherichia coli (UPEC), Neonatal meningitis Escherichia coli (NMEC) and Avian pathogenic Escherichia coli (APEC) pathovars. CONCLUSION Hybrid ExPEC/IPEC E. coli strains were found at a very high frequency in faecal samples and were in fact the predominant species present. A sequenced hybrid isolate was confirmed to be a cross-pathovar strain possessing recognised hallmarks of several pathovars, and a genome heavily influenced by horizontal gene transfer.
Collapse
Affiliation(s)
- Bjørn-Arne Lindstedt
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, N-1432, Ås, Norway.
| | - Misti D Finton
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, N-1432, Ås, Norway
| | - Davide Porcellato
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, P.O. Box 5003, N-1432, Ås, Norway
| | - Lin T Brandal
- Department of Zoonotic, Food- and Waterborne Infections, Norwegian Institute of Public Health, Oslo, Norway
| |
Collapse
|
18
|
Czerwińska J, Nowak M, Wojtczak P, Dziuban-Lech D, Cieśla JM, Kołata D, Gajewska B, Barańczyk-Kuźma A, Robinson AR, Shane HL, Gregg SQ, Rigatti LH, Yousefzadeh MJ, Gurkar AU, McGowan SJ, Kosicki K, Bednarek M, Zarakowska E, Gackowski D, Oliński R, Speina E, Niedernhofer LJ, Tudek B. ERCC1-deficient cells and mice are hypersensitive to lipid peroxidation. Free Radic Biol Med 2018; 124:79-96. [PMID: 29860127 PMCID: PMC6098728 DOI: 10.1016/j.freeradbiomed.2018.05.088] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 01/01/2023]
Abstract
Lipid peroxidation (LPO) products are relatively stable and abundant metabolites, which accumulate in tissues of mammals with aging, being able to modify all cellular nucleophiles, creating protein and DNA adducts including crosslinks. Here, we used cells and mice deficient in the ERCC1-XPF endonuclease required for nucleotide excision repair and the repair of DNA interstrand crosslinks to ask if specifically LPO-induced DNA damage contributes to loss of cell and tissue homeostasis. Ercc1-/- mouse embryonic fibroblasts were more sensitive than wild-type (WT) cells to the LPO products: 4-hydroxy-2-nonenal (HNE), crotonaldehyde and malondialdehyde. ERCC1-XPF hypomorphic mice were hypersensitive to CCl4 and a diet rich in polyunsaturated fatty acids, two potent inducers of endogenous LPO. To gain insight into the mechanism of how LPO influences DNA repair-deficient cells, we measured the impact of the major endogenous LPO product, HNE, on WT and Ercc1-/- cells. HNE inhibited proliferation, stimulated ROS and LPO formation, induced DNA base damage, strand breaks, error-prone translesion DNA synthesis and cellular senescence much more potently in Ercc1-/- cells than in DNA repair-competent control cells. HNE also deregulated base excision repair and energy production pathways. Our observations that ERCC1-deficient cells and mice are hypersensitive to LPO implicates LPO-induced DNA damage in contributing to cellular demise and tissue degeneration, notably even when the source of LPO is dietary polyunsaturated fats.
Collapse
Affiliation(s)
- Jolanta Czerwińska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
| | - Małgorzata Nowak
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Patrycja Wojtczak
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Dorota Dziuban-Lech
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
| | - Jarosław M Cieśla
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
| | - Daria Kołata
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Beata Gajewska
- Department of Biochemistry, Medical University of Warsaw, Warsaw, Poland.
| | | | - Andria R Robinson
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA.
| | - Hillary L Shane
- University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA.
| | - Siobhán Q Gregg
- University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA; Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Lora H Rigatti
- University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA.
| | - Matthew J Yousefzadeh
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, FL, USA.
| | - Aditi U Gurkar
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, FL, USA.
| | - Sara J McGowan
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, FL, USA.
| | - Konrad Kosicki
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Małgorzata Bednarek
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Ewelina Zarakowska
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland.
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland.
| | - Ryszard Oliński
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland.
| | - Elżbieta Speina
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
| | - Laura J Niedernhofer
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA; Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, FL, USA.
| | - Barbara Tudek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| |
Collapse
|
19
|
Wang Q, Wang G, Wang Y, Liu C, He X. Association of AlkB homolog 3 expression with tumor recurrence and unfavorable prognosis in hepatocellular carcinoma. J Gastroenterol Hepatol 2018; 33:1617-1625. [PMID: 29415318 DOI: 10.1111/jgh.14117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/13/2018] [Accepted: 01/29/2018] [Indexed: 01/05/2023]
Abstract
BACKGROUND AND AIM The mammalian AlkB homolog protein family has been reported to promote tumor cell invasion and metastasis of human cancer. However, the expression status and clinical significance of AlkB homolog 3 (ALKBH3) in hepatocellular carcinoma (HCC) have not been reported yet. METHODS In the present study, we investigated the protein expression of ALKBH3 by immunohistochemistry assay and evaluated its association with tumor progression, recurrence, and prognosis in 272 patients with HCC. In addition, we explored ALKBH3 function via gene overexpression and knockdown of ALKBH3. RESULTS AlkB homolog 3 was overexpressed in HCC compared with adjacent non-tumorous specimens. Moreover, ALKBH3 expression was closely related to tumor differentiation and tumor-node-metastasis stage. Interestingly, the ALKBH3 high expression in tumor tissues of HCC patients had more poor disease-free survival and overall survival than low-expression patients. Consistently, we found that knockdown of ALKBH3 inhibits HCC cell proliferation in vitro and xenograft tumor formation in vivo and overexpressing ALKBH3 showed the opposite results. ALKBH3 knockdown may inhibit cell proliferation, presumably through p21/p27-mediated cell-cycle arrest at G1 phase in human HCC. ALKBH3 may also play some role on chemosensitivity to certain genotoxic reagents, such as cisplatin (CDDP) and epirubicin. CONCLUSIONS These findings reveal an important role of ALKBH3 in HCC, indicating that ALKBH3 could be used as a new therapeutic target in future.
Collapse
Affiliation(s)
- Qian Wang
- Department of General Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Gang Wang
- Department of General Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Yi Wang
- Laboratory Animal Center, Fourth Military Medical University, Xi'an, China
| | - Chaoxu Liu
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Xianli He
- Department of General Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| |
Collapse
|
20
|
Chatterjee N, Walker GC. Mechanisms of DNA damage, repair, and mutagenesis. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2017; 58:235-263. [PMID: 28485537 PMCID: PMC5474181 DOI: 10.1002/em.22087] [Citation(s) in RCA: 997] [Impact Index Per Article: 142.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 03/16/2017] [Indexed: 05/08/2023]
Abstract
Living organisms are continuously exposed to a myriad of DNA damaging agents that can impact health and modulate disease-states. However, robust DNA repair and damage-bypass mechanisms faithfully protect the DNA by either removing or tolerating the damage to ensure an overall survival. Deviations in this fine-tuning are known to destabilize cellular metabolic homeostasis, as exemplified in diverse cancers where disruption or deregulation of DNA repair pathways results in genome instability. Because routinely used biological, physical and chemical agents impact human health, testing their genotoxicity and regulating their use have become important. In this introductory review, we will delineate mechanisms of DNA damage and the counteracting repair/tolerance pathways to provide insights into the molecular basis of genotoxicity in cells that lays the foundation for subsequent articles in this issue. Environ. Mol. Mutagen. 58:235-263, 2017. © 2017 Wiley Periodicals, Inc.
Collapse
|
21
|
Limbach PA, June Paulines M. Going global: the new era of mapping modifications in RNA. WILEY INTERDISCIPLINARY REVIEWS. RNA 2017; 8:10.1002/wrna.1367. [PMID: 27251302 PMCID: PMC5133204 DOI: 10.1002/wrna.1367] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Revised: 04/22/2016] [Accepted: 04/28/2016] [Indexed: 12/30/2022]
Abstract
The post-transcriptional modification of RNA by the addition of one or more chemical groups has been known for over 50 years. These chemical modifications, once thought to be static, are now being discovered to play key regulatory roles in gene expression. The advent of massive parallel sequencing of RNA (RNA-seq) now allows us to probe the complexity of cellular RNA and how chemically altering RNA structure expands the RNA vocabulary. Here we present an overview of the various strategies and technologies that are available to profile RNA chemical modifications at the cellular level. These strategies can be characterized as targeted and untargeted approaches: targeted strategies are developed for one single chemical modification while untargeted strategies are more broadly applicable to a range of such chemical changes. Key for all of these approaches is the ability to locate modifications within the RNA sequence. While most of these methods are built upon an RNA-Seq pipeline, alternative approaches based on mass spectrometry or conventional DNA sequencing retain value in the overall analysis process. We also look forward toward future opportunities and technologies that may expand the types of modifications that can be globally profiled. Given the ever increasing recognition that these RNA chemical modifications play important biological roles, a variety of methods, preferably orthogonal approaches, will be required to globally identify, validate and quantify RNA chemical modifications found in the transcriptome. WIREs RNA 2017, 8:e1367. doi: 10.1002/wrna.1367 For further resources related to this article, please visit the WIREs website.
Collapse
|
22
|
Abstract
The non-heme Fe enzymes are ubiquitous in nature and perform a wide range of functions involving O2 activation. These had been difficult to study relative to heme enzymes; however, spectroscopic methods that provide significant insight into the correlation of structure with function have now been developed. This Current Topics article summarizes both the molecular mechanism these enzymes use to control O2 activation in the presence of cosubstrates and the oxygen intermediates these reactions generate. Three types of O2 activation are observed. First, non-heme reactivity is shown to be different from heme chemistry where a low-spin FeIII-OOH non-heme intermediate directly reacts with substrate. Also, two subclasses of non-heme Fe enzymes generate high-spin FeIV═O intermediates that provide both σ and π frontier molecular orbitals that can control selectivity. Finally, for several subclasses of non-heme Fe enzymes, binding of the substrate to the FeII site leads to the one-electron reductive activation of O2 to an FeIII-superoxide capable of H atom abstraction and electrophilic attack.
Collapse
Affiliation(s)
- Edward I Solomon
- Department of Chemistry, Stanford University , Stanford, California 94305, United States.,SLAC National Accelerator Laboratory , Menlo Park, California 94025, United States
| | - Serra Goudarzi
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Kyle D Sutherlin
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| |
Collapse
|
23
|
Postal K, Maluf DF, Valdameri G, Rüdiger A, Hughes DL, de Sá EL, Ribeiro RR, de Souza EM, Soares JF, Nunes GG. Chemoprotective activity of mixed valence polyoxovanadates against diethylsulphate in E. coli cultures: insights from solution speciation studies. RSC Adv 2016. [DOI: 10.1039/c6ra15826a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Cell survival after treatment with dimethylsulphate in the presence of polyoxovanadates.
Collapse
Affiliation(s)
- K. Postal
- Departamento de Química
- Universidade Federal do Paraná
- 81530-900 – Curitiba-PR
- Brazil
| | - D. F. Maluf
- Departamento de Química
- Universidade Federal do Paraná
- 81530-900 – Curitiba-PR
- Brazil
| | - G. Valdameri
- Departamento de Bioquímica e Biologia Molecular
- Universidade Federal do Paraná
- 81530-900 – Curitiba-PR
- Brazil
| | - A. L. Rüdiger
- Departamento de Química
- Universidade Federal do Paraná
- 81530-900 – Curitiba-PR
- Brazil
| | - D. L. Hughes
- School of Chemistry
- University of East Anglia
- Norwich NR4 7TJ
- UK
| | - E. L. de Sá
- Departamento de Química
- Universidade Federal do Paraná
- 81530-900 – Curitiba-PR
- Brazil
| | - R. R. Ribeiro
- Departamento de Química
- Universidade Federal do Paraná
- 81530-900 – Curitiba-PR
- Brazil
| | - E. M. de Souza
- Departamento de Bioquímica e Biologia Molecular
- Universidade Federal do Paraná
- 81530-900 – Curitiba-PR
- Brazil
| | - J. F. Soares
- Departamento de Química
- Universidade Federal do Paraná
- 81530-900 – Curitiba-PR
- Brazil
| | - G. G. Nunes
- Departamento de Química
- Universidade Federal do Paraná
- 81530-900 – Curitiba-PR
- Brazil
| |
Collapse
|
24
|
Li F, Kennedy S, Hajian T, Gibson E, Seitova A, Xu C, Arrowsmith CH, Vedadi M. A Radioactivity-Based Assay for Screening Human m6A-RNA Methyltransferase, METTL3-METTL14 Complex, and Demethylase ALKBH5. ACTA ACUST UNITED AC 2015; 21:290-7. [PMID: 26701100 DOI: 10.1177/1087057115623264] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 11/30/2015] [Indexed: 11/15/2022]
Abstract
N(6)-methyladenosine (m(6)A) is the most common reversible internal modification in mammalian RNA. Changes in m(6)A levels have been implicated in a variety of cellular processes, including nuclear RNA export, control of protein translation, and protein splicing, and they have been linked to obesity, cancer, and other human diseases. METTL3 and METTL14 are N(6)-adenosine methyltransferases that work more efficiently in a stable METTL3-METTL14 heterodimer complex (METTL3-14). ALKBH5 is an m(6)A-RNA demethylase that belongs to the AlkB family of dioxygenases. We report the development of radioactivity-based assays for kinetic characterization of m(6)A-RNA modifications by METTL3-14 complex and ALKBH5 and provide optimal assay conditions suitable for screening for ligands in a 384-well format with Z' factors of 0.78 and 0.77, respectively.
Collapse
Affiliation(s)
- Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Steven Kennedy
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Taraneh Hajian
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Elisa Gibson
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Alma Seitova
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Chao Xu
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
25
|
Abstract
Hydroxylation is an emerging modification generally catalyzed by a family of ∼70 enzymes that are dependent on oxygen, Fe(II), ascorbate, and the Kreb's cycle intermediate 2-oxoglutarate (2OG). These "2OG oxygenases" sit at the intersection of nutrient availability and metabolism where they have the potential to regulate gene expression and growth in response to changes in co-factor abundance. Characterized 2OG oxygenases regulate fundamental cellular processes by catalyzing the hydroxylation or demethylation (via hydroxylation) of DNA, RNA, or protein. As such they have been implicated in various syndromes and diseases, but particularly cancer. In this review we discuss the emerging role of 2OG oxygenases in gene expression control, examine the regulation of these unique enzymes by nutrient availability and metabolic intermediates, and describe these properties in relation to the expanding role of these enzymes in cancer.
Collapse
|
26
|
Fedeles BI, Singh V, Delaney JC, Li D, Essigmann JM. The AlkB Family of Fe(II)/α-Ketoglutarate-dependent Dioxygenases: Repairing Nucleic Acid Alkylation Damage and Beyond. J Biol Chem 2015; 290:20734-20742. [PMID: 26152727 DOI: 10.1074/jbc.r115.656462] [Citation(s) in RCA: 272] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The AlkB family of Fe(II)- and α-ketoglutarate-dependent dioxygenases is a class of ubiquitous direct reversal DNA repair enzymes that remove alkyl adducts from nucleobases by oxidative dealkylation. The prototypical and homonymous family member is an Escherichia coli "adaptive response" protein that protects the bacterial genome against alkylation damage. AlkB has a wide variety of substrates, including monoalkyl and exocyclic bridged adducts. Nine mammalian AlkB homologs exist (ALKBH1-8, FTO), but only a subset functions as DNA/RNA repair enzymes. This minireview presents an overview of the AlkB proteins including recent data on homologs, structural features, substrate specificities, and experimental strategies for studying DNA repair by AlkB family proteins.
Collapse
Affiliation(s)
- Bogdan I Fedeles
- Departments of Chemistry and Biological Engineering and the Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Vipender Singh
- Departments of Chemistry and Biological Engineering and the Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - James C Delaney
- Departments of Chemistry and Biological Engineering and the Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139
| | - Deyu Li
- Departments of Chemistry and Biological Engineering and the Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139.
| | - John M Essigmann
- Departments of Chemistry and Biological Engineering and the Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139.
| |
Collapse
|
27
|
Müller TA, Hausinger RP. AlkB and Its Homologues – DNA Repair and Beyond. 2-OXOGLUTARATE-DEPENDENT OXYGENASES 2015. [DOI: 10.1039/9781782621959-00246] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
AlkB is an Fe(ii)/2-oxoglutarate-dependent dioxygenase that is part of the adaptive response to alkylating agents in Escherichia coli. AlkB hydroxylates a wide variety of alkylated DNA bases producing unstable intermediates which decompose to restore the non-alkylated bases. Homologues exist in other bacteria, metazoa (e.g. nine in humans), plants and viruses, but not in archaea, with many catalysing the same oxidative demethylation reactions as for AlkB. The mammalian enzymes Alkbh2 and Alkbh3 catalyse direct DNA repair, Alkbh5 and FTO (Alkbh9) are RNA demethylases, and Alkbh8 is used to synthesize a tRNA, while the remaining mammalian homologues have alternative functions. Alkbh1 is an apurinic/apyrimidinic lyase in addition to exhibiting demethylase activities, but no clear role for the Alkbh1 protein has emerged. Alkbh4 is involved in cell division and potentially demethylates actin, whereas the mitochondrial homologue Alkbh7 has a role in obesity; however, no enzymatic activity has been linked to Alkbh4 or Alkbh7. Here, we discuss AlkB as the ‘archetype’ of this class of hydroxylases, compare it to Alkbh2 and Alkbh3, and then briefly review the diverse (and largely unknown) functions of Alkbh1, Alkbh4, Alkbh6 and Alkbh7. Alkbh5, Alkbh8 and Alkbh9 (FTO) are described separately.
Collapse
Affiliation(s)
- Tina A. Müller
- Department of Microbiology and Molecular Genetics, Michigan State University East Lansing MI 48824 USA
| | - Robert P. Hausinger
- Department of Microbiology and Molecular Genetics, Michigan State University East Lansing MI 48824 USA
- Department of Biochemistry and Molecular Biology, Michigan State University East Lansing MI 48824 USA
| |
Collapse
|
28
|
Horita S, Scotti JS, Thinnes C, Mottaghi-Taromsari YS, Thalhammer A, Ge W, Aik W, Loenarz C, Schofield CJ, McDonough MA. Structure of the ribosomal oxygenase OGFOD1 provides insights into the regio- and stereoselectivity of prolyl hydroxylases. Structure 2015; 23:639-52. [PMID: 25728928 PMCID: PMC4396695 DOI: 10.1016/j.str.2015.01.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 01/13/2015] [Accepted: 01/21/2015] [Indexed: 01/24/2023]
Abstract
Post-translational ribosomal protein hydroxylation is catalyzed by 2-oxoglutarate (2OG) and ferrous iron dependent oxygenases, and occurs in prokaryotes and eukaryotes. OGFOD1 catalyzes trans-3 prolyl hydroxylation at Pro62 of the small ribosomal subunit protein uS12 (RPS23) and is conserved from yeasts to humans. We describe crystal structures of the human uS12 prolyl 3-hydroxylase (OGFOD1) and its homolog from Saccharomyces cerevisiae (Tpa1p): OGFOD1 in complex with the broad-spectrum 2OG oxygenase inhibitors; N-oxalylglycine (NOG) and pyridine-2,4-dicarboxylate (2,4-PDCA) to 2.1 and 2.6 Å resolution, respectively; and Tpa1p in complex with NOG, 2,4-PDCA, and 1-chloro-4-hydroxyisoquinoline-3-carbonylglycine (a more selective prolyl hydroxylase inhibitor) to 2.8, 1.9, and 1.9 Å resolution, respectively. Comparison of uS12 hydroxylase structures with those of other prolyl hydroxylases, including the human hypoxia-inducible factor (HIF) prolyl hydroxylases (PHDs), reveals differences between the prolyl 3- and prolyl 4-hydroxylase active sites, which can be exploited for developing selective inhibitors of the different subfamilies.
Collapse
Affiliation(s)
- Shoichiro Horita
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK; Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3PT, UK
| | - John S Scotti
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Cyrille Thinnes
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Yousef S Mottaghi-Taromsari
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Armin Thalhammer
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Wei Ge
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - WeiShen Aik
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Christoph Loenarz
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
| | - Michael A McDonough
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford OX1 3TA, UK.
| |
Collapse
|
29
|
Huang Y, Yan J, Li Q, Li J, Gong S, Zhou H, Gan J, Jiang H, Jia GF, Luo C, Yang CG. Meclofenamic acid selectively inhibits FTO demethylation of m6A over ALKBH5. Nucleic Acids Res 2015; 43:373-84. [PMID: 25452335 PMCID: PMC4288171 DOI: 10.1093/nar/gku1276] [Citation(s) in RCA: 446] [Impact Index Per Article: 49.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2014] [Revised: 11/18/2014] [Accepted: 11/20/2014] [Indexed: 12/21/2022] Open
Abstract
Two human demethylases, the fat mass and obesity-associated (FTO) enzyme and ALKBH5, oxidatively demethylate abundant N(6)-methyladenosine (m(6)A) residues in mRNA. Achieving a method for selective inhibition of FTO over ALKBH5 remains a challenge, however. Here, we have identified meclofenamic acid (MA) as a highly selective inhibitor of FTO. MA is a non-steroidal, anti-inflammatory drug that mechanistic studies indicate competes with FTO binding for the m(6)A-containing nucleic acid. The structure of FTO/MA has revealed much about the inhibitory function of FTO. Our newfound understanding, revealed herein, of the part of the nucleotide recognition lid (NRL) in FTO, for example, has helped elucidate the principles behind the selectivity of FTO over ALKBH5. Treatment of HeLa cells with the ethyl ester form of MA (MA2) has led to elevated levels of m(6)A modification in mRNA. Our collective results highlight the development of functional probes of the FTO enzyme that will (i) enable future biological studies and (ii) pave the way for the rational design of potent and specific inhibitors of FTO for use in medicine.
Collapse
Affiliation(s)
- Yue Huang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jingli Yan
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Qi Li
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jiafei Li
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Shouzhe Gong
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Hu Zhou
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jianhua Gan
- School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Hualiang Jiang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Gui-Fang Jia
- Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Cheng Luo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Cai-Guang Yang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| |
Collapse
|
30
|
Shivange G, Kodipelli N, Monisha M, Anindya R. A role for Saccharomyces cerevisiae Tpa1 protein in direct alkylation repair. J Biol Chem 2014; 289:35939-52. [PMID: 25381260 DOI: 10.1074/jbc.m114.590216] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Alkylating agents induce cytotoxic DNA base adducts. In this work, we provide evidence to suggest, for the first time, that Saccharomyces cerevisiae Tpa1 protein is involved in DNA alkylation repair. Little is known about Tpa1 as a repair protein beyond the initial observation from a high-throughput analysis indicating that deletion of TPA1 causes methyl methane sulfonate sensitivity in S. cerevisiae. Using purified Tpa1, we demonstrate that Tpa1 repairs both single- and double-stranded methylated DNA. Tpa1 is a member of the Fe(II) and 2-oxoglutarate-dependent dioxygenase family, and we show that mutation of the amino acid residues involved in cofactor binding abolishes the Tpa1 DNA repair activity. Deletion of TPA1 along with the base excision repair pathway DNA glycosylase MAG1 renders the tpa1Δmag1Δ double mutant highly susceptible to methylation-induced toxicity. We further demonstrate that the trans-lesion synthesis DNA polymerase Polζ (REV3) plays a key role in tolerating DNA methyl-base lesions and that tpa1Δmag1revΔ3 triple mutant is extremely susceptible to methylation-induced toxicity. Our results indicate a synergism between the base excision repair pathway and direct alkylation repair by Tpa1 in S. cerevisiae. We conclude that Tpa1 is a hitherto unidentified DNA repair protein in yeast and that it plays a crucial role in reverting alkylated DNA base lesions and cytotoxicity.
Collapse
Affiliation(s)
- Gururaj Shivange
- From the Department of Biotechnology, Indian Institute of Technology Hyderabad, Ordnance Factory Estate, Yeddumailaram 502205, Hyderabad, India
| | - Naveena Kodipelli
- From the Department of Biotechnology, Indian Institute of Technology Hyderabad, Ordnance Factory Estate, Yeddumailaram 502205, Hyderabad, India
| | - Mohan Monisha
- From the Department of Biotechnology, Indian Institute of Technology Hyderabad, Ordnance Factory Estate, Yeddumailaram 502205, Hyderabad, India
| | - Roy Anindya
- From the Department of Biotechnology, Indian Institute of Technology Hyderabad, Ordnance Factory Estate, Yeddumailaram 502205, Hyderabad, India
| |
Collapse
|
31
|
Shivange G, Kodipelli N, Anindya R. A nonradioactive restriction enzyme-mediated assay to detect DNA repair by Fe(II)/2-oxoglutarate-dependent dioxygenase. Anal Biochem 2014; 465:35-7. [PMID: 25062850 DOI: 10.1016/j.ab.2014.07.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 07/01/2014] [Accepted: 07/03/2014] [Indexed: 11/25/2022]
Abstract
The Escherichia coli DNA repair enzyme AlkB belongs to the Fe(II)/2-oxoglutarate-dependent dioxygenase family. It removes methyl groups from 1-methyl adenine (1-meA) and 3-methyl cytosine (3-meC) lesions present in single-stranded DNA by oxidative decarboxylation. In the current article, we describe an in vitro assay that permits rapid detection of AlkB activity. To achieve this, we generated methylated oligonucleotide using methyl methanesulfonate and then monitored DNA repair using a methylation-sensitive restriction enzyme and novel agarose gel electrophoresis system capable of resolving small oligonucleotides. Our approach overcomes several drawbacks of NAD(+)-dependent formaldehyde dehydrogenase-coupled assay and radioisotope-based assay for determining AlkB DNA repair activity.
Collapse
Affiliation(s)
- Gururaj Shivange
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Ordnance Factory Estate, Yeddumailaram 502205, Hyderabad, India
| | - Naveena Kodipelli
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Ordnance Factory Estate, Yeddumailaram 502205, Hyderabad, India
| | - Roy Anindya
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Ordnance Factory Estate, Yeddumailaram 502205, Hyderabad, India.
| |
Collapse
|
32
|
Mechanisms and consequences of developmental acceleration in tadpoles responding to pond drying. PLoS One 2013; 8:e84266. [PMID: 24358352 PMCID: PMC3865288 DOI: 10.1371/journal.pone.0084266] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 11/21/2013] [Indexed: 11/19/2022] Open
Abstract
Many amphibian species exploit temporary or even ephemeral aquatic habitats for reproduction by maximising larval growth under benign conditions but accelerating development to rapidly undergo metamorphosis when at risk of desiccation from pond drying. Here we determine mechanisms enabling developmental acceleration in response to decreased water levels in western spadefoot toad tadpoles (Pelobates cultripes), a species with long larval periods and large size at metamorphosis but with a high degree of developmental plasticity. We found that P. cultripes tadpoles can shorten their larval period by an average of 30% in response to reduced water levels. We show that such developmental acceleration was achieved via increased endogenous levels of corticosterone and thyroid hormone, which act synergistically to achieve metamorphosis, and also by increased expression of the thyroid hormone receptor TRΒ, which increases tissue sensitivity and responsivity to thyroid hormone. However, developmental acceleration had morphological and physiological consequences. In addition to resulting in smaller juveniles with proportionately shorter limbs, tadpoles exposed to decreased water levels incurred oxidative stress, indicated by increased activity of the antioxidant enzymes catalase, superoxide dismutase, and glutathione peroxidase. Such increases were apparently sufficient to neutralise the oxidative damage caused by presumed increased metabolic activity. Thus, developmental acceleration allows spadefoot toad tadpoles to evade drying ponds, but it comes at the expense of reduced size at metamorphosis and increased oxidative stress.
Collapse
|
33
|
Lazcano A. Planetary change and biochemical adaptation: molecular evolution of corrinoid and heme biosyntheses. Hematology 2013; 17 Suppl 1:S7-10. [DOI: 10.1179/102453312x13336169155015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
|
34
|
Saletore Y, Chen-Kiang S, Mason CE. Novel RNA regulatory mechanisms revealed in the epitranscriptome. RNA Biol 2013; 10:342-6. [PMID: 23434792 PMCID: PMC3672275 DOI: 10.4161/rna.23812] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Methyl-6-adenosine (m (6)A) has been hypothesized to exist since the 1970s, (1) but little has been known about the specific RNAs, or sites within them, that are affected by this RNA modification. Here, we report that recent work has shown RNA modifications like m (6)A, collectively called the "epitranscriptome," are a pervasive feature of mammalian cells and likely play a role in development and disease. An enrichment of m (6)A near the last CDS of thousands of genes has implicated m (6)A in transcript processing, translational regulation and potentially a mechanism for regulating miRNA maturation. Also, because the sites of m (6)A show strong evolutionary conservation and have been replicated in nearly identical sites between mouse and human, strong evolutionary pressures are likely being maintained for this mark. (2)(,) (3) Finally, we note that m (6)A is one of over 100 modifications of RNA that have been reported, (4) and with the combination of high-throughput, next-generation sequencing (NGS) techniques, immunoprecipitation with appropriate antibodies and splicing-aware peak-finding, the dynamics of the epitranscriptome can now be mapped and characterized to discern their specific cellular roles.
Collapse
Affiliation(s)
- Yogesh Saletore
- Department of Physiology and Biophysics; Weill Cornell Medical College; New York, NY USA; The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine; Weill Cornell Medical College; New York, NY USA; Tri-Institutional Training Program in Computational Biology and Medicine; New York, NY USA
| | | | | |
Collapse
|
35
|
Abstract
Endogenous and exogenous factors constantly challenge cellular DNA, generating cytotoxic and/or mutagenic DNA adducts. As a result, organisms have evolved different mechanisms to defend against the deleterious effects of DNA damage. Among these diverse repair pathways, direct DNA-repair systems provide cells with simple yet efficient solutions to reverse covalent DNA adducts. In this review, we focus on recent advances in the field of direct DNA repair, namely, photolyase-, alkyltransferase-, and dioxygenase-mediated repair processes. We present specific examples to describe new findings of known enzymes and appealing discoveries of new proteins. At the end of this article, we also briefly discuss the influence of direct DNA repair on other fields of biology and its implication on the discovery of new biology.
Collapse
Affiliation(s)
- Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | | |
Collapse
|
36
|
Niu Y, Zhao X, Wu YS, Li MM, Wang XJ, Yang YG. N6-methyl-adenosine (m6A) in RNA: an old modification with a novel epigenetic function. GENOMICS PROTEOMICS & BIOINFORMATICS 2012; 11:8-17. [PMID: 23453015 PMCID: PMC4357660 DOI: 10.1016/j.gpb.2012.12.002] [Citation(s) in RCA: 318] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Revised: 12/10/2012] [Accepted: 12/11/2012] [Indexed: 12/02/2022]
Abstract
N6-methyl-adenosine (m6A) is one of the most common and abundant modifications on RNA molecules present in eukaryotes. However, the biological significance of m6A methylation remains largely unknown. Several independent lines of evidence suggest that the dynamic regulation of m6A may have a profound impact on gene expression regulation. The m6A modification is catalyzed by an unidentified methyltransferase complex containing at least one subunit methyltransferase like 3 (METTL3). m6A modification on messenger RNAs (mRNAs) mainly occurs in the exonic regions and 3′-untranslated region (3′-UTR) as revealed by high-throughput m6A-seq. One significant advance in m6A research is the recent discovery of the first two m6A RNA demethylases fat mass and obesity-associated (FTO) gene and ALKBH5, which catalyze m6A demethylation in an α-ketoglutarate (α-KG)- and Fe2+-dependent manner. Recent studies in model organisms demonstrate that METTL3, FTO and ALKBH5 play important roles in many biological processes, ranging from development and metabolism to fertility. Moreover, perturbation of activities of these enzymes leads to the disturbed expression of thousands of genes at the cellular level, implicating a regulatory role of m6A in RNA metabolism. Given the vital roles of DNA and histone methylations in epigenetic regulation of basic life processes in mammals, the dynamic and reversible chemical m6A modification on RNA may also serve as a novel epigenetic marker of profound biological significances.
Collapse
Affiliation(s)
- Yamei Niu
- Disease Genomics and Individualized Medicine Laboratory, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | | | | | | | | | | |
Collapse
|
37
|
Mello LV, Rigden DJ. A new family of bacterial DNA repair proteins annotated by the integration of non-homology, distant homology and structural bioinformatic methods. FEBS Lett 2012; 586:3908-13. [DOI: 10.1016/j.febslet.2012.09.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Revised: 09/13/2012] [Accepted: 09/14/2012] [Indexed: 10/27/2022]
|
38
|
Franchini DM, Schmitz KM, Petersen-Mahrt SK. 5-Methylcytosine DNA demethylation: more than losing a methyl group. Annu Rev Genet 2012; 46:419-41. [PMID: 22974304 DOI: 10.1146/annurev-genet-110711-155451] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Demethylation of 5-methylcytosine in DNA is integral to the maintenance of an intact epigenome. The balance between the presence or absence of 5-methylcytosine determines many physiological aspects of cell metabolism, with a turnover that can be measured in minutes to years. Biochemically, addition of the methyl group is shared among all living kingdoms and has been well characterized, whereas the removal or reversion of this mark seems diverse and much less understood. Here, we present a summary of how DNA demethylation can be initiated directly, utilizing the ten-eleven translocation (TET) family of proteins, activation-induced deaminase (AID), or other DNA modifying enzymes, or indirectly, via transcription, RNA metabolism, or DNA repair; how intermediates in those pathways are substrates of the DNA repair machinery; and how demethylation pathways are linked and possibly balanced, avoiding mutations.
Collapse
Affiliation(s)
- Don-Marc Franchini
- DNA Editing in Immunity and Epigenetics, IFOM-Fondazione Istituto FIRC di Oncologia Molecolare, 20139 Milano, Italy.
| | | | | |
Collapse
|
39
|
Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons. Cell 2012; 149:1635-46. [PMID: 22608085 DOI: 10.1016/j.cell.2012.05.003] [Citation(s) in RCA: 2845] [Impact Index Per Article: 237.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Revised: 03/15/2012] [Accepted: 03/27/2012] [Indexed: 02/07/2023]
Abstract
Methylation of the N(6) position of adenosine (m(6)A) is a posttranscriptional modification of RNA with poorly understood prevalence and physiological relevance. The recent discovery that FTO, an obesity risk gene, encodes an m(6)A demethylase implicates m(6)A as an important regulator of physiological processes. Here, we present a method for transcriptome-wide m(6)A localization, which combines m(6)A-specific methylated RNA immunoprecipitation with next-generation sequencing (MeRIP-Seq). We use this method to identify mRNAs of 7,676 mammalian genes that contain m(6)A, indicating that m(6)A is a common base modification of mRNA. The m(6)A modification exhibits tissue-specific regulation and is markedly increased throughout brain development. We find that m(6)A sites are enriched near stop codons and in 3' UTRs, and we uncover an association between m(6)A residues and microRNA-binding sites within 3' UTRs. These findings provide a resource for identifying transcripts that are substrates for adenosine methylation and reveal insights into the epigenetic regulation of the mammalian transcriptome.
Collapse
|
40
|
Krylova SM, Koshkin V, Bagg E, Schofield CJ, Krylov SN. Mechanistic studies on the application of DNA aptamers as inhibitors of 2-oxoglutarate-dependent oxygenases. J Med Chem 2012; 55:3546-52. [PMID: 22471443 PMCID: PMC4681096 DOI: 10.1021/jm300243h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Escherichia coli (E. coli) AlkB protein and its functional human homologues belong to a subfamily of 2-oxoglutarate (2OG) dependent oxygenases (2OG oxygenases for simplicity) that enable the repair of cytotoxic methylation damage in nucleic acids and that catalyze t-RNA oxidations. DNA alkylation is a major mechanism of action for cytotoxic anticancer drugs. Thus, the inhibition of oxidative demethylation, catalyzed by these enzymes, has the potential to improve the efficacy of chemotherapies. Here we report that oligonucleotide aptamers constitute a new class of potent inhibitors of 2OG oxygenases. DNA aptamers can selectively bind to AlkB, with nanomolar affinity, and efficiently inhibit catalysis. The mechanism of inhibition was studied by capillary electrophoresis (CE) with laser-induced fluorescence (LIF) detection. Inhibition constants of the aptamers were determined and shown to correlate well with K(d) values. The results of kinetic analyses imply that the aptamers bind AlkB away from the active site. Our findings should stimulate the development of oligonucleotide aptamers for human homologues of AlkB and further their study as potential enhancers of chemotherapy efficiency.
Collapse
Affiliation(s)
- Svetlana M. Krylova
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Vasilij Koshkin
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, M3J 1P3, Canada
| | - Eleanor Bagg
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, OX1 3TA, United Kingdom
| | - Christopher J. Schofield
- Department of Chemistry and the Oxford Centre for Integrative Systems Biology, University of Oxford, Oxford, OX1 3TA, United Kingdom
| | - Sergey N. Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, M3J 1P3, Canada
| |
Collapse
|
41
|
Pastore C, Topalidou I, Forouhar F, Yan AC, Levy M, Hunt JF. Crystal structure and RNA binding properties of the RNA recognition motif (RRM) and AlkB domains in human AlkB homolog 8 (ABH8), an enzyme catalyzing tRNA hypermodification. J Biol Chem 2011; 287:2130-43. [PMID: 22065580 DOI: 10.1074/jbc.m111.286187] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Humans express nine paralogs of the bacterial DNA repair enzyme AlkB, an iron/2-oxoglutarate-dependent dioxygenase that reverses alkylation damage to nucleobases. The biochemical and physiological roles of these paralogs remain largely uncharacterized, hampering insight into the evolutionary expansion of the AlkB family. However, AlkB homolog 8 (ABH8), which contains RNA recognition motif (RRM) and methyltransferase domains flanking its AlkB domain, recently was demonstrated to hypermodify the anticodon loops in some tRNAs. To deepen understanding of this activity, we performed physiological and biophysical studies of ABH8. Using GFP fusions, we demonstrate that expression of the Caenorhabditis elegans ABH8 ortholog is widespread in larvae but restricted to a small number of neurons in adults, suggesting that its function becomes more specialized during development. In vitro RNA binding studies on several human ABH8 constructs indicate that binding affinity is enhanced by a basic α-helix at the N terminus of the RRM domain. The 3.0-Å-resolution crystal structure of a construct comprising the RRM and AlkB domains shows disordered loops flanking the active site in the AlkB domain and a unique structural Zn(II)-binding site at its C terminus. Although the catalytic iron center is exposed to solvent, the 2-oxoglutarate co-substrate likely adopts an inactive conformation in the absence of tRNA substrate, which probably inhibits uncoupled free radical generation. A conformational change in the active site coupled to a disorder-to-order transition in the flanking protein segments likely controls ABH8 catalytic activity and tRNA binding specificity. These results provide insight into the functional and structural adaptations underlying evolutionary diversification of AlkB domains.
Collapse
Affiliation(s)
- Chiara Pastore
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | | | | | | | | | | |
Collapse
|
42
|
Korvald H, Mølstad Moe AM, Cederkvist FH, Thiede B, Laerdahl JK, Bjørås M, Alseth I. Schizosaccharomyces pombe Ofd2 is a nuclear 2-oxoglutarate and iron dependent dioxygenase interacting with histones. PLoS One 2011; 6:e25188. [PMID: 21949882 PMCID: PMC3175000 DOI: 10.1371/journal.pone.0025188] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 08/29/2011] [Indexed: 11/18/2022] Open
Abstract
2-oxoglutarate (2OG) dependent dioxygenases are ubiquitous iron containing enzymes that couple substrate oxidation to the conversion of 2OG to succinate and carbon dioxide. They participate in a wide range of biological processes including collagen biosynthesis, fatty acid metabolism, hypoxic sensing and demethylation of nucleic acids and histones. Although substantial progress has been made in elucidating their function, the role of many 2OG dioxygenases remains enigmatic. Here we have studied the 2OG and iron (Fe(II)) dependent dioxygenase Ofd2 in Schizosaccharomyces pombe, a member of the AlkB subfamily of dioxygenases. We show that decarboxylation of 2OG by recombinant Ofd2 is dependent on Fe(II) and a histidine residue predicted to be involved in Fe(II) coordination. The decarboxylase activity of Ofd2 is stimulated by histones, and H2A has the strongest effect. Ofd2 interacts with all four core histones, however, only very weakly with H4. Our results define a new subclass of AlkB proteins interacting with histones, which also might comprise some of the human AlkB homologs with unknown function.
Collapse
Affiliation(s)
- Hanne Korvald
- Department of Microbiology, Oslo University Hospital HF Rikshospitalet, Oslo, Norway
- Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo, Oslo, Norway
| | - Anne Margrethe Mølstad Moe
- Department of Microbiology, Oslo University Hospital HF Rikshospitalet, Oslo, Norway
- Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo, Oslo, Norway
| | - F. Henning Cederkvist
- Department of Microbiology, Oslo University Hospital HF Rikshospitalet, Oslo, Norway
- Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo, Oslo, Norway
- Department of Medical Biochemistry, University of Oslo, Oslo, Norway
| | - Bernd Thiede
- The Biotechnology Centre of Oslo, University of Oslo, Oslo, Norway
| | - Jon K. Laerdahl
- Department of Microbiology, Oslo University Hospital HF Rikshospitalet, Oslo, Norway
- Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo, Oslo, Norway
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital HF Rikshospitalet, Oslo, Norway
- Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo, Oslo, Norway
- Department of Medical Biochemistry, University of Oslo, Oslo, Norway
| | - Ingrun Alseth
- Department of Microbiology, Oslo University Hospital HF Rikshospitalet, Oslo, Norway
- Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo, Oslo, Norway
- * E-mail:
| |
Collapse
|
43
|
Bjørnstad L, Zoppellaro G, Tomter A, Falnes P, Andersson K. Spectroscopic and magnetic studies of wild-type and mutant forms of the Fe(II)- and 2-oxoglutarate-dependent decarboxylase ALKBH4. Biochem J 2011; 434:391-8. [PMID: 21166655 PMCID: PMC3048578 DOI: 10.1042/bj20101667] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 12/14/2010] [Accepted: 12/20/2010] [Indexed: 11/24/2022]
Abstract
The Fe(II)/2OG (2-oxoglutarate)-dependent dioxygenase superfamily comprises proteins that couple substrate oxidation to decarboxylation of 2OG to succinate. A member of this class of mononuclear non-haem Fe proteins is the Escherichia coli DNA/RNA repair enzyme AlkB. In the present work, we describe the magnetic and optical properties of the yet uncharacterized human ALKBH4 (AlkB homologue). Through EPR and UV-visible spectroscopy studies, we address the Fe-binding environment of the proposed catalytic centre of wild-type ALKBH4 and an Fe(II)-binding mutant. We could observe a novel unusual Fe(III) high-spin EPR-active species in the presence of sulfide with a g(max) of 8.2. The Fe(II) site was probed with NO. An intact histidine-carboxylate site is necessary for productive Fe binding. We also report the presence of a unique cysteine-rich motif conserved in the N-terminus of ALKBH4 orthologues, and investigate its possible Fe-binding ability. Furthermore, we show that recombinant ALKBH4 mediates decarboxylation of 2OG in absence of primary substrate. This activity is dependent on Fe as well as on residues predicted to be involved in Fe(II) co-ordination. The present results demonstrate that ALKBH4 represents an active Fe(II)/2OG-dependent decarboxylase and suggest that the cysteine cluster is involved in processes other than Fe co-ordination.
Collapse
Key Words
- alkb
- alkb homologue (alkbh4)
- epr
- non-haem fe
- uv–visible spectroscopy
- alkbh, alkb homologue
- fto, fat mass and obesity-associated protein
- gst, glutathione transferase
- icp-aep, inductively coupled plasma atomic emission spectroscopy
- ipns, isopenicillin n synthase
- iptg, isopropyl β-d-thiogalactopyranoside
- mv•+, methyl viologen radical cation
- 2og, 2-oxoglutarate
- pah, phenylalanine hydroxylase
- 4,5-pcd, protocatechuate 4,5-dioxygenase
- taud, taurine dioxygenase
- uv–vis, uv–visible
- zfs, zero-field splitting
Collapse
Affiliation(s)
- Linn G. Bjørnstad
- Department of Molecular Biosciences, University of Oslo, P.O. Box 1041, Blindern, NO-0316 Oslo, Norway
| | - Giorgio Zoppellaro
- Department of Molecular Biosciences, University of Oslo, P.O. Box 1041, Blindern, NO-0316 Oslo, Norway
| | - Ane B. Tomter
- Department of Molecular Biosciences, University of Oslo, P.O. Box 1041, Blindern, NO-0316 Oslo, Norway
| | - Pål Ø. Falnes
- Department of Molecular Biosciences, University of Oslo, P.O. Box 1041, Blindern, NO-0316 Oslo, Norway
| | - K. Kristoffer Andersson
- Department of Molecular Biosciences, University of Oslo, P.O. Box 1041, Blindern, NO-0316 Oslo, Norway
| |
Collapse
|
44
|
Krylova SM, Karkhanina AA, Musheev MU, Bagg EAL, Schofield CJ, Krylov SN. DNA aptamers for as analytical tools for the quantitative analysis of DNA-dealkylating enzymes. Anal Biochem 2011; 414:261-5. [PMID: 21402046 DOI: 10.1016/j.ab.2011.03.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 03/06/2011] [Accepted: 03/08/2011] [Indexed: 11/27/2022]
Abstract
The AlkB family of oxygenases catalyze the removal of alkyl groups from nucleic acid substrates in an iron and 2-oxoglutarate-dependent manner and have roles including in DNA repair. To understand the biological functions of these DNA-dealkylating enzymes it is desirable to measure their expression levels in vitro and in vivo in complex biological matrixes. Quantitative analyses of the enzymes require affinity probes capable of binding AlkB family members selectively and with high affinity. Here we report that DNA aptamers can serve as efficient affinity probes for quantitative detection of such enzymes in vitro. Nonequilibrium capillary electrophoresis of equilibrium mixtures (NECEEM) was applied as a general tool for: (i) selection of DNA aptamers, (ii) characterization of binding parameters for the aptamers, and (iii) quantitative detection of the target in an aptamer-based affinity analysis. The selected aptamers have a range of K(d) values between 20 and 240nM. The aptamers enabled accurate quantitative analysis of AlkB even in the presence of the Escherichia coli cell lysate. Aptamers can likely be developed for other nucleic acid repair enzymes. They may also be developed for use in in vitro and potentially in vivo studies of known nucleic acid-modifying enzymes including for functional analysis.
Collapse
Affiliation(s)
- Svetlana M Krylova
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario, Canada
| | | | | | | | | | | |
Collapse
|
45
|
ALKBH3, a human AlkB homologue, contributes to cell survival in human non-small-cell lung cancer. Br J Cancer 2011; 104:700-6. [PMID: 21285982 PMCID: PMC3049579 DOI: 10.1038/sj.bjc.6606012] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND We have demonstrated for the first time that a novel human AlkB homologue, ALKBH3, contributes to prostate cancer development, but its clinical and biological roles in lung cancer remain unclear. METHODS Expression of both mRNA and protein of PCA-1 was examined by RT-PCR and western blotting. We also assessed association with senescence and in vivo ALKBH3 treatment on orthotopic tumour cell inoculation, and analysed it clinicopathologically. RESULTS We have since found novel biological roles for ALKBH3 in human lung cancers, particularly in adenocarcinoma. Our immunohistochemical analysis of human adenocarcinomas and squamous cell carcinomas of the lung not only showed overexpression of ALKBH3 in these tumours but the percentage of cells positive for ALKBH3 also correlated statistically to recurrence-free survival in adenocarcinoma. Knockdown of ALKBH3 by siRNA transfection induced expression of p21(WAF1/Cip1) and p27(Kip1) in the human lung adenocarcinoma cell line A549, resulting in cell cycle arrest, senescence and strong suppression of cell growth in vitro. In vivo, peritoneal tumour growth and dissemination was inhibited in nude mice, previously inoculated with the A549 cell line, by intraperitoneal injection of ALKBH3 siRNA + atelocollagen, as demonstrated by the reduction in both number and diameter of tumours developing in the peritoneum. CONCLUSION We suggest that ALKBH3 contributes significantly to cancer cell survival and may be a therapeutic target for human adenocarcinoma of the lung.
Collapse
|
46
|
Vad MS, Nielsen A, Lennartson A, Bond AD, McGrady JE, McKenzie CJ. Switching on oxygen activation by cobalt complexes of pentadentate ligands. Dalton Trans 2011; 40:10698-707. [DOI: 10.1039/c1dt10594a] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
47
|
Affiliation(s)
- M. V. Kovalchuk
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine
| |
Collapse
|
48
|
Nordstrand LM, Svärd J, Larsen E, Nilsen A, Ougland R, Furu K, Lien GF, Rognes T, Namekawa SH, Lee JT, Klungland A. Mice lacking Alkbh1 display sex-ratio distortion and unilateral eye defects. PLoS One 2010; 5:e13827. [PMID: 21072209 PMCID: PMC2972218 DOI: 10.1371/journal.pone.0013827] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 10/14/2010] [Indexed: 11/26/2022] Open
Abstract
Background Eschericia coli AlkB is a 2-oxoglutarate- and iron-dependent dioxygenase that reverses alkylated DNA damage by oxidative demethylation. Mouse AlkB homolog 1 (Alkbh1) is one of eight members of the newly discovered family of mammalian dioxygenases. Methods and Findings In the present study we show non-Mendelian inheritance of the Alkbh1 targeted allele in mice. Both Alkbh1−/− and heterozygous Alkbh1+/− offspring are born at a greatly reduced frequency. Additionally, the sex-ratio is considerably skewed against female offspring, with one female born for every three to four males. Most mechanisms that cause segregation distortion, act in the male gametes and affect male fertility. The skewing of the sexes appears to be of paternal origin, and might be set in the pachythene stage of meiosis during spermatogenesis, in which Alkbh1 is upregulated more than 10-fold. In testes, apoptotic spermatids were revealed in 5–10% of the tubules in Alkbh1−/− adults. The deficiency of Alkbh1 also causes misexpression of Bmp2, 4 and 7 at E11.5 during embryonic development. This is consistent with the incompletely penetrant phenotypes observed, particularly recurrent unilateral eye defects and craniofacial malformations. Conclusions Genetic and phenotypic assessment suggests that Alkbh1 mediates gene regulation in spermatogenesis, and that Alkbh1 is essential for normal sex-ratio distribution and embryonic development in mice.
Collapse
Affiliation(s)
- Line M. Nordstrand
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Jessica Svärd
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Elisabeth Larsen
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Anja Nilsen
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Rune Ougland
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Kari Furu
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Guro F. Lien
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Torbjørn Rognes
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Satoshi H. Namekawa
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Jeannie T. Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Arne Klungland
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- * E-mail:
| |
Collapse
|
49
|
Maciejewska AM, Ruszel KP, Nieminuszczy J, Lewicka J, Sokołowska B, Grzesiuk E, Kuśmierek JT. Chloroacetaldehyde-induced mutagenesis in Escherichia coli: the role of AlkB protein in repair of 3,N(4)-ethenocytosine and 3,N(4)-alpha-hydroxyethanocytosine. Mutat Res 2010; 684:24-34. [PMID: 19941873 DOI: 10.1016/j.mrfmmm.2009.11.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 11/06/2009] [Accepted: 11/18/2009] [Indexed: 05/28/2023]
Abstract
Etheno (epsilon) adducts are formed in reaction of DNA bases with various environmental carcinogens and endogenously created products of lipid peroxidation. Chloroacetaldehyde (CAA), a metabolite of carcinogen vinyl chloride, is routinely used to generate epsilon-adducts. We studied the role of AlkB, along with AlkA and Mug proteins, all engaged in repair of epsilon-adducts, in CAA-induced mutagenesis. The test system used involved pIF102 and pIF104 plasmids bearing the lactose operon of CC102 or CC104 origin (Cupples and Miller (1989) [17]) which allowed to monitor Lac(+) revertants, the latter arose by GC-->AT or GC-->TA substitutions, respectively, as a result of modification of guanine and cytosine. The plasmids were CAA-damaged in vitro and replicated in Escherichia coli of various genetic backgrounds. To modify the levels of AlkA and AlkB proteins, mutagenesis was studied in E. coli cells induced or not in adaptive response. Formation of varepsilonC proceeds via a relatively stable intermediate, 3,N(4)-alpha-hydroxyethanocytosine (HEC), which allowed to compare repair of both adducts. The results indicate that all three genes, alkA, alkB and microg, are engaged in alleviation of CAA-induced mutagenesis. The frequency of mutation was higher in AlkA-, AlkB- and Mug-deficient strains in comparison to alkA(+), alkB(+), and microg(+) controls. Considering the levels of CAA-induced Lac(+) revertants in strains harboring the pIF plasmids and induced or not in adaptive response, we conclude that AlkB protein is engaged in the repair of epsilonC and HEC in vivo. Using the modified TTCTT 5-mers as substrates, we confirmed in vitro that AlkB protein repairs epsilonC and HEC although far less efficiently than the reference adduct 3-methylcytosine. The pH optimum for repair of HEC and epsilonC is significantly different from that for 3-methylcytosine. We propose that the protonated form of adduct interact in active site of AlkB protein.
Collapse
Affiliation(s)
- Agnieszka M Maciejewska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, 5A Pawińskiego Str, Poland
| | | | | | | | | | | | | |
Collapse
|
50
|
Pulk A, Liiv A, Peil L, Maiväli Ü, Nierhaus K, Remme J. Ribosome reactivation by replacement of damaged proteins. Mol Microbiol 2010; 75:801-14. [DOI: 10.1111/j.1365-2958.2009.07002.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|