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Wei Q, Chen L, Luo W, Chen C, Shi Y, Xie J, Xie X, Luo HB. PDE12 disrupts mitochondrial oxidative phosphorylation and mediates mitochondrial dysfunction to induce oral mucosal epithelial barrier damage in oral submucous fibrosis. Eur J Pharmacol 2024; 967:176353. [PMID: 38325798 DOI: 10.1016/j.ejphar.2024.176353] [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: 11/01/2023] [Revised: 01/16/2024] [Accepted: 01/22/2024] [Indexed: 02/09/2024]
Abstract
Oral submucous fibrosis (OSF) is a chronic oral mucosal disease. The pathological changes of OSF include epithelial damage and subepithelial matrix fibrosis. This study aimed to reveal the epithelial injury mechanism of OSF. A histopathological method was used to analyze oral mucosal tissue from OSF patients and OSF rats. The expression of PDE12 in the oral epithelium was analyzed by immunohistochemistry. The epithelial-mesenchymal transition (EMT) and tight junction proteins in arecoline-treated HOKs were explored by western blotting. Epithelial leakage was assessed by transepithelial electrical resistance and lucifer yellow permeability. The expression of PDE12 and the mitochondrial morphology, mitochondrial permeability transition pore opening, mitochondrial membrane potential, and mitochondrial reactive oxygen species (mtROS) were evaluated in arecoline-induced HOKs. Oxidative phosphorylation (OXPHOS) complexes and ATP content were also explored in HOKs. The results showed significant overexpression of PDE12 in oral mucosal tissue from OSF patients and rats. PDE12 was also overexpressed and aggregated in mitochondria in arecoline-induced HOKs, resulting in dysfunction of OXPHOS and impaired mitochondrial function. An EMT, disruption of tight junctions with epithelial leakage, and extracellular matrix remodeling were also observed. PDE12 overexpression induced by PDE12 plasmid transfection enhanced the mtROS level and interfered with occludin protein localization in HOKs. Interestingly, knockdown of PDE12 clearly ameliorated arecoline-induced mitochondrial dysfunction and epithelial barrier dysfunction in HOKs. Therefore, we concluded that overexpression of PDE12 impaired mitochondrial OXPHOS and mitochondrial function and subsequently impaired epithelial barrier function, ultimately leading to OSF. We suggest that PDE12 may be a new potential target against OSF.
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Affiliation(s)
- Qihui Wei
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, Hainan Province, China
| | - Linlin Chen
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, Hainan Province, China
| | - Wen Luo
- Department of Stomatology, The First Affiliated Hospital of Hainan Medical University, Haikou, 570102, Hainan Province, China
| | - Cailian Chen
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, Hainan Province, China
| | - Yuqing Shi
- School of Life Sciences, Hainan University, Haikou, 570228, Hainan Province, China
| | - Jinmei Xie
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, Hainan Province, China
| | - Xi Xie
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, Hainan Province, China.
| | - Hai-Bin Luo
- Key Laboratory of Tropical Biological Resources of Ministry of Education, School of Pharmaceutical Sciences, Hainan University, Haikou, 570228, Hainan Province, China.
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2
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Chitwood DG, Uy L, Fu W, Klaubert SR, Harcum SW, Saski CA. Dynamics of Amino Acid Metabolism, Gene Expression, and Circulomics in a Recombinant Chinese Hamster Ovary Cell Line Adapted to Moderate and High Levels of Extracellular Lactate. Genes (Basel) 2023; 14:1576. [PMID: 37628627 PMCID: PMC10454118 DOI: 10.3390/genes14081576] [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: 07/10/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023] Open
Abstract
The accumulation of metabolic wastes in cell cultures can diminish product quality, reduce productivity, and trigger apoptosis. The limitation or removal of unintended waste products from Chinese hamster ovary (CHO) cell cultures has been attempted through multiple process and genetic engineering avenues with varied levels of success. One study demonstrated a simple method to reduce lactate and ammonia production in CHO cells with adaptation to extracellular lactate; however, the mechanism behind adaptation was not certain. To address this profound gap, this study characterizes the phenotype of a recombinant CHO K-1 cell line that was gradually adapted to moderate and high levels of extracellular lactate and examines the genomic content and role of extrachromosomal circular DNA (eccDNA) and gene expression on the adaptation process. More than 500 genes were observed on eccDNAs. Notably, more than 1000 genes were observed to be differentially expressed at different levels of lactate adaptation, while only 137 genes were found to be differentially expressed between unadapted cells and cells adapted to grow in high levels of lactate; this suggests stochastic switching as a potential stress adaptation mechanism in CHO cells. Further, these data suggest alanine biosynthesis as a potential stress-mitigation mechanism for excess lactate in CHO cells.
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Affiliation(s)
- Dylan G. Chitwood
- Department of Bioengineering, Clemson University, Clemson, SC 29634, USA; (D.G.C.); (L.U.); (S.W.H.)
| | - Lisa Uy
- Department of Bioengineering, Clemson University, Clemson, SC 29634, USA; (D.G.C.); (L.U.); (S.W.H.)
| | - Wanfang Fu
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA;
| | - Stephanie R. Klaubert
- Department of Chemical & Biomolecular Engineering, Clemson University, Clemson, SC 29634, USA;
| | - Sarah W. Harcum
- Department of Bioengineering, Clemson University, Clemson, SC 29634, USA; (D.G.C.); (L.U.); (S.W.H.)
- Department of Chemical & Biomolecular Engineering, Clemson University, Clemson, SC 29634, USA;
| | - Christopher A. Saski
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA;
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3
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Ma J, Sun L, Gao W, Li Y, Dong D. RNA binding protein: coordinated expression between the nuclear and mitochondrial genomes in tumors. J Transl Med 2023; 21:512. [PMID: 37507746 PMCID: PMC10386658 DOI: 10.1186/s12967-023-04373-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Mitochondria are the only organelles regulated by two genomes. The coordinated translation of nuclear DNA (nDNA) and mitochondrial DNA (mtDNA), which together co-encode the subunits of the oxidative phosphorylation (OXPHOS) complex, is critical for determining the metabolic plasticity of tumor cells. RNA-binding protein (RBP) is a post-transcriptional regulatory factor that plays a pivotal role in determining the fate of mRNA. RBP rapidly and effectively reshapes the mitochondrial proteome in response to intracellular and extracellular stressors, mediating the cytoplasmic and mitochondrial translation balance to adjust mitochondrial respiratory capacity and provide energy for tumor cells to adapt to different environmental pressures and growth needs. This review highlights the ability of RBPs to use liquid-liquid phase separation (LLPS) as a platform for translation regulation, integrating nuclear-mitochondrial positive and retrograde signals to coordinate cross-department translation, reshape mitochondrial energy metabolism, and promote the development and survival of tumor cells.
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Affiliation(s)
- Jiaoyan Ma
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Liankun Sun
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Weinan Gao
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Yang Li
- Department of Physiology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China
| | - Delu Dong
- Department of Pathophysiology, College of Basic Medical Sciences, Jilin University, Changchun, 130021, China.
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4
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ANGEL2 phosphatase activity is required for non-canonical mitochondrial RNA processing. Nat Commun 2022; 13:5750. [PMID: 36180430 PMCID: PMC9525292 DOI: 10.1038/s41467-022-33368-9] [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: 03/15/2022] [Accepted: 09/14/2022] [Indexed: 11/18/2022] Open
Abstract
Canonical RNA processing in mammalian mitochondria is defined by tRNAs acting as recognition sites for nucleases to release flanking transcripts. The relevant factors, their structures, and mechanism are well described, but not all mitochondrial transcripts are punctuated by tRNAs, and their mode of processing has remained unsolved. Using Drosophila and mouse models, we demonstrate that non-canonical processing results in the formation of 3′ phosphates, and that phosphatase activity by the carbon catabolite repressor 4 domain-containing family member ANGEL2 is required for their hydrolysis. Furthermore, our data suggest that members of the FAST kinase domain-containing protein family are responsible for these 3′ phosphates. Our results therefore propose a mechanism for non-canonical RNA processing in metazoan mitochondria, by identifying the role of ANGEL2. A subset of mitochondrial transcripts is not flanked by tRNAs and thus does not conform to the canonical mode of processing. Here, Clemente et al. demonstrate that phosphatase activity of ANGEL2 is required for correct processing of these transcripts.
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5
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Jiang H, Zhang Y, Yue J, Shi Y, Xiao B, Xiao W, Luo Z. Non-coding RNAs: The Neuroinflammatory Regulators in Neurodegenerative Diseases. Front Neurol 2022; 13:929290. [PMID: 36034298 PMCID: PMC9414873 DOI: 10.3389/fneur.2022.929290] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/23/2022] [Indexed: 01/09/2023] Open
Abstract
As a common indication of nervous system diseases, neuroinflammation has attracted more and more attention, especially in the process of a variety of neurodegenerative diseases, such as Alzheimer's disease and Parkinson's disease. Two types of non-coding RNAs (ncRNAs) are widely involved in the process of neuroinflammation in neurodegenerative diseases, namely long non-coding RNAs (lncRNAs) and microRNAs (miRNAs). However, no research has systematically summarized that lncRNAs and miRNAs regulate neurodegenerative diseases through neuroinflammatory mechanisms. In this study, we summarize four main mechanisms of lncRNAs and miRNAs involved in neuroinflammation in neurodegenerative diseases, including the imbalance between proinflammatory and neuroprotective cells in microglia and astrocytes, NLRP3 inflammasome, oxidative stress, and mitochondrial dysfunction, and inflammatory mediators. We hope to clarify the regulatory mechanism of lncRNAs and miRNAs in neurodegenerative diseases and provide new insights into the etiological treatment of neurodegenerative diseases from the perspective of neuroinflammation.
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Affiliation(s)
- Hao Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- Xiangya School of Medicine, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Ying Zhang
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Juan Yue
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Yuchen Shi
- Xiangya School of Medicine, Central South University, Changsha, China
| | - Bo Xiao
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Clinical Research Center for Epileptic Disease of Hunan Province, Central South University, Changsha, China
| | - Wenbiao Xiao
- Department of Geriatrics, The Second Xiangya Hospital of Central South University, Changsha, China
- *Correspondence: Wenbiao Xiao
| | - Zhaohui Luo
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- Clinical Research Center for Epileptic Disease of Hunan Province, Central South University, Changsha, China
- Zhaohui Luo
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6
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How RNases Shape Mitochondrial Transcriptomes. Int J Mol Sci 2022; 23:ijms23116141. [PMID: 35682820 PMCID: PMC9181182 DOI: 10.3390/ijms23116141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/17/2022] Open
Abstract
Mitochondria are the power houses of eukaryote cells. These endosymbiotic organelles of prokaryote origin are considered as semi-autonomous since they have retained a genome and fully functional gene expression mechanisms. These pathways are particularly interesting because they combine features inherited from the bacterial ancestor of mitochondria with characteristics that appeared during eukaryote evolution. RNA biology is thus particularly diverse in mitochondria. It involves an unexpectedly vast array of factors, some of which being universal to all mitochondria and others being specific from specific eukaryote clades. Among them, ribonucleases are particularly prominent. They play pivotal functions such as the maturation of transcript ends, RNA degradation and surveillance functions that are required to attain the pool of mature RNAs required to synthesize essential mitochondrial proteins such as respiratory chain proteins. Beyond these functions, mitochondrial ribonucleases are also involved in the maintenance and replication of mitochondrial DNA, and even possibly in the biogenesis of mitochondrial ribosomes. The diversity of mitochondrial RNases is reviewed here, showing for instance how in some cases a bacterial-type enzyme was kept in some eukaryotes, while in other clades, eukaryote specific enzymes were recruited for the same function.
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7
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Organization and expression of the mammalian mitochondrial genome. Nat Rev Genet 2022; 23:606-623. [PMID: 35459860 DOI: 10.1038/s41576-022-00480-x] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 02/07/2023]
Abstract
The mitochondrial genome encodes core subunits of the respiratory chain that drives oxidative phosphorylation and is, therefore, essential for energy conversion. Advances in high-throughput sequencing technologies and cryoelectron microscopy have shed light on the structure and organization of the mitochondrial genome and revealed unique mechanisms of mitochondrial gene regulation. New animal models of impaired mitochondrial protein synthesis have shown how the coordinated regulation of the cytoplasmic and mitochondrial translation machineries ensures the correct assembly of the respiratory chain complexes. These new technologies and disease models are providing a deeper understanding of mitochondrial genome organization and expression and of the diseases caused by impaired energy conversion, including mitochondrial, neurodegenerative, cardiovascular and metabolic diseases. They also provide avenues for the development of treatments for these conditions.
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8
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Specificity and Mechanism of Coronavirus, Rotavirus, and Mammalian Two-Histidine Phosphoesterases That Antagonize Antiviral Innate Immunity. mBio 2021; 12:e0178121. [PMID: 34372695 PMCID: PMC8406329 DOI: 10.1128/mbio.01781-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The 2′,5′-oligoadenylate (2-5A)-dependent endoribonuclease, RNase L, is a principal mediator of the interferon (IFN) antiviral response. Therefore, the regulation of cellular levels of 2-5A is a key point of control in antiviral innate immunity. Cellular 2-5A levels are determined by IFN-inducible 2′,5′-oligoadenylate synthetases (OASs) and by enzymes that degrade 2-5A. Importantly, many coronaviruses (CoVs) and rotaviruses encode 2-5A-degrading enzymes, thereby antagonizing RNase L and its antiviral effects. A-kinase-anchoring protein 7 (AKAP7), a mammalian counterpart, could possibly limit tissue damage from excessive or prolonged RNase L activation during viral infections or from self-double-stranded RNAs that activate OAS. We show that these enzymes, members of the two-histidine phosphoesterase (2H-PE) superfamily, constitute a subfamily referred here as 2′,5′-PEs. 2′,5′-PEs from the mouse CoV mouse hepatitis virus (MHV) (NS2), Middle East respiratory syndrome coronavirus (MERS-CoV) (NS4b), group A rotavirus (VP3), and mouse (AKAP7) were investigated for their evolutionary relationships and activities. While there was no activity against 3′,5′-oligoribonucleotides, they all cleaved 2′,5′-oligoadenylates efficiently but with variable activity against other 2′,5′-oligonucleotides. The 2′,5′-PEs are shown to be metal ion-independent enzymes that cleave trimer 2-5A (2′,5′-p3A3) producing mono- or diadenylates with 2′,3′-cyclic phosphate termini. Our results suggest that the elimination of 2-5A might be the sole function of viral 2′,5′-PEs, thereby promoting viral escape from innate immunity by preventing or limiting the activation of RNase L.
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9
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Yang H, Desai N. Purification of Mitochondrial Ribosomes with the Translocase Oxa1L from HEK Cells. Bio Protoc 2021; 11:e4110. [PMID: 34458404 PMCID: PMC8376546 DOI: 10.21769/bioprotoc.4110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/18/2021] [Accepted: 04/20/2021] [Indexed: 11/02/2022] Open
Abstract
Mitochondrial ribosomes (mitoribosomes) perform protein synthesis inside mitochondria, the organelles responsible for energy conversion and adenosine triphosphate (ATP) production in eukaryotic cells. To investigate their functions and structures, large-scale purification of intact mitoribosomes from mitochondria-rich animal tissues or HEK cells have been developed. However, the fast purification of mitoribosomes anchored to the mitochondrial inner membrane in complex with the Oxa1L translocase remains particularly challenging. Herein, we present a protocol recently developed and modified in our lab that provides details for the efficient isolation of intact mitoribosomes with its translocase Oxa1L. We combined the cell culture of PDE12-/- or wild-type HEK293 cell lines with the isolation of mitochondria and the purification steps used for the biochemical and structural studies of mitoribosomes and Oxa1L. Graphic abstract: Schematic procedure for the purification of mitoribosomes from HEK cells. The protocol described herein includes two main sections: 1) isolation of mitochondria from HEK cells; and 2) purification of mitoribosome-Oxa1L from mitochondria. RB: Resuspension Buffer (see Recipes) (Created with BioRender.com).
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10
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D’Souza AR, Van Haute L, Powell CA, Mutti CD, Páleníková P, Rebelo-Guiomar P, Rorbach J, Minczuk M. YbeY is required for ribosome small subunit assembly and tRNA processing in human mitochondria. Nucleic Acids Res 2021; 49:5798-5812. [PMID: 34037799 PMCID: PMC8191802 DOI: 10.1093/nar/gkab404] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 04/20/2021] [Accepted: 05/06/2021] [Indexed: 12/12/2022] Open
Abstract
Mitochondria contain their own translation apparatus which enables them to produce the polypeptides encoded in their genome. The mitochondrially-encoded RNA components of the mitochondrial ribosome require various post-transcriptional processing steps. Additional protein factors are required to facilitate the biogenesis of the functional mitoribosome. We have characterized a mitochondrially-localized protein, YbeY, which interacts with the assembling mitoribosome through the small subunit. Loss of YbeY leads to a severe reduction in mitochondrial translation and a loss of cell viability, associated with less accurate mitochondrial tRNASer(AGY) processing from the primary transcript and a defect in the maturation of the mitoribosomal small subunit. Our results suggest that YbeY performs a dual, likely independent, function in mitochondria being involved in precursor RNA processing and mitoribosome biogenesis. Issue Section: Nucleic Acid Enzymes.
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Affiliation(s)
- Aaron R D’Souza
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Lindsey Van Haute
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Christopher A Powell
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Christian D Mutti
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Petra Páleníková
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Pedro Rebelo-Guiomar
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Joanna Rorbach
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Hills Road, Cambridge CB2 0XY, UK
| | - Michal Minczuk
- To whom correspondence should be addressed. Tel: +44 122 325 2750;
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11
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Kron NS, Fieber LA. Co-expression analysis identifies neuro-inflammation as a driver of sensory neuron aging in Aplysia californica. PLoS One 2021; 16:e0252647. [PMID: 34116561 PMCID: PMC8195618 DOI: 10.1371/journal.pone.0252647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 05/20/2021] [Indexed: 01/08/2023] Open
Abstract
Aging of the nervous system is typified by depressed metabolism, compromised proteostasis, and increased inflammation that results in cognitive impairment. Differential expression analysis is a popular technique for exploring the molecular underpinnings of neural aging, but technical drawbacks of the methodology often obscure larger expression patterns. Co-expression analysis offers a robust alternative that allows for identification of networks of genes and their putative central regulators. In an effort to expand upon previous work exploring neural aging in the marine model Aplysia californica, we used weighted gene correlation network analysis to identify co-expression networks in a targeted set of aging sensory neurons in these animals. We identified twelve modules, six of which were strongly positively or negatively associated with aging. Kyoto Encyclopedia of Genes analysis and investigation of central module transcripts identified signatures of metabolic impairment, increased reactive oxygen species, compromised proteostasis, disrupted signaling, and increased inflammation. Although modules with immune character were identified, there was no correlation between genes in Aplysia that increased in expression with aging and the orthologous genes in oyster displaying long-term increases in expression after a virus-like challenge. This suggests anti-viral response is not a driver of Aplysia sensory neuron aging.
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Affiliation(s)
- N. S. Kron
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States of America
| | - L. A. Fieber
- Department of Marine Biology and Ecology, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL, United States of America
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12
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Ramnani B, Manivannan P, Jaggernauth S, Malathi K. ABCE1 Regulates RNase L-Induced Autophagy during Viral Infections. Viruses 2021; 13:v13020315. [PMID: 33670646 PMCID: PMC7922175 DOI: 10.3390/v13020315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/14/2021] [Accepted: 02/16/2021] [Indexed: 12/15/2022] Open
Abstract
Host response to a viral infection includes the production of type I interferon (IFN) and the induction of interferon-stimulated genes that have broad antiviral effects. One of the key antiviral effectors is the IFN-inducible oligoadenylate synthetase/ribonuclease L (OAS/RNase L) pathway, which is activated by double-stranded RNA to synthesize unique oligoadenylates, 2-5A, to activate RNase L. RNase L exerts an antiviral effect by cleaving diverse RNA substrates, limiting viral replication; many viruses have evolved mechanisms to counteract the OAS/RNase L pathway. Here, we show that the ATP-binding cassette E1 (ABCE1) transporter, identified as an inhibitor of RNase L, regulates RNase L activity and RNase L-induced autophagy during viral infections. ABCE1 knockdown cells show increased RNase L activity when activated by 2-5A. Compared to parental cells, the autophagy-inducing activity of RNase L in ABCE1-depleted cells is enhanced with early onset. RNase L activation in ABCE1-depleted cells inhibits cellular proliferation and sensitizes cells to apoptosis. Increased activity of caspase-3 causes premature cleavage of autophagy protein, Beclin-1, promoting a switch from autophagy to apoptosis. ABCE1 regulates autophagy during EMCV infection, and enhanced autophagy in ABCE1 knockdown cells promotes EMCV replication. We identify ABCE1 as a host protein that inhibits the OAS/RNase L pathway by regulating RNase L activity, potentially affecting antiviral effects.
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13
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Mechanisms and regulation of protein synthesis in mitochondria. Nat Rev Mol Cell Biol 2021; 22:307-325. [PMID: 33594280 DOI: 10.1038/s41580-021-00332-2] [Citation(s) in RCA: 154] [Impact Index Per Article: 51.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2021] [Indexed: 02/06/2023]
Abstract
Mitochondria are cellular organelles responsible for generation of chemical energy in the process called oxidative phosphorylation. They originate from a bacterial ancestor and maintain their own genome, which is expressed by designated, mitochondrial transcription and translation machineries that differ from those operating for nuclear gene expression. In particular, the mitochondrial protein synthesis machinery is structurally and functionally very different from that governing eukaryotic, cytosolic translation. Despite harbouring their own genetic information, mitochondria are far from being independent of the rest of the cell and, conversely, cellular fitness is closely linked to mitochondrial function. Mitochondria depend heavily on the import of nuclear-encoded proteins for gene expression and function, and hence engage in extensive inter-compartmental crosstalk to regulate their proteome. This connectivity allows mitochondria to adapt to changes in cellular conditions and also mediates responses to stress and mitochondrial dysfunction. With a focus on mammals and yeast, we review fundamental insights that have been made into the biogenesis, architecture and mechanisms of the mitochondrial translation apparatus in the past years owing to the emergence of numerous near-atomic structures and a considerable amount of biochemical work. Moreover, we discuss how cellular mitochondrial protein expression is regulated, including aspects of mRNA and tRNA maturation and stability, roles of auxiliary factors, such as translation regulators, that adapt mitochondrial translation rates, and the importance of inter-compartmental crosstalk with nuclear gene expression and cytosolic translation and how it enables integration of mitochondrial translation into the cellular context.
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14
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Abshire ET, Hughes KL, Diao R, Pearce S, Gopalakrishna S, Trievel RC, Rorbach J, Freddolino PL, Goldstrohm AC. Differential processing and localization of human Nocturnin controls metabolism of mRNA and nicotinamide adenine dinucleotide cofactors. J Biol Chem 2020; 295:15112-15133. [PMID: 32839274 PMCID: PMC7606674 DOI: 10.1074/jbc.ra120.012618] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 08/06/2020] [Indexed: 01/02/2023] Open
Abstract
Nocturnin (NOCT) is a eukaryotic enzyme that belongs to a superfamily of exoribonucleases, endonucleases, and phosphatases. In this study, we analyze the expression, processing, localization, and cellular functions of human NOCT. We find that NOCT protein is differentially expressed and processed in a cell and tissue type-specific manner to control its localization to the cytoplasm or mitochondrial exterior or interior. The N terminus of NOCT is necessary and sufficient to confer import and processing in the mitochondria. We measured the impact of cytoplasmic NOCT on the transcriptome and observed that it affects mRNA levels of hundreds of genes that are significantly enriched in osteoblast, neuronal, and mitochondrial functions. Recent biochemical data indicate that NOCT dephosphorylates NADP(H) metabolites, and thus we measured the effect of NOCT on these cofactors in cells. We find that NOCT increases NAD(H) and decreases NADP(H) levels in a manner dependent on its intracellular localization. Collectively, our data indicate that NOCT can regulate levels of both mRNAs and NADP(H) cofactors in a manner specified by its location in cells.
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Affiliation(s)
- Elizabeth T Abshire
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA; Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Kelsey L Hughes
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Rucheng Diao
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Sarah Pearce
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institute, Solna, Sweden; Max Planck Institute Biology of Ageing - Karolinska Institute Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Shreekara Gopalakrishna
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institute, Solna, Sweden
| | - Raymond C Trievel
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Joanna Rorbach
- Department of Medical Biochemistry and Biophysics, Division of Molecular Metabolism, Karolinska Institute, Solna, Sweden; Max Planck Institute Biology of Ageing - Karolinska Institute Laboratory, Karolinska Institute, Stockholm, Sweden
| | - Peter L Freddolino
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan, USA; Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Aaron C Goldstrohm
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA.
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15
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Chan KH, Petrychenko V, Mueller C, Maracci C, Holtkamp W, Wilson DN, Fischer N, Rodnina MV. Mechanism of ribosome rescue by alternative ribosome-rescue factor B. Nat Commun 2020; 11:4106. [PMID: 32796827 PMCID: PMC7427801 DOI: 10.1038/s41467-020-17853-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/15/2020] [Indexed: 12/11/2022] Open
Abstract
Alternative ribosome-rescue factor B (ArfB) rescues ribosomes stalled on non-stop mRNAs by releasing the nascent polypeptide from the peptidyl-tRNA. By rapid kinetics we show that ArfB selects ribosomes stalled on short truncated mRNAs, rather than on longer mRNAs mimicking pausing on rare codon clusters. In combination with cryo-electron microscopy we dissect the multistep rescue pathway of ArfB, which first binds to ribosomes very rapidly regardless of the mRNA length. The selectivity for shorter mRNAs arises from the subsequent slow engagement step, as it requires longer mRNA to shift to enable ArfB binding. Engagement results in specific interactions of the ArfB C-terminal domain with the mRNA entry channel, which activates peptidyl-tRNA hydrolysis by the N-terminal domain. These data reveal how protein dynamics translate into specificity of substrate recognition and provide insights into the action of a putative rescue factor in mitochondria. Rescue of ribosomes stalled on non-stop mRNA is essential for cell viability, and several rescue systems to resolve stalling exist in bacteria. Here, the authors use rapid kinetics and cryo-EM to reveal the pathway and selectivity mechanism of ArfB-mediated ribosome rescue.
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Affiliation(s)
- Kai-Hsin Chan
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Valentyn Petrychenko
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Claudia Mueller
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Cristina Maracci
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany
| | - Wolf Holtkamp
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.,Paul-Ehrlich-Institut, Paul-Ehrlich-Straße 51-59, 63225, Langen, Germany
| | - Daniel N Wilson
- Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Niels Fischer
- Department of Structural Dynamics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
| | - Marina V Rodnina
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077, Göttingen, Germany.
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16
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Liudkovska V, Dziembowski A. Functions and mechanisms of RNA tailing by metazoan terminal nucleotidyltransferases. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1622. [PMID: 33145994 PMCID: PMC7988573 DOI: 10.1002/wrna.1622] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/28/2022]
Abstract
Termini often determine the fate of RNA molecules. In recent years, 3' ends of almost all classes of RNA species have been shown to acquire nontemplated nucleotides that are added by terminal nucleotidyltransferases (TENTs). The best-described role of 3' tailing is the bulk polyadenylation of messenger RNAs in the cell nucleus that is catalyzed by canonical poly(A) polymerases (PAPs). However, many other enzymes that add adenosines, uridines, or even more complex combinations of nucleotides have recently been described. This review focuses on metazoan TENTs, which are either noncanonical PAPs or terminal uridylyltransferases with varying processivity. These enzymes regulate RNA stability and RNA functions and are crucial in early development, gamete production, and somatic tissues. TENTs regulate gene expression at the posttranscriptional level, participate in the maturation of many transcripts, and protect cells against viral invasion and the transposition of repetitive sequences. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Processing > 3' End Processing RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Vladyslava Liudkovska
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology, International Institute of Molecular and Cell Biology, Warsaw, Poland.,Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
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17
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Oxidative Stress and Neuroinflammation Potentiate Each Other to Promote Progression of Dopamine Neurodegeneration. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2020; 2020:6137521. [PMID: 32714488 PMCID: PMC7354668 DOI: 10.1155/2020/6137521] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 01/07/2023]
Abstract
Parkinson's disease (PD) is a chronic and complex disease of the central nervous system (CNS). Progressive loss of dopamine (DA) neurons in midbrain substantia nigra is considered to be the main cause of PD. The hallmark of PD pathology is the formation of Lewy bodies and the deposition of α-synuclein (α-syn). The mechanisms responsible for the progressive feature of DA neurodegeneration are not fully illustrated. Recently, oxidative stress and neuroinflammation have received extensive attention as two important entry points in the pathogenesis of PD. The occurrence of oxidative stress and neuroinflammation is usually derived from external influences or changes in internal environment, such as the accumulation of reactive oxygen species, exposure to a toxic environment, and the transformation of systemic inflammation. However, PD never results from a single independent factor and the simultaneous participation of oxidative stress and neuroinflammation contributed to PD development. Oxidative stress and neuroinflammation could potentiate each other to promote progression of PD. In this review, we briefly summarized the conditions of oxidative stress and neuroinflammation and the crosstalk between oxidative stress and neuroinflammation on the development of PD.
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18
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Abstract
Mitochondria are essential organelles in eukaryotes. Most mitochondrial proteins are encoded by the nuclear genome and translated in the cytosol. Nuclear-encoded mitochondrial proteins need to be imported, processed, folded, and assembled into their functional states. To maintain protein homeostasis (proteostasis), mitochondria are equipped with a distinct set of quality control machineries. Deficiencies in such systems lead to mitochondrial dysfunction, which is a hallmark of aging and many human diseases, such as neurodegenerative diseases, cardiovascular diseases, and cancer. In this review, we discuss the unique challenges and solutions of proteostasis in mitochondria. The import machinery coordinates with mitochondrial proteases and chaperones to maintain the mitochondrial proteome. Moreover, mitochondrial proteostasis depends on cytosolic protein quality control mechanisms during crises. In turn, mitochondria facilitate cytosolic proteostasis. Increasing evidence suggests that enhancing mitochondrial proteostasis may hold therapeutic potential to protect against protein aggregation-associated cellular defects.
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Affiliation(s)
- Linhao Ruan
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; , , , , ,
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Yuhao Wang
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; , , , , ,
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Xi Zhang
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; , , , , ,
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Alexis Tomaszewski
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; , , , , ,
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Joshua T McNamara
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; , , , , ,
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Rong Li
- Center for Cell Dynamics, Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA; , , , , ,
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
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19
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Ceddia RP, Collins S. A compendium of G-protein-coupled receptors and cyclic nucleotide regulation of adipose tissue metabolism and energy expenditure. Clin Sci (Lond) 2020; 134:473-512. [PMID: 32149342 PMCID: PMC9137350 DOI: 10.1042/cs20190579] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/17/2020] [Accepted: 02/24/2020] [Indexed: 12/15/2022]
Abstract
With the ever-increasing burden of obesity and Type 2 diabetes, it is generally acknowledged that there remains a need for developing new therapeutics. One potential mechanism to combat obesity is to raise energy expenditure via increasing the amount of uncoupled respiration from the mitochondria-rich brown and beige adipocytes. With the recent appreciation of thermogenic adipocytes in humans, much effort is being made to elucidate the signaling pathways that regulate the browning of adipose tissue. In this review, we focus on the ligand-receptor signaling pathways that influence the cyclic nucleotides, cAMP and cGMP, in adipocytes. We chose to focus on G-protein-coupled receptor (GPCR), guanylyl cyclase and phosphodiesterase regulation of adipocytes because they are the targets of a large proportion of all currently available therapeutics. Furthermore, there is a large overlap in their signaling pathways, as signaling events that raise cAMP or cGMP generally increase adipocyte lipolysis and cause changes that are commonly referred to as browning: increasing mitochondrial biogenesis, uncoupling protein 1 (UCP1) expression and respiration.
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Affiliation(s)
- Ryan P Ceddia
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, U.S.A
| | - Sheila Collins
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, U.S.A
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20
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Kanazawa M, Ikeda Y, Nishihama R, Yamaoka S, Lee NH, Yamato KT, Kohchi T, Hirayama T. Regulation of the Poly(A) Status of Mitochondrial mRNA by Poly(A)-Specific Ribonuclease Is Conserved among Land Plants. PLANT & CELL PHYSIOLOGY 2020; 61:470-480. [PMID: 31722408 DOI: 10.1093/pcp/pcz212] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 11/08/2019] [Indexed: 06/10/2023]
Abstract
Regulation of the stability and the quality of mitochondrial RNA is essential for the maintenance of mitochondrial and cellular functions in eukaryotes. We have previously reported that the eukaryotic poly(A)-specific ribonuclease (PARN) and the prokaryotic poly(A) polymerase encoded by AHG2 and AGS1, respectively, coordinately regulate the poly(A) status and the stability of mitochondrial mRNA in Arabidopsis. Mitochondrial function of PARN has not been reported in any other eukaryotes. To know how much this PARN-based mitochondrial mRNA regulation is conserved among plants, we studied the AHG2 and AGS1 counterparts of the liverwort, Marchantia polymorpha, a member of basal land plant lineage. We found that M. polymorpha has one ortholog each for AHG2 and AGS1, named MpAHG2 and MpAGS1, respectively. Their Citrine-fused proteins were detected in mitochondria of the liverwort. Molecular genetic analysis showed that MpAHG2 is essential and functionally interacts with MpAGS1 as observed in Arabidopsis. A recombinant MpAHG2 protein had a deadenylase activity in vitro. Overexpression of MpAGS1 and the reduced expression of MpAHG2 caused an accumulation of polyadenylated Mpcox1 mRNA. Furthermore, MpAHG2 suppressed Arabidopsis ahg2-1 mutant phenotype. These results suggest that the PARN-based mitochondrial mRNA regulatory system is conserved in land plants.
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Affiliation(s)
- Mai Kanazawa
- Division of Science for Bioresources, Graduate School of Environment and Life Science, Okayama University, 2-20-1 Chuo, Kurashiki, 710-0046 Japan
| | - Yoko Ikeda
- Division of Science for Bioresources, Graduate School of Environment and Life Science, Okayama University, 2-20-1 Chuo, Kurashiki, 710-0046 Japan
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, 710-0046 Japan
| | - Ryuichi Nishihama
- Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Shohei Yamaoka
- Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Nam-Hee Lee
- Department of Life Sciences, Faculty of Science and Engineering, Sorbonne University, 4 Place Jussieu, Paris 75005, France
| | - Katsuyuki T Yamato
- Department of Biotechnological Science, Faculty of Biology-Oriented Science and Technology, Kindai University, 930 Nishimitani, Kinokawa, Wakayama, 649-6493 Japan
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8502 Japan
| | - Takashi Hirayama
- Division of Science for Bioresources, Graduate School of Environment and Life Science, Okayama University, 2-20-1 Chuo, Kurashiki, 710-0046 Japan
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, 710-0046 Japan
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21
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Kotrys AV, Szczesny RJ. Mitochondrial Gene Expression and Beyond-Novel Aspects of Cellular Physiology. Cells 2019; 9:cells9010017. [PMID: 31861673 PMCID: PMC7017415 DOI: 10.3390/cells9010017] [Citation(s) in RCA: 40] [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: 11/28/2019] [Revised: 12/15/2019] [Accepted: 12/17/2019] [Indexed: 02/06/2023] Open
Abstract
Mitochondria are peculiar organelles whose proper function depends on the crosstalk between two genomes, mitochondrial and nuclear. The human mitochondrial genome (mtDNA) encodes only 13 proteins; nevertheless, its proper expression is essential for cellular homeostasis, as mtDNA-encoded proteins are constituents of mitochondrial respiratory complexes. In addition, mtDNA expression results in the production of RNA molecules, which influence cell physiology once released from the mitochondria into the cytoplasm. As a result, dysfunctions of mtDNA expression may lead to pathologies in humans. Here, we review the mechanisms of mitochondrial gene expression with a focus on recent findings in the field. We summarize the complex turnover of mitochondrial transcripts and present an increasing body of evidence indicating new functions of mitochondrial transcripts. We discuss mitochondrial gene regulation in different cellular contexts, focusing on stress conditions. Finally, we highlight the importance of emerging aspects of mitochondrial gene regulation in human health and disease.
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22
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Grover R, Burse SA, Shankrit S, Aggarwal A, Kirty K, Narta K, Srivastav R, Ray AK, Malik G, Vats A, Motiani RK, Thukral L, Roy SS, Bhattacharya S, Sharma R, Natarajan K, Mukerji M, Pandey R, Gokhale RS, Natarajan VT. Myg1 exonuclease couples the nuclear and mitochondrial translational programs through RNA processing. Nucleic Acids Res 2019; 47:5852-5866. [PMID: 31081026 PMCID: PMC6582341 DOI: 10.1093/nar/gkz371] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 04/12/2019] [Accepted: 04/30/2019] [Indexed: 01/25/2023] Open
Abstract
Semi-autonomous functioning of mitochondria in eukaryotic cell necessitates coordination with nucleus. Several RNA species fine-tune mitochondrial processes by synchronizing with the nuclear program, however the involved components remain enigmatic. In this study, we identify a widely conserved dually localized protein Myg1, and establish its role as a 3′-5′ RNA exonuclease. We employ mouse melanoma cells, and knockout of the Myg1 ortholog in Saccharomyces cerevisiae with complementation using human Myg1 to decipher the conserved role of Myg1 in selective RNA processing. Localization of Myg1 to nucleolus and mitochondrial matrix was studied through imaging and confirmed by sub-cellular fractionation studies. We developed Silexoseqencing, a methodology to map the RNAse trail at single-nucleotide resolution, and identified in situ cleavage by Myg1 on specific transcripts in the two organelles. In nucleolus, Myg1 processes pre-ribosomal RNA involved in ribosome assembly and alters cytoplasmic translation. In mitochondrial matrix, Myg1 processes 3′-termini of the mito-ribosomal and messenger RNAs and controls translation of mitochondrial proteins. We provide a molecular link to the possible involvement of Myg1 in chronic depigmenting disorder vitiligo. Our study identifies a key component involved in regulating spatially segregated organellar RNA processing and establishes the evolutionarily conserved ribonuclease as a coordinator of nucleo-mitochondrial crosstalk.
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Affiliation(s)
- Ritika Grover
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research, Rafi Marg, New Delhi, India
| | - Shaunak A Burse
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research, Rafi Marg, New Delhi, India
| | - Shambhavi Shankrit
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Ayush Aggarwal
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research, Rafi Marg, New Delhi, India
| | - Kritika Kirty
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Kiran Narta
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Rajpal Srivastav
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Ashwini Kumar Ray
- School of environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Garima Malik
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Archana Vats
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Rajender K Motiani
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Lipi Thukral
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Soumya Sinha Roy
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Sudha Bhattacharya
- School of environmental Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rakesh Sharma
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | | | - Mitali Mukerji
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Rajesh Pandey
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India
| | - Rajesh S Gokhale
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi, India
| | - Vivek T Natarajan
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi, India.,Academy of Scientific and Innovative Research, Rafi Marg, New Delhi, India
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23
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Mammalian mitochondrial translation - revealing consequences of divergent evolution. Biochem Soc Trans 2019; 47:1429-1436. [PMID: 31551356 DOI: 10.1042/bst20190265] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/15/2019] [Accepted: 08/19/2019] [Indexed: 12/16/2022]
Abstract
Mitochondria are ubiquitous organelles present in the cytoplasm of all nucleated eukaryotic cells. These organelles are described as arising from a common ancestor but a comparison of numerous aspects of mitochondria between different organisms provides remarkable examples of divergent evolution. In humans, these organelles are of dual genetic origin, comprising ∼1500 nuclear-encoded proteins and thirteen that are encoded by the mitochondrial genome. Of the various functions that these organelles perform, it is only oxidative phosphorylation, which provides ATP as a source of chemical energy, that is dependent on synthesis of these thirteen mitochondrially encoded proteins. A prerequisite for this process of translation are the mitoribosomes. The recent revolution in cryo-electron microscopy has generated high-resolution mitoribosome structures and has undoubtedly revealed some of the most distinctive molecular aspects of the mitoribosomes from different organisms. However, we still lack a complete understanding of the mechanistic aspects of this process and many of the factors involved in post-transcriptional gene expression in mitochondria. This review reflects on the current knowledge and illustrates some of the striking differences that have been identified between mitochondria from a range of organisms.
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24
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Barros MH, McStay GP. Modular biogenesis of mitochondrial respiratory complexes. Mitochondrion 2019; 50:94-114. [PMID: 31669617 DOI: 10.1016/j.mito.2019.10.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 09/04/2019] [Accepted: 10/10/2019] [Indexed: 11/29/2022]
Abstract
Mitochondrial function relies on the activity of oxidative phosphorylation to synthesise ATP and generate an electrochemical gradient across the inner mitochondrial membrane. These coupled processes are mediated by five multi-subunit complexes that reside in this inner membrane. These complexes are the product of both nuclear and mitochondrial gene products. Defects in the function or assembly of these complexes can lead to mitochondrial diseases due to deficits in energy production and mitochondrial functions. Appropriate biogenesis and function are mediated by a complex number of assembly factors that promote maturation of specific complex subunits to form the active oxidative phosphorylation complex. The understanding of the biogenesis of each complex has been informed by studies in both simple eukaryotes such as Saccharomyces cerevisiae and human patients with mitochondrial diseases. These studies reveal each complex assembles through a pathway using specific subunits and assembly factors to form kinetically distinct but related assembly modules. The current understanding of these complexes has embraced the revolutions in genomics and proteomics to further our knowledge on the impact of mitochondrial biology in genetics, medicine, and evolution.
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Affiliation(s)
- Mario H Barros
- Departamento de Microbiologia - Instituto de Ciências Biomédicas, Universidade de São Paulo, Brazil.
| | - Gavin P McStay
- Department of Biological Sciences, Staffordshire University, Stoke-on-Trent, United Kingdom.
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25
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Toompuu M, Tuomela T, Laine P, Paulin L, Dufour E, Jacobs HT. Polyadenylation and degradation of structurally abnormal mitochondrial tRNAs in human cells. Nucleic Acids Res 2019. [PMID: 29518244 PMCID: PMC6007314 DOI: 10.1093/nar/gky159] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
RNA 3' polyadenylation is known to serve diverse purposes in biology, in particular, regulating mRNA stability and translation. Here we determined that, upon exposure to high levels of the intercalating agent ethidium bromide (EtBr), greater than those required to suppress mitochondrial transcription, mitochondrial tRNAs in human cells became polyadenylated. Relaxation of the inducing stress led to rapid turnover of the polyadenylated tRNAs. The extent, kinetics and duration of tRNA polyadenylation were EtBr dose-dependent, with mitochondrial tRNAs differentially sensitive to the stress. RNA interference and inhibitor studies indicated that ongoing mitochondrial ATP synthesis, plus the mitochondrial poly(A) polymerase and SUV3 helicase were required for tRNA polyadenylation, while polynucleotide phosphorylase counteracted the process and was needed, along with SUV3, for degradation of the polyadenylated tRNAs. Doxycycline treatment inhibited both tRNA polyadenylation and turnover, suggesting a possible involvement of the mitoribosome, although other translational inhibitors had only minor effects. The dysfunctional tRNALeu(UUR) bearing the pathological A3243G mutation was constitutively polyadenylated at a low level, but this was markedly enhanced after doxycycline treatment. We propose that polyadenylation of structurally and functionally abnormal mitochondrial tRNAs entrains their PNPase/SUV3-mediated destruction, and that this pathway could play an important role in mitochondrial diseases associated with tRNA mutations.
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Affiliation(s)
- Marina Toompuu
- Faculty of Medicine and Life Sciences, BioMediTech Institute and Tampere University Hospital, FI-33014 University of Tampere, Finland
| | - Tea Tuomela
- Faculty of Medicine and Life Sciences, BioMediTech Institute and Tampere University Hospital, FI-33014 University of Tampere, Finland
| | - Pia Laine
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Lars Paulin
- Institute of Biotechnology, FI-00014 University of Helsinki, Finland
| | - Eric Dufour
- Faculty of Medicine and Life Sciences, BioMediTech Institute and Tampere University Hospital, FI-33014 University of Tampere, Finland
| | - Howard T Jacobs
- Faculty of Medicine and Life Sciences, BioMediTech Institute and Tampere University Hospital, FI-33014 University of Tampere, Finland.,Institute of Biotechnology, FI-00014 University of Helsinki, Finland
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26
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Abshire ET, Chasseur J, Bohn JA, Del Rizzo PA, Freddolino PL, Goldstrohm AC, Trievel RC. The structure of human Nocturnin reveals a conserved ribonuclease domain that represses target transcript translation and abundance in cells. Nucleic Acids Res 2019; 46:6257-6270. [PMID: 29860338 PMCID: PMC6158716 DOI: 10.1093/nar/gky412] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 05/09/2018] [Indexed: 12/22/2022] Open
Abstract
The circadian protein Nocturnin (NOCT) belongs to the exonuclease, endonuclease and phosphatase superfamily and is most similar to the CCR4-class of deadenylases that degrade the poly-adenosine tails of mRNAs. NOCT-deficient mice are resistant to high-fat diet induced weight gain, and exhibit dysregulation of bone formation. However, the mechanisms by which NOCT regulates these processes remain to be determined. Here, we describe a pair of high-resolution crystal structures of the human NOCT catalytic domain. The active site of NOCT is highly conserved with other exoribonucleases, and when directed to a transcript in cells, NOCT can reduce translation and abundance of that mRNA in a manner dependent on key active site residues. In contrast to the related deadenylase CNOT6L, purified recombinant NOCT lacks in vitro ribonuclease activity, suggesting that unidentified factors are necessary for enzymatic activity. We also find the ability of NOCT to repress reporter mRNAs in cells depends upon the 3' end of the mRNA, as reporters terminating with a 3' MALAT1 structure cannot be repressed by NOCT. Together, these data demonstrate that NOCT is an exoribonuclease that can degrade mRNAs to inhibit protein expression, suggesting a molecular mechanism for its regulatory role in lipid metabolism and bone development.
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Affiliation(s)
- Elizabeth T Abshire
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer Chasseur
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer A Bohn
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Paul A Del Rizzo
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
| | - Peter L Freddolino
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Aaron C Goldstrohm
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Raymond C Trievel
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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27
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Huang J, Wang G. Improved Mammalian Mitochondrial RNA Isolation. Bio Protoc 2019; 9:e3247. [PMID: 33654773 PMCID: PMC7854245 DOI: 10.21769/bioprotoc.3247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 04/24/2019] [Accepted: 04/30/2019] [Indexed: 11/02/2022] Open
Abstract
Mitochondria have two sets of RNAs. One is encoded in mitochondrial genome, and the other that consists of imported RNAs within mitochondria and cytosolic RNAs associated with mitochondrial outer membrane is encoded in the nucleus. These mitochondrial RNAs play important roles in mitochondrion biosynthesis and signaling in and out of mitochondria. Isolation and analysis of mitochondrial RNAs can provide useful information on understanding the mitochondrial regulation of cellular processes. However, several ribonuclease activities have been found in mitochondria, which will degrade mitochondrial RNAs during the isolation process if they are not properly inactivated. Here, we describe an improved method to inactivate the ribonuclease activities prior to RNA extraction, and thus provide a reliable protocol to isolate mammalian mitochondrial RNAs for quantitative RT-PCR and other assays.
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Affiliation(s)
- Jinliang Huang
- Ministry of Education Key Laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Geng Wang
- Ministry of Education Key Laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing 100084, China
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28
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Transcription, Processing, and Decay of Mitochondrial RNA in Health and Disease. Int J Mol Sci 2019; 20:ijms20092221. [PMID: 31064115 PMCID: PMC6540609 DOI: 10.3390/ijms20092221] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 05/01/2019] [Accepted: 05/03/2019] [Indexed: 12/16/2022] Open
Abstract
Although the large majority of mitochondrial proteins are nuclear encoded, for their correct functioning mitochondria require the expression of 13 proteins, two rRNA, and 22 tRNA codified by mitochondrial DNA (mtDNA). Once transcribed, mitochondrial RNA (mtRNA) is processed, mito-ribosomes are assembled, and mtDNA-encoded proteins belonging to the respiratory chain are synthesized. These processes require the coordinated spatio-temporal action of several enzymes, and many different factors are involved in the regulation and control of protein synthesis and in the stability and turnover of mitochondrial RNA. In this review, we describe the essential steps of mitochondrial RNA synthesis, maturation, and degradation, the factors controlling these processes, and how the alteration of these processes is associated with human pathologies.
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29
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Le PT, Bornstein SA, Motyl KJ, Tian L, Stubblefield JJ, Hong HK, Takahashi JS, Green CB, Rosen CJ, Guntur AR. A novel mouse model overexpressing Nocturnin results in decreased fat mass in male mice. J Cell Physiol 2019; 234:20228-20239. [PMID: 30953371 DOI: 10.1002/jcp.28623] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/09/2019] [Accepted: 03/19/2019] [Indexed: 12/13/2022]
Abstract
Nocturnin (NOCT) belongs to the Mg2+ dependent Exonucleases, Endonucleases, Phosphatase (EEP) family of enzymes that exhibit various functions in vitro and in vivo. NOCT is known to function as a deadenylase, cleaving poly-A tails from mRNA (messenger RNA) transcripts. Previously, we reported a role for NOCT in regulating bone marrow stromal cell differentiation through its interactions with PPARγ. In this study, we characterized the skeletal and adipose tissue phenotype when we globally overexpressed Noct in vivo. After 12 weeks of Noct overexpression, transgenic male mice had lower fat mass compared to controls, with no significant differences in the skeleton. Based on the presence of a mitochondrial target sequence in NOCT, we determined that mouse NOCT protein localizes to the mitochondria; subsequently, we found that NOCT overexpression led to a significant increase in the preadipocytes ability to utilize oxidative phosphorylation for ATP (adenosine triphosphate) generation. In summary, the effects of NOCT on adipocytes are likely through its novel role as a mediator of mitochondrial function.
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Affiliation(s)
- Phuong T Le
- Center for Clinical and Translational Research, Maine Medical Center Research Institute, Scarborough, Maine
| | - Sheila A Bornstein
- Center for Clinical and Translational Research, Maine Medical Center Research Institute, Scarborough, Maine
| | - Katherine J Motyl
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, Maine
| | - Li Tian
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, Maine
| | - Jeremy J Stubblefield
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Hee-Kyung Hong
- Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Joseph S Takahashi
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Carla B Green
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Clifford J Rosen
- Center for Clinical and Translational Research, Maine Medical Center Research Institute, Scarborough, Maine.,Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, Maine
| | - Anyonya R Guntur
- Center for Clinical and Translational Research, Maine Medical Center Research Institute, Scarborough, Maine.,Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, Maine
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30
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Rebelo-Guiomar P, Powell CA, Van Haute L, Minczuk M. The mammalian mitochondrial epitranscriptome. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2019; 1862:429-446. [PMID: 30529456 PMCID: PMC6414753 DOI: 10.1016/j.bbagrm.2018.11.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/16/2018] [Accepted: 11/23/2018] [Indexed: 01/08/2023]
Abstract
Correct expression of the mitochondrially-encoded genes is critical for the production of the components of the oxidative phosphorylation machinery. Post-transcriptional modifications of mitochondrial transcripts have been emerging as an important regulatory feature of mitochondrial gene expression. Here we review the current knowledge on how the mammalian mitochondrial epitranscriptome participates in regulating mitochondrial homeostasis. In particular, we focus on the latest breakthroughs made towards understanding the roles of the modified nucleotides in mitochondrially-encoded ribosomal and transfer RNAs, the enzymes responsible for introducing these modifications and on recent transcriptome-wide studies reporting modifications to mitochondrial messenger RNAs. This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Matthias Soller and Dr. Rupert Fray.
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Affiliation(s)
- Pedro Rebelo-Guiomar
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK; Graduate Program in Areas of Basic and Applied Biology (GABBA), University of Porto, Porto, Portugal
| | | | - Lindsey Van Haute
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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31
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Huang J, Liu P, Wang G. Regulation of mitochondrion-associated cytosolic ribosomes by mammalian mitochondrial ribonuclease T2 (RNASET2). J Biol Chem 2018; 293:19633-19644. [PMID: 30385512 PMCID: PMC6314140 DOI: 10.1074/jbc.ra118.005433] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/15/2018] [Indexed: 11/12/2022] Open
Abstract
Mitochondrial proteins are encoded in both mitochondrial and nuclear genomes. The expression levels of these two pools of mitochondrial genes are co-regulated and synchronized. Import and assembly of the nucleus-encoded oxidative phosphorylation (OXPHOS) subunits affect protein synthesis in the mitochondrial matrix by engaging the mitochondrial ribosomes. How the ribosomes at the outside of mitochondria are regulated by mitochondria, however, remains mostly unexplored. Here, using an array of biochemical assays and genetic knockdown and overexpression in HEK293 or mouse cells, we show that cytosolic rRNAs that are associated with the mitochondrial outer membrane have very different decay patterns from those of both endoplasmic reticulum–associated and –nonassociated cytosolic rRNAs. Mitochondrial intermembrane space RNase T2 (RNASET2), which has been previously shown to degrade mitochondrial RNAs, is also responsible for selective degradation of the cytosolic rRNAs on the outer membrane. We noted that the degradation activity also has a positive effect on nuclear transcription of rRNAs, suggesting a compensatory feedback mechanism, and affects protein translations in and out of mitochondria. These findings establish a mechanism for the co-regulation of gene expression programs inside and outside of mitochondria in mammalian cells.
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Affiliation(s)
- Jinliang Huang
- From the Ministry of Education Key Laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Peipei Liu
- From the Ministry of Education Key Laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Geng Wang
- From the Ministry of Education Key Laboratory of Bioinformatics, Cell Biology and Development Center, School of Life Sciences, Tsinghua University, Beijing 100084, China
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32
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Hughes KL, Abshire ET, Goldstrohm AC. Regulatory roles of vertebrate Nocturnin: insights and remaining mysteries. RNA Biol 2018; 15:1255-1267. [PMID: 30257600 PMCID: PMC6284557 DOI: 10.1080/15476286.2018.1526541] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Post-transcriptional control of messenger RNA (mRNA) is an important layer of gene regulation that modulates mRNA decay, translation, and localization. Eukaryotic mRNA decay begins with the catalytic removal of the 3' poly-adenosine tail by deadenylase enzymes. Multiple deadenylases have been identified in vertebrates and are known to have distinct biological roles; among these proteins is Nocturnin, which has been linked to circadian biology, adipogenesis, osteogenesis, and obesity. Multiple studies have investigated Nocturnin's involvement in these processes; however, a full understanding of its molecular function remains elusive. Recent studies have provided new insights by identifying putative Nocturnin-regulated mRNAs in mice and by determining the structure and regulatory activities of human Nocturnin. This review seeks to integrate these new discoveries into our understanding of Nocturnin's regulatory functions and highlight the important remaining unanswered questions surrounding its regulation, biochemical activities, protein partners, and target mRNAs.
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Affiliation(s)
- Kelsey L Hughes
- a Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Minneapolis , MN , USA
| | - Elizabeth T Abshire
- a Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Minneapolis , MN , USA.,b Department of Biological Chemistry , University of Michigan , Ann Arbor , MI , USA
| | - Aaron C Goldstrohm
- a Department of Biochemistry, Molecular Biology and Biophysics , University of Minnesota , Minneapolis , MN , USA
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33
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van Esveld SL, Huynen MA. Does mitochondrial DNA evolution in metazoa drive the origin of new mitochondrial proteins? IUBMB Life 2018; 70:1240-1250. [PMID: 30281911 DOI: 10.1002/iub.1940] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/14/2018] [Accepted: 08/21/2018] [Indexed: 01/10/2023]
Abstract
Most eukaryotic cells contain mitochondria with a genome that evolved from their α-proteobacterial ancestor. In the course of eukaryotic evolution, the mitochondrial genome underwent a dramatic reduction in size, caused by the loss and translocation of genes. This required adjustments in mitochondrial gene expression mechanisms and resulted in a complex collaborative system of mitochondrially encoded transfer RNAs and ribosomal RNAs with nuclear encoded proteins to express the mitochondrial encoded oxidative phosphorylation (OXPHOS) proteins. In this review, we examine mitochondrial gene expression from an evolutionary point of view: to what extent can we correlate changes in the mitochondrial genome in the evolutionary lineage leading to human with the origin of new nuclear encoded proteins. We dated the evolutionary origin of mitochondrial proteins that interact with mitochondrial DNA or its RNA and/or protein products in a systematic manner and compared them with documented changes in the mitochondrial DNA. We find anecdotal but accumulating evidence that metazoan RNA-interacting proteins arose in conjunction with changes of the mitochondrial DNA. We find no substantial evidence for such compensatory evolution in new OXPHOS proteins, which appear to be constrained by the ability to form supercomplexes. © 2018 IUBMB Life, 70(12):1240-1250, 2018.
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Affiliation(s)
- S L van Esveld
- Radboud Center for Mitochondrial Medicine, Radboudumc, Nijmegen, The Netherlands.,Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, The Netherlands
| | - M A Huynen
- Radboud Center for Mitochondrial Medicine, Radboudumc, Nijmegen, The Netherlands
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34
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Lopp A, Reintamm T, Kuusksalu A, Olspert A, Kelve M. Identification of a novel member of 2H phosphoesterases, 2',5'-oligoadenylate degrading ribonuclease from the oyster Crassostrea gigas. Biochimie 2018; 156:181-195. [PMID: 30195052 DOI: 10.1016/j.biochi.2018.09.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 09/03/2018] [Indexed: 11/16/2022]
Abstract
Several genes of IFN-mediated pathways in vertebrates, among them the genes that participate in the 2',5'-oligoadenylate synthetase (OAS)/RNase L pathway, have been identified in C. gigas. In the present study, we identified genes, which encode proteins having 2',5'-oligoadenylate degrading activity in C. gigas. These proteins belong to the 2H phosphoesterase superfamily and have sequence similarity to the mammalian A kinase anchoring protein 7 (AKAP7) central domain, which is responsible for the 2',5'-phosphodiesterase (2',5'-PDE) activity. Comparison of the genomic structures of C. gigas proteins with that of AKAP7 suggests that these enzymes originate from a direct common ancestor. However, the identified nucleases are not typical 2',5'-PDEs. The found enzymes catalyse the degradation of 2',5'-linked oligoadenylates in a metal-ion-independent way, yielding products with 2',3' -cyclic phosphate and 5'-OH termini similarly to the 3'-5' bond cleavage in RNA, catalyzed by metal-independent ribonucleases. 3',5'-linked oligoadenylates are not substrates for them. The preferred substrates for the C. gigas enzymes are 5'-triphosphorylated 2',5'-oligoadenylates, whose major cleavage reaction results in the removal of the 5'-triphosphorylated 2',3'-cyclic phosphate derivative, leaving behind the respective unphosphorylated 2',5'-oligoadenylate. Such a cleavage reaction results in the direct inactivation of the biologically active 2-5A molecule. The 2',5'-ribonucleases (2',5'-RNases) from C. gigas could be members of the ancient group of ribonucleases, specific to 2'-5' phosphodiester bond, together with the enzyme that was characterized previously from the marine sponge Tethya aurantium. The novel 2',5'-RNases may play a role in the control of cellular 2-5A levels, thereby limiting damage to host cells after viral infection.
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Affiliation(s)
- Annika Lopp
- Department of Chemistry and Biotechnology, Division of Gene Technology, Tallinn University of Technology, Akadeemia Tee 15, Tallinn, 12618, Estonia.
| | - Tõnu Reintamm
- Department of Chemistry and Biotechnology, Division of Gene Technology, Tallinn University of Technology, Akadeemia Tee 15, Tallinn, 12618, Estonia
| | - Anne Kuusksalu
- Department of Chemistry and Biotechnology, Division of Gene Technology, Tallinn University of Technology, Akadeemia Tee 15, Tallinn, 12618, Estonia
| | - Allan Olspert
- Department of Chemistry and Biotechnology, Division of Gene Technology, Tallinn University of Technology, Akadeemia Tee 15, Tallinn, 12618, Estonia
| | - Merike Kelve
- Department of Chemistry and Biotechnology, Division of Gene Technology, Tallinn University of Technology, Akadeemia Tee 15, Tallinn, 12618, Estonia
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35
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Mitochondrial transcription and translation: overview. Essays Biochem 2018; 62:309-320. [PMID: 30030363 PMCID: PMC6056719 DOI: 10.1042/ebc20170102] [Citation(s) in RCA: 165] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 05/14/2018] [Accepted: 05/14/2018] [Indexed: 12/13/2022]
Abstract
Mitochondria are the major source of ATP in the cell. Five multi-subunit complexes in the inner membrane of the organelle are involved in the oxidative phosphorylation required for ATP production. Thirteen subunits of these complexes are encoded by the mitochondrial genome often referred to as mtDNA. For this reason, the expression of mtDNA is vital for the assembly and functioning of the oxidative phosphorylation complexes. Defects of the mechanisms regulating mtDNA gene expression have been associated with deficiencies in assembly of these complexes, resulting in mitochondrial diseases. Recently, numerous factors involved in these processes have been identified and characterized leading to a deeper understanding of the mechanisms that underlie mitochondrial diseases.
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36
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Szczesny RJ, Kowalska K, Klosowska-Kosicka K, Chlebowski A, Owczarek EP, Warkocki Z, Kulinski TM, Adamska D, Affek K, Jedroszkowiak A, Kotrys AV, Tomecki R, Krawczyk PS, Borowski LS, Dziembowski A. Versatile approach for functional analysis of human proteins and efficient stable cell line generation using FLP-mediated recombination system. PLoS One 2018; 13:e0194887. [PMID: 29590189 PMCID: PMC5874048 DOI: 10.1371/journal.pone.0194887] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 03/12/2018] [Indexed: 12/21/2022] Open
Abstract
Deciphering a function of a given protein requires investigating various biological aspects. Usually, the protein of interest is expressed with a fusion tag that aids or allows subsequent analyses. Additionally, downregulation or inactivation of the studied gene enables functional studies. Development of the CRISPR/Cas9 methodology opened many possibilities but in many cases it is restricted to non-essential genes. Recombinase-dependent gene integration methods, like the Flp-In system, are very good alternatives. The system is widely used in different research areas, which calls for the existence of compatible vectors and efficient protocols that ensure straightforward DNA cloning and generation of stable cell lines. We have created and validated a robust series of 52 vectors for streamlined generation of stable mammalian cell lines using the FLP recombinase-based methodology. Using the sequence-independent DNA cloning method all constructs for a given coding-sequence can be made with just three universal PCR primers. Our collection allows tetracycline-inducible expression of proteins with various tags suitable for protein localization, FRET, bimolecular fluorescence complementation (BiFC), protein dynamics studies (FRAP), co-immunoprecipitation, the RNA tethering assay and cell sorting. Some of the vectors contain a bidirectional promoter for concomitant expression of miRNA and mRNA, so that a gene can be silenced and its product replaced by a mutated miRNA-insensitive version. Our toolkit and protocols have allowed us to create more than 500 constructs with ease. We demonstrate the efficacy of our vectors by creating stable cell lines with various tagged proteins (numatrin, fibrillarin, coilin, centrin, THOC5, PCNA). We have analysed transgene expression over time to provide a guideline for future experiments and compared the effectiveness of commonly used inducers for tetracycline-responsive promoters. As proof of concept we examined the role of the exoribonuclease XRN2 in transcription termination by RNAseq.
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Affiliation(s)
- Roman J. Szczesny
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- * E-mail: (RJS); (AD)
| | - Katarzyna Kowalska
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kamila Klosowska-Kosicka
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Aleksander Chlebowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Ewelina P. Owczarek
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Zbigniew Warkocki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Tomasz M. Kulinski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Dorota Adamska
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kamila Affek
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Agata Jedroszkowiak
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Anna V. Kotrys
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Rafal Tomecki
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Pawel S. Krawczyk
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Lukasz S. Borowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Andrzej Dziembowski
- Laboratory of RNA Biology and Functional Genomics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland
- * E-mail: (RJS); (AD)
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37
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Skeparnias I, Αnastasakis D, Shaukat AN, Grafanaki K, Stathopoulos C. Expanding the repertoire of deadenylases. RNA Biol 2017; 14:1320-1325. [PMID: 28267419 PMCID: PMC5711463 DOI: 10.1080/15476286.2017.1300222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 02/13/2017] [Accepted: 02/23/2017] [Indexed: 12/20/2022] Open
Abstract
Deadenylases belong to an expanding family of exoribonucleases involved mainly in mRNA stability and turnover, with the exception of PARN which has additional roles in the biogenesis of several important non-coding RNAs, including miRNAs and piRNAs. Recently, PARN in C. elegans and its homolog PNLDC1 in B. mori were reported as the elusive trimmers mediating piRNA biogenesis. In addition, characterization of mammalian PNLDC1 in comparison to PARN, showed that is specifically expressed in embryonic stem and germ cells, as well as during early embryo development. Moreover, its expression is correlated with epigenetic events mediated by the de novo DNMT3b methyltransferase and knockdown in stem cells upregulates important genes that regulate multipotency. The recent data suggest that at least some new deadenylases may have expanded roles in cell metabolism as regulators of gene expression, through mRNA deadenylation, ncRNAs biogenesis and ncRNA-mediated mRNA targeting, linking essential mechanisms that regulate epigenetic control and transition events during differentiation. The possible roles of mammalian PNLDC1 along those dynamic networks are discussed in the light of new extremely important findings.
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Affiliation(s)
- Ilias Skeparnias
- Department of Biochemistry, School of Medicine, University of Patras, Greece
| | | | | | - Katerina Grafanaki
- Department of Biochemistry, School of Medicine, University of Patras, Greece
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38
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Chrzanowska-Lightowlers Z, Rorbach J, Minczuk M. Human mitochondrial ribosomes can switch structural tRNAs - but when and why? RNA Biol 2017; 14:1668-1671. [PMID: 28786741 PMCID: PMC5731804 DOI: 10.1080/15476286.2017.1356551] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
High resolution cryoEM of mammalian mitoribosomes revealed the unexpected presence of mitochondrially encoded tRNA as a structural component of mitochondrial large ribosomal subunit (mt-LSU). Our previously published data identified that only mitochondrial (mt-) tRNAPhe and mt-tRNAVal can be incorporated into mammalian mt-LSU and within an organism there is no evidence of tissue specific variation. When mt-tRNAVal is limiting, human mitoribosomes can integrate mt-tRNAPhe instead to generate a translationally competent monosome. Here we discuss the possible reasons for and consequences of the observed plasticity of the structural mt-tRNA integration. We also indicate potential direction for further research that could help our understanding of the mechanistic and evolutionary aspects of this unprecedented system.
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Affiliation(s)
- Zofia Chrzanowska-Lightowlers
- a The Wellcome Trust Centre for Mitochondrial Research, Institute of Neuroscience , Newcastle University , Newcastle upon Tyne , England , UK
| | - Joanna Rorbach
- b Department of Medical Biochemistry and Biophysics , Karolinska Institutet , Retzius väg 8, Stockholm , Sweden
| | - Michal Minczuk
- c MRC Mitochondrial Biology Unit , Wellcome Trust/MRC Building, Hills Road, Cambridge, England , UK
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39
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Pearce SF, Rorbach J, Haute LV, D’Souza AR, Rebelo-Guiomar P, Powell CA, Brierley I, Firth AE, Minczuk M. Maturation of selected human mitochondrial tRNAs requires deadenylation. eLife 2017; 6:e27596. [PMID: 28745585 PMCID: PMC5544427 DOI: 10.7554/elife.27596] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/21/2017] [Indexed: 02/02/2023] Open
Abstract
Human mitochondria contain a genome (mtDNA) that encodes essential subunits of the oxidative phosphorylation system. Expression of mtDNA entails multi-step maturation of precursor RNA. In other systems, the RNA life cycle involves surveillance mechanisms, however, the details of RNA quality control have not been extensively characterised in human mitochondria. Using a mitochondrial ribosome profiling and mitochondrial poly(A)-tail RNA sequencing (MPAT-Seq) assay, we identify the poly(A)-specific exoribonuclease PDE12 as a major factor for the quality control of mitochondrial non-coding RNAs. The lack of PDE12 results in a spurious polyadenylation of the 3' ends of the mitochondrial (mt-) rRNA and mt-tRNA. While the aberrant adenylation of 16S mt-rRNA did not affect the integrity of the mitoribosome, spurious poly(A) additions to mt-tRNA led to reduced levels of aminoacylated pool of certain mt-tRNAs and mitoribosome stalling at the corresponding codons. Therefore, our data uncover a new, deadenylation-dependent mtRNA maturation pathway in human mitochondria.
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Affiliation(s)
- Sarah F Pearce
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Joanna Rorbach
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Lindsey Van Haute
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Aaron R D’Souza
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Pedro Rebelo-Guiomar
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
- Graduate Program in Areas of Basic and Applied Biology, University of Porto, Porto, Portugal
| | - Christopher A Powell
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Ian Brierley
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Andrew E Firth
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
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40
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Polyadenylation and degradation of RNA in the mitochondria. Biochem Soc Trans 2017; 44:1475-1482. [PMID: 27911729 DOI: 10.1042/bst20160126] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 06/24/2016] [Accepted: 06/28/2016] [Indexed: 12/20/2022]
Abstract
Mitochondria have their own gene expression machinery and the relative abundance of RNA products in these organelles in animals is mostly dictated by their rate of degradation. The molecular mechanisms regulating the differential accumulation of the transcripts in this organelle remain largely elusive. Here, we summarize the present knowledge of how RNA is degraded in human mitochondria and describe the coexistence of stable poly(A) tails and the nonabundant tails, which have been suggested to play a role in the RNA degradation process.
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41
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Regulation of Mammalian Mitochondrial Gene Expression: Recent Advances. Trends Biochem Sci 2017; 42:625-639. [PMID: 28285835 PMCID: PMC5538620 DOI: 10.1016/j.tibs.2017.02.003] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/02/2017] [Accepted: 02/10/2017] [Indexed: 01/03/2023]
Abstract
Perturbation of mitochondrial DNA (mtDNA) gene expression can lead to human pathologies. Therefore, a greater appreciation of the basic mechanisms of mitochondrial gene expression is desirable to understand the pathophysiology of associated disorders. Although the purpose of the mitochondrial gene expression machinery is to provide only 13 proteins of the oxidative phosphorylation (OxPhos) system, recent studies have revealed its remarkable and unexpected complexity. We review here the latest breakthroughs in our understanding of the post-transcriptional processes of mitochondrial gene expression, focusing on advances in analyzing the mitochondrial epitranscriptome, the role of mitochondrial RNA granules (MRGs), the benefits of recently obtained structures of the mitochondrial ribosome, and the coordination of mitochondrial and cytosolic translation to orchestrate the biogenesis of OxPhos complexes. The genetic system required for mitochondrial gene expression is housed within the mitochondrial matrix, with all the necessary RNAs being provided by transcription of the mtDNA itself. Our understanding of the extent and nature of post-transcriptional modifications of mtRNA, the epitranscriptome, is rapidly expanding. Several required nucleus-encoded enzymes have recently been identified. mtRNA maturation factors localize in distinct foci, termed mtRNA granules, with newly transcribed RNA. These foci may allow spatiotemporal control of mtRNA processing. Recent high-resolution structures obtained via cryo-electron microscopy have rapidly advanced our understanding of the specialized adaptations of the mitochondrial ribosome. Production of respiratory complexes requires tight coordination between the cytoplasmic and mitochondrial translation systems.
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Bruni F, Lightowlers RN, Chrzanowska-Lightowlers ZM. Human mitochondrial nucleases. FEBS J 2017; 284:1767-1777. [PMID: 27926991 PMCID: PMC5484287 DOI: 10.1111/febs.13981] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 11/22/2016] [Accepted: 11/30/2016] [Indexed: 12/26/2022]
Abstract
Mitochondria are cytosolic organelles that have many essential roles including ATP production via oxidative phosphorylation, apoptosis, iron‐sulfur cluster biogenesis, heme and steroid synthesis, calcium homeostasis, and regulation of cellular redox state. One of the unique features of these organelles is the presence of an extrachromosomal mitochondrial genome (mtDNA), together with all the machinery required to replicate and transcribe mtDNA. The accurate maintenance of mitochondrial gene expression is essential for correct organellar metabolism, and is in part dependent on the levels of mtDNA and mtRNA, which are regulated by balancing synthesis against degradation. It is clear that although a number of mitochondrial nucleases have been identified, not all those responsible for the degradation of DNA or RNA have been characterized. Recent investigations, however, have revealed the contribution that mutations in the genes coding for these enzymes has made to causing pathogenic mitochondrial diseases.
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Affiliation(s)
- Francesco Bruni
- The Wellcome Trust Centre for Mitochondrial Research, The Medical School, Newcastle University, UK
| | - Robert N Lightowlers
- The Wellcome Trust Centre for Mitochondrial Research, The Medical School, Newcastle University, UK
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Chou WL, Chung YL, Fang JC, Lu CA. Novel interaction between CCR4 and CAF1 in rice CCR4-NOT deadenylase complex. PLANT MOLECULAR BIOLOGY 2017; 93:79-96. [PMID: 27714489 DOI: 10.1007/s11103-016-0548-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 09/28/2016] [Indexed: 06/06/2023]
Abstract
Rice is an important crop in the world. However, little is known about rice mRNA deadenylation, which is an important regulation step of gene expression at the post-transcriptional level. The CCR4-NOT1 complex contains two key components, CCR4 and CAF1, which are the main cytoplasmic deadenylases in eukaryotic cells. In yeast and humans, CCR4 can interact with CAF1 via its N-terminal LRR domain. However, no CCR4 protein containing N-terminal LRR motifs have been found in plants. In this manuscript, we demonstrate a novel pattern of interaction between OsCCR4 and OsCAF1 in the rice CCR4-NOT complex, and that OsCAF1 acts as a bridge between OsCCR4 and OsNOT1 in this complex. Our results revealed that the Mynd-like domain at the N-terminus of rice CCR4 proteins and the PXLXP motif at the rice CAF1 N-terminus play critical roles in OsCCR4-OsCAF1 interaction. Deadenylation, also called poly(A) tail shortening, is the first rate-limiting step in general cytoplasmic mRNA degradation in eukaryotic cells. Carbon catabolite repressor (CCR)4 and CCR4-associated factor (CAF)1 in the CCR4-NOT complex function in mRNA poly(A) tail shortening. CCR4s contain N-terminal leucine-rich repeat (LRR) motifs that interact with CAF1s in yeast, fruit fly and mammals. In silico analysis has not identified any plant CCR4 proteins that contain LRR motifs. Here, two rice CCR4 homologous genes, OsCCR4a and OsCCR4b, were identified. The isolated recombinant exonuclease-endonuclease-phosphatase domain of OsCCR4a and OsCCR4b exhibited 3'-5' exonuclease activity in vitro, and point mutation of a catalytic residue in this domain disrupted the deadenylase activity. Both OsCCR4a and OsCCR4b fluorescent fusion proteins were localized in the rice cytoplasm and nucleus, and both associated with processing bodies via their N-terminus. Binding analyses showed that OsCCR4a and OsCCR4b directly interacted with three rice CAF1 family members: OsCAF1A, OsCAF1G and OsCAF1H. The zf-MYND-like domain at the N terminus of rice CCR4 and the PXLXP motif of rice CAF1 play critical roles in OsCCR4-OsCAF1 interaction. OsCAF1 proteins, but not OsCCR4 proteins, can interact with the MIG4G domain of rice OsNOT1. Our studies thus reveal a hitherto undiscovered novel interaction pattern that connects OsCCR4 and OsCAF1 in the rice CCR4-NOT complex.
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Affiliation(s)
- Wei-Lun Chou
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, ROC
| | - Yue-Lin Chung
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, ROC
| | - Jhen-Cheng Fang
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, ROC
| | - Chung-An Lu
- Department of Life Sciences, National Central University, Jhongli City, Taoyuan County 320, Taiwan, ROC.
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44
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Inhibition of innate immune cytosolic surveillance by an M. tuberculosis phosphodiesterase. Nat Chem Biol 2016; 13:210-217. [PMID: 28106876 DOI: 10.1038/nchembio.2254] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 10/05/2016] [Indexed: 12/18/2022]
Abstract
Mycobacterium tuberculosis infection leads to cytosolic release of the bacterial cyclic dinucleotide (CDN) c-di-AMP and a host-generated CDN, cGAMP, both of which trigger type I interferon (IFN) expression in a STING-dependent manner. Here we report that M. tuberculosis has developed a mechanism to inhibit STING activation and the type I IFN response via the bacterial phosphodiesterase (PDE) CdnP, which mediates hydrolysis of both bacterial-derived c-di-AMP and host-derived cGAMP. Mutation of cdnP attenuates M. tuberculosis virulence, as does loss of a host CDN PDE known as ENPP1. CdnP is inhibited by both US Food and Drug Administration (FDA)-approved PDE inhibitors and nonhydrolyzable dinucleotide mimetics specifically designed to target the enzyme. These findings reveal a crucial role of CDN homeostasis in governing the outcome of M. tuberculosis infection as well as a unique mechanism of subversion of the host's cytosolic surveillance pathway (CSP) by a bacterial PDE that may serve as an attractive antimicrobial target.
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45
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Gusho E, Baskar D, Banerjee S. New advances in our understanding of the "unique" RNase L in host pathogen interaction and immune signaling. Cytokine 2016; 133:153847. [PMID: 27595182 PMCID: PMC7128181 DOI: 10.1016/j.cyto.2016.08.009] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 08/08/2016] [Accepted: 08/08/2016] [Indexed: 12/22/2022]
Abstract
Ever since the discovery of the existence of an interferon (IFN)-regulated ribonuclease, significant advances have been made in understanding the mechanism and associated regulatory effects of its action. What had been studied initially as a "unique" endoribonuclease is currently known as ribonuclease L (RNase L where "L" stands for latent). Some of the key developments include discovery of the RNase L signaling pathway, its structural characterization, and its molecular cloning. RNase L has been implicated in antiviral and antibacterial defense, as well as in hereditary prostate cancer. RNase L is activated by 2'-5' linked oligoadenylates (2-5A), which are synthesized by the oligoadenylate synthetases (OASs), a family of IFN-regulated pathogen recognition receptors that sense double-stranded RNAs. Activated RNase L cleaves single stranded RNAs, including viral RNAs and cellular RNAs. The catalytic activity of RNase L has been found to lead into the activation of several cellular signaling pathways, including those involved in autophagy, apoptosis, IFN-β production, NLRP3 inflammasome activation leading to IL-1β secretion, inhibition of cell migration, and cell adhesion. In this review, we will highlight the newest advances in our understanding of the catalytic role of RNase L in the context of different cellular pathways and extend the scope of these findings to discussion of potential therapeutic targets for antimicrobial drug development.
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Affiliation(s)
- Elona Gusho
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue Cleveland, OH 44195, USA
| | - Danika Baskar
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue Cleveland, OH 44195, USA; Pediatrics Division Office, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA(1)
| | - Shuvojit Banerjee
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, 9500 Euclid Avenue Cleveland, OH 44195, USA.
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Wedatilake Y, Niazi R, Fassone E, Powell CA, Pearce S, Plagnol V, Saldanha JW, Kleta R, Chong WK, Footitt E, Mills PB, Taanman JW, Minczuk M, Clayton PT, Rahman S. TRNT1 deficiency: clinical, biochemical and molecular genetic features. Orphanet J Rare Dis 2016; 11:90. [PMID: 27370603 PMCID: PMC4930608 DOI: 10.1186/s13023-016-0477-0] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 06/24/2016] [Indexed: 11/10/2022] Open
Abstract
Background TRNT1 (CCA-adding transfer RNA nucleotidyl transferase) enzyme deficiency is a new metabolic disease caused by defective post-transcriptional modification of mitochondrial and cytosolic transfer RNAs (tRNAs). Results We investigated four patients from two families with infantile-onset cyclical, aseptic febrile episodes with vomiting and diarrhoea, global electrolyte imbalance during these episodes, sideroblastic anaemia, B lymphocyte immunodeficiency, retinitis pigmentosa, hepatosplenomegaly, exocrine pancreatic insufficiency and renal tubulopathy. Other clinical features found in children include sensorineural deafness, cerebellar atrophy, brittle hair, partial villous atrophy and nephrocalcinosis. Whole exome sequencing and bioinformatic filtering were utilised to identify recessive compound heterozygous TRNT1 mutations (missense mutation c.668T>C, p.Ile223Thr and a novel splice mutation c.342+5G>T) segregating with disease in the first family. The second family was found to have a homozygous TRNT1 mutation (c.569G>T), p.Arg190Ile, (previously published). We found normal mitochondrial translation products using passage matched controls and functional perturbation of 3’ CCA addition to mitochondrial tRNAs (tRNACys, tRNALeuUUR and tRNAHis) in fibroblasts from two patients, demonstrating a pathomechanism affecting the CCA addition to mt-tRNAs. Acute management of these patients included transfusion for anaemia, fluid and electrolyte replacement and immunoglobulin therapy. We also describe three-year follow-up findings after treatment by bone marrow transplantation in one patient, with resolution of fever and reversal of the abnormal metabolic profile. Conclusions Our report highlights that TRNT1 mutations cause a spectrum of disease ranging from a childhood-onset complex disease with manifestations in most organs to an adult-onset isolated retinitis pigmentosa presentation. Systematic review of all TRNT1 cases and mutations reported to date revealed a distinctive phenotypic spectrum and metabolic and other investigative findings, which will facilitate rapid clinical recognition of future cases.
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Affiliation(s)
- Yehani Wedatilake
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | - Rojeen Niazi
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | - Elisa Fassone
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | | | | | | | - José W Saldanha
- Division of Mathematical Biology, National Institute for Medical Research, Mill Hill, London, UK
| | - Robert Kleta
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK.,UCL Genetics Institute, London, UK.,Division of Medicine, UCL, London, UK
| | - W Kling Chong
- Radiology Department, Great Ormond Street Hospital, London, UK
| | - Emma Footitt
- Metabolic medicine department, Great Ormond Street Hospital, London, UK
| | - Philippa B Mills
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | - Jan-Willem Taanman
- Department of Clinical Neurosciences, UCL Institute of Neurology, London, UK
| | | | - Peter T Clayton
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK
| | - Shamima Rahman
- Genetics and Genomic Medicine Programme, UCL Institute of Child Health, London, UK. .,Mitochondrial Research Group, Genetics and Genomic Medicine Programme, UCL Institute of Child Health, 30, Guilford Street, London, WC1N 1EH, UK.
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47
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Bratic A, Clemente P, Calvo-Garrido J, Maffezzini C, Felser A, Wibom R, Wedell A, Freyer C, Wredenberg A. Mitochondrial Polyadenylation Is a One-Step Process Required for mRNA Integrity and tRNA Maturation. PLoS Genet 2016; 12:e1006028. [PMID: 27176048 PMCID: PMC4866704 DOI: 10.1371/journal.pgen.1006028] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 04/14/2016] [Indexed: 12/20/2022] Open
Abstract
Polyadenylation has well characterised roles in RNA turnover and translation in a variety of biological systems. While polyadenylation on mitochondrial transcripts has been suggested to be a two-step process required to complete translational stop codons, its involvement in mitochondrial RNA turnover is less well understood. We studied knockdown and knockout models of the mitochondrial poly(A) polymerase (MTPAP) in Drosophila melanogaster and demonstrate that polyadenylation of mitochondrial mRNAs is exclusively performed by MTPAP. Further, our results show that mitochondrial polyadenylation does not regulate mRNA stability but protects the 3' terminal integrity, and that despite a lack of functioning 3' ends, these trimmed transcripts are translated, suggesting that polyadenylation is not required for mitochondrial translation. Additionally, loss of MTPAP leads to reduced steady-state levels and disturbed maturation of tRNACys, indicating that polyadenylation in mitochondria might be important for the stability and maturation of specific tRNAs. The polyadenylation of cellular RNAs is a well-studied signal for gene expression, with a defined function in either RNA turnover or translation, in the majority of systems. In mammalian mitochondria the role of polyadenylation is less clear, and can to date only be attributed to completing the translational stop signal on several mitochondrial transcripts. Previous work though demonstrated that mitochondrial polyadenylation requires a certain length and shortening of the poly(A) tail signal has detrimental effects on mitochondrial function. In this study we deleted the mitochondrial polymerase responsible for polyadenylation in the fly, Drosophila melanogaster, and demonstrate that the mitochondrial poly(A) tail is essential for preserving the 3’ ends of mitochondrial transcripts, with no other enzyme capable of completing stop signals. Our study also shows that polyadenylation does not regulate transcript stability nor is it required for translation, but might be involved in the maturation of certain mitochondrial tRNAs. We therefore conclude that besides completing translational stop signals, mitochondrial polyadenylation protects the 3’ termini from degradation.
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Affiliation(s)
- Ana Bratic
- Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Paula Clemente
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Javier Calvo-Garrido
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Camilla Maffezzini
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Andrea Felser
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Rolf Wibom
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Wedell
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
| | - Christoph Freyer
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
- * E-mail: (CF); (AW)
| | - Anna Wredenberg
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Centre for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden
- * E-mail: (CF); (AW)
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48
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Levy S, Allerston CK, Liveanu V, Habib MR, Gileadi O, Schuster G. Identification of LACTB2, a metallo-β-lactamase protein, as a human mitochondrial endoribonuclease. Nucleic Acids Res 2016; 44:1813-32. [PMID: 26826708 PMCID: PMC4770246 DOI: 10.1093/nar/gkw050] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 01/19/2016] [Indexed: 11/23/2022] Open
Abstract
Post-transcriptional control of mitochondrial gene expression, including the
processing and generation of mature transcripts as well as their degradation, is a
key regulatory step in gene expression in human mitochondria. Consequently,
identification of the proteins responsible for RNA processing and degradation in this
organelle is of great importance. The metallo-β-lactamase (MBL) is a candidate
protein family that includes ribo- and deoxyribonucleases. In this study, we
discovered a function for LACTB2, an orphan MBL protein found in mammalian
mitochondria. Solving its crystal structure revealed almost perfect alignment of the
MBL domain with CPSF73, as well as to other ribonucleases of the MBL superfamily.
Recombinant human LACTB2 displayed robust endoribonuclease activity on ssRNA with a
preference for cleavage after purine-pyrimidine sequences. Mutational analysis
identified an extended RNA-binding site. Knockdown of LACTB2 in cultured cells caused
a moderate but significant accumulation of many mitochondrial transcripts, and its
overexpression led to the opposite effect. Furthermore, manipulation of LACTB2
expression resulted in cellular morphological deformation and cell death. Together,
this study discovered that LACTB2 is an endoribonuclease that is involved in the
turnover of mitochondrial RNA, and is essential for mitochondrial function in human
cells.
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Affiliation(s)
- Shiri Levy
- Faculty of Biology, Technion- Israel Institute of Technology, Haifa 32000, Israel
| | - Charles K Allerston
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Varda Liveanu
- Faculty of Biology, Technion- Israel Institute of Technology, Haifa 32000, Israel
| | - Mouna R Habib
- Faculty of Biology, Technion- Israel Institute of Technology, Haifa 32000, Israel
| | - Opher Gileadi
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Gadi Schuster
- Faculty of Biology, Technion- Israel Institute of Technology, Haifa 32000, Israel
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49
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Fiedler M, Rossmanith W, Wahle E, Rammelt C. Mitochondrial poly(A) polymerase is involved in tRNA repair. Nucleic Acids Res 2015; 43:9937-49. [PMID: 26354863 PMCID: PMC4787750 DOI: 10.1093/nar/gkv891] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 08/26/2015] [Indexed: 11/12/2022] Open
Abstract
Transcription of the mitochondrial genome results in polycistronic precursors, which are processed mainly by the release of tRNAs interspersed between rRNAs and mRNAs. In many metazoan mitochondrial genomes some tRNA genes overlap with downstream genes; in the case of human mitochondria the genes for tRNATyr and tRNACys overlap by one nucleotide. It has previously been shown that processing of the common precursor releases an incomplete tRNATyr lacking the 3′-adenosine. The 3′-terminal adenosine has to be added before addition of the CCA end and subsequent aminoacylation. We show that the mitochondrial poly(A) polymerase (mtPAP) is responsible for this A addition. In vitro, a tRNATyr lacking the discriminator is a substrate for mtPAP. In vivo, an altered mtPAP protein level affected tRNATyr maturation, as shown by sequencing the 3′ ends of mitochondrial tRNAs. Complete repair could be reconstituted in vitro with three enzymes: mtPAP frequently added more than one A to the 3′ end of the truncated tRNA, and either the mitochondrial deadenylase PDE12 or the endonuclease RNase Z trimmed the oligo(A) tail to a single A before CCA addition. An enzyme machinery that evolved primarily for other purposes thus allows to tolerate the frequent evolutionary occurrence of gene overlaps.
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Affiliation(s)
- Mario Fiedler
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Walter Rossmanith
- Center for Anatomy & Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Elmar Wahle
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
| | - Christiane Rammelt
- Institute of Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
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50
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Wood ER, Bledsoe R, Chai J, Daka P, Deng H, Ding Y, Harris-Gurley S, Kryn LH, Nartey E, Nichols J, Nolte RT, Prabhu N, Rise C, Sheahan T, Shotwell JB, Smith D, Tai V, Taylor JD, Tomberlin G, Wang L, Wisely B, You S, Xia B, Dickson H. The Role of Phosphodiesterase 12 (PDE12) as a Negative Regulator of the Innate Immune Response and the Discovery of Antiviral Inhibitors. J Biol Chem 2015; 290:19681-96. [PMID: 26055709 PMCID: PMC4528132 DOI: 10.1074/jbc.m115.653113] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Revised: 05/20/2015] [Indexed: 11/06/2022] Open
Abstract
2',5'-Oligoadenylate synthetase (OAS) enzymes and RNase-L constitute a major effector arm of interferon (IFN)-mediated antiviral defense. OAS produces a unique oligonucleotide second messenger, 2',5'-oligoadenylate (2-5A), that binds and activates RNase-L. This pathway is down-regulated by virus- and host-encoded enzymes that degrade 2-5A. Phosphodiesterase 12 (PDE12) was the first cellular 2-5A- degrading enzyme to be purified and described at a molecular level. Inhibition of PDE12 may up-regulate the OAS/RNase-L pathway in response to viral infection resulting in increased resistance to a variety of viral pathogens. We generated a PDE12-null cell line, HeLaΔPDE12, using transcription activator-like effector nuclease-mediated gene inactivation. This cell line has increased 2-5A levels in response to IFN and poly(I-C), a double-stranded RNA mimic compared with the parental cell line. Moreover, HeLaΔPDE12 cells were resistant to viral pathogens, including encephalomyocarditis virus, human rhinovirus, and respiratory syncytial virus. Based on these results, we used DNA-encoded chemical library screening to identify starting points for inhibitor lead optimization. Compounds derived from this effort raise 2-5A levels and exhibit antiviral activity comparable with the effects observed with PDE12 gene inactivation. The crystal structure of PDE12 complexed with an inhibitor was solved providing insights into the structure-activity relationships of inhibitor potency and selectivity.
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Affiliation(s)
| | | | - Jing Chai
- ELT Boston, GlaxoSmithKline, Waltham, Massachusetts 02451
| | - Philias Daka
- Antiviral Discovery Performance Unit, GlaxoSmithKline, Research Triangle Park, North Carolina 27709 and
| | - Hongfeng Deng
- ELT Boston, GlaxoSmithKline, Waltham, Massachusetts 02451
| | - Yun Ding
- ELT Boston, GlaxoSmithKline, Waltham, Massachusetts 02451
| | | | | | | | | | | | - Ninad Prabhu
- ELT Boston, GlaxoSmithKline, Waltham, Massachusetts 02451
| | - Cecil Rise
- ELT Boston, GlaxoSmithKline, Waltham, Massachusetts 02451
| | - Timothy Sheahan
- Antiviral Discovery Performance Unit, GlaxoSmithKline, Research Triangle Park, North Carolina 27709 and
| | - J Brad Shotwell
- Antiviral Discovery Performance Unit, GlaxoSmithKline, Research Triangle Park, North Carolina 27709 and
| | | | - Vince Tai
- Antiviral Discovery Performance Unit, GlaxoSmithKline, Research Triangle Park, North Carolina 27709 and
| | | | | | | | | | - Shihyun You
- Antiviral Discovery Performance Unit, GlaxoSmithKline, Research Triangle Park, North Carolina 27709 and
| | - Bing Xia
- ELT Boston, GlaxoSmithKline, Waltham, Massachusetts 02451
| | - Hamilton Dickson
- Antiviral Discovery Performance Unit, GlaxoSmithKline, Research Triangle Park, North Carolina 27709 and
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