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Silva GLA, Tosi LRO, McCulloch R, Black JA. Unpicking the Roles of DNA Damage Protein Kinases in Trypanosomatids. Front Cell Dev Biol 2021; 9:636615. [PMID: 34422791 PMCID: PMC8377203 DOI: 10.3389/fcell.2021.636615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 07/13/2021] [Indexed: 12/31/2022] Open
Abstract
To preserve genome integrity when faced with DNA lesions, cells activate and coordinate a multitude of DNA repair pathways to ensure timely error correction or tolerance, collectively called the DNA damage response (DDR). These interconnecting damage response pathways are molecular signal relays, with protein kinases (PKs) at the pinnacle. Focused efforts in model eukaryotes have revealed intricate aspects of DNA repair PK function, including how they direct DDR pathways and how repair reactions connect to wider cellular processes, including DNA replication and transcription. The Kinetoplastidae, including many parasites like Trypanosoma spp. and Leishmania spp. (causative agents of debilitating, neglected tropical infections), exhibit peculiarities in several core biological processes, including the predominance of multigenic transcription and the streamlining or repurposing of DNA repair pathways, such as the loss of non-homologous end joining and novel operation of nucleotide excision repair (NER). Very recent studies have implicated ATR and ATM kinases in the DDR of kinetoplastid parasites, whereas DNA-dependent protein kinase (DNA-PKcs) displays uncertain conservation, questioning what functions it fulfills. The wide range of genetic manipulation approaches in these organisms presents an opportunity to investigate DNA repair kinase roles in kinetoplastids and to ask if further kinases are involved. Furthermore, the availability of kinase inhibitory compounds, targeting numerous eukaryotic PKs, could allow us to test the suitability of DNA repair PKs as novel chemotherapeutic targets. Here, we will review recent advances in the study of trypanosomatid DNA repair kinases.
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Affiliation(s)
- Gabriel L A Silva
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom.,Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Luiz R O Tosi
- Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Richard McCulloch
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Jennifer Ann Black
- The Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom.,Department of Cell and Molecular Biology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
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2
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Paull TT. DNA damage and regulation of protein homeostasis. DNA Repair (Amst) 2021; 105:103155. [PMID: 34116476 DOI: 10.1016/j.dnarep.2021.103155] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 10/21/2022]
Abstract
The accumulation of unrepaired DNA lesions is associated with many pathological outcomes in humans, particularly in neurodegenerative diseases and in normal aging. Evidence supporting a causal role for DNA damage in the onset and progression of neurodegenerative disease has come from rare human patients with mutations in DNA damage response genes as well as from model organisms; however, the generality of this relationship in the normal population is unclear. In addition, the relevance of DNA damage in the context of proteotoxic stress-the widely accepted paradigm for pathology during neurodegeneration-is not well understood. Here, observations supporting intertwined roles of DNA damage and proteotoxicity in aging-related neurological outcomes are reviewed, with particular emphasis on recent insights into the relationships between DNA repair and autophagy, the ubiquitin proteasome system, formation of protein aggregates, poly-ADP-ribose polymerization, and transcription-driven DNA lesions.
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Affiliation(s)
- Tanya T Paull
- The University of Texas at Austin, Department of Molecular Biosciences, Austin, TX, 78712, United States.
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Schmidt H, Malik A, Bicker A, Poetzsch G, Avivi A, Shams I, Hankeln T. Hypoxia tolerance, longevity and cancer-resistance in the mole rat Spalax - a liver transcriptomics approach. Sci Rep 2017; 7:14348. [PMID: 29084988 PMCID: PMC5662568 DOI: 10.1038/s41598-017-13905-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 09/29/2017] [Indexed: 12/20/2022] Open
Abstract
The blind subterranean mole rat Spalax shows a remarkable tolerance to hypoxia, cancer-resistance and longevity. Unravelling the genomic basis of these adaptations will be important for biomedical applications. RNA-Seq gene expression data were obtained from normoxic and hypoxic Spalax and rat liver tissue. Hypoxic Spalax broadly downregulates genes from major liver function pathways. This energy-saving response is likely a crucial adaptation to low oxygen levels. In contrast, the hypoxia-sensitive rat shows massive upregulation of energy metabolism genes. Candidate genes with plausible connections to the mole rat’s phenotype, such as important key genes related to hypoxia-tolerance, DNA damage repair, tumourigenesis and ageing, are substantially higher expressed in Spalax than in rat. Comparative liver transcriptomics highlights the importance of molecular adaptations at the gene regulatory level in Spalax and pinpoints a variety of starting points for subsequent functional studies.
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Affiliation(s)
- Hanno Schmidt
- Molecular Genetics and Genome Analysis, Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University, Johann Joachim Becher-Weg 30 A, D-55128, Mainz, Germany.,Genomic Evolution and Climate, Senckenberg Biodiversity and Climate Research Centre (SBiK-F), D-60325, Frankfurt am Main, Germany
| | - Assaf Malik
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa, 31905, Israel
| | - Anne Bicker
- Molecular Genetics and Genome Analysis, Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University, Johann Joachim Becher-Weg 30 A, D-55128, Mainz, Germany
| | - Gesa Poetzsch
- Molecular Genetics and Genome Analysis, Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University, Johann Joachim Becher-Weg 30 A, D-55128, Mainz, Germany
| | - Aaron Avivi
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa, 31905, Israel
| | - Imad Shams
- Institute of Evolution, University of Haifa, Mount Carmel, Haifa, 31905, Israel.
| | - Thomas Hankeln
- Molecular Genetics and Genome Analysis, Institute of Organismic and Molecular Evolution, Johannes Gutenberg-University, Johann Joachim Becher-Weg 30 A, D-55128, Mainz, Germany.
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Yu X, Long YC, Shen HM. Differential regulatory functions of three classes of phosphatidylinositol and phosphoinositide 3-kinases in autophagy. Autophagy 2015; 11:1711-28. [PMID: 26018563 PMCID: PMC4824607 DOI: 10.1080/15548627.2015.1043076] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 04/11/2015] [Accepted: 04/14/2015] [Indexed: 02/06/2023] Open
Abstract
Autophagy is an evolutionarily conserved and exquisitely regulated self-eating cellular process with important biological functions. Phosphatidylinositol 3-kinases (PtdIns3Ks) and phosphoinositide 3-kinases (PI3Ks) are involved in the autophagic process. Here we aim to recapitulate how 3 classes of these lipid kinases differentially regulate autophagy. Generally, activation of the class I PI3K suppresses autophagy, via the well-established PI3K-AKT-MTOR (mechanistic target of rapamycin) complex 1 (MTORC1) pathway. In contrast, the class III PtdIns3K catalytic subunit PIK3C3/Vps34 forms a protein complex with BECN1 and PIK3R4 and produces phosphatidylinositol 3-phosphate (PtdIns3P), which is required for the initiation and progression of autophagy. The class II enzyme emerged only recently as an alternative source of PtdIns3P and autophagic initiator. However, the orthodox paradigm is challenged by findings that the PIK3CB catalytic subunit of class I PI3K acts as a positive regulator of autophagy, and PIK3C3 was thought to be an amino acid sensor for MTOR, which curbs autophagy. At present, a number of PtdIns3K and PI3K inhibitors, including specific PIK3C3 inhibitors, have been developed for suppression of autophagy and for clinical applications in autophagy-related human diseases.
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Affiliation(s)
- Xinlei Yu
- a Department of Biochemistry; Yong Loo Lin School of Medicine, National University of Singapore ; Singapore
| | - Yun Chau Long
- a Department of Biochemistry; Yong Loo Lin School of Medicine, National University of Singapore ; Singapore
| | - Han-Ming Shen
- b Department of Physiology; Yong Loo Lin School of Medicine, National University of Singapore ; Singapore
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Suetomi K, Mereiter S, Mori C, Takanami T, Higashitani A. Caenorhabditis elegans ATR checkpoint kinase ATL-1 influences life span through mitochondrial maintenance. Mitochondrion 2013; 13:729-35. [PMID: 23434802 DOI: 10.1016/j.mito.2013.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 01/24/2013] [Accepted: 02/13/2013] [Indexed: 11/17/2022]
Abstract
ATR is highly conserved in all eukaryotes and functions as a cell-cycle nuclear checkpoint kinase. In mammals, ATR is essential whose complete absence results in early embryonic lethality and its hypomorphic mutation causes a complex disease known as Seckel syndrome. However, molecular mechanisms that cause a wide variety of symptoms including accelerated aging have remained unclear. Similarly, in the nematode Caenorhabditis elegans, a deletion mutant of ATR ortholog atl-1 appears to develop into normal adults, but their eggs do not hatch and die at early embryogenesis. Here we show that the parental worms of atl-1 defective mutant achieved longevity. Transcription levels of certain superoxide dismutase genes, sod-3 and -5 and enzymatic activity of superoxide dismutases significantly increased in the mutant. Furthermore, lipid peroxidation such as a formation of malondialdehyde was attenuated. Expressions of other genes regulated by DAF-16/FOXO transcription factor were also altered. In contrast, the mutant became hypersensitive to rotenone and ethidium bromide. Compared with the wild type the mitochondrial DNA copy number in the mutant was lesser and its proliferation is more severely inhibited in the presence of rotenone. These results suggest that C. elegans ATL-1 is involved not only in the nuclear checkpoint control but also in the mitochondrial maintenance, and its dysfunction activates mild oxidative stress response, resulting in an alteration of life span.
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Affiliation(s)
- Kazuhiro Suetomi
- Graduate School of Life Sciences, Tohoku University, Sendai, 980-8577, Japan
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