My Bibliography

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Kahne SC, Darwin KH. Structural determinants of regulated proteolysis in pathogenic bacteria by ClpP and the proteasome. Curr Opin Struct Biol. 2020 Nov 19;67:120-126. doi: 10.1016/j.sbi.2020.09.012. [Epub ahead of print] Review. PubMed PMID: 33221704; NIHMSID:NIHMS1638377.

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Darwin KH. Bandwagoning. EMBO Rep. 2020 Nov 5;21(11):e51765. doi: 10.15252/embr.202051765. Epub 2020 Oct 15. PubMed PMID: 33063444; PubMed Central PMCID: PMC7645171.

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Becker SH, Ulrich K, Dhabaria A, Ueberheide B, Beavers W, Skaar EP, Iyer LM, Aravind L, Jakob U, Darwin KH. Mycobacterium tuberculosis Rv0991c Is a Redox-Regulated Molecular Chaperone. mBio. 2020 Aug 25;11(4). doi: 10.1128/mBio.01545-20. PubMed PMID: 32843553; PubMed Central PMCID: PMC7448276.

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Ji DX, Yamashiro LH, Chen KJ, Mukaida N, Kramnik I, Darwin KH, Vance RE. Type I interferon-driven susceptibility to Mycobacterium tuberculosis is mediated by IL-1Ra. Nat Microbiol. 2019 Dec;4(12):2128-2135. doi: 10.1038/s41564-019-0578-3. Epub 2019 Oct 14. PubMed PMID: 31611644; PubMed Central PMCID: PMC6879852.

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Ballister ER, Samanovic MI, Darwin KH. Mycobacterium tuberculosis Rv2700 Contributes to Cell Envelope Integrity and Virulence. J Bacteriol. 2019 Oct 1;201(19). doi: 10.1128/JB.00228-19. Print 2019 Oct 1. PubMed PMID: 31285241; PubMed Central PMCID: PMC6755743.

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Hu K, Jordan AT, Zhang S, Dhabaria A, Kovach A, Rangel MV, Ueberheide B, Li H, Darwin KH. Characterization of Guided Entry of Tail-Anchored Proteins 3 Homologues in Mycobacterium tuberculosis. J Bacteriol. 2019 Jul 15;201(14). doi: 10.1128/JB.00159-19. Print 2019 Jul 15. PubMed PMID: 31036728; PubMed Central PMCID: PMC6597400.

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Becker SH, Jastrab JB, Dhabaria A, Chaton CT, Rush JS, Korotkov KV, Ueberheide B, Darwin KH. The Mycobacterium tuberculosis Pup-proteasome system regulates nitrate metabolism through an essential protein quality control pathway. Proc Natl Acad Sci U S A. 2019 Feb 19;116(8):3202-3210. doi: 10.1073/pnas.1819468116. Epub 2019 Feb 5. PubMed PMID: 30723150; PubMed Central PMCID: PMC6386731.

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Becker SH, Li H, Heran Darwin K. Biology and Biochemistry of Bacterial Proteasomes. Subcell Biochem. 2019;93:339-358. doi: 10.1007/978-3-030-28151-9_11. Review. PubMed PMID: 31939157; PubMed Central PMCID: PMC7155931.

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Samanovic MI, Hsu HC, Jones MB, Jones V, McNeil MR, Becker SH, Jordan AT, Strnad M, Xu C, Jackson M, Li H, Darwin KH. Cytokinin Signaling in Mycobacterium tuberculosis. mBio. 2018 Jun 19;9(3). doi: 10.1128/mBio.00989-18. PubMed PMID: 29921668; PubMed Central PMCID: PMC6016246.

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Hu K, Jastrab JB, Zhang S, Kovach A, Zhao G, Darwin KH, Li H. Proteasome substrate capture and gate opening by the accessory factor PafE from Mycobacterium tuberculosis. J Biol Chem. 2018 Mar 30;293(13):4713-4723. doi: 10.1074/jbc.RA117.001471. Epub 2018 Feb 5. PubMed PMID: 29414791; PubMed Central PMCID: PMC5880150.

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Wu Y, Hu K, Li D, Bai L, Yang S, Jastrab JB, Xiao S, Hu Y, Zhang S, Darwin KH, Wang T, Li H. Mycobacterium tuberculosis proteasomal ATPase Mpa has a β-grasp domain that hinders docking with the proteasome core protease. Mol Microbiol. 2017 Jul;105(2):227-241. doi: 10.1111/mmi.13695. Epub 2017 May 3. PubMed PMID: 28419599; PubMed Central PMCID: PMC5575984.

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Bai L, Jastrab JB, Isasa M, Hu K, Yu H, Gygi SP, Darwin KH, Li H. Structural Analysis of Mycobacterium tuberculosis Homologues of the Eukaryotic Proteasome Assembly Chaperone 2 (PAC2). J Bacteriol. 2017 May 1;199(9). doi: 10.1128/JB.00846-16. Print 2017 May 1. PubMed PMID: 28193903; PubMed Central PMCID: PMC5388811.

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Jastrab JB, Samanovic MI, Copin R, Shopsin B, Darwin KH. Loss-of-Function Mutations in HspR Rescue the Growth Defect of a Mycobacterium tuberculosis Proteasome Accessory Factor E (pafE) Mutant. J Bacteriol. 2017 Apr 1;199(7). doi: 10.1128/JB.00850-16. Print 2017 Apr 1. PubMed PMID: 28096448; PubMed Central PMCID: PMC5350283.

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Becker SH, Darwin KH. Bacterial Proteasomes: Mechanistic and Functional Insights. Microbiol Mol Biol Rev. 2017 Mar;81(1). doi: 10.1128/MMBR.00036-16. Print 2017 Mar. Review. PubMed PMID: 27974513; PubMed Central PMCID: PMC5312241.

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Bai L, Hu K, Wang T, Jastrab JB, Darwin KH, Li H. Structural analysis of the dodecameric proteasome activator PafE in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A. 2016 Apr 5;113(14):E1983-92. doi: 10.1073/pnas.1512094113. Epub 2016 Mar 21. PubMed PMID: 27001842; PubMed Central PMCID: PMC4833279.

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Nowicka U, Hoffman M, Randles L, Shi X, Khavrutskii L, Stefanisko K, Tarasova NI, Darwin KH, Walters KJ. Mycobacterium tuberculosis copper-regulated protein SocB is an intrinsically disordered protein that folds upon interaction with a synthetic phospholipid bilayer. Proteins. 2016 Feb;84(2):193-200. doi: 10.1002/prot.24970. Epub 2015 Dec 29. PubMed PMID: 26650755; PubMed Central PMCID: PMC4718776.

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Samanovic MI, Darwin KH. Game of 'Somes: Protein Destruction for Mycobacterium tuberculosis Pathogenesis. Trends Microbiol. 2016 Jan;24(1):26-34. doi: 10.1016/j.tim.2015.10.001. Epub 2015 Oct 29. Review. PubMed PMID: 26526503; PubMed Central PMCID: PMC4698092.

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Clevers H, Firestein S, Ringrose L, Bernards R, Darwin KH, Vance RE. Radical Sabbaticals. Cell. 2015 Nov 5;163(4):788-9. doi: 10.1016/j.cell.2015.10.058. PubMed PMID: 26544929.

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Darwin KH. Mycobacterium tuberculosis and Copper: A Newly Appreciated Defense against an Old Foe?. J Biol Chem. 2015 Jul 31;290(31):18962-6. doi: 10.1074/jbc.R115.640193. Epub 2015 Jun 8. Review. PubMed PMID: 26055711; PubMed Central PMCID: PMC4521017.

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Shi X, Darwin KH. Copper homeostasis in Mycobacterium tuberculosis. Metallomics. 2015 Jun;7(6):929-34. doi: 10.1039/c4mt00305e. Review. PubMed PMID: 25614981; PubMed Central PMCID: PMC4465026.

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Jastrab JB, Wang T, Murphy JP, Bai L, Hu K, Merkx R, Huang J, Chatterjee C, Ovaa H, Gygi SP, Li H, Darwin KH. An adenosine triphosphate-independent proteasome activator contributes to the virulence of Mycobacterium tuberculosis. Proc Natl Acad Sci U S A. 2015 Apr 7;112(14):E1763-72. doi: 10.1073/pnas.1423319112. Epub 2015 Mar 23. PubMed PMID: 25831519; PubMed Central PMCID: PMC4394314.

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Samanovic MI, Tu S, Novák O, Iyer LM, McAllister FE, Aravind L, Gygi SP, Hubbard SR, Strnad M, Darwin KH. Proteasomal control of cytokinin synthesis protects Mycobacterium tuberculosis against nitric oxide. Mol Cell. 2015 Mar 19;57(6):984-994. doi: 10.1016/j.molcel.2015.01.024. Epub 2015 Feb 26. PubMed PMID: 25728768; PubMed Central PMCID: PMC4369403.

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Jastrab JB, Darwin KH. Bacterial Proteasomes. Annu Rev Microbiol. 2015;69:109-27. doi: 10.1146/annurev-micro-091014-104201. Review. PubMed PMID: 26488274; PubMed Central PMCID: PMC4702487.

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Bode NJ, Darwin KH. The Pup-Proteasome System of Mycobacteria. Microbiol Spectr. 2014 Oct;2(5). doi: 10.1128/microbiolspec.MGM2-0008-2013. Review. PubMed PMID: 26104367; PubMed Central PMCID: PMC4232953.

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Shi X, Festa RA, Ioerger TR, Butler-Wu S, Sacchettini JC, Darwin KH, Samanovic MI. The copper-responsive RicR regulon contributes to Mycobacterium tuberculosis virulence. mBio. 2014 Feb 18;5(1). doi: 10.1128/mBio.00876-13. PubMed PMID: 24549843; PubMed Central PMCID: PMC3944814.

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Samanovic MI, Li H, Darwin KH. The pup-proteasome system of Mycobacterium tuberculosis. Subcell Biochem. 2013;66:267-95. doi: 10.1007/978-94-007-5940-4_10. Review. PubMed PMID: 23479444; PubMed Central PMCID: PMC4212895.

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Burns KE, McAllister FE, Schwerdtfeger C, Mintseris J, Cerda-Maira F, Noens EE, Wilmanns M, Hubbard SR, Melandri F, Ovaa H, Gygi SP, Darwin KH. Mycobacterium tuberculosis prokaryotic ubiquitin-like protein-deconjugating enzyme is an unusual aspartate amidase. J Biol Chem. 2012 Oct 26;287(44):37522-9. doi: 10.1074/jbc.M112.384784. Epub 2012 Aug 31. PubMed PMID: 22942282; PubMed Central PMCID: PMC3481346.

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Merkx R, Burns KE, Slobbe P, El Oualid F, El Atmioui D, Darwin KH, Ovaa H. Synthesis and evaluation of a selective fluorogenic Pup derived assay reagent for Dop, a potential drug target in Mycobacterium tuberculosis. Chembiochem. 2012 Sep 24;13(14):2056-60. doi: 10.1002/cbic.201200460. Epub 2012 Aug 24. PubMed PMID: 22927162; PubMed Central PMCID: PMC3474595.

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Samanovic MI, Ding C, Thiele DJ, Darwin KH. Copper in microbial pathogenesis: meddling with the metal. Cell Host Microbe. 2012 Feb 16;11(2):106-15. doi: 10.1016/j.chom.2012.01.009. Review. PubMed PMID: 22341460; PubMed Central PMCID: PMC3285254.

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Burns KE, Darwin KH. Pupylation: proteasomal targeting by a protein modifier in bacteria. Methods Mol Biol. 2012;832:151-60. doi: 10.1007/978-1-61779-474-2_10. PubMed PMID: 22350883; PubMed Central PMCID: PMC3619960.

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Cerda-Maira FA, McAllister F, Bode NJ, Burns KE, Gygi SP, Darwin KH. Reconstitution of the Mycobacterium tuberculosis pupylation pathway in Escherichia coli. EMBO Rep. 2011 Jul 8;12(8):863-70. doi: 10.1038/embor.2011.109. PubMed PMID: 21738222; PubMed Central PMCID: PMC3147258.

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Festa RA, Jones MB, Butler-Wu S, Sinsimer D, Gerads R, Bishai WR, Peterson SN, Darwin KH. A novel copper-responsive regulon in Mycobacterium tuberculosis. Mol Microbiol. 2011 Jan;79(1):133-48. doi: 10.1111/j.1365-2958.2010.07431.x. Epub 2010 Oct 29. PubMed PMID: 21166899; PubMed Central PMCID: PMC3052634.

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Wang T, Darwin KH, Li H. Binding-induced folding of prokaryotic ubiquitin-like protein on the Mycobacterium proteasomal ATPase targets substrates for degradation. Nat Struct Mol Biol. 2010 Nov;17(11):1352-7. doi: 10.1038/nsmb.1918. Epub 2010 Oct 17. PubMed PMID: 20953180; PubMed Central PMCID: PMC2988878.

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Burns KE, Cerda-Maira FA, Wang T, Li H, Bishai WR, Darwin KH. "Depupylation" of prokaryotic ubiquitin-like protein from mycobacterial proteasome substrates. Mol Cell. 2010 Sep 10;39(5):821-7. doi: 10.1016/j.molcel.2010.07.019. Epub 2010 Aug 12. PubMed PMID: 20705495; PubMed Central PMCID: PMC2939144.

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Cerda-Maira FA, Pearce MJ, Fuortes M, Bishai WR, Hubbard SR, Darwin KH. Molecular analysis of the prokaryotic ubiquitin-like protein (Pup) conjugation pathway in Mycobacterium tuberculosis. Mol Microbiol. 2010 Sep;77(5):1123-35. doi: 10.1111/j.1365-2958.2010.07276.x. PubMed PMID: 20636328; PubMed Central PMCID: PMC2975802.

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Darwin KH, Hofmann K. SAMPyling proteins in archaea. Trends Biochem Sci. 2010 Jun;35(6):348-51. doi: 10.1016/j.tibs.2010.03.003. Epub 2010 May 23. Review. PubMed PMID: 20547064; PubMed Central PMCID: PMC2892244.

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Burns KE, Pearce MJ, Darwin KH. Prokaryotic ubiquitin-like protein provides a two-part degron to Mycobacterium proteasome substrates. J Bacteriol. 2010 Jun;192(11):2933-5. doi: 10.1128/JB.01639-09. Epub 2010 Mar 16. PubMed PMID: 20233925; PubMed Central PMCID: PMC2876485.

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Burns KE, Darwin KH. Pupylation versus ubiquitylation: tagging for proteasome-dependent degradation. Cell Microbiol. 2010 Apr 1;12(4):424-31. doi: 10.1111/j.1462-5822.2010.01447.x. Epub 2010 Jan 26. Review. PubMed PMID: 20109157; PubMed Central PMCID: PMC3647454.

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Festa RA, McAllister F, Pearce MJ, Mintseris J, Burns KE, Gygi SP, Darwin KH. Prokaryotic ubiquitin-like protein (Pup) proteome of Mycobacterium tuberculosis [corrected] . PLoS One. 2010 Jan 6;5(1):e8589. doi: 10.1371/journal.pone.0008589. PubMed PMID: 20066036; PubMed Central PMCID: PMC2797603.

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Burns KE, Darwin KH. Pupylation : A Signal for Proteasomal Degradation in Mycobacterium tuberculosis. Subcell Biochem. 2010;54:149-57. doi: 10.1007/978-1-4419-6676-6_12. PubMed PMID: 21222280; PubMed Central PMCID: PMC6544877.

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Cerda-Maira F, Darwin KH. The Mycobacterium tuberculosis proteasome: more than just a barrel-shaped protease. Microbes Infect. 2009 Dec;11(14-15):1150-5. doi: 10.1016/j.micinf.2009.08.003. Epub 2009 Aug 9. Review. PubMed PMID: 19671445; PubMed Central PMCID: PMC2788230.

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Wang T, Li H, Lin G, Tang C, Li D, Nathan C, Darwin KH, Li H. Structural insights on the Mycobacterium tuberculosis proteasomal ATPase Mpa. Structure. 2009 Oct 14;17(10):1377-85. doi: 10.1016/j.str.2009.08.010. PubMed PMID: 19836337; PubMed Central PMCID: PMC2775066.

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Chen X, Solomon WC, Kang Y, Cerda-Maira F, Darwin KH, Walters KJ. Prokaryotic ubiquitin-like protein pup is intrinsically disordered. J Mol Biol. 2009 Sep 11;392(1):208-17. doi: 10.1016/j.jmb.2009.07.018. Epub 2009 Jul 14. PubMed PMID: 19607839; PubMed Central PMCID: PMC2734869.

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Darwin KH. Prokaryotic ubiquitin-like protein (Pup), proteasomes and pathogenesis. Nat Rev Microbiol. 2009 Jul;7(7):485-91. doi: 10.1038/nrmicro2148. Epub 2009 Jun 1. Review. PubMed PMID: 19483713; PubMed Central PMCID: PMC3662484.

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Pearce MJ, Mintseris J, Ferreyra J, Gygi SP, Darwin KH. Ubiquitin-like protein involved in the proteasome pathway of Mycobacterium tuberculosis. Science. 2008 Nov 14;322(5904):1104-7. doi: 10.1126/science.1163885. Epub 2008 Oct 2. PubMed PMID: 18832610; PubMed Central PMCID: PMC2698935.

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Festa RA, Pearce MJ, Darwin KH. Characterization of the proteasome accessory factor (paf) operon in Mycobacterium tuberculosis. J Bacteriol. 2007 Apr;189(8):3044-50. doi: 10.1128/JB.01597-06. Epub 2007 Feb 2. PubMed PMID: 17277063; PubMed Central PMCID: PMC1855869.

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Pearce MJ, Arora P, Festa RA, Butler-Wu SM, Gokhale RS, Darwin KH. Identification of substrates of the Mycobacterium tuberculosis proteasome. EMBO J. 2006 Nov 15;25(22):5423-32. doi: 10.1038/sj.emboj.7601405. Epub 2006 Nov 2. PubMed PMID: 17082771; PubMed Central PMCID: PMC1636610.

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Butler SM, Festa RA, Pearce MJ, Darwin KH. Self-compartmentalized bacterial proteases and pathogenesis. Mol Microbiol. 2006 May;60(3):553-62. doi: 10.1111/j.1365-2958.2006.05128.x. Review. PubMed PMID: 16629660.

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Darwin KH, Nathan CF. Role for nucleotide excision repair in virulence of Mycobacterium tuberculosis. Infect Immun. 2005 Aug;73(8):4581-7. doi: 10.1128/IAI.73.8.4581-4587.2005. PubMed PMID: 16040969; PubMed Central PMCID: PMC1201236.

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Hisert KB, MacCoss M, Shiloh MU, Darwin KH, Singh S, Jones RA, Ehrt S, Zhang Z, Gaffney BL, Gandotra S, Holden DW, Murray D, Nathan C. A glutamate-alanine-leucine (EAL) domain protein of Salmonella controls bacterial survival in mice, antioxidant defence and killing of macrophages: role of cyclic diGMP. Mol Microbiol. 2005 Jun;56(5):1234-45. doi: 10.1111/j.1365-2958.2005.04632.x. PubMed PMID: 15882417.