DOCSLIB.ORG

Mouse Ndufb3 Conditional Knockout Project (CRISPR/Cas9)

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Mouse Ndufb3 Conditional Knockout Project (CRISPR/Cas9) https://www.alphaknockout.com Mouse Ndufb3 Conditional Knockout Project (CRISPR/Cas9) Objective: To create a Ndufb3 conditional knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Ndufb3 gene (NCBI Reference Sequence: NM_025597 ; Ensembl: ENSMUSG00000026032 ) is located on Mouse chromosome 1. 3 exons are identified, with the ATG start codon in exon 2 and the TGA stop codon in exon 3 (Transcript: ENSMUST00000027193). Exon 2 will be selected as conditional knockout region (cKO region). Deletion of this region should result in the loss of function of the Mouse Ndufb3 gene. To engineer the targeting vector, homologous arms and cKO region will be generated by PCR using BAC clone RP23-67I5 as template. Cas9, gRNA and targeting vector will be co-injected into fertilized eggs for cKO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Exon 2 starts from about 100% of the coding region. The knockout of Exon 2 will result in frameshift of the gene. The size of intron 1 for 5'-loxP site insertion: 4419 bp, and the size of intron 2 for 3'-loxP site insertion: 4399 bp. The size of effective cKO region: ~658 bp. The cKO region does not have any other known gene. Page 1 of 7 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele gRNA region 5' gRNA region 3' 1 2 3 Targeting vector Targeted allele Constitutive KO allele (After Cre recombination) Legends Exon of mouse Ndufb3 Homology arm cKO region loxP site Page 2 of 7 https://www.alphaknockout.com Overview of the Dot Plot Window size: 10 bp Forward Reverse Complement Sequence 12 Note: The sequence of homologous arms and cKO region is aligned with itself to determine if there are tandem repeats. No significant tandem repeat is found in the dot plot matrix. So this region is suitable for PCR screening or sequencing analysis. Overview of the GC Content Distribution Window size: 300 bp Sequence 12 Summary: Full Length(7158bp) | A(27.7% 1983) | C(19.1% 1367) | T(35.04% 2508) | G(18.16% 1300) Note: The sequence of homologous arms and cKO region is analyzed to determine the GC content. No significant high GC-content region is found. So this region is suitable for PCR screening or sequencing analysis. Page 3 of 7 https://www.alphaknockout.com BLAT Search Results (up) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 3000 1 3000 3000 100.0% chr1 + 58587843 58590842 3000 browser details YourSeq 196 174 1090 3000 92.0% chr1 + 155407821 155524076 116256 browser details YourSeq 174 178 1073 3000 87.9% chr17 - 70732707 70842196 109490 browser details YourSeq 150 181 1082 3000 90.9% chr11 + 18010811 18127043 116233 browser details YourSeq 111 956 1090 3000 91.2% chr4 + 41139647 41139781 135 browser details YourSeq 109 954 1090 3000 89.8% chr9 - 114399985 114400121 137 browser details YourSeq 107 956 1090 3000 89.7% chr14 - 63592359 63592493 135 browser details YourSeq 106 956 1091 3000 89.0% chrX + 8269347 8269482 136 browser details YourSeq 105 956 1086 3000 90.1% chr17 - 87634310 87634440 131 browser details YourSeq 105 956 1086 3000 90.1% chr9 + 109938252 109938382 131 browser details YourSeq 105 957 1091 3000 88.9% chr2 + 130511142 130511276 135 browser details YourSeq 105 956 1090 3000 88.9% chr10 + 84616147 84616281 135 browser details YourSeq 105 956 1087 3000 90.1% chr1 + 118379472 118379604 133 browser details YourSeq 104 962 1091 3000 90.0% chr15 + 96793119 96793248 130 browser details YourSeq 103 962 1090 3000 90.0% chr4 - 123705151 123705279 129 browser details YourSeq 103 953 1090 3000 87.6% chr3 - 95876825 95876983 159 browser details YourSeq 103 956 1087 3000 89.4% chr14 - 122185755 122185890 136 browser details YourSeq 103 956 1086 3000 89.4% chr14 - 26509965 26510095 131 browser details YourSeq 103 956 1090 3000 88.2% chr15 + 61996687 61996821 135 browser details YourSeq 103 956 1091 3000 88.2% chr12 + 76848669 76849041 373 Note: The 3000 bp section upstream of Exon 2 is BLAT searched against the genome. No significant similarity is found. BLAT Search Results (down) QUERY SCORE START END QSIZE IDENTITY CHROM STRAND START END SPAN ----------------------------------------------------------------------------------------------- browser details YourSeq 3000 1 3000 3000 100.0% chr1 + 58591501 58594500 3000 browser details YourSeq 281 2503 2785 3000 99.0% chr10 - 66588787 66589068 282 browser details YourSeq 280 2505 2785 3000 100.0% chr18 + 17345959 17346248 290 browser details YourSeq 280 2504 2785 3000 99.7% chr15 + 52730822 52731103 282 browser details YourSeq 280 2505 2785 3000 100.0% chr10 + 119066246 119066558 313 browser details YourSeq 280 2504 2785 3000 100.0% chr1 + 105013715 105013998 284 browser details YourSeq 279 2506 2785 3000 100.0% chr15 - 18320727 18321030 304 browser details YourSeq 279 2506 2785 3000 100.0% chr13 - 6764247 6764552 306 browser details YourSeq 279 2503 2785 3000 99.7% chr10 + 14709279 14709578 300 browser details YourSeq 278 2508 2785 3000 100.0% chr12 - 64732742 64733019 278 browser details YourSeq 278 2508 2785 3000 100.0% chr10 - 29625847 29626124 278 browser details YourSeq 278 2503 2785 3000 99.3% chr1 - 146010942 146011297 356 browser details YourSeq 276 2504 2785 3000 99.3% chr16 - 40531757 40559118 27362 browser details YourSeq 276 2504 2785 3000 97.9% chr15 - 45932257 45932533 277 browser details YourSeq 276 2508 2785 3000 99.7% chr1 + 123318931 123319208 278 browser details YourSeq 275 2508 2785 3000 99.7% chr15 - 56891882 56892173 292 browser details YourSeq 275 2499 2785 3000 98.6% chr11 - 29444892 29445201 310 browser details YourSeq 275 2508 2785 3000 99.7% chr10 - 48058527 48058807 281 browser details YourSeq 275 2505 2785 3000 99.0% chr15 + 54204683 54204963 281 browser details YourSeq 275 2510 2785 3000 100.0% chr14 + 43662277 43662558 282 Note: The 3000 bp section downstream of Exon 2 is BLAT searched against the genome. No significant similarity is found. Page 4 of 7 https://www.alphaknockout.com Gene and protein information: Ndufb3 NADH:ubiquinone oxidoreductase subunit B3 [ Mus musculus (house mouse) ] Gene ID: 66495, updated on 12-Aug-2019 Gene summary Official Symbol Ndufb3 provided by MGI Official Full Name NADH:ubiquinone oxidoreductase subunit B3 provided by MGI Primary source MGI:MGI:1913745 See related Ensembl:ENSMUSG00000026032 Gene type protein coding RefSeq status VALIDATED Organism Mus musculus Lineage Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus Also known as CI-B12; 2700033I16Rik Expression Ubiquitous expression in heart adult (RPKM 65.8), bladder adult (RPKM 47.1) and 26 other tissues See more Orthologs human all Genomic context Location: 1; 1 C1.3 See Ndufb3 in Genome Data Viewer Exon count: 3 Annotation release Status Assembly Chr Location 108 current GRCm38.p6 (GCF_000001635.26) 1 NC_000067.6 (58586397..58595964) Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 1 NC_000067.5 (58643443..58652792) Chromosome 1 - NC_000067.6 Page 5 of 7 https://www.alphaknockout.com Transcript information: This gene has 1 transcript Gene: Ndufb3 ENSMUSG00000026032 Description NADH:ubiquinone oxidoreductase subunit B3 [Source:MGI Symbol;Acc:MGI:1913745] Gene Synonyms 2700033I16Rik Location Chromosome 1: 58,586,384-58,595,964 forward strand. GRCm38:CM000994.2 About this gene This gene has 1 transcript (splice variant), 206 orthologues and is a member of 1 Ensembl protein family. Transcripts Name Transcript ID bp Protein Translation ID Biotype CCDS UniProt Flags Ndufb3-201 ENSMUST00000027193.8 763 104aa ENSMUSP00000027193.8 Protein coding CCDS14977 Q9CQZ6 TSL:1 GENCODE basic APPRIS P1 29.58 kb Forward strand 58.58Mb 58.59Mb 58.60Mb Genes (Comprehensive set... Ndufb3-201 >protein coding Contigs AC118698.7 > Genes < Fam126b-207protein coding (Comprehensive set... < Fam126b-202protein coding < Fam126b-201protein coding < Fam126b-206protein coding < Fam126b-205lncRNA < Fam126b-204retained intron < Fam126b-203retained intron Regulatory Build 58.58Mb 58.59Mb 58.60Mb Reverse strand 29.58 kb Regulation Legend CTCF Enhancer Open Chromatin Promoter Promoter Flank Transcription Factor Binding Site Gene Legend Protein Coding Ensembl protein coding merged Ensembl/Havana Non-Protein Coding RNA gene processed transcript Page 6 of 7 https://www.alphaknockout.com Transcript: ENSMUST00000027193 9.58 kb Forward strand Ndufb3-201 >protein coding ENSMUSP00000027... PDB-ENSP mappings Low complexity (Seg) Pfam NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 PANTHER PTHR15082:SF2 NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 3 All sequence SNPs/i... Sequence variants (dbSNP and all other sources) YR M M R R Variant Legend inframe insertion missense variant synonymous variant Scale bar 0 10 20 30 40 50 60 70 80 90 104 We wish to acknowledge the following valuable scientific information resources: Ensembl, MGI, NCBI, UCSC. Page 7 of 7.
Load more

Recommended publications
  • Proteomic and Metabolomic Analyses of Mitochondrial Complex I-Deficient
    THE JOURNAL OF BIOLOGICAL CHEMISTRY VOL. 287, NO. 24, pp. 20652–20663, June 8, 2012 © 2012 by The American Society for Biochemistry and Molecular Biology, Inc. Published in the U.S.A. Proteomic and Metabolomic Analyses of Mitochondrial Complex I-deficient Mouse Model Generated by Spontaneous B2 Short Interspersed Nuclear Element (SINE) Insertion into NADH Dehydrogenase (Ubiquinone) Fe-S Protein 4 (Ndufs4) Gene*□S Received for publication, November 25, 2011, and in revised form, April 5, 2012 Published, JBC Papers in Press, April 25, 2012, DOI 10.1074/jbc.M111.327601 Dillon W. Leong,a1 Jasper C. Komen,b1 Chelsee A. Hewitt,a Estelle Arnaud,c Matthew McKenzie,d Belinda Phipson,e Melanie Bahlo,e,f Adrienne Laskowski,b Sarah A. Kinkel,a,g,h Gayle M. Davey,g William R. Heath,g Anne K. Voss,a,h René P. Zahedi,i James J. Pitt,j Roman Chrast,c Albert Sickmann,i,k Michael T. Ryan,l Gordon K. Smyth,e,f,h b2 a,h,m,n3 David R. Thorburn, and Hamish S. Scott Downloaded from From the aMolecular Medicine Division, gImmunology Division, and eBioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia, the bMurdoch Childrens Research Institute, Royal Children’s Hospital and Department of Paediatrics, University of Melbourne, Parkville, Victoria 3052, Australia, the cDépartement de Génétique Médicale, Université de Lausanne, 1005 Lausanne, Switzerland, the dCentre for Reproduction and Development, Monash Institute of Medical Research, Clayton, Victoria 3168, Australia, the hDepartment of Medical Biology
    [Show full text]
  • Low Abundance of the Matrix Arm of Complex I in Mitochondria Predicts Longevity in Mice
    ARTICLE Received 24 Jan 2014 | Accepted 9 Apr 2014 | Published 12 May 2014 DOI: 10.1038/ncomms4837 OPEN Low abundance of the matrix arm of complex I in mitochondria predicts longevity in mice Satomi Miwa1, Howsun Jow2, Karen Baty3, Amy Johnson1, Rafal Czapiewski1, Gabriele Saretzki1, Achim Treumann3 & Thomas von Zglinicki1 Mitochondrial function is an important determinant of the ageing process; however, the mitochondrial properties that enable longevity are not well understood. Here we show that optimal assembly of mitochondrial complex I predicts longevity in mice. Using an unbiased high-coverage high-confidence approach, we demonstrate that electron transport chain proteins, especially the matrix arm subunits of complex I, are decreased in young long-living mice, which is associated with improved complex I assembly, higher complex I-linked state 3 oxygen consumption rates and decreased superoxide production, whereas the opposite is seen in old mice. Disruption of complex I assembly reduces oxidative metabolism with concomitant increase in mitochondrial superoxide production. This is rescued by knockdown of the mitochondrial chaperone, prohibitin. Disrupted complex I assembly causes premature senescence in primary cells. We propose that lower abundance of free catalytic complex I components supports complex I assembly, efficacy of substrate utilization and minimal ROS production, enabling enhanced longevity. 1 Institute for Ageing and Health, Newcastle University, Newcastle upon Tyne NE4 5PL, UK. 2 Centre for Integrated Systems Biology of Ageing and Nutrition, Newcastle University, Newcastle upon Tyne NE4 5PL, UK. 3 Newcastle University Protein and Proteome Analysis, Devonshire Building, Devonshire Terrace, Newcastle upon Tyne NE1 7RU, UK. Correspondence and requests for materials should be addressed to T.v.Z.
    [Show full text]
  • Mouse Ndufb3 Knockout Project (CRISPR/Cas9)
    https://www.alphaknockout.com Mouse Ndufb3 Knockout Project (CRISPR/Cas9) Objective: To create a Ndufb3 knockout Mouse model (C57BL/6J) by CRISPR/Cas-mediated genome engineering. Strategy summary: The Ndufb3 gene (NCBI Reference Sequence: NM_025597 ; Ensembl: ENSMUSG00000026032 ) is located on Mouse chromosome 1. 3 exons are identified, with the ATG start codon in exon 2 and the TGA stop codon in exon 3 (Transcript: ENSMUST00000027193). Exon 2~3 will be selected as target site. Cas9 and gRNA will be co-injected into fertilized eggs for KO Mouse production. The pups will be genotyped by PCR followed by sequencing analysis. Note: Exon 2 starts from about 0.32% of the coding region. Exon 2~3 covers 100.0% of the coding region. The size of effective KO region: ~4711 bp. The KO region does not have any other known gene. Page 1 of 8 https://www.alphaknockout.com Overview of the Targeting Strategy Wildtype allele 5' gRNA region gRNA region 3' 1 2 3 Legends Exon of mouse Ndufb3 Knockout region Page 2 of 8 https://www.alphaknockout.com Overview of the Dot Plot (up) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section upstream of start codon is aligned with itself to determine if there are tandem repeats. No significant tandem repeat is found in the dot plot matrix. So this region is suitable for PCR screening or sequencing analysis. Overview of the Dot Plot (down) Window size: 15 bp Forward Reverse Complement Sequence 12 Note: The 2000 bp section downstream of stop codon is aligned with itself to determine if there are tandem repeats.
    [Show full text]
  • Electron Transport Chain Activity Is a Predictor and Target for Venetoclax Sensitivity in Multiple Myeloma
    ARTICLE https://doi.org/10.1038/s41467-020-15051-z OPEN Electron transport chain activity is a predictor and target for venetoclax sensitivity in multiple myeloma Richa Bajpai1,7, Aditi Sharma 1,7, Abhinav Achreja2,3, Claudia L. Edgar1, Changyong Wei1, Arusha A. Siddiqa1, Vikas A. Gupta1, Shannon M. Matulis1, Samuel K. McBrayer 4, Anjali Mittal3,5, Manali Rupji 6, Benjamin G. Barwick 1, Sagar Lonial1, Ajay K. Nooka 1, Lawrence H. Boise 1, Deepak Nagrath2,3,5 & ✉ Mala Shanmugam 1 1234567890():,; The BCL-2 antagonist venetoclax is highly effective in multiple myeloma (MM) patients exhibiting the 11;14 translocation, the mechanistic basis of which is unknown. In evaluating cellular energetics and metabolism of t(11;14) and non-t(11;14) MM, we determine that venetoclax-sensitive myeloma has reduced mitochondrial respiration. Consistent with this, low electron transport chain (ETC) Complex I and Complex II activities correlate with venetoclax sensitivity. Inhibition of Complex I, using IACS-010759, an orally bioavailable Complex I inhibitor in clinical trials, as well as succinate ubiquinone reductase (SQR) activity of Complex II, using thenoyltrifluoroacetone (TTFA) or introduction of SDHC R72C mutant, independently sensitize resistant MM to venetoclax. We demonstrate that ETC inhibition increases BCL-2 dependence and the ‘primed’ state via the ATF4-BIM/NOXA axis. Further, SQR activity correlates with venetoclax sensitivity in patient samples irrespective of t(11;14) status. Use of SQR activity in a functional-biomarker informed manner may better select for MM patients responsive to venetoclax therapy. 1 Department of Hematology and Medical Oncology, Winship Cancer Institute, School of Medicine, Emory University, Atlanta, GA, USA.
    [Show full text]
  • A High-Fat Diet Coordinately Downregulates Genes Required for Mitochondrial Oxidative Phosphorylation in Skeletal Muscle Lauren M
    A High-Fat Diet Coordinately Downregulates Genes Required for Mitochondrial Oxidative Phosphorylation in Skeletal Muscle Lauren M. Sparks, Hui Xie, Robert A. Koza, Randall Mynatt, Matthew W. Hulver, George A. Bray, and Steven R. Smith Obesity and type 2 diabetes have been associated with a ray studies have shown that genes involved in oxidative high-fat diet (HFD) and reduced mitochondrial mass phosphorylation (OXPHOS) exhibit reduced expression and function. We hypothesized a HFD may affect expres- levels in the skeletal muscle of type 2 diabetic subjects and sion of genes involved in mitochondrial function and prediabetic subjects. These changes may be mediated by biogenesis. To test this hypothesis, we fed 10 insulin- the peroxisome proliferator–activated receptor ␥ coacti- sensitive males an isoenergetic HFD for 3 days with vator-1 (PGC1) pathway. PGC1␣- and PGC1␤-responsive muscle biopsies before and after intervention. Oligonu- cleotide microarray analysis revealed 297 genes were OXPHOS genes show reduced expression in the muscle of differentially regulated by the HFD (Bonferonni ad- patients with type 2 diabetes (3,4). In addition to the justed P < 0.001). Six genes involved in oxidative cellular energy sensor AMP kinase, the peroxisome prolif- phosphorylation (OXPHOS) decreased. Four were mem- erator–activated receptor cofactors PGC1␣ (5–7) and pos- bers of mitochondrial complex I: NDUFB3, NDUFB5, sibly PGC1␤ (8) activate mitochondrial biogenesis and NDUFS1, and NDUFV1; one was SDHB in complex II and increase OXPHOS gene expression by increasing the tran- a mitochondrial carrier protein SLC25A12. Peroxisome scription, translation, and activation of the transcription proliferator–activated receptor ␥ coactivator-1 (PGC1) -and PGC1␤ mRNA were decreased by ؊20%, P < 0.01, factors necessary for mitochondrial DNA (mtDNA) repli ␣ and ؊25%, P < 0.01, respectively.
    [Show full text]
  • Bayesian Hidden Markov Tree Models for Clustering Genes with Shared Evolutionary History
    Submitted to the Annals of Applied Statistics arXiv: arXiv:0000.0000 BAYESIAN HIDDEN MARKOV TREE MODELS FOR CLUSTERING GENES WITH SHARED EVOLUTIONARY HISTORY By Yang Liy,{,∗, Shaoyang Ningy,∗, Sarah E. Calvoz,x,{, Vamsi K. Moothak,z,x,{ and Jun S. Liuy Harvard Universityy, Broad Institutez, Harvard Medical Schoolx, Massachusetts General Hospital{, and Howard Hughes Medical Institutek Determination of functions for poorly characterized genes is cru- cial for understanding biological processes and studying human dis- eases. Functionally associated genes are often gained and lost together through evolution. Therefore identifying co-evolution of genes can predict functional gene-gene associations. We describe here the full statistical model and computational strategies underlying the orig- inal algorithm CLustering by Inferred Models of Evolution (CLIME 1.0) recently reported by us [Li et al., 2014]. CLIME 1.0 employs a mixture of tree-structured hidden Markov models for gene evolution process, and a Bayesian model-based clustering algorithm to detect gene modules with shared evolutionary histories (termed evolutionary conserved modules, or ECMs). A Dirichlet process prior was adopted for estimating the number of gene clusters and a Gibbs sampler was developed for posterior sampling. We further developed an extended version, CLIME 1.1, to incorporate the uncertainty on the evolution- ary tree structure. By simulation studies and benchmarks on real data sets, we show that CLIME 1.0 and CLIME 1.1 outperform traditional methods that use simple metrics (e.g., the Hamming distance or Pear- son correlation) to measure co-evolution between pairs of genes. 1. Introduction. The human genome encodes more than 20,000 protein- coding genes, of which a large fraction do not have annotated function to date [Galperin and Koonin, 2010].
    [Show full text]
  • Arabidopsis Thaliana Alternative Dehydrogenases: a Potential
    Catania et al. Orphanet Journal of Rare Diseases (2019) 14:236 https://doi.org/10.1186/s13023-019-1185-3 RESEARCH Open Access Arabidopsis thaliana alternative dehydrogenases: a potential therapy for mitochondrial complex I deficiency? Perspectives and pitfalls Alessia Catania1,2† , Arcangela Iuso3,4†, Juliette Bouchereau1,5†, Laura S. Kremer3,4, Marina Paviolo1,5, Caterina Terrile3, Paule Bénit1, Allan G. Rasmusson6, Thomas Schwarzmayr3,7, Valeria Tiranti2, Pierre Rustin1†, Malgorzata Rak1†, Holger Prokisch3,4*† and Manuel Schiff1,5† Abstract Background: Complex I (CI or NADH:ubiquinone oxidoreductase) deficiency is the most frequent cause of mitochondrial respiratory chain defect. Successful attempts to rescue CI function by introducing an exogenous NADH dehydrogenase, such as the NDI1 from Saccharomyces cerevisiae (ScNDI1), have been reported although with drawbacks related to competition with CI. In contrast to ScNDI1, which is permanently active in yeast naturally devoid of CI, plant alternative NADH dehydrogenases (NDH-2) support the oxidation of NADH only when the CI is metabolically inactive and conceivably when the concentration of matrix NADH exceeds a certain threshold. We therefore explored the feasibility of CI rescue by NDH-2 from Arabidopsis thaliana (At) in human CI defective fibroblasts. Results: We showed that, other than ScNDI1, two different NDH-2 (AtNDA2 and AtNDB4) targeted to the mitochondria were able to rescue CI deficiency and decrease oxidative stress as indicated by a normalization of SOD activity in human CI-defective fibroblasts. We further demonstrated that when expressed in human control fibroblasts, AtNDA2 shows an affinity for NADH oxidation similar to that of CI, thus competing with CI for the oxidation of NADH as opposed to our initial hypothesis.
    [Show full text]
  • Transcriptomic and Proteomic Landscape of Mitochondrial
    TOOLS AND RESOURCES Transcriptomic and proteomic landscape of mitochondrial dysfunction reveals secondary coenzyme Q deficiency in mammals Inge Ku¨ hl1,2†*, Maria Miranda1†, Ilian Atanassov3, Irina Kuznetsova4,5, Yvonne Hinze3, Arnaud Mourier6, Aleksandra Filipovska4,5, Nils-Go¨ ran Larsson1,7* 1Department of Mitochondrial Biology, Max Planck Institute for Biology of Ageing, Cologne, Germany; 2Department of Cell Biology, Institute of Integrative Biology of the Cell (I2BC) UMR9198, CEA, CNRS, Univ. Paris-Sud, Universite´ Paris-Saclay, Gif- sur-Yvette, France; 3Proteomics Core Facility, Max Planck Institute for Biology of Ageing, Cologne, Germany; 4Harry Perkins Institute of Medical Research, The University of Western Australia, Nedlands, Australia; 5School of Molecular Sciences, The University of Western Australia, Crawley, Australia; 6The Centre National de la Recherche Scientifique, Institut de Biochimie et Ge´ne´tique Cellulaires, Universite´ de Bordeaux, Bordeaux, France; 7Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden Abstract Dysfunction of the oxidative phosphorylation (OXPHOS) system is a major cause of human disease and the cellular consequences are highly complex. Here, we present comparative *For correspondence: analyses of mitochondrial proteomes, cellular transcriptomes and targeted metabolomics of five [email protected] knockout mouse strains deficient in essential factors required for mitochondrial DNA gene (IKu¨ ); expression, leading to OXPHOS dysfunction. Moreover,
    [Show full text]
  • MLRQ Subunit of NADH:Ubiquinone Oxidoreductase in the Human Mitochondrial Respiratory Chain
    The Molecular and Biochernical Characterization of the MLRQ Subunit of NADH:Ubiquinone Oxidoreductase in the Human Mitochondrial Respiratory Chain Dhush y Kanagarajah A Thesis submitted in codormity with the requirements for the degree of Master of Science Graduate Department of Biochemistry University of Toronto " Copyright by Dhushy Kanagarajah. 200 1 National Library Bibliothèque nationale I*l of Canada du Canada Acquisitions and Acquisitions et Bibliographie Services services bibliographiques 395 Wellington Street 395. rue Wellington Ottawa ON K1A ON4 ûttawa ON K1A ON4 Canada Canada The author has granted a non- L'auteur a accordé une licence non exclusive licence ailowing the exclusive permettant à la National Library of Canada to Bibliothèque nationale du Canada de reproduce, loan, distriie or seil reproduire, prêter, distribuer ou copies of this thesis in microform, vendre des copies de cette thèse sous paper or electronic formats. la forme de microfiche/fh, de reproduction sur papier ou sur format électronique. The author retains ownership of the L'auteur conserve la propriété du copyright in this thesis. Neither the droit d'auteur qui protège cette thèse. thesis nor substantial extracts fiom it Ni la thèse ni des extraits substantiels may be printed or othenirise de celle-ci ne doivent être imprimés reproduced without the author' s ou autrement reproduits sans son permission. autorisation. The Molecular and Biochemical Characterization of the MLRQ Subunit of NADH:Ubiquinone Oxidoreductase in the Humsn Mitochondrîal Respiratory Chain Master of Science, 200 1 Dhushy Kanagarajah Department of Biochemistry University of Toronto Abstract Isolated deficiency of NADH:ubiquinone oxidoreductase (Complex 1), the first enzyme of the mitochondrial respiratory chah is the most comrnon cause of human mitochondriocytopathies.
    [Show full text]
  • Table S1. 103 Ferroptosis-Related Genes Retrieved from the Genecards
    Table S1. 103 ferroptosis-related genes retrieved from the GeneCards. Gene Symbol Description Category GPX4 Glutathione Peroxidase 4 Protein Coding AIFM2 Apoptosis Inducing Factor Mitochondria Associated 2 Protein Coding TP53 Tumor Protein P53 Protein Coding ACSL4 Acyl-CoA Synthetase Long Chain Family Member 4 Protein Coding SLC7A11 Solute Carrier Family 7 Member 11 Protein Coding VDAC2 Voltage Dependent Anion Channel 2 Protein Coding VDAC3 Voltage Dependent Anion Channel 3 Protein Coding ATG5 Autophagy Related 5 Protein Coding ATG7 Autophagy Related 7 Protein Coding NCOA4 Nuclear Receptor Coactivator 4 Protein Coding HMOX1 Heme Oxygenase 1 Protein Coding SLC3A2 Solute Carrier Family 3 Member 2 Protein Coding ALOX15 Arachidonate 15-Lipoxygenase Protein Coding BECN1 Beclin 1 Protein Coding PRKAA1 Protein Kinase AMP-Activated Catalytic Subunit Alpha 1 Protein Coding SAT1 Spermidine/Spermine N1-Acetyltransferase 1 Protein Coding NF2 Neurofibromin 2 Protein Coding YAP1 Yes1 Associated Transcriptional Regulator Protein Coding FTH1 Ferritin Heavy Chain 1 Protein Coding TF Transferrin Protein Coding TFRC Transferrin Receptor Protein Coding FTL Ferritin Light Chain Protein Coding CYBB Cytochrome B-245 Beta Chain Protein Coding GSS Glutathione Synthetase Protein Coding CP Ceruloplasmin Protein Coding PRNP Prion Protein Protein Coding SLC11A2 Solute Carrier Family 11 Member 2 Protein Coding SLC40A1 Solute Carrier Family 40 Member 1 Protein Coding STEAP3 STEAP3 Metalloreductase Protein Coding ACSL1 Acyl-CoA Synthetase Long Chain Family Member 1 Protein
    [Show full text]
  • Early‐Onset Coenzyme Q10 Deficiency Associated with Ataxia And
    LJMU Research Online Cotta, A, Alston, CL, Baptista-Junior, S, Paim, JF, Carvalho, E, Navarro, MM, Appleton, M, Shiau Ng, Y, Valicek, J, da-Cunha-Junior, AL, Lima, MI, de la Rocque Ferreira, A, Takata, RI, Hargreaves, IP, Gorman, GS, McFarland, R, Pierre, G and Taylor, RW Early‐ onset coenzyme Q10 deficiency associated with ataxia and respiratory chain dysfunction due to novel pathogenic COQ8A variants, including a large intragenic deletion http://researchonline.ljmu.ac.uk/id/eprint/13044/ Article Citation (please note it is advisable to refer to the publisher’s version if you intend to cite from this work) Cotta, A, Alston, CL, Baptista-Junior, S, Paim, JF, Carvalho, E, Navarro, MM, Appleton, M, Shiau Ng, Y, Valicek, J, da-Cunha-Junior, AL, Lima, MI, de la Rocque Ferreira, A, Takata, RI, Hargreaves, IP, Gorman, GS, McFarland, R, Pierre, G and Taylor, RW (2020) Early‐ onset coenzyme Q10 deficiency LJMU has developed LJMU Research Online for users to access the research output of the University more effectively. Copyright © and Moral Rights for the papers on this site are retained by the individual authors and/or other copyright owners. Users may download and/or print one copy of any article(s) in LJMU Research Online to facilitate their private study or for non-commercial research. You may not engage in further distribution of the material or use it for any profit-making activities or any commercial gain. The version presented here may differ from the published version or from the version of the record. Please see the repository URL above for details on accessing the published version and note that access may require a subscription.
    [Show full text]
  • Reveals of Candidate Active Ingredients in Justicia and Its Anti-Thrombotic Action of Mechanism Based on Network Pharmacology Ap
    www.nature.com/scientificreports OPEN Reveals of candidate active ingredients in Justicia and its anti‑thrombotic action of mechanism based on network pharmacology approach and experimental validation Zongchao Hong1,5, Ting Zhang2,5, Ying Zhang1, Zhoutao Xie1, Yi Lu1, Yunfeng Yao1, Yanfang Yang1,3,4*, Hezhen Wu1,3,4* & Bo Liu1,3* Thrombotic diseases seriously threaten human life. Justicia, as a common Chinese medicine, is usually used for anti‑infammatory treatment, and further studies have found that it has an inhibitory efect on platelet aggregation. Therefore, it can be inferred that Justicia can be used as a therapeutic drug for thrombosis. This work aims to reveal the pharmacological mechanism of the anti‑thrombotic efect of Justicia through network pharmacology combined with wet experimental verifcation. During the analysis, 461 compound targets were predicted from various databases and 881 thrombus‑related targets were collected. Then, herb‑compound‑target network and protein–protein interaction network of disease and prediction targets were constructed and cluster analysis was applied to further explore the connection between the targets. In addition, Gene Ontology (GO) and pathway (KEGG) enrichment were used to further determine the association between target proteins and diseases. Finally, the expression of hub target proteins of the core component and the anti‑thrombotic efect of Justicia’s core compounds were verifed by experiments. In conclusion, the core bioactive components, especially justicidin D, can reduce thrombosis by regulating F2, MMP9, CXCL12, MET, RAC1, PDE5A, and ABCB1. The combination of network pharmacology and the experimental research strategies proposed in this paper provides a comprehensive method for systematically exploring the therapeutic mechanism of multi‑component medicine.
    [Show full text]