Recent Publications

Recent Publications

  1. Fortune SM, Rubin EJ. Host transcription in active and latent tuberculosis. Genome Biol. 2010;11(9):135. doi: 10.1186/gb-2010-11-9-135. Epub 2010 Sep 28. PubMed PMID: 20920149; PubMed Central PMCID: PMC2965379.
  2. Chao MC, Rubin EJ. Letting sleeping dos lie: does dormancy play a role in tuberculosis? Annu Rev Microbiol. 2010;64:293-311. doi: 10.1146/annurev.micro.112408.134043. Review. PubMed PMID: 20825351.
  3. Dutton RJ, Wayman A, Wei JR, Rubin EJ, Beckwith J, Boyd D. Inhibition of bacterial disulfide bond formation by the anticoagulant warfarin. Proc Natl Acad Sci U S A. 2010 Jan 5;107(1):297-301. doi: 10.1073/pnas.0912952107. Epub 2009 Dec 15. PubMed PMID: 20018758; PubMed Central PMCID: PMC2806739.
  4. Sassetti CM, Rubin EJ. Relics of selection in the mycobacterial genome. Nat Genet. 2010 Jun;42(6):476-8. doi: 10.1038/ng0610-476. PubMed PMID: 20502489; PubMed Central PMCID: PMC4043303.
  5. Hett EC, Chao MC, Rubin EJ. Interaction and modulation of two antagonistic cell wall enzymes of mycobacteria. PLoS Pathog. 2010 Jul 29;6(7):e1001020. doi: 10.1371/journal.ppat.1001020. PubMed PMID: 20686708; PubMed Central PMCID: PMC2912383.
  6. Freundlich JS, Lalgondar M, Wei JR, Swanson S, Sorensen EJ, Rubin EJ, Sacchettini JC. The abyssomicin C family as in vitro inhibitors of Mycobacterium tuberculosis. Tuberculosis (Edinb). 2010 Sep;90(5):298-300. doi: 10.1016/ Epub 2010 Aug 23. PubMed PMID: 20739223; PubMed Central PMCID: PMC3213896.
  7. Kim JH, Wei JR, Wallach JB, Robbins RS, Rubin EJ, Schnappinger D. Protein inactivation in mycobacteria by controlled proteolysis and its application to deplete the beta subunit of RNA polymerase. Nucleic Acids Res. 2011 Mar;39(6):2210-20. doi: 10.1093/nar/gkq1149. Epub 2010 Nov 12. PubMed PMID: 21075796; PubMed Central PMCID: PMC3064785.
  8. Wei JR, Krishnamoorthy V, Murphy K, Kim JH, Schnappinger D, Alber T, Sassetti CM, Rhee KY, Rubin EJ. Depletion of antibiotic targets has widely varying effects on growth. Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):4176-81. doi: 10.1073/pnas.1018301108. Epub 2011 Feb 22. PubMed PMID: 21368134; PubMed Central PMCID: PMC3053961.
  9. Horsburgh CR Jr, Rubin EJ. Clinical practice. Latent tuberculosis infection in the United States. N Engl J Med. 2011 Apr 14;364(15):1441-8. doi: 10.1056/NEJMcp1005750. Review. PubMed PMID: 21488766.
  10. La Rosa V, Poce G, Canseco JO, Buroni S, Pasca MR, Biava M, Raju RM, Porretta GC, Alfonso S, Battilocchio C, Javid B, Sorrentino F, Ioerger TR, Sacchettini JC, Manetti F, Botta M, De Logu A, Rubin EJ, De Rossi E. MmpL3 is the cellular target of the antitubercular pyrrole derivative BM212. Antimicrob Agents Chemother. 2012 Jan;56(1):324-31. doi: 10.1128/AAC.05270-11. Epub 2011 Oct 24. PubMed PMID: 22024828; PubMed Central PMCID: PMC3256021.
  11. Gee CL, Papavinasasundaram KG, Blair SR, Baer CE, Falick AM, King DS, Griffin JE, Venghatakrishnan H, Zukauskas A, Wei JR, Dhiman RK, Crick DC, Rubin EJ, Sassetti CM, Alber T. A phosphorylated pseudokinase complex controls cell wall synthesis in mycobacteria. Sci Signal. 2012 Jan 24;5(208):ra7. doi: 10.1126/scisignal.2002525. PubMed PMID: 22275220; PubMed Central PMCID: PMC3664666.
  12. Madigan CA, Cheng TY, Layre E, Young DC, McConnell MJ, Debono CA, Murry JP, Wei JR, Barry CE 3rd, Rodriguez GM, Matsunaga I, Rubin EJ, Moody DB. Lipidomic discovery of deoxysiderophores reveals a revised mycobactin biosynthesis pathway in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A. 2012 Jan 24;109(4):1257-62. doi: 10.1073/pnas.1109958109. Epub 2012 Jan 9. PubMed PMID: 22232695; PubMed Central PMCID: PMC3268331.
  13. Raju RM, Unnikrishnan M, Rubin DH, Krishnamoorthy V, Kandror O, Akopian TN, Goldberg AL, Rubin EJ. Mycobacterium tuberculosis ClpP1 and ClpP2 function together in protein degradation and are required for viability in vitro and during infection. PLoS Pathog. 2012 Feb;8(2):e1002511. doi: 10.1371/journal.ppat.1002511. Epub 2012 Feb 16. PubMed PMID: 22359499; PubMed Central PMCID: PMC3280978.
  14. Akopian T, Kandror O, Raju RM, Unnikrishnan M, Rubin EJ, Goldberg AL. The active ClpP protease from M. tuberculosis is a complex composed of a heptameric ClpP1 and a ClpP2 ring. EMBO J. 2012 Mar 21;31(6):1529-41. doi: 10.1038/emboj.2012.5. Epub 2012 Jan 27. PubMed PMID: 22286948; PubMed Central PMCID: PMC3321190.
  15. Zhang YJ, Ioerger TR, Huttenhower C, Long JE, Sassetti CM, Sacchettini JC, Rubin EJ. Global assessment of genomic regions required for growth in Mycobacterium tuberculosis. PLoS Pathog. 2012 Sep;8(9):e1002946. doi: 10.1371/journal.ppat.1002946. Epub 2012 Sep 27. Erratum in: PLoS Pathog. 2013;9(7). doi:10.1371/annotation/4669e9e7-fd12-4a01-be2a-617b956ec0bb. PubMed PMID: 23028335; PubMed Central PMCID: PMC3460630.
  16. Raju RM, Goldberg AL, Rubin EJ. Bacterial proteolytic complexes as therapeutic targets. Nat Rev Drug Discov. 2012 Oct;11(10):777-89. doi: 10.1038/nrd3846. Review. PubMed PMID: 23023677.
  17. Ioerger TR, O’Malley T, Liao R, Guinn KM, Hickey MJ, Mohaideen N, Murphy KC, Boshoff HI, Mizrahi V, Rubin EJ, Sassetti CM, Barry CE 3rd, Sherman DR, Parish T, Sacchettini JC. Identification of new drug targets and resistance mechanisms in Mycobacterium tuberculosis. PLoS One. 2013 Sep 23;8(9):e75245. doi: 10.1371/journal.pone.0075245. eCollection 2013. PubMed PMID: 24086479; PubMed Central PMCID: PMC3781026.
  18. Ngubane NA, Gresh L, Ioerger TR, Sacchettini JC, Zhang YJ, Rubin EJ, Pym A, Khati M. High-throughput sequencing enhanced phage display identifies peptides that bind mycobacteria. PLoS One. 2013 Nov 12;8(11):e77844. doi: 10.1371/journal.pone.0077844. eCollection 2013. PubMed PMID: 24265677; PubMed Central PMCID: PMC3827053.
  19. Chao MC, Kieser KJ, Minami S, Mavrici D, Aldridge BB, Fortune SM, Alber T, Rubin EJ. Protein complexes and proteolytic activation of the cell wall hydrolase RipA regulate septal resolution in mycobacteria. PLoS Pathog. 2013 Feb;9(2):e1003197. doi: 10.1371/journal.ppat.1003197. Epub 2013 Feb 28. PubMed PMID: 23468634; PubMed Central PMCID: PMC3585148.
  20. DeJesus MA, Zhang YJ, Sassetti CM, Rubin EJ, Sacchettini JC, Ioerger TR. Bayesian analysis of gene essentiality based on sequencing of transposon insertion libraries. Bioinformatics. 2013 Mar 15;29(6):695-703. doi: 10.1093/bioinformatics/btt043. Epub 2013 Jan 29. PubMed PMID: 23361328; PubMed Central PMCID: PMC3597147.
  21. Zhang YJ, Rubin EJ. Feast or famine: the host-pathogen battle over amino acids. Cell Microbiol. 2013 Jul;15(7):1079-87. doi: 10.1111/cmi.12140. Epub 2013 Apr 5. Review. PubMed PMID: 23521858.
  22. Stanley SA, Kawate T, Iwase N, Shimizu M, Clatworthy AE, Kazyanskaya E, Sacchettini JC, Ioerger TR, Siddiqi NA, Minami S, Aquadro JA, Grant SS, Rubin EJ, Hung DT. Diarylcoumarins inhibit mycolic acid biosynthesis and kill Mycobacterium tuberculosis by targeting FadD32. Proc Natl Acad Sci U S A. 2013 Jul 9;110(28):11565-70. doi: 10.1073/pnas.1302114110. Epub 2013 Jun 24. PubMed PMID: 23798446; PubMed Central PMCID: PMC3710825.
  23. Zheng J, Rubin EJ, Bifani P, Mathys V, Lim V, Au M, Jang J, Nam J, Dick T, Walker JR, Pethe K, Camacho LR. para-Aminosalicylic acid is a prodrug targeting dihydrofolate reductase in Mycobacterium tuberculosis. J Biol Chem. 2013 Aug 9;288(32):23447-56. doi: 10.1074/jbc.M113.475798. Epub 2013 Jun 18. Erratum in: J Biol Chem. 2013 Oct 4;288(40):28951. PubMed PMID: 23779105.
  24. Chao MC, Pritchard JR, Zhang YJ, Rubin EJ, Livny J, Davis BM, Waldor MK. High-resolution definition of the Vibrio cholerae essential gene set with hidden Markov model-based analyses of transposon-insertion sequencing data. Nucleic Acids Res. 2013 Oct;41(19):9033-48. doi: 10.1093/nar/gkt654. Epub 2013 Jul 30. PubMed PMID: 23901011; PubMed Central PMCID: PMC3799429.
  25. Farhat MR, Shapiro BJ, Kieser KJ, Sultana R, Jacobson KR, Victor TC, Warren RM, Streicher EM, Calver A, Sloutsky A, Kaur D, Posey JE, Plikaytis B, Oggioni MR, Gardy JL, Johnston JC, Rodrigues M, Tang PK, Kato-Maeda M, Borowsky ML, Muddukrishna B, Kreiswirth BN, Kurepina N, Galagan J, Gagneux S, Birren B, Rubin EJ, Lander ES, Sabeti PC, Murray M. Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nat Genet. 2013 Oct;45(10):1183-9. doi: 10.1038/ng.2747. Epub 2013 Sep 1. PubMed PMID: 23995135; PubMed Central PMCID: PMC3887553.
  26. Zhang YJ, Reddy MC, Ioerger TR, Rothchild AC, Dartois V, Schuster BM, Trauner A, Wallis D, Galaviz S, Huttenhower C, Sacchettini JC, Behar SM, Rubin EJ. Tryptophan biosynthesis protects mycobacteria from CD4 T-cell-mediated killing. Cell. 2013 Dec 5;155(6):1296-308. doi: 10.1016/j.cell.2013.10.045. PubMed PMID: 24315099; PubMed Central PMCID: PMC3902092.
  27. Javid B, Sorrentino F, Toosky M, Zheng W, Pinkham JT, Jain N, Pan M, Deighan P, Rubin EJ. Mycobacterial mistranslation is necessary and sufficient for rifampicin phenotypic resistance. Proc Natl Acad Sci U S A. 2014 Jan 21;111(3):1132-7. doi: 10.1073/pnas.1317580111. Epub 2014 Jan 6. PubMed PMID: 24395793; PubMed Central PMCID: PMC3903211.
  28. Stanley SA, Barczak AK, Silvis MR, Luo SS, Sogi K, Vokes M, Bray MA, Carpenter AE, Moore CB, Siddiqi N, Rubin EJ, Hung DT. Identification of host-targeted small molecules that restrict intracellular Mycobacterium tuberculosis growth. PLoS Pathog. 2014 Feb 20;10(2):e1003946. doi: 10.1371/journal.ppat.1003946. eCollection 2014 Feb. PubMed PMID: 24586159; PubMed Central PMCID: PMC3930586.
  29. Rodionova IA, Schuster BM, Guinn KM, Sorci L, Scott DA, Li X, Kheterpal I, Shoen C, Cynamon M, Locher C, Rubin EJ, Osterman AL. Metabolic and bactericidal effects of targeted suppression of NadD and NadE enzymes in mycobacteria. MBio. 2014 Feb 18;5(1). pii: e00747-13. doi: 10.1128/mBio.00747-13. PubMed PMID: 24549842; PubMed Central PMCID: PMC3944813.
  30. Layre E, Lee HJ, Young DC, Martinot AJ, Buter J, Minnaard AJ, Annand JW, Fortune SM, Snider BB, Matsunaga I, Rubin EJ, Alber T, Moody DB. Molecular profiling of Mycobacterium tuberculosis identifies tuberculosinyl nucleoside products of the virulence-associated enzyme Rv3378c. Proc Natl Acad Sci U S A. 2014 Feb 25;111(8):2978-83. doi: 10.1073/pnas.1315883111. Epub 2014 Feb 10. PubMed PMID: 24516143; PubMed Central PMCID: PMC3939896.
  31. Raju RM, Jedrychowski MP, Wei JR, Pinkham JT, Park AS, O’Brien K, Rehren G, Schnappinger D, Gygi SP, Rubin EJ. Post-translational regulation via Clp protease is critical for survival of Mycobacterium tuberculosis. PLoS Pathog. 2014 Mar 6;10(3):e1003994. doi: 10.1371/journal.ppat.1003994. eCollection 2014 Mar. PubMed PMID: 24603869; PubMed Central PMCID: PMC3946367.
  32. Rubin EJ, O’Brien JP, Ivanov PL, Brodbelt JS, Trent MS. Identification of a broad family of lipid A late acyltransferases with non-canonical substrate specificity. Mol Microbiol. 2014 Mar;91(5):887-99. doi: 10.1111/mmi.12501. Epub 2014 Jan 14. PubMed PMID: 24372821; PubMed Central PMCID: PMC3947442.
  33. Siegrist MS, Steigedal M, Ahmad R, Mehra A, Dragset MS, Schuster BM, Philips JA, Carr SA, Rubin EJ. Mycobacterial Esx-3 requires multiple components for iron acquisition. MBio. 2014 May 6;5(3):e01073-14. doi: 10.1128/mBio.01073-14. PubMed PMID: 24803520; PubMed Central PMCID: PMC4010830.
  34. Mavrici D, Marakalala MJ, Holton JM, Prigozhin DM, Gee CL, Zhang YJ, Rubin EJ, Alber T. Mycobacterium tuberculosis FtsX extracellular domain activates the peptidoglycan hydrolase, RipC. Proc Natl Acad Sci U S A. 2014 Jun 3;111(22):8037-42. doi: 10.1073/pnas.1321812111. Epub 2014 May 19. PubMed PMID: 24843173; PubMed Central PMCID: PMC4050617.
  35. Ngubane NA, Gresh L, Pym A, Rubin EJ, Khati M. Selection of RNA aptamers against the M. tuberculosis EsxG protein using surface plasmon resonance-based SELEX. Biochem Biophys Res Commun. 2014 Jun 20;449(1):114-9. doi: 10.1016/j.bbrc.2014.04.163. Epub 2014 May 9. PubMed PMID: 24813997.
  36. Kieser KJ, Rubin EJ. How sisters grow apart: mycobacterial growth and division. Nat Rev Microbiol. 2014 Aug;12(8):550-62. doi: 10.1038/nrmicro3299. Epub 2014 Jul 7. Review. PubMed PMID: 24998739.
  37. Santa Maria JP Jr, Sadaka A, Moussa SH, Brown S, Zhang YJ, Rubin EJ, Gilmore MS, Walker S. Compound-gene interaction mapping reveals distinct roles for Staphylococcus aureus teichoic acids. Proc Natl Acad Sci U S A. 2014 Aug 26;111(34):12510-5. doi: 10.1073/pnas.1404099111. Epub 2014 Aug 7. PubMed PMID: 25104751; PubMed Central PMCID: PMC4151746.
  38. Mir M, Prisic S, Kang CM, Lun S, Guo H, Murry JP, Rubin EJ, Husson RN. Mycobacterial gene cuvA is required for optimal nutrient utilization and virulence. Infect Immun. 2014 Oct;82(10):4104-17. doi: 10.1128/IAI.02207-14. Epub 2014 Jul 21. PubMed PMID: 25047842; PubMed Central PMCID: PMC4187881.
  39. Pritchard JR, Chao MC, Abel S, Davis BM, Baranowski C, Zhang YJ, Rubin EJ, Waldor MK. ARTIST: high-resolution genome-wide assessment of fitness using transposon-insertion sequencing. PLoS Genet. 2014 Nov 6;10(11):e1004782. doi: 10.1371/journal.pgen.1004782. eCollection 2014 Nov. PubMed PMID: 25375795; PubMed Central PMCID: PMC4222735.
  40. Madigan CA, Martinot AJ, Wei JR, Madduri A, Cheng TY, Young DC, Layre E, Murry JP, Rubin EJ, Moody DB. Lipidomic Analysis Links Mycobactin Synthase K to Iron Uptake and Virulence in M. tuberculosis. PLoS Pathog. 2015 Mar 27;11(3):e1004792. doi: 10.1371/journal.ppat.1004792. eCollection 2015 Mar. PubMed PMID: 25815898; PubMed Central PMCID: PMC4376628.
  41. Baer CE, Rubin EJ, Sassetti CM. New insights into TB physiology suggest untapped therapeutic opportunities. Immunol Rev. 2015 Mar;264(1):327-43. doi: 10.1111/imr.12267. PubMed PMID: 25703570; PubMed Central PMCID: PMC4339208.
  42. Akopian T, Kandror O, Tsu C, Lai JH, Wu W, Liu Y, Zhao P, Park A, Wolf L, Dick LR, Rubin EJ, Bachovchin W, Goldberg AL. Cleavage specificity of Mycobacterium tuberculosis ClpP1P2 protease and identification of novel peptide substrates and boronate inhibitors with anti-bacterial activity. J Biol Chem. 2015 Mar 10. pii: jbc.M114.625640. [Epub ahead of print] PubMed PMID: 25759383.
  43. Rodionova IA, Zuccola HJ, Sorci L, Aleshin AE, Kazanov MD, Ma CT, Sergienko E, Rubin EJ, Locher CP, Osterman AL. Mycobacterial Nicotinate Mononucleotide Adenylyltransferase: STRUCTURE, MECHANISM, AND IMPLICATIONS FOR DRUG DISCOVERY. J Biol Chem. 2015 Mar 20;290(12):7693-706. doi: 10.1074/jbc.M114.628016. Epub 2015 Jan 28. PubMed PMID: 25631047; PubMed Central PMCID: PMC4367272.
  44. Landeta C, Blazyk JL, Hatahet F, Meehan BM, Eser M, Myrick A, Bronstain L, Minami S, Arnold H, Ke N, Rubin EJ, Furie BC, Furie B, Beckwith J, Dutton R, Boyd D. Compounds targeting disulfide bond forming enzyme DsbB of Gram-negative bacteria. Nat Chem Biol. 2015 Apr;11(4):292-8. doi: 10.1038/nchembio.1752. Epub 2015 Feb 16. PubMed PMID: 25686372; PubMed Central PMCID: PMC4366281.
  45. Dragset MS, Poce G, Alfonso S, Padilla-Benavides T, Ioerger TR, Kaneko T, Sacchettini JC, Biava M, Parish T, Argüello JM, Steigedal M, Rubin EJ. A novel antimycobacterial compound acts as an intracellular iron chelator. Antimicrob Agents Chemother. 2015 Apr;59(4):2256-64. doi: 10.1128/AAC.05114-14. Epub 2015 Feb 2. PubMed PMID: 25645825; PubMed Central PMCID: PMC4356758.