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Article

Single-Cell Analysis of Ribonucleotide Reductase Transcriptional and Translational Response to DNA Damage

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Pages 635-642 | Received 27 Sep 2012, Accepted 20 Nov 2012, Published online: 20 Mar 2023

REFERENCES

  • Friedberg EC, Walker GC, Siede W, Wood RD, Schultz RA, Ellenberger T. 2006. DNA repair and mutagenesis. ASM Press, Washington, DC.
  • Hoeijmakers JH. 2007. Genome maintenance mechanisms are critical for preventing cancer as well as other aging-associated diseases. Mech. Ageing Dev. 128:460–462.
  • Nordlund P, Reichard P. 2006. Ribonucleotide reductases. Annu. Rev. Biochem. 75:681–706.
  • Yao R, Zhang Z, An X, Bucci B, Perlstein DL, Stubbe J, Huang M. 2003. Subcellular localization of yeast ribonucleotide reductase regulated by the DNA replication and damage checkpoint pathways. Proc. Natl. Acad. Sci. U. S. A. 100:6628–6633.
  • Zhao X, Muller EG, Rothstein R. 1998. A suppressor of two essential checkpoint genes identifies a novel protein that negatively affects dNTP pools. Mol. Cell 2:329–340.
  • Chabes A, Domkin V, Larsson G, Liu A, Graslund A, Wijmenga S, Thelander L. 2000. Yeast ribonucleotide reductase has a heterodimeric iron-radical-containing subunit. Proc. Natl. Acad. Sci. U. S. A. 97:2474–2479.
  • Perlstein DL, Ge J, Ortigosa AD, Robblee JH, Zhang Z, Huang M, Stubbe J. 2005. The active form of the Saccharomyces cerevisiae ribonucleotide reductase small subunit is a heterodimer in vitro and in vivo. Biochemistry 44:15366–15377.
  • An X, Zhang Z, Yang K, Huang M. 2006. Cotransport of the heterodimeric small subunit of the Saccharomyces cerevisiae ribonucleotide reductase between the nucleus and the cytoplasm. Genetics 173:63–73.
  • Huang M, Zhou Z, Elledge SJ. 1998. The DNA replication and damage checkpoint pathways induce transcription by inhibition of the Crt1 repressor. Cell 94:595–605.
  • Tsaponina O, Barsoum E, Astrom SU, Chabes A. 2011. Ixr1 is required for the expression of the ribonucleotide reductase Rnr1 and maintenance of dNTP pools. PLoS Genet. 7:e1002061. doi:10.1371/journal.pgen.1002061.
  • Lee YD, Wang J, Stubbe J, Elledge SJ. 2008. Dif1 is a DNA-damage-regulated facilitator of nuclear import for ribonucleotide reductase. Mol. Cell 32:70–80.
  • Zhao X, Chabes A, Domkin V, Thelander L, Rothstein R. 2001. The ribonucleotide reductase inhibitor Sml1 is a new target of the Mec1/Rad53 kinase cascade during growth and in response to DNA damage. EMBO J. 20:3544–3553.
  • Zhao X, Rothstein R. 2002. The Dun1 checkpoint kinase phosphorylates and regulates the ribonucleotide reductase inhibitor Sml1. Proc. Natl. Acad. Sci. U. S. A. 99:3746–3751.
  • Elledge SJ, Davis RW. 1989. DNA damage induction of ribonucleotide reductase. Mol. Cell. Biol. 9:4932–4940.
  • Elledge SJ, Davis RW. 1990. Two genes differentially regulated in the cell cycle and by DNA-damaging agents encode alternative regulatory subunits of ribonucleotide reductase. Genes Dev. 4:740–751.
  • Huang M, Elledge SJ. 1997. Identification of RNR4, encoding a second essential small subunit of ribonucleotide reductase in Saccharomyces cerevisiae. Mol. Cell. Biol. 17:6105–6113.
  • Altschuler SJ, Wu LF. 2010. Cellular heterogeneity: do differences make a difference? Cell 141:559–563.
  • Cai L, Friedman N, Xie XS. 2006. Stochastic protein expression in individual cells at the single molecule level. Nature 440:358–362.
  • Raj A, van Oudenaarden A. 2009. Single-molecule approaches to stochastic gene expression. Annu. Rev. Biophys. 38:255–270.
  • Taniguchi Y, Choi PJ, Li GW, Chen H, Babu M, Hearn J, Emili A, Xie XS. 2010. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 329:533–538.
  • Lee MV, Topper SE, Hubler SL, Hose J, Wenger CD, Coon JJ, Gasch AP. 2011. A dynamic model of proteome changes reveals new roles for transcript alteration in yeast. Mol. Syst. Biol. 7:514.
  • de Godoy LM, Olsen JV, Cox J, Nielsen ML, Hubner NC, Frohlich F, Walther TC, Mann M. 2008. Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature 455:1251–1254.
  • Gygi SP, Rochon Y, Franza BR, Aebersold R. 1999. Correlation between protein and mRNA abundance in yeast. Mol. Cell. Biol. 19:1720–1730.
  • Bregman A, Avraham-Kelbert M, Barkai O, Duek L, Guterman A, Choder M. 2011. Promoter elements regulate cytoplasmic mRNA decay. Cell 147:1473–1483.
  • Trcek T, Larson DR, Moldon A, Query CC, Singer RH. 2011. Single-molecule mRNA decay measurements reveal promoter-regulated mRNA stability in yeast. Cell 147:1484–1497.
  • Raj A, van den Bogaard P, Rifkin SA, van Oudenaarden A, Tyagi S. 2008. Imaging individual mRNA molecules using multiple singly labeled probes. Nat. Methods 5:877–879.
  • Tan RZ, van Oudenaarden A. 2010. Transcript counting in single cells reveals dynamics of rDNA transcription. Mol. Syst. Biol. 6:358.
  • Youk H, Raj A, van Oudenaarden A. 2010. Imaging single mRNA molecules in yeast. Methods Enzymol. 470:429–446.
  • Zenklusen D, Larson DR, Singer RH. 2008. Single-RNA counting reveals alternative modes of gene expression in yeast. Nat. Struct. Mol. Biol. 15:1263–1271.
  • Domkin V, Thelander L, Chabes A. 2002. Yeast DNA damage-inducible Rnr3 has a very low catalytic activity strongly stimulated after the formation of a cross-talking Rnr1/Rnr3 complex. J. Biol. Chem. 277:18574–18578.
  • Puddu F, Piergiovanni G, Plevani P, Muzi-Falconi M. 2011. Sensing of replication stress and Mec1 activation act through two independent pathways involving the 9-1-1 complex and DNA polymerase epsilon. PLoS Genet. 7:e1002022. doi:10.1371/journal.pgen.1002022.
  • Chabes A, Stillman B. 2007. Constitutively high dNTP concentration inhibits cell cycle progression and the DNA damage checkpoint in yeast Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. U. S. A. 104:1183–1188.
  • Sabouri N, Viberg J, Goyal DK, Johansson E, Chabes A. 2008. Evidence for lesion bypass by yeast replicative DNA polymerases during DNA damage. Nucleic Acids Res. 36:5660–5667.
  • Nick McElhinny SA, Watts BE, Kumar D, Watt DL, Lundstrom EB, Burgers PM, Johansson E, Chabes A, Kunkel TA. 2010. Abundant ribonucleotide incorporation into DNA by yeast replicative polymerases. Proc. Natl. Acad. Sci. U. S. A. 107:4949–4954.
  • Chabes A, Georgieva B, Domkin V, Zhao X, Rothstein R, Thelander L. 2003. Survival of DNA damage in yeast directly depends on increased dNTP levels allowed by relaxed feedback inhibition of ribonucleotide reductase. Cell 112:391–401.
  • Bar-Even A, Paulsson J, Maheshri N, Carmi M, O'Shea E, Pilpel Y, Barkai N. 2006. Noise in protein expression scales with natural protein abundance. Nat. Genet. 38:636–643.
  • Basehoar AD, Zanton SJ, Pugh BF. 2004. Identification and distinct regulation of yeast TATA box-containing genes. Cell 116:699–709.
  • Tomar RS, Zheng S, Brunke-Reese D, Wolcott HN, Reese JC. 2008. Yeast Rap1 contributes to genomic integrity by activating DNA damage repair genes. EMBO J. 27:1575–1584.
  • Cerqueira NM, Fernandes PA, Ramos MJ. 2007. Ribonucleotide reductase: a critical enzyme for cancer chemotherapy and antiviral agents. Recent Pat. Anticancer Drug Discov. 2:11–29.
  • Cerqueira NM, Fernandes PA, Ramos MJ. 2007. Understanding ribonucleotide reductase inactivation by gemcitabine. Chemistry 13:8507–8515.
  • Jordheim LP, Seve P, Tredan O, Dumontet C. 2011. The ribonucleotide reductase large subunit (RRM1) as a predictive factor in patients with cancer. Lancet Oncol. 12:693–702.

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