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Yılmaz M, Kamaşak T, Teralı K, Çebi AH, Türkyılmaz A. The first Turkish family with a novel biallelic missense variant of the ALKBH8 gene: A study on the clinical and variant spectrum of ALKBH8-related intellectual developmental disorders. Am J Med Genet A 2024; 194:e63535. [PMID: 38189198 DOI: 10.1002/ajmg.a.63535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 12/12/2023] [Accepted: 12/26/2023] [Indexed: 01/09/2024]
Abstract
ABH8, the protein encoded by the ALKBH8 gene, modifies tRNAs by methylating their anticodon wobble uridine residues. The variations in the ALKBH8 gene are associated with the "intellectual developmental disorder, autosomal recessive type 71" (MIM: 618504) phenotype in the OMIM database. This phenotype is characterized by global developmental delay, facial dysmorphic features, and psychiatric problems. To date, 12 patients from five distinct families carrying variants of the ALKBH8 gene have been reported in the literature. In the present study, we report the first Turkish family harboring a novel homozygous missense variant, NM_138775.3:c.1874G > C (p.Arg625Pro), in the last exon of the ALKBH8 gene. Two affected siblings in this family showed signs of global developmental delay and intellectual disability. Based on the dysmorphological assessment of the cases, fifth finger clinodactyly and fetal fingertip pads were prominent, in addition to the dysmorphic findings similar to those reported in previous studies. Minor dysmorphic limb anomalies in relation to this phenotype have not yet been previously reported in the literature. Our computational studies revealed the potential deleterious effects of the Arg-to-Pro substitution on the structure and stability of the ABH8 methyltransferase domain. In the present report, the first Turkish family with an ultrarare disease associated with the ALKBH8 gene was reported, and a novel deleterious variant in the ALKBH8 gene and additional clinical features that were not reported with this condition have been reported.
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Affiliation(s)
- Mustafa Yılmaz
- Department of Medical Genetics, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Tülay Kamaşak
- Department of Pediatric Neurology, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Kerem Teralı
- Department of Medical Biochemistry, Faculty of Medicine, Cyprus International University, Nicosia, Cyprus
| | - Alper Han Çebi
- Department of Medical Genetics, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
| | - Ayberk Türkyılmaz
- Department of Medical Genetics, Faculty of Medicine, Karadeniz Technical University, Trabzon, Turkey
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2
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DeAngelo SL, Dziechciarz S, Solanki S, Shin M, Zhao L, Balia A, El-Derany MO, Das NK, Castillo C, Bell HN, Paulo JA, Zhang Y, Rossiter NJ, McCulla EC, He J, Talukder I, Schafer ZT, Neamati N, Mancias JD, Koutmos M, Shah YM. Recharacterization of RSL3 reveals that the selenoproteome is a druggable target in colorectal cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.29.587381. [PMID: 38617233 PMCID: PMC11014488 DOI: 10.1101/2024.03.29.587381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Ferroptosis is an iron-dependent, non-apoptotic form of cell death resulting from the accumulation of lipid peroxides. Colorectal cancer (CRC) accumulates high levels of intracellular iron and reactive oxygen species (ROS), thereby sensitizing cells to ferroptosis. The selenoprotein glutathione peroxidase (GPx4) is a key enzyme in the detoxification of lipid peroxides and can be inhibited by the compound (S)-RSL3 ([1S,3R]-RSL3). However, the stereoisomer (R)-RSL3 ([1R,3R]-RSL3), which does not inhibit GPx4, exhibits equipotent activity to (S)-RSL3 across a panel of CRC cell lines. Utilizing CRC cell lines with an inducible knockdown of GPx4, we demonstrate that (S)-RSL3 sensitivity does not align with GPx4 dependency. Subsequently, a biotinylated (S)-RSL3 was then synthesized to perform affinity purification-mass spectrometry (AP-MS), revealing that (S)-RSL3 acts as a pan-inhibitor of the selenoproteome, targeting both the glutathione and thioredoxin peroxidase systems as well as multiple additional selenoproteins. To investigate the therapeutic potential of broadly disrupting the selenoproteome as a therapeutic strategy in CRC, we employed further chemical and genetic approaches to disrupt selenoprotein function. The findings demonstrate that the selenoprotein inhibitor Auranofin can induce ferroptosis and/or oxidative cell death both in-vitro and in-vivo. Consistent with this data we observe that AlkBH8, a tRNA-selenocysteine methyltransferase required for the translational incorporation of selenocysteine, is essential for CRC growth. In summary, our research elucidates the complex mechanisms underlying ferroptosis in CRC and reveals that modulation of the selenoproteome provides multiple new therapeutic targets and opportunities in CRC.
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Affiliation(s)
- Stephen L DeAngelo
- Doctoral Program in Cancer Biology, University of Michigan Medical School, Ann Arbor, MI, United States
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States
| | - Sofia Dziechciarz
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
| | - Sumeet Solanki
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
| | - Myungsun Shin
- Department of Cell Biology, Harvard Medical School, Boston, MA, United States
- Dana-Farber Cancer Institute, Boston, Massachusetts, United States
| | - Liang Zhao
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
| | - Andrii Balia
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, United States
| | - Marwa O El-Derany
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
| | - Nupur K Das
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
| | - Cristina Castillo
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
| | - Hannah N Bell
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, United States
- Dana-Farber Cancer Institute, Boston, Massachusetts, United States
| | - Yuezhong Zhang
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
| | - Nicholas J Rossiter
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States
| | - Elizabeth C McCulla
- Doctoral Program in Cancer Biology, University of Michigan Medical School, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States
| | - Jianping He
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Indrani Talukder
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
| | - Zachary T Schafer
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, United States
| | - Nouri Neamati
- Department of Biochemistry, Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States
| | - Joseph D Mancias
- Dana-Farber Cancer Institute, Boston, Massachusetts, United States
- Division of Radiation and Genome Stability, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA. United States
| | - Markos Koutmos
- Department of Chemistry, University of Michigan, Ann Arbor, MI, United States
- Department of Biophysics, University of Michigan, Ann Arbor, MI, United States
| | - Yatrik M Shah
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, United States
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, United States
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, United States
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3
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Yu R, Zhang W, Li Y, Tang J, Kim K, Li B. Functional characterisation of Fe (II) and 2OG-dependent dioxygenase TcALKBH4 in the red flour beetle, Tribolium castaneum. INSECT MOLECULAR BIOLOGY 2023; 32:676-688. [PMID: 37462221 DOI: 10.1111/imb.12865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 07/03/2023] [Indexed: 11/08/2023]
Abstract
Alpha-ketoglutarate-dependent dioxygenase ALKB homologue 4 (ALKBH4) is a member of the Fe (II) and 2-oxoglutarate-dependent ALKB homologue family that plays important roles in epigenetic regulation by alkyl lesions removal in mammals. However, the roles of ALKBH4 in insects are not clear. Here, TcALKBH4 was cloned and functionally characterised in Tribolium castaneum. Temporal expression revealed that TcALKBH4 was highly expressed in early embryos and early pupae. Spatial expression showed that TcALKBH4 was highly expressed in the adult testis, and followed by the ovary. RNA interference targeting TcALKBH4 at different developmental stages in T. castaneum led to apparent phenotypes including the failure of development in larvae, the reduction of food intake and the deficiency of fertility in adult. However, further dot blot analyses showed that TcALKBH4 RNAi does not seem to influence 6 mA levels in vivo. qRT-PCR was used to further explore the underlying molecular mechanisms; the result showed that TcALKBH4 mediates the development of larvae possibly through 20E signalling pathway, and the fertility of female and male adult might be regulated by the expression of vitellogenesis and JH signalling pathway, respectively. Altogether, these findings will provide new insights into the potential function of ALKBH4 in insects.
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Affiliation(s)
- Runnan Yu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Wenjing Zhang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Yanxiao Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Jing Tang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - KumChol Kim
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
- Department of Life-Science, University of Science, Pyongyang, Democratic People's Republic of Korea
| | - Bin Li
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, China
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Madhwani KR, Sayied S, Ogata CH, Hogan CA, Lentini JM, Mallik M, Dumouchel JL, Storkebaum E, Fu D, O’Connor-Giles KM. tRNA modification enzyme-dependent redox homeostasis regulates synapse formation and memory. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.14.566895. [PMID: 38014328 PMCID: PMC10680711 DOI: 10.1101/2023.11.14.566895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Post-transcriptional modification of RNA regulates gene expression at multiple levels. ALKBH8 is a tRNA modifying enzyme that methylates wobble uridines in specific tRNAs to modulate translation. Through methylation of tRNA-selenocysteine, ALKBH8 promotes selenoprotein synthesis and regulates redox homeostasis. Pathogenic variants in ALKBH8 have been linked to intellectual disability disorders in the human population, but the role of ALKBH8 in the nervous system is unknown. Through in vivo studies in Drosophila, we show that ALKBH8 controls oxidative stress in the brain to restrain synaptic growth and support learning and memory. ALKBH8 null animals lack wobble uridine methylation and exhibit a global reduction in protein synthesis, including a specific decrease in selenoprotein levels. Loss of ALKBH8 or independent disruption of selenoprotein synthesis results in ectopic synapse formation. Genetic expression of antioxidant enzymes fully suppresses synaptic overgrowth in ALKBH8 null animals, confirming oxidative stress as the underlying cause of dysregulation. ALKBH8 animals also exhibit associative learning and memory impairments that are reversed by pharmacological antioxidant treatment. Together, these findings demonstrate the critical role of tRNA modification in redox homeostasis in the nervous system and reveal antioxidants as a potential therapy for ALKBH8-associated intellectual disability.
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Affiliation(s)
| | - Shanzeh Sayied
- Department of Neuroscience, Brown University, Providence, RI, USA
| | | | - Caley A. Hogan
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Jenna M. Lentini
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Moushami Mallik
- Molecular Neurobiology Laboratory, Donders Institute for Brain, Cognition, and Behaviour, Radboud University, Nijmegen, NL
| | | | - Erik Storkebaum
- Molecular Neurobiology Laboratory, Donders Institute for Brain, Cognition, and Behaviour, Radboud University, Nijmegen, NL
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Kate M. O’Connor-Giles
- Department of Neuroscience, Brown University, Providence, RI, USA
- Carney Institute for Brain Sciences, Brown University, Providence, RI, USA
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5
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Hogan CA, Gratz SJ, Dumouchel JL, Thakur RS, Delgado A, Lentini JM, Madhwani KR, Fu D, O'Connor‐Giles KM. Expanded tRNA methyltransferase family member TRMT9B regulates synaptic growth and function. EMBO Rep 2023; 24:e56808. [PMID: 37642556 PMCID: PMC10561368 DOI: 10.15252/embr.202356808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 08/03/2023] [Accepted: 08/14/2023] [Indexed: 08/31/2023] Open
Abstract
Nervous system function rests on the formation of functional synapses between neurons. We have identified TRMT9B as a new regulator of synapse formation and function in Drosophila. TRMT9B has been studied for its role as a tumor suppressor and is one of two metazoan homologs of yeast tRNA methyltransferase 9 (Trm9), which methylates tRNA wobble uridines. Whereas Trm9 homolog ALKBH8 is ubiquitously expressed, TRMT9B is enriched in the nervous system. However, in the absence of animal models, TRMT9B's role in the nervous system has remained unstudied. Here, we generate null alleles of TRMT9B and find it acts postsynaptically to regulate synaptogenesis and promote neurotransmission. Through liquid chromatography-mass spectrometry, we find that ALKBH8 catalyzes canonical tRNA wobble uridine methylation, raising the question of whether TRMT9B is a methyltransferase. Structural modeling studies suggest TRMT9B retains methyltransferase function and, in vivo, disruption of key methyltransferase residues blocks TRMT9B's ability to rescue synaptic overgrowth, but not neurotransmitter release. These findings reveal distinct roles for TRMT9B in the nervous system and highlight the significance of tRNA methyltransferase family diversification in metazoans.
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Affiliation(s)
- Caley A Hogan
- Genetics Training ProgramUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Scott J Gratz
- Department of NeuroscienceBrown UniversityProvidenceRIUSA
| | | | - Rajan S Thakur
- Department of NeuroscienceBrown UniversityProvidenceRIUSA
| | - Ambar Delgado
- Department of NeuroscienceBrown UniversityProvidenceRIUSA
| | - Jenna M Lentini
- Department of Biology, Center for RNA BiologyUniversity of RochesterRochesterNYUSA
| | | | - Dragony Fu
- Department of Biology, Center for RNA BiologyUniversity of RochesterRochesterNYUSA
| | - Kate M O'Connor‐Giles
- Department of NeuroscienceBrown UniversityProvidenceRIUSA
- Carney Institute for Brain ScienceProvidenceRIUSA
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6
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Dai Z, Asgari S. ALKBH8 as a potential N 6 -methyladenosine (m 6 A) eraser in insects. INSECT MOLECULAR BIOLOGY 2023; 32:461-468. [PMID: 37119026 DOI: 10.1111/imb.12843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 04/13/2023] [Indexed: 06/19/2023]
Abstract
The N6 -methyladenosine (m6 A) machinery functions through three groups of proteins in eukaryotic cells, including m6 A writers, erasers and readers. The m6 A cellular machinery has mostly been characterised in mammalian species, and the relevant literature on insects is currently scant. While homologues of m6 A writers and readers have been reported from insects, no erasers have been described so far. Here, using BLAST search, we searched for potential erasers in insects. While we found homologues of human m6 A eraser ALKBH5 in termites, beetles and true bugs, they could not be found in representative dipteran and lepidopteran species. However, a potential m6 A eraser, ALKBH8, was identified and experimentally investigated. Our results showed that ALKBH8 can reduce the m6 A levels of Aedes aegypti and Drosophila melanogaster RNAs, suggesting that AeALKBH8 could be a candidate m6 A eraser in insects.
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Affiliation(s)
- Zhenkai Dai
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Sassan Asgari
- Australian Infectious Disease Research Centre, School of Biological Sciences, The University of Queensland, Brisbane, Queensland, Australia
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7
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Kogaki T, Hase H, Tanimoto M, Tashiro A, Kitae K, Ueda Y, Jingushi K, Tsujikawa K. ALKBH4 is a novel enzyme that promotes translation through modified uridine regulation. J Biol Chem 2023; 299:105093. [PMID: 37507018 PMCID: PMC10465949 DOI: 10.1016/j.jbc.2023.105093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Epitranscriptomics studies the mechanisms of acquired RNA modifications. The epitranscriptome is dynamically regulated by specific enzymatic reactions, and the proper execution of these enzymatic RNA modifications regulates a variety of physiological RNA functions. However, the lack of experimental tools, such as antibodies for RNA modification, limits the development of epitranscriptomic research. Furthermore, the regulatory enzymes of many RNA modifications have not yet been identified. Herein, we aimed to identify new molecular mechanisms involved in RNA modification by focusing on the AlkB homolog (ALKBH) family molecules, a family of RNA demethylases. We demonstrated that ALKBH4 interacts with small RNA, regulating the formation and metabolism of the (R)-5-carboxyhydroxymethyl uridine methyl ester. We also found that the reaction of ALKBH4 with small RNA enhances protein translation efficiency in an in vitro assay system. These findings indicate that ALKBH4 is involved in the regulation of uridine modification and expand on the role of tRNA-mediated translation control through ALKBH4.
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Affiliation(s)
- Takahiro Kogaki
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Hiroaki Hase
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.
| | - Masaya Tanimoto
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Atyuya Tashiro
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Kaori Kitae
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Yuko Ueda
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Kentaro Jingushi
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Kazutake Tsujikawa
- Laboratory of Molecular and Cellular Physiology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
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Abstract
The study of eukaryotic tRNA processing has given rise to an explosion of new information and insights in the last several years. We now have unprecedented knowledge of each step in the tRNA processing pathway, revealing unexpected twists in biochemical pathways, multiple new connections with regulatory pathways, and numerous biological effects of defects in processing steps that have profound consequences throughout eukaryotes, leading to growth phenotypes in the yeast Saccharomyces cerevisiae and to neurological and other disorders in humans. This review highlights seminal new results within the pathways that comprise the life of a tRNA, from its birth after transcription until its death by decay. We focus on new findings and revelations in each step of the pathway including the end-processing and splicing steps, many of the numerous modifications throughout the main body and anticodon loop of tRNA that are so crucial for tRNA function, the intricate tRNA trafficking pathways, and the quality control decay pathways, as well as the biogenesis and biology of tRNA-derived fragments. We also describe the many interactions of these pathways with signaling and other pathways in the cell.
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Affiliation(s)
- Eric M Phizicky
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine, Rochester, New York 14642, USA
| | - Anita K Hopper
- Department of Molecular Genetics and Center for RNA Biology, Ohio State University, Columbus, Ohio 43235, USA
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9
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Kietzmann T. Vitamin C: From nutrition to oxygen sensing and epigenetics. Redox Biol 2023; 63:102753. [PMID: 37263060 DOI: 10.1016/j.redox.2023.102753] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/09/2023] [Accepted: 05/16/2023] [Indexed: 06/03/2023] Open
Abstract
Vitamin C is unbeatable - at least when it comes to sales. Of all the vitamin preparations, those containing vitamin C sell best. This is surprising because vitamin C deficiency is extremely rare. Nevertheless, there is still controversy about whether the additional intake of vitamin C supplements is essential for our health. In this context, the possible additional benefit is in most cases merely reduced to the known effect as an antioxidant. However, new findings in recent years on the mechanisms of oxygen-sensing and epigenetic control underpin the multifaceted role of vitamin C in a biological context and have therefore renewed interest in it. In the present article, therefore, known facts are linked to these new key data. In addition, available clinical data on vitamin C use of cancer therapy are summarized.
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Affiliation(s)
- Thomas Kietzmann
- University of Oulu, Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, P.O. Box 3000, 90014, Oulu, Finland.
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10
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Li Q, Zhu Q. The role of demethylase AlkB homologs in cancer. Front Oncol 2023; 13:1153463. [PMID: 37007161 PMCID: PMC10060643 DOI: 10.3389/fonc.2023.1153463] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/03/2023] [Indexed: 03/18/2023] Open
Abstract
The AlkB family (ALKBH1-8 and FTO), a member of the Fe (II)- and α-ketoglutarate-dependent dioxygenase superfamily, has shown the ability to catalyze the demethylation of a variety of substrates, including DNA, RNA, and histones. Methylation is one of the natural organisms’ most prevalent forms of epigenetic modifications. Methylation and demethylation processes on genetic material regulate gene transcription and expression. A wide variety of enzymes are involved in these processes. The methylation levels of DNA, RNA, and histones are highly conserved. Stable methylation levels at different stages can coordinate the regulation of gene expression, DNA repair, and DNA replication. Dynamic methylation changes are essential for the abilities of cell growth, differentiation, and division. In some malignancies, the methylation of DNA, RNA, and histones is frequently altered. To date, nine AlkB homologs as demethylases have been identified in numerous cancers’ biological processes. In this review, we summarize the latest advances in the research of the structures, enzymatic activities, and substrates of the AlkB homologs and the role of these nine homologs as demethylases in cancer genesis, progression, metastasis, and invasion. We provide some new directions for the AlkB homologs in cancer research. In addition, the AlkB family is expected to be a new target for tumor diagnosis and treatment.
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Affiliation(s)
- Qiao Li
- Department of Orthopedic Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
- Department of Spine Surgery, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Qingsan Zhu
- Department of Orthopedic Surgery, China-Japan Union Hospital of Jilin University, Changchun, Jilin, China
- *Correspondence: Qingsan Zhu,
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11
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Hori H. Transfer RNA Modification Enzymes with a Thiouridine Synthetase, Methyltransferase and Pseudouridine Synthase (THUMP) Domain and the Nucleosides They Produce in tRNA. Genes (Basel) 2023; 14:genes14020382. [PMID: 36833309 PMCID: PMC9957541 DOI: 10.3390/genes14020382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
The existence of the thiouridine synthetase, methyltransferase and pseudouridine synthase (THUMP) domain was originally predicted by a bioinformatic study. Since the prediction of the THUMP domain more than two decades ago, many tRNA modification enzymes containing the THUMP domain have been identified. According to their enzymatic activity, THUMP-related tRNA modification enzymes can be classified into five types, namely 4-thiouridine synthetase, deaminase, methyltransferase, a partner protein of acetyltransferase and pseudouridine synthase. In this review, I focus on the functions and structures of these tRNA modification enzymes and the modified nucleosides they produce. Biochemical, biophysical and structural studies of tRNA 4-thiouridine synthetase, tRNA methyltransferases and tRNA deaminase have established the concept that the THUMP domain captures the 3'-end of RNA (in the case of tRNA, the CCA-terminus). However, in some cases, this concept is not simply applicable given the modification patterns observed in tRNA. Furthermore, THUMP-related proteins are involved in the maturation of other RNAs as well as tRNA. Moreover, the modified nucleosides, which are produced by the THUMP-related tRNA modification enzymes, are involved in numerous biological phenomena, and the defects of genes for human THUMP-related proteins are implicated in genetic diseases. In this review, these biological phenomena are also introduced.
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Affiliation(s)
- Hiroyuki Hori
- Department of Materials Science and Biotechnology, Graduate School of Science and Engineering, Ehime University, Matsuyama 790-8577, Japan
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12
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Papadopoulou A, Meyer F, Buller RM. Engineering Fe(II)/α-Ketoglutarate-Dependent Halogenases and Desaturases. Biochemistry 2023; 62:229-240. [PMID: 35446547 DOI: 10.1021/acs.biochem.2c00115] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Fe(II)/α-ketoglutarate-dependent dioxygenases (α-KGDs) are widespread enzymes in aerobic biology and serve a remarkable array of biological functions, including roles in collagen biosynthesis, plant and animal development, transcriptional regulation, nucleic acid modification, and secondary metabolite biosynthesis. This functional diversity is reflected in the enzymes' catalytic flexibility as α-KGDs can catalyze an intriguing set of synthetically valuable reactions, such as hydroxylations, halogenations, and desaturations, capturing the interest of scientists across disciplines. Mechanistically, all α-KGDs are understood to follow a similar activation pathway to generate a substrate radical, yet how individual members of the enzyme family direct this key intermediate toward the different reaction outcomes remains elusive, triggering structural, computational, spectroscopic, kinetic, and enzyme engineering studies. In this Perspective, we will highlight how first enzyme and substrate engineering examples suggest that the chemical reaction pathway within α-KGDs can be intentionally tailored using rational design principles. We will delineate the structural and mechanistic investigations of the reprogrammed enzymes and how they begin to inform about the enzymes' structure-function relationships that determine chemoselectivity. Application of this knowledge in future enzyme and substrate engineering campaigns will lead to the development of powerful C-H activation catalysts for chemical synthesis.
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Affiliation(s)
- Athena Papadopoulou
- Competence Center for Biocatalysis, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Fabian Meyer
- Competence Center for Biocatalysis, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
| | - Rebecca M Buller
- Competence Center for Biocatalysis, Zurich University of Applied Sciences, Einsiedlerstrasse 31, 8820 Wädenswil, Switzerland
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13
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Cavallin I, Bartosovic M, Skalicky T, Rengaraj P, Demko M, Schmidt-Dengler MC, Drino A, Helm M, Vanacova S. HITS-CLIP analysis of human ALKBH8 reveals interactions with fully processed substrate tRNAs and with specific noncoding RNAs. RNA (NEW YORK, N.Y.) 2022; 28:1568-1581. [PMID: 36192131 PMCID: PMC9670814 DOI: 10.1261/rna.079421.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Transfer RNAs acquire a large plethora of chemical modifications. Among those, modifications of the anticodon loop play important roles in translational fidelity and tRNA stability. Four human wobble U-containing tRNAs obtain 5-methoxycarbonylmethyluridine (mcm5U34) or 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U34), which play a role in decoding. This mark involves a cascade of enzymatic activities. The last step is mediated by alkylation repair homolog 8 (ALKBH8). In this study, we performed a transcriptome-wide analysis of the repertoire of ALKBH8 RNA targets. Using a combination of HITS-CLIP and RIP-seq analyses, we uncover ALKBH8-bound RNAs. We show that ALKBH8 targets fully processed and CCA modified tRNAs. Our analyses uncovered the previously known set of wobble U-containing tRNAs. In addition, both our approaches revealed ALKBH8 binding to several other types of noncoding RNAs, in particular C/D box snoRNAs.
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Affiliation(s)
- Ivana Cavallin
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Marek Bartosovic
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Tomas Skalicky
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Praveenkumar Rengaraj
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Martin Demko
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | | | - Aleksej Drino
- Medical University of Vienna, Center for Anatomy and Cell Biology, 1090 Vienna, Austria
| | - Mark Helm
- Johannes Gutenberg-Universität Mainz, Institute of Pharmaceutical and Biomedical Science (IPBS), D-55128 Mainz, Germany
| | - Stepanka Vanacova
- Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
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14
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Liu H, Xie Y, Wang X, Abboud MI, Ma C, Ge W, Schofield CJ. Exploring links between 2-oxoglutarate-dependent oxygenases and Alzheimer's disease. Alzheimers Dement 2022; 18:2637-2668. [PMID: 35852137 PMCID: PMC10083964 DOI: 10.1002/alz.12733] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/12/2022] [Accepted: 06/10/2022] [Indexed: 01/31/2023]
Abstract
Hypoxia, that is, an inadequate oxygen supply, is linked to neurodegeneration and patients with cardiovascular disease are prone to Alzheimer's disease (AD). 2-Oxoglutarate and ferrous iron-dependent oxygenases (2OGDD) play a key role in the regulation of oxygen homeostasis by acting as hypoxia sensors. 2OGDD also have roles in collagen biosynthesis, lipid metabolism, nucleic acid repair, and the regulation of transcription and translation. Many biological processes in which the >60 human 2OGDD are involved are altered in AD patient brains, raising the question as to whether 2OGDD are involved in the transition from normal aging to AD. Here we give an overview of human 2OGDD and critically discuss their potential roles in AD, highlighting possible relationships with synapse dysfunction/loss. 2OGDD may regulate neuronal/glial differentiation through enzyme activity-dependent mechanisms and modulation of their activity has potential to protect against synapse loss. Work linking 2OGDD and AD is at an early stage, especially from a therapeutic perspective; we suggest integrated pathology and in vitro discovery research to explore their roles in AD is merited. We hope to help enable long-term research on the roles of 2OGDD and, more generally, oxygen/hypoxia in AD. We also suggest shorter term empirically guided clinical studies concerning the exploration of 2OGDD/oxygen modulators to help maintain synaptic viability are of interest for AD treatment.
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Affiliation(s)
- Haotian Liu
- State Key Laboratory of Medical Molecular Biology & Department of ImmunologyInstitute of Basic Medical Sciences Chinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Yong Xie
- State Key Laboratory of Medical Molecular Biology & Department of ImmunologyInstitute of Basic Medical Sciences Chinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
- National Clinical Research Center for OrthopedicsSports Medicine & RehabilitationDepartment of OrthopedicsGeneral Hospital of Chinese PLABeijingChina
| | - Xia Wang
- State Key Laboratory of Medical Molecular Biology & Department of ImmunologyInstitute of Basic Medical Sciences Chinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Martine I. Abboud
- The Chemistry Research LaboratoryDepartment of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordOxfordUK
| | - Chao Ma
- Department of Human Anatomy, Histology and EmbryologyNeuroscience CenterNational Human Brain Bank for Development and FunctionInstitute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Wei Ge
- State Key Laboratory of Medical Molecular Biology & Department of ImmunologyInstitute of Basic Medical Sciences Chinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijingChina
| | - Christopher J. Schofield
- The Chemistry Research LaboratoryDepartment of Chemistry and the Ineos Oxford Institute for Antimicrobial ResearchUniversity of OxfordOxfordUK
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15
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Lee MY, Ojeda-Britez S, Ehrbar D, Samwer A, Begley TJ, Melendez JA. Selenoproteins and the senescence-associated epitranscriptome. Exp Biol Med (Maywood) 2022; 247:2090-2102. [PMID: 36036467 PMCID: PMC9837304 DOI: 10.1177/15353702221116592] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Selenium is a naturally found trace element, which provides multiple benefits including antioxidant, anticancer, and antiaging, as well as boosting immunity. One unique feature of selenium is its incorporation as selenocysteine, a rare 21st amino acid, into selenoproteins. Twenty-five human selenoproteins have been discovered, and a majority of these serve as crucial antioxidant enzymes for redox homeostasis. Unlike other amino acids, incorporation of selenocysteine requires a distinctive UGA stop codon recoding mechanism. Although many studies correlating selenium, selenoproteins, aging, and senescence have been performed, it has not yet been explored if the upstream events regulating selenoprotein synthesis play a role in senescence-associated pathologies. The epitranscriptomic writer alkylation repair homolog 8 (ALKBH8) is critical for selenoprotein production, and its deficiency can significantly decrease levels of selenoproteins that are essential for reactive oxygen species (ROS) detoxification, and increase oxidative stress, one of the major drivers of cellular senescence. Here, we review the potential role of epitranscriptomic marks that govern selenocysteine utilization in regulating the senescence program.
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Affiliation(s)
- May Y Lee
- College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY 12203, USA
- The RNA Institute, University at Albany, Albany, NY 12222, USA
| | - Stephen Ojeda-Britez
- College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY 12203, USA
| | - Dylan Ehrbar
- The RNA Institute, University at Albany, Albany, NY 12222, USA
- Department of Biological Sciences, University at Albany, Albany, NY 12222, USA
- RNA Epitranscriptomics and Proteomics Resource, University at Albany, Albany, NY 12222, USA
| | | | - Thomas J Begley
- The RNA Institute, University at Albany, Albany, NY 12222, USA
- Department of Biological Sciences, University at Albany, Albany, NY 12222, USA
- RNA Epitranscriptomics and Proteomics Resource, University at Albany, Albany, NY 12222, USA
| | - J Andres Melendez
- College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY 12203, USA
- The RNA Institute, University at Albany, Albany, NY 12222, USA
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16
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Pan-Cancer Analysis Reveals the Relation between TRMT112 and Tumor Microenvironment. JOURNAL OF ONCOLOGY 2022; 2022:1445932. [PMID: 36081672 PMCID: PMC9448524 DOI: 10.1155/2022/1445932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/29/2022] [Accepted: 08/09/2022] [Indexed: 11/17/2022]
Abstract
Dysregulated epigenetic modifications play a critical role in cancer development where TRMT112 is a member of the transfer RNA (tRNA) methyltransferase family. Till now, no studies have revealed the linkage between TRMT112 expression and diverse types of tumors. Based on TCGA data, we first probed into the relation between TRMT112 and prognosis and the potential role of TRMT112 in tumor microenvironment across 33 types of tumor. TRMT112 presented with increased expression in most cancers, which was significantly prognostic. Furthermore, TRMT112 was associated with tumor-associated fibroblasts in a variety of cancers. Additionally, a positive relationship was identified between TRMT112 expression and multiple tumor-related immune infiltrations, such as dendritic cells, CD8+ T cells, macrophages, CD4+ T cells, neutrophils, and B cells in lung adenocarcinoma and breast invasive carcinoma. In summary, our results suggest that TRMT112 might be a potential prognostic predictor of cancers and involved in regulating multiple cancer-related immune responses to some extent.
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Waqas A, Nayab A, Shaheen S, Abbas S, Latif M, Rafeeq MM, Al-Dhuayan IS, Alqosaibi AI, Alnamshan MM, Sain ZM, Habib AH, Alam Q, Umair M, Saqib MAN. Case Report: Biallelic Variant in the tRNA Methyltransferase Domain of the AlkB Homolog 8 Causes Syndromic Intellectual Disability. Front Genet 2022; 13:878274. [PMID: 35571055 PMCID: PMC9096442 DOI: 10.3389/fgene.2022.878274] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/18/2022] [Indexed: 11/23/2022] Open
Abstract
Intellectual disability (ID) has become very common and is an extremely heterogeneous disorder, where the patients face many challenges with deficits in intellectual functioning and adaptive behaviors. A single affected family revealed severe disease phenotypes such as ID, developmental delay, dysmorphic facial features, postaxial polydactyly type B, and speech impairment. DNA of a single affected individual was directly subjected to whole exome sequencing (WES), followed by Sanger sequencing. Data analysis revealed a novel biallelic missense variant (c.1511G>C; p.(Trp504Ser)) in the ALKBH8 gene, which plays a significant role in tRNA modifications. Our finding adds another variant to the growing list of ALKBH8-associated tRNA modifications causing ID and additional phenotypic manifestations. The present study depicts the key role of the genes associated with tRNA modifications, such as ALKBH8, in the development and pathophysiology of the human brain.
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Affiliation(s)
- Ahmed Waqas
- Department of Zoology, Division of Science and Technology, University of Education, Lahore, Pakistan
| | - Anam Nayab
- Microbiology and Biotechnology Research Lab, Department of Biotechnology, Fatima Jinnah Women University, The Mall, Rawalpindi, Pakistan
| | - Shabnam Shaheen
- Department of Higher Education, Government Girls Degree College Lakki Marwat, Lakki Marwat, Pakistan
| | - Safdar Abbas
- Department of Biological Science, Darmouth College, Hanover, NH, United States
| | - Muhammad Latif
- Department of Zoology, Division of Science and Technology, University of Education, Lahore, Pakistan
| | - Misbahuddin M Rafeeq
- Department of Pharmacology, Faculty of Medicine, Rabigh, King Abduaziz University, Jeddah, Saudi Arabia
| | - Ibtesam S Al-Dhuayan
- Department of Biology, College of Science, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Amany I Alqosaibi
- Department of Biology, College of Science, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Mashael M Alnamshan
- Department of Biology, College of Science, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Ziaullah M Sain
- Department of Microbiology, Faculty of Medicine, Rabigh, King Abduaziz University, Jeddah, Saudi Arabia
| | - Alaa Hamed Habib
- Department of Physiology, Faculty of Medicine, King Abduaziz University, Jeddah, Saudi Arabia
| | - Qamre Alam
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia.,Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
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18
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Sheng Y, Zhou M, You C, Dai X. Dynamics and biological relevance of epigenetic N6-methyladenine DNA modification in eukaryotic cells. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.08.109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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19
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Nishida Y, Ohmori S, Kakizono R, Kawai K, Namba M, Okada K, Yamagami R, Hirata A, Hori H. Required Elements in tRNA for Methylation by the Eukaryotic tRNA (Guanine- N2-) Methyltransferase (Trm11-Trm112 Complex). Int J Mol Sci 2022; 23:ijms23074046. [PMID: 35409407 PMCID: PMC8999500 DOI: 10.3390/ijms23074046] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/03/2022] [Accepted: 04/04/2022] [Indexed: 12/10/2022] Open
Abstract
The Saccharomyces cerevisiae Trm11 and Trm112 complex (Trm11-Trm112) methylates the 2-amino group of guanosine at position 10 in tRNA and forms N2-methylguanosine. To determine the elements required in tRNA for methylation by Trm11-Trm112, we prepared 60 tRNA transcript variants and tested them for methylation by Trm11-Trm112. The results show that the precursor tRNA is not a substrate for Trm11-Trm112. Furthermore, the CCA terminus is essential for methylation by Trm11-Trm112, and Trm11-Trm112 also only methylates tRNAs with a regular-size variable region. In addition, the G10-C25 base pair is required for methylation by Trm11-Trm112. The data also demonstrated that Trm11-Trm112 recognizes the anticodon-loop and that U38 in tRNAAla acts negatively in terms of methylation. Likewise, the U32-A38 base pair in tRNACys negatively affects methylation. The only exception in our in vitro study was tRNAValAAC1. Our experiments showed that the tRNAValAAC1 transcript was slowly methylated by Trm11-Trm112. However, position 10 in this tRNA was reported to be unmodified G. We purified tRNAValAAC1 from wild-type and trm11 gene deletion strains and confirmed that a portion of tRNAValAAC1 is methylated by Trm11-Trm112 in S. cerevisiae. Thus, our study explains the m2G10 modification pattern of all S. cerevisiae class I tRNAs and elucidates the Trm11-Trm112 binding sites.
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20
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Evke S, Lin Q, Melendez JA, Begley TJ. Epitranscriptomic Reprogramming Is Required to Prevent Stress and Damage from Acetaminophen. Genes (Basel) 2022; 13:genes13030421. [PMID: 35327975 PMCID: PMC8955276 DOI: 10.3390/genes13030421] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/13/2022] [Accepted: 02/16/2022] [Indexed: 02/06/2023] Open
Abstract
Epitranscriptomic marks, in the form of enzyme catalyzed RNA modifications, play important gene regulatory roles in response to environmental and physiological conditions. However, little is known with respect to how acute toxic doses of pharmaceuticals influence the epitranscriptome. Here we define how acetaminophen (APAP) induces epitranscriptomic reprogramming and how the writer Alkylation Repair Homolog 8 (Alkbh8) plays a key gene regulatory role in the response. Alkbh8 modifies tRNA selenocysteine (tRNASec) to translationally regulate the production of glutathione peroxidases (Gpx’s) and other selenoproteins, with Gpx enzymes known to play protective roles during APAP toxicity. We demonstrate that APAP increases toxicity and markers of damage, and decreases selenoprotein levels in Alkbh8 deficient mouse livers, when compared to wildtype. APAP also promotes large scale reprogramming of many RNA marks comprising the liver tRNA epitranscriptome including: 5-methoxycarbonylmethyluridine (mcm5U), isopentenyladenosine (i6A), pseudouridine (Ψ), and 1-methyladenosine (m1A) modifications linked to tRNASec and many other tRNA’s. Alkbh8 deficiency also leads to wide-spread epitranscriptomic dysregulation in response to APAP, demonstrating that a single writer defect can promote downstream changes to a large spectrum of RNA modifications. Our study highlights the importance of RNA modifications and translational responses to APAP, identifies writers as key modulators of stress responses in vivo and supports the idea that the epitranscriptome may play important roles in responses to pharmaceuticals.
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Affiliation(s)
- Sara Evke
- Nanobioscience Constellation, College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY 12203, USA; (S.E.); (J.A.M.)
- The RNA Institute, University at Albany, Albany, NY 12222, USA;
| | - Qishan Lin
- The RNA Institute, University at Albany, Albany, NY 12222, USA;
- Department of Biological Sciences, University at Albany, Albany, NY 12222, USA
- RNA Epitranscriptomics and Proteomics Resource, University at Albany, Albany, NY 12222, USA
| | - Juan Andres Melendez
- Nanobioscience Constellation, College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY 12203, USA; (S.E.); (J.A.M.)
- The RNA Institute, University at Albany, Albany, NY 12222, USA;
| | - Thomas John Begley
- The RNA Institute, University at Albany, Albany, NY 12222, USA;
- Department of Biological Sciences, University at Albany, Albany, NY 12222, USA
- RNA Epitranscriptomics and Proteomics Resource, University at Albany, Albany, NY 12222, USA
- Correspondence:
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21
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Wang L, Feng X, Jiao Z, Gan J, Meng Q. Characterization of the prognostic and diagnostic values of ALKBH family members in non-small cell lung cancer. Pathol Res Pract 2022; 231:153809. [DOI: 10.1016/j.prp.2022.153809] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 01/27/2022] [Accepted: 02/11/2022] [Indexed: 01/26/2023]
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Evolutionary History of RNA Modifications at N6-Adenosine Originating from the R-M System in Eukaryotes and Prokaryotes. BIOLOGY 2022; 11:biology11020214. [PMID: 35205080 PMCID: PMC8868631 DOI: 10.3390/biology11020214] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 01/13/2022] [Accepted: 01/24/2022] [Indexed: 12/11/2022]
Abstract
Simple Summary The m6A is the most abundant and well-studied modification of mRNA, and plays an important role in transcription and translation. It is known to be evolutionarily conserved machinery present in the last eukaryotic common ancestor (LECA). The writers and erasers responsible for adding or removing m6A belong to specific protein families, respectively, suggesting that these members are evolutionarily related. However, only some of these mRNA m6A modification-associated proteins have been studied from an evolutionary perspective, while there has been no comprehensive and systematic analysis of the distributions and evolutionary history of N6mA-associated proteins in the three kingdoms of life. In this study, we identified orthologues of all the reported N6mA-associated proteins in 88 organisms from three kingdoms of life and comprehensively reconstructed the evolutionary history of the RNA N6mA modification machinery. The results demonstrate that RNA N6mA-MTases are derived from at least two different types of prokaryotic DNA MTases (class α and β MTases). As the m6A reader, YTH proteins may be acquired by LECA from an individual prokaryotic YTH-domain protein that evolved from the N-terminals of an R-M system endonuclease. In addition, the origin of eukaryotic ALKBH family proteins is inferred to be driven by at least two occasions of independent HTG from the bacterial ALKB family. Abstract Methylation at the N6-position of adenosine (N6mA) on mRNA (m6A) is one of the most widespread, highly selective and dynamically regulated RNA modifications and plays an important role in transcription and translation. In the present study, a comprehensive analysis of phylogenetic relationships, conserved domain sequence characteristics and protein structure comparisons were employed to explore the distribution of RNA N6mA modification (m6A, m6,6A, m6Am, m6, 6Am and m6t6A)-associated proteins (writers, readers and erasers) in three kingdoms of life and reveal the evolutionary history of these modifications. These findings further confirmed that the restriction-modification (R-M) system is the origin of DNA and RNA N6mA modifications. Among them, the existing mRNA m6A modification system derived from the last eukaryotic common ancestor (LECA) is the evolutionary product of elements from the last universal common ancestor (LUCA) or driven by horizontal gene transfer (HGT) from bacterial elements. The subsequent massive gene gains and losses contribute to the development of unique and diverse functions in distinct species. Particularly, RNA methyltransferases (MTases) as the writer responsible for adding N6mA marks on mRNA and ncRNAs may have evolved from class α and β prokaryotic “orphan” MTases originating from the R-M system. The reader, YTH proteins that specifically recognize the m6A deposit, may be acquired by LECA from an individual prokaryotic YTH-domain protein that evolved from N-terminals of an R-M system endonuclease. The eraser, which emerged from the ALKB family (ALKBH5 and FTO) in eukaryotes, may be driven by independent HTG from bacterial ALKB proteins. The evolutionary history of RNA N6mA modifications was inferred in the present study, which will deepen our understanding of these modifications in different species.
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23
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Schmidl D, Jonasson NSW, Menke A, Schneider S, Daumann L. Spectroscopic and in vitro investigations of Fe2+/α-Ketoglutarate-dependent enzymes involved in nucleic acid repair and modification. Chembiochem 2022; 23:e202100605. [PMID: 35040547 PMCID: PMC9401043 DOI: 10.1002/cbic.202100605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 01/14/2022] [Indexed: 11/08/2022]
Abstract
The activation of molecular oxygen for the highly selective functionalization and repair of DNA and RNA nucleobases is achieved by α-ketoglutarate (α-KG)/iron-dependent dioxygenases. Enzymes of special interest are the human homologs AlkBH of Escherichia coli EcAlkB and ten-eleven translocation (TET) enzymes. These enzymes are involved in demethylation or dealkylation of DNA and RNA, although additional physiological functions are continuously being revealed. Given their importance, studying enzyme-substrate interactions, turnover and kinetic parameters is pivotal for the understanding of the mode of action of these enzymes. Diverse analytical methods, including X-ray crystallography, UV/Vis absorption, electron paramagnetic resonance (EPR), circular dichroism (CD) and NMR spectroscopy have been employed to study the changes in the active site and the overall enzyme structure upon substrate, cofactor and inhibitor addition. Several methods are now available to assess activity of these enzymes. By discussing limitations and possibilities of these techniques for EcAlkB, AlkBH and TET we aim to give a comprehensive synopsis from a bioinorganic point of view, addressing researchers from different disciplines working in the highly interdisciplinary and rapidly evolving field of epigenetic processes and DNA/RNA repair and modification.
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Affiliation(s)
- David Schmidl
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Niko S W Jonasson
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Annika Menke
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Sabine Schneider
- Ludwig-Maximilians-Universität München: Ludwig-Maximilians-Universitat Munchen, Chemistry, GERMANY
| | - Lena Daumann
- Ludwig-Maximilians-Universität München, Department of Chemistry, Butenandtstr. 5-13, 81377, München, GERMANY
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24
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Brūmele B, Mutso M, Telanne L, Õunap K, Spunde K, Abroi A, Kurg R. Human TRMT112-Methyltransferase Network Consists of Seven Partners Interacting with a Common Co-Factor. Int J Mol Sci 2021; 22:ijms222413593. [PMID: 34948388 PMCID: PMC8708615 DOI: 10.3390/ijms222413593] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/07/2021] [Accepted: 12/15/2021] [Indexed: 01/22/2023] Open
Abstract
Methylation is an essential epigenetic modification mainly catalysed by S-Adenosyl methionine-dependent methyltransferases (MTases). Several MTases require a cofactor for their metabolic stability and enzymatic activity. TRMT112 is a small evolutionary conserved protein that acts as a co-factor and activator for different MTases involved in rRNA, tRNA and protein methylation. Using a SILAC screen, we pulled down seven methyltransferases-N6AMT1, WBSCR22, METTL5, ALKBH8, THUMPD2, THUMPD3 and TRMT11-as interaction partners of TRMT112. We showed that TRMT112 stabilises all seven MTases in cells. TRMT112 and MTases exhibit a strong mutual feedback loop when expressed together in cells. TRMT112 interacts with its partners in a similar way; however, single amino acid mutations on the surface of TRMT112 reveal several differences as well. In summary, mammalian TRMT112 can be considered as a central "hub" protein that regulates the activity of at least seven methyltransferases.
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Affiliation(s)
| | | | | | | | | | | | - Reet Kurg
- Correspondence: ; Tel.: +372-737-5040
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25
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Maddirevula S, Alameer S, Ewida N, de Sousa MML, Bjørås M, Vågbø CB, Alkuraya FS. Insight into ALKBH8-related intellectual developmental disability based on the first pathogenic missense variant. Hum Genet 2021; 141:209-215. [PMID: 34757492 DOI: 10.1007/s00439-021-02391-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 10/20/2021] [Indexed: 12/23/2022]
Abstract
ALKBH8 is a methyltransferase that modifies tRNAs by methylating the anticodon wobble uridine residue. The syndrome of ALKBH8-related intellectual developmental disability (MRT71) has thus far been reported solely in the context of homozygous truncating variants that cluster in the last exon. This raises interesting questions about the disease mechanism, because these variants are predicted to escape nonsense mediated decay and yet they appear to be loss of function. Furthermore, the limited class of reported variants complicates the future interpretation of missense variants in ALKBH8. Here, we report a consanguineous family in which two children with MRT71-compatible phenotype are homozygous for a novel missense variant in the methyltransferase domain. We confirm the pathogenicity of this variant by demonstrating complete absence of ALKBH8-dependent modifications in patient cells. Targeted proteomics analysis of ALKBH8 indicates that the variant does not lead to loss of ALKBH8 protein expression. This report adds to the clinical delineation of MRT71, confirms loss of function of ALKBH8 as the disease mechanism and expands the repertoire of its molecular lesions.
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Affiliation(s)
- Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, 11211, Saudi Arabia
| | - Seham Alameer
- Department of Pediatrics, Ministry of the National Guard-Health Affairs, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Nour Ewida
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, 11211, Saudi Arabia
| | | | - Magnar Bjørås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Cathrine Broberg Vågbø
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, 7491, Trondheim, Norway.,Proteomics and Modomics Experimental Core and St. Olavs Hospital Central Staff, Trondheim, Norway
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, 11211, Saudi Arabia. .,Department of Anatomy and Cell Biology, College of Medicine, Alfaisal University, Riyadh, 11533, Saudi Arabia.
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26
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Tsao N, Brickner JR, Rodell R, Ganguly A, Wood M, Oyeniran C, Ahmad T, Sun H, Bacolla A, Zhang L, Lukinović V, Soll JM, Townley BA, Casanova AG, Tainer JA, He C, Vindigni A, Reynoird N, Mosammaparast N. Aberrant RNA methylation triggers recruitment of an alkylation repair complex. Mol Cell 2021; 81:4228-4242.e8. [PMID: 34686315 DOI: 10.1016/j.molcel.2021.09.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 07/18/2021] [Accepted: 09/21/2021] [Indexed: 12/13/2022]
Abstract
Central to genotoxic responses is their ability to sense highly specific signals to activate the appropriate repair response. We previously reported that the activation of the ASCC-ALKBH3 repair pathway is exquisitely specific to alkylation damage in human cells. Yet the mechanistic basis for the selectivity of this pathway was not immediately obvious. Here, we demonstrate that RNA but not DNA alkylation is the initiating signal for this process. Aberrantly methylated RNA is sufficient to recruit ASCC, while an RNA dealkylase suppresses ASCC recruitment during chemical alkylation. In turn, recruitment of ASCC during alkylation damage, which is mediated by the E3 ubiquitin ligase RNF113A, suppresses transcription and R-loop formation. We further show that alkylated pre-mRNA is sufficient to activate RNF113A E3 ligase in vitro in a manner dependent on its RNA binding Zn-finger domain. Together, our work identifies an unexpected role for RNA damage in eliciting a specific response to genotoxins.
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Affiliation(s)
- Ning Tsao
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Joshua R Brickner
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Rebecca Rodell
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Adit Ganguly
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Matthew Wood
- Division of Oncology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA; Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Clement Oyeniran
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Tanveer Ahmad
- Institute for Advanced Biosciences, Grenoble Alpes University, CNRS UMR5309, INSERM U1209, Grenoble, France
| | - Hua Sun
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Albino Bacolla
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Lisheng Zhang
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Institute for Biophysical Dynamics, University of Chicago, Chicago IL 60637, USA
| | - Valentina Lukinović
- Institute for Advanced Biosciences, Grenoble Alpes University, CNRS UMR5309, INSERM U1209, Grenoble, France
| | - Jennifer M Soll
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Brittany A Townley
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Alexandre G Casanova
- Institute for Advanced Biosciences, Grenoble Alpes University, CNRS UMR5309, INSERM U1209, Grenoble, France
| | - John A Tainer
- Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA; Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Chuan He
- Department of Biochemistry and Molecular Biology, Department of Chemistry, and Institute for Biophysical Dynamics, University of Chicago, Chicago IL 60637, USA; Howard Hughes Medical Institute, University of Chicago, Chicago IL 60637, USA
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Nicolas Reynoird
- Institute for Advanced Biosciences, Grenoble Alpes University, CNRS UMR5309, INSERM U1209, Grenoble, France
| | - Nima Mosammaparast
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA.
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27
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Kusnadi EP, Timpone C, Topisirovic I, Larsson O, Furic L. Regulation of gene expression via translational buffering. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1869:119140. [PMID: 34599983 DOI: 10.1016/j.bbamcr.2021.119140] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 09/19/2021] [Accepted: 09/21/2021] [Indexed: 12/28/2022]
Abstract
Translation of an mRNA represents a critical step during the expression of protein-coding genes. As mechanisms governing post-transcriptional regulation of gene expression are progressively unveiled, it is becoming apparent that transcriptional programs are not fully reflected in the proteome. Herein, we highlight a previously underappreciated post-transcriptional mode of regulation of gene expression termed translational buffering. In principle, translational buffering opposes the impact of alterations in mRNA levels on the proteome. We further describe three types of translational buffering: compensation, which maintains protein levels e.g. across species or individuals; equilibration, which retains pathway stoichiometry; and offsetting, which acts as a reversible mechanism that maintains the levels of selected subsets of proteins constant despite genetic alteration and/or stress-induced changes in corresponding mRNA levels. While mechanisms underlying compensation and equilibration have been reviewed elsewhere, the principal focus of this review is on the less-well understood mechanism of translational offsetting. Finally, we discuss potential roles of translational buffering in homeostasis and disease.
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Affiliation(s)
- Eric P Kusnadi
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia; Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia
| | - Clelia Timpone
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia
| | - Ivan Topisirovic
- Lady Davis Institute, Gerald Bronfman Department of Oncology and Departments of Biochemistry and Experimental Medicine, McGill University, Montreal, QC, Canada.
| | - Ola Larsson
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, Solna, Sweden.
| | - Luc Furic
- Translational Prostate Cancer Research Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia; Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Victoria, Australia; Cancer Program, Biomedicine Discovery Institute and Department of Anatomy and Developmental Biology, Monash University, Clayton, Victoria, Australia.
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28
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DNA Demethylation in the Processes of Repair and Epigenetic Regulation Performed by 2-Ketoglutarate-Dependent DNA Dioxygenases. Int J Mol Sci 2021; 22:ijms221910540. [PMID: 34638881 PMCID: PMC8508711 DOI: 10.3390/ijms221910540] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 12/05/2022] Open
Abstract
Site-specific DNA methylation plays an important role in epigenetic regulation of gene expression. Chemical methylation of DNA, including the formation of various methylated nitrogenous bases, leads to the formation of genotoxic modifications that impair DNA functions. Despite the fact that different pathways give rise to methyl groups in DNA, the main pathway for their removal is oxidative demethylation, which is catalyzed by nonheme Fe(II)/α-ketoglutarate–dependent DNA dioxygenases. DNA dioxygenases share a common catalytic mechanism of the oxidation of the alkyl groups on nitrogenous bases in nucleic acids. This review presents generalized data on the catalytic mechanism of action of DNA dioxygenases and on the participation of typical representatives of this superfamily, such as prokaryotic enzyme AlkB and eukaryotic enzymes ALKBH1–8 and TET1–3, in both processes of direct repair of alkylated DNA adducts and in the removal of an epigenetic mark (5-methylcytosine).
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29
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Graille M. Division of labor in epitranscriptomics: What have we learnt from the structures of eukaryotic and viral multimeric RNA methyltransferases? WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1673. [PMID: 34044474 DOI: 10.1002/wrna.1673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 02/06/2023]
Abstract
The translation of an mRNA template into the corresponding protein is a highly complex and regulated choreography performed by ribosomes, tRNAs, and translation factors. Most RNAs involved in this process are decorated by multiple chemical modifications (known as epitranscriptomic marks) contributing to the efficiency, the fidelity, and the regulation of the mRNA translation process. Many of these epitranscriptomic marks are written by holoenzymes made of a catalytic subunit associated with an activating subunit. These holoenzymes play critical roles in cell development. Indeed, several mutations being identified in the genes encoding for those proteins are linked to human pathologies such as cancers and intellectual disorders for instance. This review describes the structural and functional properties of RNA methyltransferase holoenzymes, which when mutated often result in brain development pathologies. It illustrates how structurally different activating subunits contribute to the catalytic activity of these holoenzymes through common mechanistic trends that most likely apply to other classes of holoenzymes. This article is categorized under: RNA Processing > RNA Editing and Modification RNA Processing > Capping and 5' End Modifications.
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Affiliation(s)
- Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole Polytechnique, IP Paris, Palaiseau Cedex, France
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30
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Davydova E, Shimazu T, Schuhmacher MK, Jakobsson ME, Willemen HLDM, Liu T, Moen A, Ho AYY, Małecki J, Schroer L, Pinto R, Suzuki T, Grønsberg IA, Sohtome Y, Akakabe M, Weirich S, Kikuchi M, Olsen JV, Dohmae N, Umehara T, Sodeoka M, Siino V, McDonough MA, Eijkelkamp N, Schofield CJ, Jeltsch A, Shinkai Y, Falnes PØ. The methyltransferase METTL9 mediates pervasive 1-methylhistidine modification in mammalian proteomes. Nat Commun 2021; 12:891. [PMID: 33563959 PMCID: PMC7873184 DOI: 10.1038/s41467-020-20670-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 12/10/2020] [Indexed: 12/16/2022] Open
Abstract
Post-translational methylation plays a crucial role in regulating and optimizing protein function. Protein histidine methylation, occurring as the two isomers 1- and 3-methylhistidine (1MH and 3MH), was first reported five decades ago, but remains largely unexplored. Here we report that METTL9 is a broad-specificity methyltransferase that mediates the formation of the majority of 1MH present in mouse and human proteomes. METTL9-catalyzed methylation requires a His-x-His (HxH) motif, where "x" is preferably a small amino acid, allowing METTL9 to methylate a number of HxH-containing proteins, including the immunomodulatory protein S100A9 and the NDUFB3 subunit of mitochondrial respiratory Complex I. Notably, METTL9-mediated methylation enhances respiration via Complex I, and the presence of 1MH in an HxH-containing peptide reduced its zinc binding affinity. Our results establish METTL9-mediated 1MH as a pervasive protein modification, thus setting the stage for further functional studies on protein histidine methylation.
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Affiliation(s)
- Erna Davydova
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316, Oslo, Norway
| | - Tadahiro Shimazu
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Maren Kirstin Schuhmacher
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Magnus E Jakobsson
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research (NNF-CPR), University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
- Department of Immunotechnology, Lund University, Medicon Village, 22100, Lund, Sweden
| | - Hanneke L D M Willemen
- Center for Translational Immunology (CTI), University Medical Center Utrecht, Utrecht University, 3584, Utrecht, EA, The Netherlands
| | - Tongri Liu
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Anders Moen
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316, Oslo, Norway
| | - Angela Y Y Ho
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316, Oslo, Norway
| | - Jędrzej Małecki
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316, Oslo, Norway
| | - Lisa Schroer
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316, Oslo, Norway
| | - Rita Pinto
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316, Oslo, Norway
- Department of Molecular Oncology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Takehiro Suzuki
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Ida A Grønsberg
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316, Oslo, Norway
| | - Yoshihiro Sohtome
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Mai Akakabe
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
| | - Sara Weirich
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Masaki Kikuchi
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Jesper V Olsen
- Proteomics Program, Faculty of Health and Medical Sciences, Novo Nordisk Foundation Center for Protein Research (NNF-CPR), University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Takashi Umehara
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, Yokohama, Japan
| | - Mikiko Sodeoka
- Synthetic Organic Chemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan
- RIKEN Center for Sustainable Resource Science, Wako, Saitama, Japan
| | - Valentina Siino
- Department of Immunotechnology, Lund University, Medicon Village, 22100, Lund, Sweden
| | - Michael A McDonough
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, UK
| | - Niels Eijkelkamp
- Center for Translational Immunology (CTI), University Medical Center Utrecht, Utrecht University, 3584, Utrecht, EA, The Netherlands
| | | | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
| | - Yoichi Shinkai
- Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, Japan.
| | - Pål Ø Falnes
- Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, 0316, Oslo, Norway.
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31
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Lentini JM, Fu D. Monitoring the 5-Methoxycarbonylmethyl-2-Thiouridine (mcm5s2U) Modification Utilizing the Gamma-Toxin Endonuclease. Methods Mol Biol 2021; 2298:197-216. [PMID: 34085247 DOI: 10.1007/978-1-0716-1374-0_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The post-transcriptional modification of tRNAs at the wobble position plays a critical role in proper mRNA decoding and efficient protein synthesis. In particular, certain wobble uridines in eukaryotes are converted to 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2U). The mcm5s2U modification modulates decoding during translation by increasing the stringency of the wobble uridine to base pair with its canonical nucleotide partner, thereby restricting decoding to its cognate codon. Here, we outline a technique to monitor wobble uridine status in mcm5s2U-containing tRNAs using the gamma-toxin endonuclease from the yeast Kluyveromyces lactis that naturally cleaves tRNAs containing the mcm5s2U modification. This technique is coupled to Northern blotting or reverse transcription-PCR to enable rapid and sensitive detection of changes in mcm5s2U modification state.
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Affiliation(s)
- Jenna M Lentini
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, USA
| | - Dragony Fu
- Department of Biology, Center for RNA Biology, University of Rochester, Rochester, NY, USA.
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32
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Xu B, Liu D, Wang Z, Tian R, Zuo Y. Multi-substrate selectivity based on key loops and non-homologous domains: new insight into ALKBH family. Cell Mol Life Sci 2021; 78:129-141. [PMID: 32642789 PMCID: PMC11072825 DOI: 10.1007/s00018-020-03594-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/24/2020] [Accepted: 07/03/2020] [Indexed: 12/16/2022]
Abstract
AlkB homologs (ALKBH) are a family of specific demethylases that depend on Fe2+ and α-ketoglutarate to catalyze demethylation on different substrates, including ssDNA, dsDNA, mRNA, tRNA, and proteins. Previous studies have made great progress in determining the sequence, structure, and molecular mechanism of the ALKBH family. Here, we first review the multi-substrate selectivity of the ALKBH demethylase family from the perspective of sequence and structural evolution. The construction of the phylogenetic tree and the comparison of key loops and non-homologous domains indicate that the paralogs with close evolutionary relationship have similar domain compositions. The structures show that the lack and variations of four key loops change the shape of clefts to cause the differences in substrate affinity, and non-homologous domains may be related to the compatibility of multiple substrates. We anticipate that the new insights into selectivity determinants of the ALKBH family are useful for understanding the demethylation mechanisms.
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Affiliation(s)
- Baofang Xu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Dongyang Liu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zerong Wang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Ruixia Tian
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yongchun Zuo
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
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33
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Wang C, van Tran N, Jactel V, Guérineau V, Graille M. Structural and functional insights into Archaeoglobus fulgidus m2G10 tRNA methyltransferase Trm11 and its Trm112 activator. Nucleic Acids Res 2020; 48:11068-11082. [PMID: 33035335 PMCID: PMC7641767 DOI: 10.1093/nar/gkaa830] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/11/2020] [Accepted: 09/17/2020] [Indexed: 01/20/2023] Open
Abstract
tRNAs play a central role during the translation process and are heavily post-transcriptionally modified to ensure optimal and faithful mRNA decoding. These epitranscriptomics marks are added by largely conserved proteins and defects in the function of some of these enzymes are responsible for neurodevelopmental disorders and cancers. Here, we focus on the Trm11 enzyme, which forms N2-methylguanosine (m2G) at position 10 of several tRNAs in both archaea and eukaryotes. While eukaryotic Trm11 enzyme is only active as a complex with Trm112, an allosteric activator of methyltransferases modifying factors (RNAs and proteins) involved in mRNA translation, former studies have shown that some archaeal Trm11 proteins are active on their own. As these studies were performed on Trm11 enzymes originating from archaeal organisms lacking TRM112 gene, we have characterized Trm11 (AfTrm11) from the Archaeoglobus fulgidus archaeon, which genome encodes for a Trm112 protein (AfTrm112). We show that AfTrm11 interacts directly with AfTrm112 similarly to eukaryotic enzymes and that although AfTrm11 is active as a single protein, its enzymatic activity is strongly enhanced by AfTrm112. We finally describe the first crystal structures of the AfTrm11-Trm112 complex and of Trm11, alone or bound to the methyltransferase inhibitor sinefungin.
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Affiliation(s)
- Can Wang
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, F-91128 Palaiseau, France
| | - Nhan van Tran
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, F-91128 Palaiseau, France
| | - Vincent Jactel
- Laboratoire de Synthèse Organique (LSO), CNRS, Ecole polytechnique, ENSTA, Institut Polytechnique de Paris, F-91128 Palaiseau, France
| | - Vincent Guérineau
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198, Gif-sur-Yvette, France
| | - Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, F-91128 Palaiseau, France
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34
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Reversal of nucleobase methylation by dioxygenases. Nat Chem Biol 2020; 16:1160-1169. [DOI: 10.1038/s41589-020-00675-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 09/11/2020] [Indexed: 12/12/2022]
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35
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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: 2] [Impact Index Per Article: 0.5] [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.
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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.
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36
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Xiao MZ, Liu JM, Xian CL, Chen KY, Liu ZQ, Cheng YY. Therapeutic potential of ALKB homologs for cardiovascular disease. Biomed Pharmacother 2020; 131:110645. [PMID: 32942149 DOI: 10.1016/j.biopha.2020.110645] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 08/05/2020] [Accepted: 08/16/2020] [Indexed: 02/06/2023] Open
Abstract
Cardiovascular diseases (CVDs) are the leading causes of human death. Recently, ALKB homologs, including ALKBH1-8 and FTO, have been found to have a variety of biological functions, such as histone demethylation, RNA demethylation, and DNA demethylation. These functions may regulate the physiological and pathological processes of CVDs, including inflammation, oxidative stress, cell apoptosis, and mitochondrial, endothelial, and fat metabolism dysfunction. In the present review, we summarize the biological functions of ALKB homologs and the relationship between the ALKB homologs and CVDs. Importantly, we discuss the roles of ALKB homologs in the regulation of oxidative stress, inflammation, autophagy, and DNA damage in CVDs, as well as the practical applications of ALKB homologs inhibitors or agonists in treating CVDs. In conclusion, the ALKBH family might be a promising target for CVDs therapy.
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Affiliation(s)
- Ming-Zhu Xiao
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China; School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Jia-Ming Liu
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China; School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Cui-Ling Xian
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China; School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, 510006, China
| | - Keng-Yu Chen
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China; The Second Affiliated Hospital of Guangdong Pharmaceutical University, Yunfu, 527300, China
| | - Zhong-Qiu Liu
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China.
| | - Yuan-Yuan Cheng
- Guangdong Key Laboratory for Translational Cancer Research of Chinese Medicine, Joint Laboratory for Translational Cancer Research of Chinese Medicine of the Ministry of Education of the People's Republic of China, International Institute for Translational Chinese Medicine, School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, 510006, China.
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McCown PJ, Ruszkowska A, Kunkler CN, Breger K, Hulewicz JP, Wang MC, Springer NA, Brown JA. Naturally occurring modified ribonucleosides. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1595. [PMID: 32301288 PMCID: PMC7694415 DOI: 10.1002/wrna.1595] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2020] [Revised: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 12/18/2022]
Abstract
The chemical identity of RNA molecules beyond the four standard ribonucleosides has fascinated scientists since pseudouridine was characterized as the “fifth” ribonucleotide in 1951. Since then, the ever‐increasing number and complexity of modified ribonucleosides have been found in viruses and throughout all three domains of life. Such modifications can be as simple as methylations, hydroxylations, or thiolations, complex as ring closures, glycosylations, acylations, or aminoacylations, or unusual as the incorporation of selenium. While initially found in transfer and ribosomal RNAs, modifications also exist in messenger RNAs and noncoding RNAs. Modifications have profound cellular outcomes at various levels, such as altering RNA structure or being essential for cell survival or organism viability. The aberrant presence or absence of RNA modifications can lead to human disease, ranging from cancer to various metabolic and developmental illnesses such as Hoyeraal–Hreidarsson syndrome, Bowen–Conradi syndrome, or Williams–Beuren syndrome. In this review article, we summarize the characterization of all 143 currently known modified ribonucleosides by describing their taxonomic distributions, the enzymes that generate the modifications, and any implications in cellular processes, RNA structure, and disease. We also highlight areas of active research, such as specific RNAs that contain a particular type of modification as well as methodologies used to identify novel RNA modifications. This article is categorized under:RNA Processing > RNA Editing and Modification
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Affiliation(s)
- Phillip J McCown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Agnieszka Ruszkowska
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Charlotte N Kunkler
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Kurtis Breger
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jacob P Hulewicz
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Matthew C Wang
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Noah A Springer
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
| | - Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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38
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Marcinkowski M, Pilžys T, Garbicz D, Steciuk J, Zugaj D, Mielecki D, Sarnowski TJ, Grzesiuk E. Human and Arabidopsis alpha-ketoglutarate-dependent dioxygenase homolog proteins-New players in important regulatory processes. IUBMB Life 2020; 72:1126-1144. [PMID: 32207231 DOI: 10.1002/iub.2276] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 02/20/2020] [Accepted: 03/08/2020] [Indexed: 12/31/2022]
Abstract
The family of AlkB homolog (ALKBH) proteins, the homologs of Escherichia coli AlkB 2-oxoglutarate (2OG), and Fe(II)-dependent dioxygenase are involved in a number of important regulatory processes in eukaryotic cells including repair of alkylation lesions in DNA, RNA, and nucleoprotein complexes. There are nine human and thirteen Arabidopsis thaliana ALKBH proteins described, which exhibit diversified functions. Among them, human ALKBH5 and FaT mass and Obesity-associated (FTO) protein and Arabidopsis ALKBH9B and ALKBH10B have been recognized as N6 methyladenine (N6 meA) demethylases, the most abundant posttranscriptional modification in mRNA. The FTO protein is reported to be associated with obesity and type 2 diabetes, and involved in multiple other processes, while ALKBH5 is induced by hypoxia. Arabidopsis ALKBH9B is an N6 meA demethylase influencing plant susceptibility to viral infections via m6 A/A ratio control in viral RNA. ALKBH10B has been discovered to be a functional Arabidopsis homolog of FTO; thus, it is also an RNA N6 meA demethylase involved in plant flowering and several other regulatory processes including control of metabolism. High-throughput mass spectrometry showed multiple sites of human ALKBH phosphorylation. In the case of FTO, the type of modified residue decides about the further processing of the protein. This modification may result in subsequent protein ubiquitination and proteolysis, or in the blocking of these processes. However, the impact of phosphorylation on the other ALKBH function and their downstream pathways remains nearly unexplored in both human and Arabidopsis. Therefore, the investigation of evolutionarily conserved functions of ALKBH proteins and their regulatory impact on important cellular processes is clearly called for.
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Affiliation(s)
- Michał Marcinkowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Tomaš Pilžys
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Damian Garbicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jaroslaw Steciuk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Dorota Zugaj
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Damian Mielecki
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Tomasz J Sarnowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Elżbieta Grzesiuk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
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39
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Koliadenko V, Wilanowski T. Additional functions of selected proteins involved in DNA repair. Free Radic Biol Med 2020; 146:1-15. [PMID: 31639437 DOI: 10.1016/j.freeradbiomed.2019.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/16/2019] [Accepted: 10/16/2019] [Indexed: 12/30/2022]
Abstract
Protein moonlighting is a phenomenon in which a single polypeptide chain can perform a number of different unrelated functions. Here we present our analysis of moonlighting in the case of selected DNA repair proteins which include G:T mismatch-specific thymine DNA glycosylase (TDG), methyl-CpG-binding domain protein 4 (MBD4), apurinic/apyrimidinic endonuclease 1 (APE1), AlkB homologs, poly (ADP-ribose) polymerase 1 (PARP-1) and single-strand selective monofunctional uracil DNA glycosylase 1 (SMUG1). Most of their additional functions are not accidental and clear patterns are emerging. Participation in RNA metabolism is not surprising as bases occurring in RNA are the same or very similar to those in DNA. Other common additional function involves regulation of transcription. This is not unexpected as these proteins bind to specific DNA regions for DNA repair, hence they can also be recruited to regulate transcription. Participation in demethylation and replication of DNA appears logical as well. Some of the multifunctional DNA repair proteins play major roles in many diseases, including cancer. However, their moonlighting might prove a major difficulty in the development of new therapies because it will not be trivial to target a single protein function without affecting its other functions that are not related to the disease.
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Affiliation(s)
- Vlada Koliadenko
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096, Warsaw, Poland
| | - Tomasz Wilanowski
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Ilji Miecznikowa 1, 02-096, Warsaw, Poland.
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40
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Genome-wide CRISPR screen identifies ELP5 as a determinant of gemcitabine sensitivity in gallbladder cancer. Nat Commun 2019; 10:5492. [PMID: 31792210 PMCID: PMC6889377 DOI: 10.1038/s41467-019-13420-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 11/04/2019] [Indexed: 02/05/2023] Open
Abstract
Gemcitabine is the first-line treatment for locally advanced and metastatic gallbladder cancer (GBC), but poor gemcitabine response is universal. Here, we utilize a genome-wide CRISPR screen to identify that loss of ELP5 reduces the gemcitabine-induced apoptosis in GBC cells in a P53-dependent manner through the Elongator complex and other uridine 34 (U34) tRNA-modifying enzymes. Mechanistically, loss of ELP5 impairs the integrity and stability of the Elongator complex to abrogate wobble U34 tRNA modification, and directly impedes the wobble U34 modification-dependent translation of hnRNPQ mRNA, a validated P53 internal ribosomal entry site (IRES) trans-acting factor. Downregulated hnRNPQ is unable to drive P53 IRES-dependent translation, but rescuing a U34 modification-independent hnRNPQ mutant could restore P53 translation and gemcitabine sensitivity in ELP5-depleted GBC cells. GBC patients with lower ELP5, hnRNPQ, or P53 expression have poor survival outcomes after gemcitabine chemotherapy. These results indicate that the Elongator/hnRNPQ/P53 axis controls gemcitabine sensitivity in GBC cells. Gemcitabine is used to treat gallbaldder cancer but patient responses are variable. Here, the authors use a genome-wide CRISPR screen and identify the translational elongator protein ELP5 as a protein that is important for mediating gemcitabine-induced apoptosis.
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41
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Leonardi A, Evke S, Lee M, Melendez JA, Begley TJ. Epitranscriptomic systems regulate the translation of reactive oxygen species detoxifying and disease linked selenoproteins. Free Radic Biol Med 2019; 143:573-593. [PMID: 31476365 PMCID: PMC7650020 DOI: 10.1016/j.freeradbiomed.2019.08.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/28/2019] [Accepted: 08/29/2019] [Indexed: 02/07/2023]
Abstract
Here we highlight the role of epitranscriptomic systems in post-transcriptional regulation, with a specific focus on RNA modifying writers required for the incorporation of the 21st amino acid selenocysteine during translation, and the pathologies linked to epitranscriptomic and selenoprotein defects. Epitranscriptomic marks in the form of enzyme-catalyzed modifications to RNA have been shown to be important signals regulating translation, with defects linked to altered development, intellectual impairment, and cancer. Modifications to rRNA, mRNA and tRNA can affect their structure and function, while the levels of these dynamic tRNA-specific epitranscriptomic marks are stress-regulated to control translation. The tRNA for selenocysteine contains five distinct epitranscriptomic marks and the ALKBH8 writer for the wobble uridine (U) has been shown to be vital for the translation of the glutathione peroxidase (GPX) and thioredoxin reductase (TRXR) family of selenoproteins. The reactive oxygen species (ROS) detoxifying selenocysteine containing proteins are a prime examples of how specialized translation can be regulated by specific tRNA modifications working in conjunction with distinct codon usage patterns, RNA binding proteins and specific 3' untranslated region (UTR) signals. We highlight the important role of selenoproteins in detoxifying ROS and provide details on how epitranscriptomic marks and selenoproteins can play key roles in and maintaining mitochondrial function and preventing disease.
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Affiliation(s)
- Andrea Leonardi
- Colleges of Nanoscale Science and Engineering, University at Albany, State University of New York, Albany, NY, USA
| | - Sara Evke
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA
| | - May Lee
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA
| | - J Andres Melendez
- Colleges of Nanoscale Science and Engineering, State University of New York Polytechnic Institute, Albany, NY, USA.
| | - Thomas J Begley
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA; RNA Institute, University at Albany, State University of New York, Albany, NY, USA.
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42
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Wagner A, Hofmeister O, Rolland SG, Maiser A, Aasumets K, Schmitt S, Schorpp K, Feuchtinger A, Hadian K, Schneider S, Zischka H, Leonhardt H, Conradt B, Gerhold JM, Wolf A. Mitochondrial Alkbh1 localizes to mtRNA granules and its knockdown induces the mitochondrial UPR in humans and C. elegans. J Cell Sci 2019; 132:jcs.223891. [PMID: 31434717 DOI: 10.1242/jcs.223891] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 08/13/2019] [Indexed: 12/11/2022] Open
Abstract
The Fe(II) and 2-oxoglutarate-dependent oxygenase Alkb homologue 1 (Alkbh1) has been shown to act on a wide range of substrates, like DNA, tRNA and histones. Thereby different enzymatic activities have been identified including, among others, demethylation of N 3-methylcytosine (m3C) in RNA- and single-stranded DNA oligonucleotides, demethylation of N 1-methyladenosine (m1A) in tRNA or formation of 5-formyl cytosine (f5C) in tRNA. In accordance with the different substrates, Alkbh1 has also been proposed to reside in distinct cellular compartments in human and mouse cells, including the nucleus, cytoplasm and mitochondria. Here, we describe further evidence for a role of human Alkbh1 in regulation of mitochondrial protein biogenesis, including visualizing localization of Alkbh1 into mitochondrial RNA granules with super-resolution 3D SIM microscopy. Electron microscopy and high-resolution respirometry analyses revealed an impact of Alkbh1 level on mitochondrial respiration, but not on mitochondrial structure. Downregulation of Alkbh1 impacts cell growth in HeLa cells and delays development in Caenorhabditis elegans, where the mitochondrial role of Alkbh1 seems to be conserved. Alkbh1 knockdown, but not Alkbh7 knockdown, triggers the mitochondrial unfolded protein response (UPRmt) in C. elegans.
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Affiliation(s)
- Anita Wagner
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Olga Hofmeister
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Stephane G Rolland
- Department of Biology II, Center for Integrated Protein Science Munich, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Andreas Maiser
- Department of Biology II, Center for Integrated Protein Science Munich, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Koit Aasumets
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Sabine Schmitt
- Institute of Toxicology and Environmental Hygiene, School of Medicine, Technical University Munich, 80802 Munich, Germany
| | - Kenji Schorpp
- Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Annette Feuchtinger
- Institute of Pathology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Kamyar Hadian
- Assay Development and Screening Platform, Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Sabine Schneider
- Center for Integrated Protein Science at the Department of Chemistry, Chair of Biochemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748 Garching, Germany
| | - Hans Zischka
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany.,Institute of Toxicology and Environmental Hygiene, School of Medicine, Technical University Munich, 80802 Munich, Germany
| | - Heinrich Leonhardt
- Department of Biology II, Center for Integrated Protein Science Munich, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Barbara Conradt
- Department of Biology II, Center for Integrated Protein Science Munich, Ludwig-Maximilians-University Munich, 82152 Planegg-Martinsried, Germany
| | - Joachim M Gerhold
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Alexander Wolf
- Institute of Molecular Toxicology and Pharmacology, Helmholtz Zentrum München-German Research Center for Environmental Health, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
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43
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Jaroy EG, Acosta-Jimenez L, Hotta R, Goldstein AM, Emblem R, Klungland A, Ougland R. "Too much guts and not enough brains": (epi)genetic mechanisms and future therapies of Hirschsprung disease - a review. Clin Epigenetics 2019; 11:135. [PMID: 31519213 PMCID: PMC6743154 DOI: 10.1186/s13148-019-0718-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 07/29/2019] [Indexed: 12/21/2022] Open
Abstract
Hirschsprung disease is a neurocristopathy, characterized by aganglionosis in the distal bowel. It is caused by failure of the enteric nervous system progenitors to migrate, proliferate, and differentiate in the gut. Development of an enteric nervous system is a tightly regulated process. Both the neural crest cells and the surrounding environment are regulated by different genes, signaling pathways, and morphogens. For this process to be successful, the timing of gene expression is crucial. Hence, alterations in expression of genes specific for the enteric nervous system may contribute to the pathogenesis of Hirschsprung’s disease. Several epigenetic mechanisms contribute to regulate gene expression, such as modifications of DNA and RNA, histone modifications, and microRNAs. Here, we review the current knowledge of epigenetic and epitranscriptomic regulation in the development of the enteric nervous system and its potential significance for the pathogenesis of Hirschsprung’s disease. We also discuss possible future therapies and how targeting epigenetic and epitranscriptomic mechanisms may open new avenues for novel treatment.
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Affiliation(s)
- Emilie G Jaroy
- Clinic for Diagnostics and Intervention and Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, 0027, Oslo, Norway.,Department of Pediatric Surgery, Oslo University Hospital, Rikshospitalet, 0424, Oslo, Norway.,Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317, Oslo, Norway
| | - Lourdes Acosta-Jimenez
- Clinic for Diagnostics and Intervention and Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, 0027, Oslo, Norway.,Department of Pediatric Surgery, Oslo University Hospital, Rikshospitalet, 0424, Oslo, Norway.,Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317, Oslo, Norway
| | - Ryo Hotta
- Department of Pediatric Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Allan M Goldstein
- Department of Pediatric Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Ragnhild Emblem
- Department of Pediatric Surgery, Oslo University Hospital, Rikshospitalet, 0424, Oslo, Norway.,Faculty of Medicine, Institute of Clinical Medicine, University of Oslo, 0317, Oslo, Norway
| | - Arne Klungland
- Clinic for Diagnostics and Intervention and Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, 0027, Oslo, Norway.,Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317, Oslo, Norway
| | - Rune Ougland
- Clinic for Diagnostics and Intervention and Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, 0027, Oslo, Norway. .,Department of Surgery, Baerum Hospital, Vestre Viken Hospital Trust, 3004, Drammen, Norway.
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44
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The Common Partner of Several Methyltransferases TRMT112 Regulates the Expression of N6AMT1 Isoforms in Mammalian Cells. Biomolecules 2019; 9:biom9090422. [PMID: 31466382 PMCID: PMC6769652 DOI: 10.3390/biom9090422] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 08/26/2019] [Accepted: 08/27/2019] [Indexed: 12/28/2022] Open
Abstract
Methylation is a widespread modification occurring in DNA, RNA and proteins. The N6AMT1 (HEMK2) protein has DNA N6-methyladenine as well as the protein glutamine and histone lysine methyltransferase activities. The human genome encodes two different isoforms of N6AMT1, the major isoform and the alternatively spliced isoform, where the substrate binding motif is missing. Several RNA methyltransferases involved in ribosome biogenesis, tRNA methylation and translation interact with the common partner, the TRMT112 protein. In this study, we show that TRMT112 regulates the expression of N6AMT1 isoforms in mammalian cells. Both isoforms are equally expressed on mRNA level, but only isoform 1 is detected on the protein level in human cells. We show that the alternatively spliced isoform is not able to interact with TRMT112 and when translated, is rapidly degraded from the cells. This suggests that TRMT112 is involved in cellular quality control ensuring that N6AMT1 isoform with missing substrate binding domain is eliminated from the cells. The down-regulation of TRMT112 does not affect the N6AMT1 protein levels in cells, suggesting that the two proteins of TRMT112 network, WBSCR22 and N6AMT1, are differently regulated by their common cofactor.
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45
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Salem ESB, Vonberg AD, Borra VJ, Gill RK, Nakamura T. RNAs and RNA-Binding Proteins in Immuno-Metabolic Homeostasis and Diseases. Front Cardiovasc Med 2019; 6:106. [PMID: 31482095 PMCID: PMC6710452 DOI: 10.3389/fcvm.2019.00106] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 07/17/2019] [Indexed: 12/16/2022] Open
Abstract
The increasing prevalence of worldwide obesity has emerged as a major risk factor for type 2 diabetes (T2D), hepatosteatosis, and cardiovascular disease. Accumulating evidence indicates that obesity has strong inflammatory underpinnings tightly linked to the development of metabolic diseases. However, the molecular mechanisms by which obesity induces aberrant inflammation associated with metabolic diseases are not yet clearly defined. Recently, RNAs have emerged as important regulators of stress responses and metabolism. RNAs are subject to changes in modification status, higher-order structure, and cellular localization; all of which could affect the affinity for RNA-binding proteins (RBPs) and thereby modify the RNA-RBP networks. Proper regulation and management of RNA characteristics are fundamental to cellular and organismal homeostasis, as well as paramount to health. Identification of multiple single nucleotide polymorphisms (SNPs) within loci of fat mass- and obesity-associated protein (FTO) gene, an RNA demethylase, through genome-wide association studies (GWAS) of T2D, and functional assessments of FTO in mice, support the concept that disruption in RNA modifications leads to the development of human diseases including obesity and metabolic disorder. In obesity, dynamic alterations in modification and localization of RNAs appear to modulate the RNA-RBP networks and activate proinflammatory RBPs, such as double-stranded RNA (dsRNA)-dependent protein kinase (PKR), Toll-like receptor (TLR) 3 and TLR7, and RNA silencing machinery. These changes induce aberrant inflammation and the development of metabolic diseases. This review will describe the current understanding of the underlying causes of these common and altered characteristics of RNA-RBP networks which will pave the way for developing novel approaches to tackle the pandemic issue of obesity.
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Affiliation(s)
- Esam S B Salem
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pharmacology and Systems Physiology, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Andrew D Vonberg
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Vishnupriya J Borra
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Rupinder K Gill
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | - Takahisa Nakamura
- Division of Endocrinology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, United States.,Department of Metabolic Bioregulation, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
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46
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Abstract
DNA modifications are a major form of epigenetic regulation that eukaryotic cells utilize in concert with histone modifications. While much work has been done elucidating the role of 5-methylcytosine over the past several decades, only recently has it been recognized that N(6)-methyladenine (N6-mA) is present in quantifiable and biologically active levels in the DNA of eukaryotic cells. Unlike prokaryotes which utilize N6-mA to recognize "self" from "foreign" DNA, eukaryotes have been found to use N6-mA in varying ways, from regulating transposable elements to gene regulation in response to hypoxia and stress. In this review, we examine the current state of the N6-mA in research field, and the current understanding of the biochemical mechanisms which deposit and remove N6-mA from the eukaryotic genome.
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Affiliation(s)
- Myles H Alderman
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Andrew Z Xiao
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, 06520, USA.
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47
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Monies D, Vågbø CB, Al-Owain M, Alhomaidi S, Alkuraya FS. Recessive Truncating Mutations in ALKBH8 Cause Intellectual Disability and Severe Impairment of Wobble Uridine Modification. Am J Hum Genet 2019; 104:1202-1209. [PMID: 31079898 DOI: 10.1016/j.ajhg.2019.03.026] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 03/26/2019] [Indexed: 01/17/2023] Open
Abstract
The wobble hypothesis was proposed to explain the presence of fewer tRNAs than possible codons. The wobble nucleoside position in the anticodon stem-loop undergoes a number of modifications that help maintain the efficiency and fidelity of translation. AlkB homolog 8 (ALKBH8) is an atypical member of the highly conserved AlkB family of dioxygenases and is involved in the formation of mcm5s2U, (S)-mchm5U, (R)-mchm5U, mcm5U, and mcm5Um at the anticodon wobble uridines of specific tRNAs. In two multiplex consanguineous families, we identified two homozygous truncating ALKBH8 mutations causing intellectual disability. Analysis of tRNA derived from affected individuals showed the complete absence of these modifications, consistent with the presumptive loss of function of the variants. Our results highlight the sensitivity of the brain to impaired wobble modification and expand the list of intellectual-disability syndromes caused by mutations in genes related to tRNA modification.
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48
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Moore C, Meng B. Prediction of the molecular boundary and functionality of novel viral AlkB domains using homology modelling and principal component analysis. J Gen Virol 2019; 100:691-703. [PMID: 30835193 DOI: 10.1099/jgv.0.001237] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Alkylation B (AlkB) proteins are ubiquitous among diverse cellular organisms, where they act to reverse the damage in DNA and RNA due to methylation, such as 1-methyladenine and 3-methylcytosine. This process is found in virtually all forms of life, with the notable exception of archaea and yeast. This protein family is so significant to all forms of life that it was recently discovered that an AlkB domain is encoded as part of the replicase (poly)protein in a small subset of single-stranded, positive-sense RNA viruses, mainly belonging to the families Alphaflexiviridae, Betaflexiviridae and Closteroviridae. Interestingly, these AlkB-containing viruses are mostly important pathogens of woody perennials such as fruit crops, and are responsible for significant economic losses. As a newly identified protein domain in RNA viruses, the origin and molecular boundary of the viral AlkB domain, as well as its function in viral replication, virus-host interactions and infection are unknown. This is due to the limited sequence conservation of viral AlkB domains, especially at the N-terminal region corresponding to the nucleotide recognition lid. Here we apply several independent analytical approaches (homology modelling, principal component analysis and the Shannon diversity index) for the first time, to better understand this viral domain. We conclude that a functional AlkB domain in these viruses comprises approximately 150-170 amino acids. Although the exact function of the viral AlkB domain remains unknown, we hypothesize that it counteracts a host defence mechanism that is unique in these perennial plants and was acquired to enhance the long-term survival of these RNA viruses that infect perennial plants. Interestingly, a majority of these viruses have a tissue tropism for the phloem. Furthermore, we identified several additional amino acid residues that are uniquely conserved among viral AlkBs. This work helps to provide a foundation for further investigation of the function of viral AlkBs and critical residues involved in AlkB function.
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Affiliation(s)
- Clayton Moore
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
| | - Baozhong Meng
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada
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Borowski R, Dziergowska A, Sochacka E, Leszczynska G. Novel entry to the synthesis of ( S)- and ( R)-5-methoxycarbonylhydroxymethyluridines – a diastereomeric pair of wobble tRNA nucleosides. RSC Adv 2019; 9:40507-40512. [PMID: 35542686 PMCID: PMC9076229 DOI: 10.1039/c9ra08548c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 11/28/2019] [Indexed: 11/30/2022] Open
Abstract
Two novel methods for the preparation of the virtually equimolar mixtures of (S)- and (R)-diastereomers of 5-methoxycarbonylhydroxymethyluridine (mchm5U) have been developed. The first method involved α-hydroxylation of a 5-malonate ester derivative of uridine (5) with SeO2, followed by transformation to (S)- and (R)-5-carboxymethyluridines (cm5U, 8) and, finally, into the corresponding methyl esters. In the second approach, (S)- and (R)-mchm5-uridines were obtained starting from 5-formyluridine derivative (9) by hydrolysis of the imidate salt (11) prepared in the acid catalyzed reaction of 5-cyanohydrin-containing uridine (10b) with methyl alcohol. In both methods, the (S)- and (R) diastereomers of mchm5U were effectively separated by preparative C18 RP HPLC. Two novel methods for the preparation of the virtually equimolar mixtures of (S)- and (R)-diastereomers of 5-methoxycarbonylhydroxymethyluridine (mchm5U) have been developed.![]()
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Affiliation(s)
- Robert Borowski
- Institute of Organic Chemistry
- Lodz University of Technology
- 90-924 Lodz
- Poland
| | | | - Elzbieta Sochacka
- Institute of Organic Chemistry
- Lodz University of Technology
- 90-924 Lodz
- Poland
| | - Grazyna Leszczynska
- Institute of Organic Chemistry
- Lodz University of Technology
- 90-924 Lodz
- Poland
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Vasilieva EN, Laptev IG, Sergiev PV, Dontsova OA. The Common Partner of Several Methyltransferases Modifying the Components of The Eukaryotic Translation Apparatus. Mol Biol 2018. [DOI: 10.1134/s0026893318060171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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