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Cai X, Ng CP, Jones O, Fung TS, Ryu KW, Li D, Thompson CB. Lactate activates the mitochondrial electron transport chain independently of its metabolism. Mol Cell 2023; 83:3904-3920.e7. [PMID: 37879334 PMCID: PMC10752619 DOI: 10.1016/j.molcel.2023.09.034] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 08/02/2023] [Accepted: 09/28/2023] [Indexed: 10/27/2023]
Abstract
Lactate has long been considered a cellular waste product. However, we found that as extracellular lactate accumulates, it also enters the mitochondrial matrix and stimulates mitochondrial electron transport chain (ETC) activity. The resulting increase in mitochondrial ATP synthesis suppresses glycolysis and increases the utilization of pyruvate and/or alternative respiratory substrates. The ability of lactate to increase oxidative phosphorylation does not depend on its metabolism. Both L- and D-lactate are effective at enhancing ETC activity and suppressing glycolysis. Furthermore, the selective induction of mitochondrial oxidative phosphorylation by unmetabolized D-lactate reversibly suppressed aerobic glycolysis in both cancer cell lines and proliferating primary cells in an ATP-dependent manner and enabled cell growth on respiratory-dependent bioenergetic substrates. In primary T cells, D-lactate enhanced cell proliferation and effector function. Together, these findings demonstrate that lactate is a critical regulator of the ability of mitochondrial oxidative phosphorylation to suppress glucose fermentation.
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Affiliation(s)
- Xin Cai
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Charles P Ng
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Olivia Jones
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Tak Shun Fung
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Keun Woo Ryu
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Dayi Li
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Craig B Thompson
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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2
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Cai X, Ng CC, Jones O, Fung TS, Ryu K, Li D, Thompson CB. Lactate activates the mitochondrial electron transport chain independent of its metabolism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.02.551712. [PMID: 37577602 PMCID: PMC10418154 DOI: 10.1101/2023.08.02.551712] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Lactate has long been considered a cellular waste product. However, we found that as extracellular lactate accumulates, it also enters the mitochondrial matrix and stimulates mitochondrial electron transport chain (ETC) activity. The resulting increase in mitochondrial ATP synthesis suppresses glycolysis and increases the utilization of pyruvate and/or alternative respiratory substrates. The ability of lactate to increase oxidative phosphorylation does not depend on its metabolism. Both L- and D-lactate are effective at enhancing ETC activity and suppressing glycolysis. Furthermore, the selective induction of mitochondrial oxidative phosphorylation by unmetabolized D-lactate reversibly suppressed aerobic glycolysis in both cancer cell lines and proliferating primary cells in an ATP-dependent manner and enabled cell growth on respiratory-dependent bioenergetic substrates. In primary T cells, D-lactate enhanced cell proliferation and effector function. Together, these findings demonstrate that lactate is a critical regulator of the ability of mitochondrial oxidative phosphorylation to suppress glucose fermentation.
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3
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Blanco-Fernandez J, Jourdain AA. Dead-Seq: Discovering Synthetic Lethal Interactions from Dead Cells Genomics. Methods Mol Biol 2023; 2661:329-342. [PMID: 37166646 DOI: 10.1007/978-1-0716-3171-3_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Pooled genetic screens have revolutionized the field of functional genomics, yet perturbations that decrease fitness, such as those leading to synthetic lethality, have remained difficult to quantify at the genomic level. We and colleagues previously developed "death screening," a protocol based on the purification of dead cells in genetic screens, and used it to identify a set of genes necessary for mitochondrial gene expression, translation, and oxidative phosphorylation (OXPHOS), thus offering new possibilities for the diagnosis of mitochondrial disorders. Here, we describe Dead-Seq, a refined protocol for death screening that is compatible with most pooled screening protocols, including genome-wide CRISPR/Cas9 screening. Dead-Seq converts negative-selection screens into positive-selection screens and generates high-quality data directly from dead cells, at limited sequencing costs.
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Affiliation(s)
| | - Alexis A Jourdain
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland.
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4
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Bai Z, Tao W, Zhou Y, Cao Y, Yu S, Shi Z. Xiao-Yao-San protects against anti-tuberculosis drug-induced liver injury by regulating Grsf1 in the mitochondrial oxidative stress pathway. Front Pharmacol 2022; 13:948128. [PMID: 36120303 PMCID: PMC9475289 DOI: 10.3389/fphar.2022.948128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/08/2022] [Indexed: 11/24/2022] Open
Abstract
Background: Xiao-Yao-San (XYS) is a traditional Chinese prescription that regulates gastrointestinal function, improves mental and psychological abnormalities, and enhances liver function. However, the underlying mechanism of XYS for relieving anti-tuberculosis (AT) drug-induced liver injury is not clear. Objective: The current study examined whether XYS alleviated the symptoms of AT drug-induced liver injury in mice via the mitochondrial oxidative stress pathway. Methods: BALB/c male mice were randomly divided into four groups of 12 animals, including a control group, a model group, a 0.32 g/kg XYS group, and a 0.64 g/kg XYS group. The effect of XYS on the degree of liver injury was observed using haematoxylin and eosin staining (HE) and oil red O staining of pathological sections, biochemical parameters, and reactive oxygen species (ROS) levels. The protein expression of mitochondrial synthesis-related proteins and ferroptosis-related proteins was examined using Western blotting. Results: XYS improved the pathological changes in liver tissue and reduced the level of oxidative stress in liver-injured mice. XYS increased the expression of mitochondrial synthesis-related proteins and reversed the expression of ferroptosis-related proteins. Knockdown of G-rich RNA sequence binding factor 1 (Grsf1) expression with Grsf1 shRNA blocked the protective effects of XYS in liver injury. Conclusion: Our findings suggest that XYS alleviates AT drug-induced liver injury by mediating Grsf1 in the mitochondrial oxidative stress pathway.
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Affiliation(s)
- Zijun Bai
- School of Chinese Medicine, School of Integrated Chinese and Western Medicine Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
- Ningxia Key Laboratory of Cerebrocranial Disease, Incubation Base of National Key Laboratory, College of Pharmacy, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Weiwei Tao
- School of Chinese Medicine, School of Integrated Chinese and Western Medicine Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Yiqun Zhou
- Department of Infectious Disease, Suzhou Integrated Chinese and Western Medicine Hospital, Suzhou, Jiangsu, China
| | - Yi Cao
- Institute of Literature in Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
| | - Shun Yu
- Institute of Literature in Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
- *Correspondence: Shun Yu, ; Zheng Shi,
| | - Zheng Shi
- Institute of Literature in Chinese Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu, China
- *Correspondence: Shun Yu, ; Zheng Shi,
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5
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Skolik RA, Solocinski J, Konkle ME, Chakraborty N, Menze MA. Global changes to HepG2 cell metabolism in response to galactose treatment. Am J Physiol Cell Physiol 2021; 320:C778-C793. [PMID: 33439775 DOI: 10.1152/ajpcell.00460.2020] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Tumor cell proliferation requires sufficient metabolic flux through the pentose phosphate pathway to meet the demand for biosynthetic precursors and to increase protection against oxidative stress which in turn requires an upregulation of substrate flow through glycolysis. This metabolic poise is often coupled with a shift in ATP production from mitochondrial OXPHOS to substrate-level phosphorylation. Despite major advances that were facilitated by using tumor-derived cell lines in research areas spanning from membrane to cytoskeletal biology, this distorted metabolic profile limits their impact as a model in physiology and toxicology. Substitution of glucose with galactose in the cell culture medium has been demonstrated to shift ATP production from substrate-level phosphorylation to mitochondrial OXPHOS. This increase in oxygen utilization is coupled to a global metabolic reorganization with potential impacts on macromolecule biosynthesis and cellular redox homeostasis, but a comprehensive analysis on the effects of sugar substitution in tumor-derived cells is still missing. To address this gap in knowledge we performed transcriptomic and metabolomic analyses on human hepatocellular carcinoma (HepG2) cells adapted to either glucose or galactose as the aldohexose source. We observed a shift toward oxidative metabolism in all primary metabolic pathways at both transcriptomic and metabolomic levels. We also observed a decrease in nicotinamide dinucleotide (NAD(P)) levels and subcellular NAD+-to-NADH ratios in cells cultured with galactose compared with glucose control cells. Our results suggest that galactose reduces both glycolytic and biosynthetic flux and restores a metabolic poise in HepG2 cells that closely reflects the metabolic state observed in primary hepatocytes.
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Affiliation(s)
- R A Skolik
- Department of Biology, University of Louisville, Louisville, Kentucky
| | - J Solocinski
- Department of Mechanical Engineering, University of Michigan, Dearborn, Michigan
| | - M E Konkle
- Department of Chemistry, Ball State University, Muncie, Indiana
| | - N Chakraborty
- Department of Mechanical Engineering, University of Michigan, Dearborn, Michigan
| | - M A Menze
- Department of Biology, University of Louisville, Louisville, Kentucky
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Arroyo JD, Jourdain AA, Calvo SE, Ballarano CA, Doench JG, Root DE, Mootha VK. A Genome-wide CRISPR Death Screen Identifies Genes Essential for Oxidative Phosphorylation. Cell Metab 2016; 24:875-885. [PMID: 27667664 PMCID: PMC5474757 DOI: 10.1016/j.cmet.2016.08.017] [Citation(s) in RCA: 216] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Revised: 07/15/2016] [Accepted: 08/24/2016] [Indexed: 12/18/2022]
Abstract
Oxidative phosphorylation (OXPHOS) is the major pathway for ATP production in humans. Deficiencies in OXPHOS can arise from mutations in either mitochondrial or nuclear genomes and comprise the largest collection of inborn errors of metabolism. At present we lack a complete catalog of human genes and pathways essential for OXPHOS. Here we introduce a genome-wide CRISPR "death screen" that actively selects dying cells to reveal human genes required for OXPHOS, inspired by the classic observation that human cells deficient in OXPHOS survive in glucose but die in galactose. We report 191 high-confidence hits essential for OXPHOS, including 72 underlying known OXPHOS diseases. Our screen reveals a functional module consisting of NGRN, WBSCR16, RPUSD3, RPUSD4, TRUB2, and FASTKD2 that regulates the mitochondrial 16S rRNA and intra-mitochondrial translation. Our work yields a rich catalog of genes required for OXPHOS and, more generally, demonstrates the power of death screening for functional genomic analysis.
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Affiliation(s)
- Jason D Arroyo
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexis A Jourdain
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sarah E Calvo
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carmine A Ballarano
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David E Root
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Vamsi K Mootha
- Department of Molecular Biology and Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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7
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Emperador S, Pacheu-Grau D, Bayona-Bafaluy MP, Garrido-Pérez N, Martín-Navarro A, López-Pérez MJ, Montoya J, Ruiz-Pesini E. An MRPS12 mutation modifies aminoglycoside sensitivity caused by 12S rRNA mutations. Front Genet 2015; 5:469. [PMID: 25642242 PMCID: PMC4294204 DOI: 10.3389/fgene.2014.00469] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 12/19/2014] [Indexed: 01/22/2023] Open
Abstract
Several homoplasmic pathologic mutations in mitochondrial DNA, such as those causing Leber hereditary optic neuropathy or non-syndromic hearing loss, show incomplete penetrance. Therefore, other elements must modify their pathogenicity. Discovery of these modifying factors is not an easy task because in multifactorial diseases conventional genetic approaches may not always be informative. Here, we have taken an evolutionary approach to unmask putative modifying factors for a particular homoplasmic pathologic mutation causing aminoglycoside-induced and non-syndromic hearing loss, the m.1494C>T transition in the mitochondrial DNA. The mutation is located in the decoding site of the mitochondrial ribosomal RNA. We first looked at mammalian species that had fixed the human pathologic mutation. These mutations are called compensated pathogenic deviations because an organism carrying one must also have another that suppresses the deleterious effect of the first. We found that species from the primate family Cercopithecidae (old world monkeys) harbor the m.1494T allele even if their auditory function is normal. In humans the m.1494T allele increases the susceptibility to aminoglycosides. However, in primary fibroblasts from a Cercopithecidae species, aminoglycosides do not impair cell growth, respiratory complex IV activity and quantity or the mitochondrial protein synthesis. Interestingly, this species also carries a fixed mutation in the mitochondrial ribosomal protein S12. We show that the expression of this variant in a human m.1494T cell line reduces its susceptibility to aminoglycosides. Because several mutations in this human protein have been described, they may possibly explain the absence of pathologic phenotype in some pedigree members with the most frequent pathologic mutations in mitochondrial ribosomal RNA.
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Affiliation(s)
- Sonia Emperador
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza Zaragoza, Spain ; Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza Zaragoza, Spain ; Centros de Investigación Biomédica en Red de Enfermedades Raras, Universidad de Zaragoza Zaragoza, Spain
| | - David Pacheu-Grau
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza Zaragoza, Spain
| | - M Pilar Bayona-Bafaluy
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza Zaragoza, Spain
| | - Nuria Garrido-Pérez
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza Zaragoza, Spain
| | - Antonio Martín-Navarro
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza Zaragoza, Spain
| | - Manuel J López-Pérez
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza Zaragoza, Spain ; Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza Zaragoza, Spain ; Centros de Investigación Biomédica en Red de Enfermedades Raras, Universidad de Zaragoza Zaragoza, Spain
| | - Julio Montoya
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza Zaragoza, Spain ; Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza Zaragoza, Spain ; Centros de Investigación Biomédica en Red de Enfermedades Raras, Universidad de Zaragoza Zaragoza, Spain
| | - Eduardo Ruiz-Pesini
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza Zaragoza, Spain ; Instituto de Investigación Sanitaria de Aragón, Universidad de Zaragoza Zaragoza, Spain ; Centros de Investigación Biomédica en Red de Enfermedades Raras, Universidad de Zaragoza Zaragoza, Spain ; Fundación ARAID, Universidad de Zaragoza Zaragoza, Spain
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8
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Gershoni M, Levin L, Ovadia O, Toiw Y, Shani N, Dadon S, Barzilai N, Bergman A, Atzmon G, Wainstein J, Tsur A, Nijtmans L, Glaser B, Mishmar D. Disrupting mitochondrial-nuclear coevolution affects OXPHOS complex I integrity and impacts human health. Genome Biol Evol 2014; 6:2665-80. [PMID: 25245408 PMCID: PMC4224335 DOI: 10.1093/gbe/evu208] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The mutation rate of the mitochondrial DNA (mtDNA), which is higher by an order of magnitude as compared with the nuclear genome, enforces tight mitonuclear coevolution to maintain mitochondrial activities. Interruption of such coevolution plays a role in interpopulation hybrid breakdown, speciation events, and disease susceptibility. Previously, we found an elevated amino acid replacement rate and positive selection in the nuclear DNA-encoded oxidative phosphorylation (OXPHOS) complex I subunit NDUFC2, a phenomenon important for the direct interaction of NDUFC2 with the mtDNA-encoded complex I subunit ND4. This finding underlines the importance of mitonuclear coevolution to physical interactions between mtDNA and nuclear DNA-encoded factors. Nevertheless, it remains unclear whether this interaction is important for the stability and activity of complex I. Here, we show that siRNA silencing of NDUFC2 reduced growth of human D-407 retinal pigment epithelial cells, significantly diminished mitochondrial membrane potential, and interfered with complex I integrity. Moreover, site-directed mutagenesis of a positively selected amino acid in NDUFC2 significantly interfered with the interaction of NDUFC2 with its mtDNA-encoded partner ND4. Finally, we show that a genotype combination involving this amino acid (NDUFC2 residue 46) and the mtDNA haplogroup HV likely altered susceptibility to type 2 diabetes mellitus in Ashkenazi Jews. Therefore, mitonuclear coevolution is important for maintaining mitonuclear factor interactions, OXPHOS, and for human health.
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Affiliation(s)
- Moran Gershoni
- Department of Life Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Liron Levin
- Department of Life Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Ofer Ovadia
- Department of Life Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Yasmin Toiw
- Department of Life Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Naama Shani
- Department of Life Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Sara Dadon
- Department of Life Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
| | - Nir Barzilai
- Institute of Aging, Division of Endocrinology, Departments of Medicine and Genetics, Albert Einstein College of Medicine, New York, NY, USA
| | - Aviv Bergman
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Gil Atzmon
- Institute of Aging, Division of Endocrinology, Departments of Medicine and Genetics, Albert Einstein College of Medicine, New York, NY, USA
| | | | - Anat Tsur
- Endocrine Clinic, Clalit Health Services, Jerusalem, Israel
| | - Leo Nijtmans
- Nijmegen Center for Mitochondrial Disorders, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Benjamin Glaser
- Endocrinology and Metabolism Service, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Dan Mishmar
- Department of Life Sciences, Ben Gurion University of the Negev, Beer Sheva, Israel
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Mocan L, Ilie I, Tabaran FA, Dana B, Zaharie F, Zdrehus C, Puia C, Mocan T, Muntean V, Teodora P, Ofelia M, Marcel T, Iancu C. Surface plasmon resonance-induced photoactivation of gold nanoparticles as mitochondria-targeted therapeutic agents for pancreatic cancer. Expert Opin Ther Targets 2013; 17:1383-93. [PMID: 24188208 DOI: 10.1517/14728222.2013.855200] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND Noble metal nanoparticles such as gold nanoparticles can strongly absorb light in the visible region by inducing coherent collective oscillation of conduction band electrons in strong resonance with visible frequencies of light. This phenomenon is frequently termed as surface plasmon resonance (SPR). OBJECTIVES The main objective was to study the effects of laser photoactivated gold nanoparticles (by means of SPR) on human pancreatic cancer cells. RESULTS Gold nanoparticles obtained using standard wet chemical methods (with sodium borohydride as a reducing agent) underwent photoexcitation using 2w 808 nm laser and further administered to 1.4E7 pancreatic cancer cell lines. Flow cytometry, transmission electron microscopy, phase contrast microscopy, quantitative proteomics and confocal microscopy combined with immunochemical staining were used to examine the interaction between photo excited gold nanoparticles and pancreatic cancer cells. CONCLUSION The study shows that phonon-phonon interactions following laser photoexcitation of gold nanoparticles exhibit increased intracellular uptake, as well as mitochondrial swelling, closely followed by mitochondrial inner membrane permeabilization and depolarization. This unique data may represent a major step in mitochondria-targeted anticancer therapies using laser-activated gold nanoparticles.
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Affiliation(s)
- Lucian Mocan
- "Iuliu Hatieganu" University of Medicine and Pharmacy, Regional Institute of Gastroenterology and Hepatology, Department of Nanomedicine , Croitorilor Street, Cluj-Napoca , Romania , +40264-439696 ; +40264-439696 ;
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GRSF1 regulates RNA processing in mitochondrial RNA granules. Cell Metab 2013; 17:399-410. [PMID: 23473034 PMCID: PMC3593211 DOI: 10.1016/j.cmet.2013.02.005] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Revised: 12/18/2012] [Accepted: 02/06/2013] [Indexed: 12/22/2022]
Abstract
Various specialized domains have been described in the cytosol and the nucleus; however, little is known about compartmentalization within the mitochondrial matrix. GRSF1 (G-rich sequence factor 1) is an RNA binding protein that was previously reported to localize in the cytosol. We found that an isoform of GRSF1 accumulates in discrete foci in the mitochondrial matrix. These foci are composed of nascent mitochondrial RNA and also contain RNase P, an enzyme that participates in mitochondrial RNA processing. GRSF1 was found to interact with RNase P and to be required for processing of both classical and tRNA-less RNA precursors. In its absence, cleavage of primary RNA transcripts is abnormal, leading to decreased expression of mitochondrially encoded proteins and mitochondrial dysfunction. Our findings suggest that the foci containing GRSF1 and RNase P correspond to sites where primary RNA transcripts converge to be processed. We have termed these large ribonucleoprotein structures "mitochondrial RNA granules."
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Secrier M, Pavlopoulos GA, Aerts J, Schneider R. Arena3D: visualizing time-driven phenotypic differences in biological systems. BMC Bioinformatics 2012; 13:45. [PMID: 22439608 PMCID: PMC3368716 DOI: 10.1186/1471-2105-13-45] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 03/22/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Elucidating the genotype-phenotype connection is one of the big challenges of modern molecular biology. To fully understand this connection, it is necessary to consider the underlying networks and the time factor. In this context of data deluge and heterogeneous information, visualization plays an essential role in interpreting complex and dynamic topologies. Thus, software that is able to bring the network, phenotypic and temporal information together is needed. Arena3D has been previously introduced as a tool that facilitates link discovery between processes. It uses a layered display to separate different levels of information while emphasizing the connections between them. We present novel developments of the tool for the visualization and analysis of dynamic genotype-phenotype landscapes. RESULTS Version 2.0 introduces novel features that allow handling time course data in a phenotypic context. Gene expression levels or other measures can be loaded and visualized at different time points and phenotypic comparison is facilitated through clustering and correlation display or highlighting of impacting changes through time. Similarity scoring allows the identification of global patterns in dynamic heterogeneous data. In this paper we demonstrate the utility of the tool on two distinct biological problems of different scales. First, we analyze a medium scale dataset that looks at perturbation effects of the pluripotency regulator Nanog in murine embryonic stem cells. Dynamic cluster analysis suggests alternative indirect links between Nanog and other proteins in the core stem cell network. Moreover, recurrent correlations from the epigenetic to the translational level are identified. Second, we investigate a large scale dataset consisting of genome-wide knockdown screens for human genes essential in the mitotic process. Here, a potential new role for the gene lsm14a in cytokinesis is suggested. We also show how phenotypic patterning allows for extensive comparison and identification of high impact knockdown targets. CONCLUSIONS We present a new visualization approach for perturbation screens with multiple phenotypic outcomes. The novel functionality implemented in Arena3D enables effective understanding and comparison of temporal patterns within morphological layers, to help with the system-wide analysis of dynamic processes. Arena3D is available free of charge for academics as a downloadable standalone application from: http://arena3d.org/.
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Affiliation(s)
- Maria Secrier
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, Heidelberg 69117, Germany.
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