Publications

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2022

• Dibitetto D, Marshall S, Sanchi A, Liptay M, Badar J, Lopes M, Rottenberg S, Smolka MB. DNA-PKcs promotes fork reversal and chemoresistance. Mol Cell. 2022.
• Bell ES, Shah P, Zuela-Sopilniak N, Kim D, Varlet AA, Morival JLP, McGregor AL, Isermann P, Davidson PM, Elacqua JJ, Lakins JN, Vahdat L, Weaver VM, Smolka MB, Span PN, Lammerding J. Low lamin A levels enhance confined cell migration and metastatic capacity in breast cancer. Oncogene. 2022.
• Cao X, Shami Shah A, Sanford EJ, Smolka MB, Baskin JM. Proximity Labeling Reveals Spatial Regulation of the Anaphase-Promoting Complex/Cyclosome by a Microtubule Adaptor. ACS Chem Biol. 2022.
• Sanford EJ, Smolka MB. A field guide to the proteomics of post-translational modifications in DNA repair.
  Proteomics. 2022.
• Sims JR, Faça VM, Pereira C, Ascenção C, Comstock W, Badar J, Arroyo-Martinez GA, Freire R, Cohen PE, Weiss RS, Smolka MB. Phosphoproteomics of ATR signaling in mouse testes. Elife. 2022.
• Pereira C, Arroyo-Martinez GA, Guo MZ, Downey MS, Kelly ER, Grive KJ, Mahadevaiah SK, Sims JR, Faca VM, Tsai C, Schiltz CJ, Wit N, Jacobs H, Clark NL, Freire R, Turner J, Lyndaker AM, Brieno-Enriquez MA, Cohen PE, Smolka MB, Weiss RS. Multiple 9-1-1 complexes promote homolog synapsis, DSB repair, and ATR signaling during mammalian meiosis.
  Elife. 2022.
• Caballero M, Ge T, Rebelo AR, Seo S, Kim S, Brooks K, Zuccaro M, Kanagaraj R, Vershkov D, Kim D, Smogorzewska A, Smolka M, Benvenisty N, West SC, Egli D, Mace EM, Koren A. Comprehensive analysis of DNA replication timing across 184 cell lines suggests a role for MCM10 in replication timing regulation. Human Molecular Genetics. 2022.

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2021

• Joiner AM, Phillips BP, Yugandhar K, Sanford EJ, Smolka MB, Yu H, Miller EA, Fromme JC. Structural basis of TRAPPIII-mediated Rab1 activation. EMBO J. 2021
• Pellicanò G, Al Mamun M, Jurado-Santiago D, Villa-Hernández S, Yin X, Giannattasio M, Lanz MC, Smolka MB, Yeeles J, Shirahige K, García-Díaz M, Bermejo R. Checkpoint-mediated DNA polymerase ε exonuclease activity curbing counteracts resection-driven fork collapse. Mol Cell. 2021
• Sanford EJ, Comstock WJ, Faça VM, Vega SC, Gnügge R, Symington LS, Smolka MB. Phosphoproteomics reveals a distinctive Mec1/ATR signaling response upon DNA end hyper-resection. EMBO J. 2021
• Lanz MC, Yugandhar K, Gupta S, Sanford EJ, Faça VM, Vega S, Joiner AMN, Fromme JC, Yu H, Smolka MB. In-depth and 3-dimensional exploration of the budding yeast phosphoproteome. EMBO Rep. 2021

 

2020

• Faca VM, Sanford EJ, Tieu J, Comstock W, Gupta S, Marshall S, Yu H, Smolka MB. Maximized quantitative phosphoproteomics allows high confidence dissection of the DNA damage signaling network. Sci Rep. 2020 
• Diego Dibitetto, Jennie Sims, Carolline Ascenção,… Marcus Smolka. Intrinsic ATR signaling shapes DNA end resection and suppresses toxic DNA-PKcs signaling. Nucleic Acids Research – Cancer. 2020
• David Waterman, James Haber, Marcus Smolka. Checkpoint Responses to DNA Double-Strand Breaks. Annual Review of Biochemistry. 2020
• Bruhn C, Ajazi A, Ferrari E, Lanz MC, Batrin R, Choudhary R, Walvekar A, Laxman S, Longhese MP, Fabre E, Smolka MB, Foiani M. The Rad53^CHK1/CHK2-Spt21^NPAT and Tel1^ATM axes couple glucose tolerance to histone dosage and subtelomeric silencing. Nature Communications. 2020
• Pereira C, Smolka MB, Weiss RS, Brieño-Enríquez MA. ATR signaling in mammalian meiosis: From upstream scaffolds to downstream signaling. Environ Mol Mutagen. 2020
• Beck WHJ, Kim D, Das J, Yu H, Smolka MB, Mao Y. Glucosylation by the Legionella Effector SetA Promotes the Nuclear Localization of the Transcription Factor TFEB. iScience. 2020
• Yugandhar K, Wang TY, Leung AK, Lanz MC, Motorykin I, Liang J, Shayhidin EE, Smolka MB, Zhang S, Yu H MaXLinker: Proteome-wide Cross-link Identifications with High Specificity and Sensitivity. Mol Cell Proteomics. 2020
• Shin JH, Lanz M, Smolka MB, Dörr T. Characterization of an anti-FLAG antibody binding protein in V. cholerae. Biochem Biophys Res Commun. 2020

 

2019

• Lanz M, Dibitetto D and Smolka MB. DNA Damage Kinase Signaling: Checkpoint and Repair at 30 Years. Embo Journal. 2019 (Review Article). PMID: 31393028.
• Lanz M, Yughandar K, Sanford E, Faça V, Vega S, Gupta S, Joiner A, Fromme C, Haiyuan Yu* and Smolka MB*. In Depth and 3-Dimensional Exploration of the Budding Yeast Phosphoproteome. BioRxiv. (2019). doi: https://doi.org/10.1101/700070. *Co-corresponding authors.
• Memisoglu G, Lanz MC, Eapen VV, Jordan JM, Lee K, Smolka MB, Haber JE. Mec1/ATR autophosphorylation regulates DNA damage checkpoint signaling. Cell Reports. 2019 PMID: 31340146.
• Wan M, Sulpizio AG, Akturk A, Beck WHJ, Lanz M, Faça VM, Smolka MB, Vogel JP, Mao Y. Deubiquitination of phosphoribosyl-ubiquitin conjugates by phosphodiesterase-domain-containing Legionella effectors. Proc Natl Acad Sci U S A. 2019
• Shami Shah A, Batrouni AG, Kim D, Punyala A, Cao W, Han C, Goldberg ML, Smolka MB, Baskin JM. PLEKHA4/kramer Attenuates Dishevelled Ubiquitination to Modulate Wnt and Planar Cell Polarity Signaling. Cell Reports. 2019 PMID: 31091453.
• Massey DJ, Kim D, Brooks KE, Smolka MB*, Koren A*. Next-Generation Sequencing Enables Spatiotemporal Resolution of Human Centromere Replication Timing. Genes 2019 PMID: 30987063. *Co-corresponding authors.
• Zhou X, Paushter DH, Pagan MD, Kim D, Nunez Santos M, Lieberman RL, Overkleeft HS, Sun Y, Smolka MB, Hu F Progranulin deficiency leads to reduced glucocerebrosidase activity. PLoS One. (2019) PMID: 31291241.
• Sulpizio A, Minelli ME, Wan M, Burrowes PD, Wu X, Sanford EJ, Shin JH, Williams BC, Goldberg ML, Smolka MB, Mao Y Protein polyglutamylation catalyzed by the bacterial calmodulin-dependent pseudokinase SidJ. Elife. 2019
• Baile MG, Guiney EL, Sanford EJ, MacGurn JA, Smolka MB, Emr SD Activity of a ubiquitin ligase adaptor is regulated by disordered insertions in its arrestin domain. Mol Biol Cell. 2019

 

 

2018

• Kim D, Liu Y, Oberly S, Freire R, Smolka MB. ATR-mediated proteome remodeling is a major determinant of homologous recombination capacity in cancer cells. Nucleic Acids Res. 2018 Jul 12. PMID:30010936.
  • Featured in the Chronicle: Study reveals how promising cancer drug works for best use
• Lanz MC, Oberly S, Sanford EJ, Sharma S, Chabes A, Smolka MB. Separable roles for Mec1/ATR in genome maintenance, DNA replication, and checkpoint signaling. Genes Dev. 2018 Jun 13. PMID: 29899143.
  • Recommended by Faculty1000: https://f1000.com/prime/733450126
• Bastos de Oliveira, F.M., Kim, D., Lanz, M., Smolka, M.B. 2018. Quantitative analysis of DNA damage signaling responses to chemical and genetic perturbations. Methods in Molecular Biology: 1672, pp. 645-660.

 

 

2017

• Cabrera E, Hernández-Pérez S, Koundrioukoff S, Debatisse M, Kim D, Smolka MB, Freire R, Gillespie DA. PERK inhibits DNA replication during the Unfolded Protein Response via Claspin and Chk1. Oncogene. 2017 Feb 2;36(5):678-686. doi: 10.1038/onc.2016.239. Epub 2016 Jul 4.
• Liu Y, Cussiol JR, Dibitetto D, Sims JR, Twayana S, Weiss RS, Freire R, Marini F, Pellcioli A, Smolka MB. TOPBP1/Dpb11 plays a conserved role in homologous recombination DNA repair through the coordinated recruitment of 53BP1/Rad9. J Cell Biol. 2017 Feb 22;216(3):623-39. DOI: 10.1083/jcb.201607031

          Commentary by the Gasser Lab: A game of musical chairs: Pro- and anti-resection factors compete for TOPBP1 binding after DNA damage.

 

 

2016

• Sullivan PM, Zhou X, Robins AM, Paushter DH, Kim D, Smolka MB, Hu F. The ALS/FTLD associated protein C9orf72 associates with SMCR8 and WDR41 to regulate the autophagy-lysosome pathway. Acta Neuropathol Commun. 2016 May 18;4(1):51. doi: 10.1186/s40478-016-0324-5.
• Cussiol JR, Dibitetto D, Pellicioli A, Smolka MB. Slx4 scaffolding in homologous recombination and checkpoint control: lessons from yeast. Chromosoma. 2016 May 10. [Epub ahead of print] Review.
• Dibitetto D, Ferrari M, Rawal CC, Balint A, Kim T, Zhang Z, Smolka MB, Brown GW, Marini F, Pellicioli A. Slx4 and Rtt107 control checkpoint signalling and DNA resection at double-strand breaks. Nucleic Acids Res. 2016 Jan 29;44(2):669-82. doi: 10.1093/nar/gkv1080. Epub 2015 Oct 20.
• Liu Y and Smolka MB. TOPBP1 takes RADical command in recombinational DNA repair. J Cell Biol. 2016 Jan 25;212(3):263-6. doi: 10.1083/jcb.201601028.
• Bai G, Smolka MB, Schimenti JC. Chronic DNA Replication Stress Reduces Replicative Lifespan of Cells by TRP53-Dependent, microRNA-Assisted MCM2-7 Downregulation. PLOS Genetics. 2016 Jan 14;12(1):e1005787. doi: 10.1371/journal.pgen.1005787.

2015

• Jablonowski CM, Cussiol JR, Oberly S, Yimit A, Balint A, Kim T, Zhang Z, Brown GW, Smolka MB. Termination of Replication Stress Signaling via Concerted Action of the Slx4 Scaffold and the PP4 Phosphatase. Genetics. 2015 Nov;201(3):937-49. doi: 10.1534/genetics.115.181479. Epub 2015 Sep 11.
• Silva JA, Pompeu DG, Smolka MB, Gozzo FC, Comar M Jr, Eberlin MN, Granjeiro PA, Marangoni S. Primary Structure of a Trypsin Inhibitor (Copaifera langsdorffii Trypsin Inhibitor-1) Obtained from C. langsdorffii Seeds. J Biomol Tech. 2015 Sep;26(3): 90–102. doi:  10.7171/jbt.15-2603-002
• Zhou X, Sun L, Oliveira F, Qi X, Brown WJ, Smolka M, Sun Y, Hu F. Prosaposin facilitates sortilin independent lysosomal targeting of progranulin. J Cell Biol. 2015 Sep 14;210(6):991-1002. doi: 10.1083/jcb.201502029
• Bastos de Oliveira FM, Kim DS, Cussiol JR, Das J, Jeong MC, Doerfler L, Schmidt KH, Yu H, Smolka MB. Phosphoproteomics reveals distinct modes of Mec1/ATR signaling during DNA replication. Mol Cell. 19 March 2015;57(6): 1-9.
• Cussiol JR, Jablonowski CM, Yimit A, Brown GW, Smolka MB. Dampening DNA damage checkpoint signalling via coordinated BRCT domain interactions. EMBO Journal. 15 April 2015;34(8): 975-1142.
• Balint A, Kim T, Gallo D, Cussiol JR, Bastos de Oliveira FM, Yimit A, Ou J, Nakato R, Gurevich A, Shirahige K, Smolka MB, Zhang Z, Brown GW. Assembly of Slx4 signaling complexes behind DNA replication forks. EMBO Journal. 13 August 2015;34(16): 2182-97. doi: 10.15252/embj.201591190

 

2014

Wei X, Das J, Fragoza R, Liang J, Bastos de Oliveira FM, Lee HR, Wang X, Mort M, Stenson PD, Cooper DN, Lipkin SM, Smolka MB, Yu H. A massively parallel pipeline to clone DNA variants and examine molecular phenotypes of human disease mutations. PLoS Genetics. 2014 Dec 11;10(12):e1004819. doi: 10.1371/journal.pgen.1004819. eCollection 2014.

Hsu F, Luo X, Qiu J, Teng YB, Jin J, Smolka MB, Luo ZQ, Mao Y. The Legionella effector SidC defines a unique family of ubiquitin ligases important for bacterial phagosomal remodeling. Proc Natl Acad Sci U S A. 2014 Jul 8. pii: 201402605.

 

de Oliveira FM, Smolka MB. Identification of DNA damage checkpoint-dependent protein interactions in Saccharomyces cerevisiae using quantitative mass spectrometry. Methods Mol Biol. Volume 1156, 2014, pp 251-263.

 

2013

Viswanatha R, Wayt J, Ohouo PY, Smolka MB, Bretscher A. Interactome analysis reveals ezrin can adopt multiple conformational states. J Biol Chem. December 2013; 288(49):35437-5.

Scafoglio C, Smolka M, Zhou H, Perissi V, Rosenfeld MG. The Co-Repressor SMRT Delays DNA Damage-Induced Caspase Activation by Repressing Pro-Apoptotic Genes and Modulating the Dynamics of Checkpoint Kinase 2 Activation. PLoS One. May 2013; 8(5):e59986.

Ohouo PY, Bastos de Oliveira FM, Liu Y, Ma CJ, Smolka MB. DNA-repair scaffolds dampen checkpoint signalling by counteracting the adaptor Rad9. Nature. January 2013; 493(7430):120-4.

 

2012

Ohouo PY, Smolka MB. The many roads to checkpoint activation. Cell Cycle. December 2012. 11(24). [Epub ahead of print]

Viswanatha R, Ohouo PY, Smolka MB, Bretscher A. Local phosphocycling mediated by LOK/SLK restricts ezrin function to the apical aspect of epithelial cells. J Cell Biol. December 2012. 199(6):969-84.

Smolka MB, Bastos de Oliveira FM, Harris MR, de Bruin RA. The checkpoint transcriptional response: make sure to turn it off once you are satisfied. Cell Cycle. September 2012. 11(17):3166-74.

Oliveira FB, Harris MR, Brazasuskas P, de Bruin RAM, Smolka MB. Linking DNA checkpoint to MBF cell-cycle transcription reveals a distinct class of G1/S genes. EMBO Journal. February 2012.

Travesa A, Kuo D, de Bruin RAM, Kalashnikova TI, Guaderrama M, Thai K, Aslanian A, Smolka MB, Yates JR, Ideker T, Wittenberg C.DNA replication stress differentially regulates G1/S genes via Rad53-dependent inactivation of Nrm1. EMBO Journal. February 2012.

 

2011

Ohouo, PY, Smolka, MB. A touching moment for Smc5/6: from ssDNA binding to repair. Cell Cycle. February 2011. 10(8): 1190-1191. Comment on Roy MA, et al.

Macgurn JA, Hsu PC, Smolka MB, Emr SD. TORC1 regulates endocytosis via Npr1-mediated phosphoinhibition of a ubiquitin ligase adapter. Cell. November 23, 2011; 147(5):1104-17.

 

2010

Ohouo, P., Bastos de Oliveira, F. Almeida, B. and Smolka, M. DNA damage signaling recruits the Rtt107-Slx4 scaffolds via Dpb11 to mediate replication stress response. Molecular Cell. July 2010; 39(2): 300-306.

Smolka, M. Fine-tuning the DNA damage response: protein phosphatase 2A checks on CHK2. Comment on Freeman AK, et al. Cell Cycle 2010; 9:736–47. Cell Cycle. March 2010, 9(4): 736-747.

 

2009

Wagner, M.V., Smolka, M.B., de Bruin, R.A., Zhou, H., Wittenberg, C., Dowdy, S.F. Whi5 regulation by site specific CDK-phosphorylation in Saccharomyces cerevisiae. PLoS ONE. 2009; 4(1): e4300. Jan. 2009.

 

2008

Payne, S. H., Yau, M., Smolka, M. B., Tanner, S., Zhou, H. and Bafna, V. Phosphorylation specific MS/MS scoring for rapid and efficient phosphoproteome analysis. J. Proteome Res. 2008, 7(8):3373-3381.

Pham, P., Smolka M. B., Calabrese, P., Landolph, A., Zhang, K., Zhou, H. and Goodman, M. F. Impact of phosphorylation and phosphorylation-null mutants on the activity and deamination specificity of activation-induced cytidine deaminase. J Biol Chem. 2008.

Albuquerque, C. P.*, Smolka, M. B.*, Eng, J. and Zhou, H. A Multidimensional Chromatography Technology for In-depth Phosphoproteome Analysis. Mol Cell Proteomics. 2008, 7(7):1389-96. *These authors contributed equally to this work.

 

2007

Smolka, M. B., Albuquerque, C. P., Chen, S. and Zhou, H. Proteome-wide identification of in vivo targets of DNA damage checkpoint kinases. PNAS. 2007, 104(25):10364-9.

Chen, S., Smolka, M. B. and H. Zhou. Mechanism of Dun1 activation by Rad53 phosphorylation in Saccharomyces cerevisiae. J Biol Chem.2007, 282(2):986-95.

Martins, D., Astua-Monge, G., Coletta-Filho, H. D., Winck, F. V., Baldasso, P. A., Oliveira, B. M., Marangoni, S., Machado, M. A., Novello, J. C. and Smolka, M. B. Absence of Classical Heat Shock Response in the Citrus Pathogen Xylella fastidiosa. Curr Microbiol. 2007, 54(2):119-23.

 

2006

Smolka, M. B., Chen, S., Maddox, P. S., Enserink, J. M., Albuquerque, C. P., Wei, X. X., Schmidt, K. H., Desai, A., Kolodner, R. D. and Zhou, H. An FHA Domain-Mediated Protein Interaction Network of Rad53 Reveals its Role in Polarized Cell Growth. J Cell Biol. 2006, 175(5):743-53.

Enserink, J. M., Smolka, M. B., Zhou, H. and Kolodner, R. D. Checkpoint proteins control morphogenetic events during DNA replication stress in Saccharomyces cerevisiae. J Cell Biol. 2006, 175(5):729-41.

Pereira D. R., Martins D., Winck FV, Smolka M. B., Nishimura N. F., Rabelo-Goncalves E. M., Hara N. H., Marangoni S., Zeitune J. M. and Novello J. C. Comparative analysis of two-dimensional electrophoresis maps (2-DE) of Helicobacter pylori from Brazilian patients with chronic gastritis and duodenal ulcer: a preliminary report. Rev Inst Med Trop Sao Paulo. 2006, 48(3):175-7.

 

2005

Smolka, M. B., Albuquerque, C. P., Chen, S. H., Schmidt, K. H., Wei, X. X., Kolodner, R. D. and Zhou, H. Dynamic Changes in Protein-Protein Interaction and Protein Phosphorylation Probed with Amine-reactive Isotope Tag. Mol Cell Proteomics 2005, 4(9):1358-69.

 

2004

Macedo, M. L, Freire, M. G., Martins, L. T., Martinez, D. S., Gomes, V. M., Smolka, M. B., Toyama, M. H., Marangoni, S. and Coelho, L. C. Novel protein from Labramia bojeri A. DC. seeds homologue to Kunitz-type trypsin inhibitor with lectin-like properties. J Agric Food Chem.2004, 52(25):7548-54.

 

2003

Smolka, M. B., Martins, D., Winck, F. V., Santoro, C. E., Castellari, R. R., Ferrari, F., Brum, I. J., Galembeck, E., Coletta-Filho, H. D., Machado, M. A., Marangoni, S. and Novello, J. C.. Proteome Analysis of the Plant Pathogen Xylella fastidiosa Reveals Major Cellular and Extracellular Proteins and a Peculiar Codon Bias Distribution. Proteomics. 2003, 3:224-37.

 

2002

Smolka, M., Zhou, H. and Aebersold, R. Quantitative Protein Profiling Using Two-dimensional Gel Electrophoresis, Isotope-coded Affinity Tag Labeling, and Mass Spectrometry. Mol Cell Proteomics. 2002, 1:19-29.

 

2001

Smolka, M. B., Zhou, H., Purkayastha, S. and Aebersold, R. Optimization of the isotope-coded affinity tag-labeling procedure for quantitative proteome analysis. Analytical Biochem. 2001, 297:25-31.

Freire, M. G., Machado, O. L., Smolka, M. B., Marangoni, S., Novello, J. C. and Macedo, M. L. Isolation and characterization of isolectins from Talisia esculenta seeds. J Protein Chem. 2001, 20:495-500.

 

2000

Smolka, M. B., Zoppi, C. C, Alves, A. A., Silveira, L. R., Marangoni, S., Pereira-Da-Silva, L., Novello, J. C. and Macedo, D. V. HSP72 as a complementary protection against oxidative stress induced by exercise in the soleus muscle of rats. Am J Physiology 2000, 279(5):R1539-45.

 

1998

Smolka, M. B., Marangoni, S., Oliveira, B. and Novello, J. C. Purification and partial characterization of a thrombin-like enzyme, balterobin, from the venom of Bothrops alternatus. Toxicon. 1998, 36(7):1059-63.