Publications

Clayton DA and Shadel GS: Isolation of mitochondria from cells and tissues. Cold Spring Harb Protoc. 2014 Oct 1;2014 (10) :pdb.top074542. Epub 2014 Oct 1. PMID: 25275115


Clayton DA and Shadel GS: Purification of mitochondria by sucrose step density gradient centrifugation. Cold Spring Harb Protoc. 2014 Oct 1;2014 (10) :pdb.prot080028. Epub 2014 Oct 1. PMID: 25275106


Clayton DA and Shadel GS: Isolation of mitochondria from animal tissue. Cold Spring Harb Protoc. 2014 Oct 1;2014 (10) :pdb.prot080010. Epub 2014 Oct 1. PMID: 25275105


Clayton DA and Shadel GS: Isolation of mitochondria from tissue culture cells. Cold Spring Harb Protoc. 2014 Oct 1;2014 (10) :pdb.prot080002. Epub 2014 Oct 1. PMID: 25275104


Nouws J and Shadel GS: microManaging mitochondrial translation. Cell. 2014 Jul 31;158 (3) :477-8. PMID: 25083863


Mannam P, Shinn AS, Srivastava A, Neamu RF, Walker WE, Bohanon M, Merkel J, Kang MJ, Dela Cruz CS, Ahasic AM, Pisani MA, Trentalange M, West AP, Shadel GS, Elias JA and Lee PJ: MKK3 regulates mitochondrial biogenesis and mitophagy in sepsis-induced lung injury. Am J Physiol Lung Cell Mol Physiol. 2014 Apr 1;306 (7) :L604-19. Epub 2014 Jan 31. PMID: 24487387


Christian BE and Shadel GS: Aging: it's SIRTainly possible to restore mitochondrial dysfunction. Curr Biol. 2014 Mar 3;24 (5) :R206-8. PMID: 24602889


Sharma NK, Lebedeva M, Thomas T, Kovalenko OA, Stumpf JD, Shadel GS and Santos JH: Intrinsic mitochondrial DNA repair defects in Ataxia Telangiectasia. DNA Repair (Amst). 2014 Jan;13 :22-31. Epub 2013 Dec 15. PMID: 24342190


Schroeder EA and Shadel GS: Crosstalk between mitochondrial stress signals regulates yeast chronological lifespan. Mech Ageing Dev. 2014 Jan;135 :41-9. Epub 2013 Dec 25. PMID: 24373996

Schroeder EA, Raimundo N and Shadel GS: Epigenetic silencing mediates mitochondria stress-induced longevity. Cell Metab. 2013 Jun 4;17 (6) :954-64. PMID: 23747251


Bestwick ML and Shadel GS: Accessorizing the human mitochondrial transcription machinery. Trends Biochem Sci. 2013 Jun;38 (6) :283-91. Epub 2013 Apr 27. PMID: 23632312


Surovtseva YV and Shadel GS: Transcription-independent role for human mitochondrial RNA polymerase in mitochondrial ribosome biogenesis. Nucleic Acids Res. 2013 Feb 1;41 (4) :2479-88. Epub 2013 Jan 8. PMID: 23303773


D'Souza AD, Parish IA, Krause DS, Kaech SM and Shadel GS: Reducing mitochondrial ROS improves disease-related pathology in a mouse model of ataxia-telangiectasia. Mol Ther. 2013 Jan;21 (1) :42-8. Epub 2012 Sep 25. PMID: 23011031

Ocampo A, Liu J, Schroeder EA, Shadel GS and Barrientos A: Mitochondrial respiratory thresholds regulate yeast chronological life span and its extension by caloric restriction. Cell Metab. 2012 Jul 3;16 (1) :55-67. PMID: 22768839


Longo VD, Shadel GS, Kaeberlein M and Kennedy B: Replicative and chronological aging in Saccharomyces cerevisiae. Cell Metab. 2012 Jul 3;16 (1) :18-31. PMID: 22768836


Lodeiro MF, Uchida A, Bestwick M, Moustafa IM, Arnold JJ, Shadel GS and Cameron CE: Transcription from the second heavy-strand promoter of human mtDNA is repressed by transcription factor A in vitro. Proc Natl Acad Sci U S A. 2012 Apr 24;109 (17) :6513-8. Epub 2012 Apr 9. PMID: 22493245


Schroeder EA and Shadel GS: Alternative mitochondrial fuel extends life span. Cell Metab. 2012 Apr 4;15 (4) :417-8. PMID: 22482723


Raimundo N, Song L, Shutt TE, McKay SE, Cotney J, Guan MX, Gilliland TC, Hohuan D, Santos-Sacchi J and Shadel GS: Mitochondrial stress engages E2F1 apoptotic signaling to cause deafness. Cell. 2012 Feb 17;148 (4) :716-26. PMID: 22341444


Woo DK, Green PD, Santos JH, D'Souza AD, Walther Z, Martin WD, Christian BE, Chandel NS and Shadel GS: Mitochondrial genome instability and ROS enhance intestinal tumorigenesis in APC(Min/+) mice. Am J Pathol. 2012 Jan;180 (1) :24-31. Epub 2011 Nov 3. PMID: 22056359


Malarkey CS, Bestwick M, Kuhlwilm JE, Shadel GS and Churchill ME: Transcriptional activation by mitochondrial transcription factor A involves preferential distortion of promoter DNA. Nucleic Acids Res. 2012 Jan;40 (2) :614-24. Epub 2011 Sep 23. PMID: 21948790

Liu L, Sanosaka M, Lei S, Bestwick ML, Frey JH Jr, Surovtseva YV, Shadel GS and Cooper MP: LRP130 protein remodels mitochondria and stimulates fatty acid oxidation. J Biol Chem. 2011 Dec 2;286 (48) :41253-64. Epub 2011 Oct 4. PMID: 21971050


Baysal BE, McKay SE, Kim YJ, Zhang Z, Alila L, Willett-Brozick JE, Pacak K, Kim TH and Shadel GS: Genomic imprinting at a boundary element flanking the SDHD locus. Hum Mol Genet. 2011 Nov 15;20 (22) :4452-61. Epub 2011 Aug 23. PMID: 21862453


Surovtseva YV, Shutt TE, Cotney J, Cimen H, Chen SY, Koc EC and Shadel GS: Mitochondrial ribosomal protein L12 selectively associates with human mitochondrial RNA polymerase to activate transcription. Proc Natl Acad Sci U S A. 2011 Nov 1;108 (44) :17921-6. Epub 2011 Oct 14. PMID: 22003127


Raimundo N, Baysal BE and Shadel GS: Revisiting the TCA cycle: signaling to tumor formation. Trends Mol Med. 2011 Nov;17 (11) :641-9. Epub 2011 Jul 20. PMID: 21764377


Pan Y, Schroeder EA, Ocampo A, Barrientos A and Shadel GS: Regulation of yeast chronological life span by TORC1 via adaptive mitochondrial ROS signaling. Cell Metab. 2011 Jun 8;13 (6) :668-78. PMID: 21641548


D'Souza AD, Parish IA, McKay SE, Kaech SM and Shadel GS: Aberrant CD8+ T-cell responses and memory differentiation upon viral infection of an ataxia-telangiectasia mouse model driven by hyper-activated Akt and mTORC1 signaling. Am J Pathol. 2011 Jun;178 (6) :2740-51. PMID: 21641396


West AP, Shadel GS and Ghosh S: Mitochondria in innate immune responses. Nat Rev Immunol. 2011 Jun;11 (6) :389-402. Epub 2011 May 20. PMID: 21597473


West AP, Brodsky IE, Rahner C, Woo DK, Erdjument-Bromage H, Tempst P, Walsh MC, Choi Y, Shadel GS and Ghosh S: TLR signalling augments macrophage bactericidal activity through mitochondrial ROS. Nature. 2011 Apr 28;472 (7344) :476-80. PMID: 21525932


Shutt TE, Bestwick M and Shadel GS: The core human mitochondrial transcription initiation complex: It only takes two to tango. Transcription. 2011 Mar;2 (2) :55-59. PMID: 21468229


Woo DK and Shadel GS: Mitochondrial stress signals revise an old aging theory. Cell. 2011 Jan 7;144 (1) :11-2. PMID: 21215364


Chatenay-Lapointe M and Shadel GS: Repression of mitochondrial translation, respiration and a metabolic cycle-regulated gene, SLF1, by the yeast Pumilio-family protein Puf3p. PLoS One. 2011;6 (5) :e20441. Epub 2011 May 31. PMID: 21655263

Lee HY, Choi CS, Birkenfeld AL, Alves TC, Jornayvaz FR, Jurczak MJ, Zhang D, Woo DK, Shadel GS, Ladiges W, Rabinovitch PS, Santos JH, Petersen KF, Samuel VT and Shulman GI: Targeted expression of catalase to mitochondria prevents age-associated reductions in mitochondrial function and insulin resistance. Cell Metab. 2010 Dec 1;12 (6) :668-74. PMID: 21109199


Chatenay-Lapointe M and Shadel GS: Stressed-out mitochondria get MAD. Cell Metab. 2010 Dec 1;12 (6) :559-60. PMID: 21109188


Shutt TE, Lodeiro MF, Cotney J, Cameron CE and Shadel GS: Core human mitochondrial transcription apparatus is a regulated two-component system in vitro. Proc Natl Acad Sci U S A. 2010 Jul 6;107 (27) :12133-8. Epub 2010 Jun 18. PMID: 20562347


Shutt TE and Shadel GS: A compendium of human mitochondrial gene expression machinery with links to disease. Environ Mol Mutagen. 2010 Jun;51 (5) :360-79. PMID: 20544879

Pawar V, Jingjing L, Patel N, Kaur N, Doetsch PW, Shadel GS, Zhang H and Siede W: Checkpoint kinase phosphorylation in response to endogenous oxidative DNA damage in repair-deficient stationary-phase Saccharomyces cerevisiae. Mech Ageing Dev. 2009 Aug;130 (8) :501-8. Epub 2009 Jun 18. PMID: 19540258


Shadel GS and Pan Y: Multi-faceted regulation of mitochondria by TOR. Cell Cycle. 2009 Jul 15;8 (14) :2143. Epub 2009 Jul 15. PMID: 19587547


Cotney J, McKay SE and Shadel GS: Elucidation of separate, but collaborative functions of the rRNA methyltransferase-related human mitochondrial transcription factors B1 and B2 in mitochondrial biogenesis reveals new insight into maternally inherited deafness. Hum Mol Genet. 2009 Jul 15;18 (14) :2670-82. Epub 2009 May 5. PMID: 19417006


Crouser ED, Shao G, Julian MW, Macre JE, Shadel GS, Tridandapani S, Huang Q and Wewers MD: Monocyte activation by necrotic cells is promoted by mitochondrial proteins and formyl peptide receptors. Crit Care Med. 2009 Jun;37 (6) :2000-9. PMID: 19384205


Lebedeva MA, Eaton JS and Shadel GS: Loss of p53 causes mitochondrial DNA depletion and altered mitochondrial reactive oxygen species homeostasis. Biochim Biophys Acta. 2009 May;1787 (5) :328-34. Epub 2009 Jan 20. PMID: 19413947


Suissa S, Wang Z, Poole J, Wittkopp S, Feder J, Shutt TE, Wallace DC, Shadel GS and Mishmar D: Ancient mtDNA genetic variants modulate mtDNA transcription and replication. PLoS Genet. 2009 May;5 (5) :e1000474. Epub 2009 May 8. PMID: 19424428


Raimundo N and Shadel GS: A "radical" mitochondrial view of autophagy-related pathology. Aging (Albany NY). 2009 Apr 8;1 (4) :354-6. Epub 2009 Apr 8. PMID: 20157522


Tal MC, Sasai M, Lee HK, Yordy B, Shadel GS and Iwasaki A: Absence of autophagy results in reactive oxygen species-dependent amplification of RLR signaling. Proc Natl Acad Sci U S A. 2009 Feb 24;106 (8) :2770-5. Epub 2009 Feb 5. PMID: 19196953


Pan Y and Shadel GS: Extension of chronological life span by reduced TOR signaling requires down-regulation of Sch9p and involves increased mitochondrial OXPHOS complex density. Aging (Albany NY). 2009 Jan 28;1 (1) :131-45. Epub 2009 Jan 28. PMID: 20157595


Griffiths LM, Doudican NA, Shadel GS and Doetsch PW: Mitochondrial DNA oxidative damage and mutagenesis in Saccharomyces cerevisiae. Methods Mol Biol. 2009;554 :267-86. PMID: 19513680

Shadel GS: Into the wild frontier of mitochondrial disease and aging. Methods. 2008 Dec;46 (4) :239-40. PMID: 19027636


Shadel GS: Debut of MitoMatters. Mitochondrion. 2008 Sep;8 (4) :338. Epub 2008 Sep 3. PMID: 18775517


Bonawitz ND, Chatenay-Lapointe M, Wearn CM and Shadel GS: Expression of the rDNA-encoded mitochondrial protein Tar1p is stringently controlled and responds differentially to mitochondrial respiratory demand and dysfunction. Curr Genet. 2008 Aug;54 (2) :83-94. Epub 2008 Jul 12. PMID: 18622616


Shadel GS: Expression and maintenance of mitochondrial DNA: new insights into human disease pathology. Am J Pathol. 2008 Jun;172 (6) :1445-56. Epub 2008 May 5. PMID: 18458094


Schleicher M, Shepherd BR, Suarez Y, Fernandez-Hernando C, Yu J, Pan Y, Acevedo LM, Shadel GS and Sessa WC: Prohibitin-1 maintains the angiogenic capacity of endothelial cells by regulating mitochondrial function and senescence. J Cell Biol. 2008 Jan 14;180 (1) :101-12. PMID: 18195103

D'Souza AD, Parikh N, Kaech SM and Shadel GS: Convergence of multiple signaling pathways is required to coordinately up-regulate mtDNA and mitochondrial biogenesis during T cell activation. Mitochondrion. 2007 Dec;7 (6) :374-85. Epub 2007 Aug 16. PMID: 17890163


Eaton JS, Lin ZP, Sartorelli AC, Bonawitz ND and Shadel GS: Ataxia-telangiectasia mutated kinase regulates ribonucleotide reductase and mitochondrial homeostasis. J Clin Invest. 2007 Sep;117 (9) :2723-34. PMID: 17786248


Lebedeva MA and Shadel GS: Cell cycle- and ribonucleotide reductase-driven changes in mtDNA copy number influence mtDNA Inheritance without compromising mitochondrial gene expression. Cell Cycle. 2007 Aug 15;6 (16) :2048-57. Epub 2007 Jun 7. PMID: 17721079


Bonawitz ND and Shadel GS: Rethinking the mitochondrial theory of aging: the role of mitochondrial gene expression in lifespan determination. Cell Cycle. 2007 Jul 1;6 (13) :1574-8. Epub 2007 May 22. PMID: 17603300


Wang Z, Cotney J and Shadel GS: Human mitochondrial ribosomal protein MRPL12 interacts directly with mitochondrial RNA polymerase to modulate mitochondrial gene expression. J Biol Chem. 2007 Apr 27;282 (17) :12610-8. Epub 2007 Mar 2. PMID: 17337445


Bonawitz ND, Chatenay-Lapointe M, Pan Y and Shadel GS: Reduced TOR signaling extends chronological life span via increased respiration and upregulation of mitochondrial gene expression. Cell Metab. 2007 Apr;5 (4) :265-77. PMID: 17403371


Lin ZP, Belcourt MF, Carbone R, Eaton JS, Penketh PG, Shadel GS, Cory JG and Sartorelli AC: Excess ribonucleotide reductase R2 subunits coordinate the S phase checkpoint to facilitate DNA damage repair and recovery from replication stress. Biochem Pharmacol. 2007 Mar 15;73 (6) :760-72. Epub 2006 Nov 23. PMID: 17188250


Zhang H, Luo Y, Zhang W, He Y, Dai S, Zhang R, Huang Y, Bernatchez P, Giordano FJ, Shadel G, Sessa WC and Min W: Endothelial-specific expression of mitochondrial thioredoxin improves endothelial cell function and reduces atherosclerotic lesions. Am J Pathol. 2007 Mar;170 (3) :1108-20. PMID: 17322393


Shutt TE and Shadel GS: Expanding the mitochondrial interactome. Genome Biol. 2007;8 (2) :203. PMID: 17319976


Shadel GS and Seidel-Rogol BL: Diagnostic assays for defects in mtDNA replication and transcription in yeast and humans. Methods Cell Biol. 2007;80 :465-79. PMID: 17445709


Cotney J, Wang Z and Shadel GS: Relative abundance of the human mitochondrial transcription system and distinct roles for h-mtTFB1 and h-mtTFB2 in mitochondrial biogenesis and gene expression. Nucleic Acids Res. 2007;35 (12) :4042-54. Epub 2007 Jun 8. PMID: 17557812

O'Rourke TW, Doudican NA, Zhang H, Eaton JS, Doetsch PW and Shadel GS: Differential involvement of the related DNA helicases Pif1p and Rrm3p in mtDNA point mutagenesis and stability. Gene. 2005 Jul 18;354 :86-92. PMID: 15907372


Taylor SD, Zhang H, Eaton JS, Rodeheffer MS, Lebedeva MA, O'rourke TW, Siede W and Shadel GS: The conserved Mec1/Rad53 nuclear checkpoint pathway regulates mitochondrial DNA copy number in Saccharomyces cerevisiae. Mol Biol Cell. 2005 Jun;16 (6) :3010-8. Epub 2005 Apr 13. PMID: 15829566


Doudican NA, Song B, Shadel GS and Doetsch PW: Oxidative DNA damage causes mitochondrial genomic instability in Saccharomyces cerevisiae. Mol Cell Biol. 2005 Jun;25 (12) :5196-204. PMID: 15923634


Shadel GS: Mitochondrial DNA, aconitase 'wraps' it up. Trends Biochem Sci. 2005 Jun;30 (6) :294-6. PMID: 15950872

Shadel GS: Coupling the mitochondrial transcription machinery to human disease. Trends Genet. 2004 Oct;20 (10) :513-9. PMID: 15363906


Shadel GS: A dual-function mitochondrial transcription factor tunes out deafness. Mol Genet Metab. 2004 May;82 (1) :1-3. PMID: 15110315

McCulloch V and Shadel GS: Human mitochondrial transcription factor B1 interacts with the C-terminal activation region of h-mtTFA and stimulates transcription independently of its RNA methyltransferase activity. Mol Cell Biol. 2003 Aug;23 (16) :5816-24. PMID: 12897151


Rodeheffer MS and Shadel GS: Multiple interactions involving the amino-terminal domain of yeast mtRNA polymerase determine the efficiency of mitochondrial protein synthesis. J Biol Chem. 2003 May 16;278 (20) :18695-701. Epub 2003 Mar 10. PMID: 12637560


Seidel-Rogol BL, McCulloch V and Shadel GS: Human mitochondrial transcription factor B1 methylates ribosomal RNA at a conserved stem-loop. Nat Genet. 2003 Jan;33 (1) :23-4. Epub 2002 Dec 23. PMID: 12496758

Coelho PS, Bryan AC, Kumar A, Shadel GS and Snyder M: A novel mitochondrial protein, Tar1p, is encoded on the antisense strand of the nuclear 25S rDNA. Genes Dev. 2002 Nov 1;16 (21) :2755-60. PMID: 12414727


O'Rourke TW, Doudican NA, Mackereth MD, Doetsch PW and Shadel GS: Mitochondrial dysfunction due to oxidative mitochondrial DNA damage is reduced through cooperative actions of diverse proteins. Mol Cell Biol. 2002 Jun;22 (12) :4086-93. PMID: 12024022


Seidel-Rogol BL and Shadel GS: Modulation of mitochondrial transcription in response to mtDNA depletion and repletion in HeLa cells. Nucleic Acids Res. 2002 May 1;30 (9) :1929-34. PMID: 11972329


McCulloch V, Seidel-Rogol BL and Shadel GS: A human mitochondrial transcription factor is related to RNA adenine methyltransferases and binds S-adenosylmethionine. Mol Cell Biol. 2002 Feb;22 (4) :1116-25. PMID: 11809803


Bryan AC, Rodeheffer MS, Wearn CM and Shadel GS: Sls1p is a membrane-bound regulator of transcription-coupled processes involved in Saccharomyces cerevisiae mitochondrial gene expression. Genetics. 2002 Jan;160 (1) :75-82. PMID: 11805046

Rodeheffer MS, Boone BE, Bryan AC and Shadel GS: Nam1p, a protein involved in RNA processing and translation, is coupled to transcription through an interaction with yeast mitochondrial RNA polymerase. J Biol Chem. 2001 Mar 16;276 (11) :8616-22. Epub 2000 Dec 15. PMID: 11118450


Seidel-Rogol BL and Shadel GS: Diagnostic assays for defects in mitochondrial DNA replication and transcription in yeast and human cells. Methods Cell Biol. 2001;65 :413-27. PMID: 11381607

Shadel GS, Buckenmeyer GA, Clayton DA and Schmitt ME: Mutational analysis of the RNA component of Saccharomyces cerevisiae RNase MRP reveals distinct nuclear phenotypes. Gene. 2000 Mar 7;245 (1) :175-84. PMID: 10713458


Devine JH and Shadel GS: Assay of autoinducer activity with luminescent Escherichia coli sensor strains harboring a modified Vibrio fischeri lux regulon. Methods Enzymol. 2000;305 :279-87. PMID: 10812607

Shadel GS: Yeast as a model for human mtDNA replication. Am J Hum Genet. 1999 Nov;65 (5) :1230-7. PMID: 10521287


Wang Y and Shadel GS: Stability of the mitochondrial genome requires an amino-terminal domain of yeast mitochondrial RNA polymerase. Proc Natl Acad Sci U S A. 1999 Jul 6;96 (14) :8046-51. PMID: 10393945

Shadel GS and Clayton DA: Mitochondrial DNA maintenance in vertebrates. Annu Rev Biochem. 1997;66 :409-35. PMID: 9242913

Sitnikov DM, Shadel GS and Baldwin TO: Autoinducer-independent mutants of the LuxR transcriptional activator exhibit differential effects on the two lux promoters of Vibrio fischeri. Mol Gen Genet. 1996 Oct 16;252 (5) :622-5. PMID: 8914523


Carrodeguas JA, Yun S, Shadel GS, Clayton DA and Bogenhagen DF: Functional conservation of yeast mtTFB despite extensive sequence divergence. Gene Expr. 1996;6 (4) :219-30. PMID: 9196077


Shadel GS and Clayton DA: Isolation and characterization of vertebrate mitochondrial transcription factor A homologs. Methods Enzymol. 1996;264 :149-58. PMID: 8965689


Shadel GS and Clayton DA: Mapping promoters in displacement-loop region of vertebrate mitochondrial DNA. Methods Enzymol. 1996;264 :139-48. PMID: 8965688

Dairaghi DJ, Shadel GS and Clayton DA: Addition of a 29 residue carboxyl-terminal tail converts a simple HMG box-containing protein into a transcriptional activator. J Mol Biol. 1995 May 26;249 (1) :11-28. PMID: 7776365


Dairaghi DJ, Shadel GS and Clayton DA: Human mitochondrial transcription factor A and promoter spacing integrity are required for transcription initiation. Biochim Biophys Acta. 1995 May 24;1271 (1) :127-34. PMID: 7599198


Shadel GS and Clayton DA: A Saccharomyces cerevisiae mitochondrial transcription factor, sc-mtTFB, shares features with sigma factors but is functionally distinct. Mol Cell Biol. 1995 Apr;15 (4) :2101-8. PMID: 7891705

Shadel GS and Clayton DA: Mitochondrial transcription initiation. Variation and conservation. J Biol Chem. 1993 Aug 5;268 (22) :16083-6. PMID: 8344889

Shadel GS, Young R and Baldwin TO: Use of regulated cell lysis in a lethal genetic selection in Escherichia coli: identification of the autoinducer-binding region of the LuxR protein from Vibrio fischeri ATCC 7744. J Bacteriol. 1990 Jul;172 (7) :3980-7. PMID: 2141835


Shadel GS, Devine JH and Baldwin TO: Control of the lux regulon of Vibrio fischeri. J Biolumin Chemilumin. 1990 Apr-Jun;5 (2) :99-106. PMID: 2186599

Devine JH, Shadel GS and Baldwin TO: Identification of the operator of the lux regulon from the Vibrio fischeri strain ATCC7744. Proc Natl Acad Sci U S A. 1989 Aug;86 (15) :5688-92. PMID: 2762291


Baldwin TO, Devine JH, Heckel RC, Lin JW and Shadel GS: The complete nucleotide sequence of the lux regulon of Vibrio fischeri and the luxABN region of Photobacterium leiognathi and the mechanism of control of bacterial bioluminescence. J Biolumin Chemilumin. 1989 Jul;4 (1) :326-41. PMID: 2801220