My Bibliography

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Weinert TA, Derbyshire KM, Hughson FM, Grindley ND. Replicative and conservative transpositional recombination of insertion sequences. Cold Spring Harb Symp Quant Biol. 1984;49:251-60. doi: 10.1101/sqb.1984.049.01.029. PubMed PMID: 6099240.

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Haring V, Scholz P, Scherzinger E, Frey J, Derbyshire K, Hatfull G, Willetts NS, Bagdasarian M. Protein RepC is involved in copy number control of the broad host range plasmid RSF1010. Proc Natl Acad Sci U S A. 1985 Sep;82(18):6090-4. doi: 10.1073/pnas.82.18.6090. PubMed PMID: 3898079; PubMed Central PMCID: PMC390705.

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Derbyshire KM, Grindley ND. Replicative and conservative transposition in bacteria. Cell. 1986 Nov 7;47(3):325-7. doi: 10.1016/0092-8674(86)90586-6. Review. PubMed PMID: 3021339.

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Derbyshire KM, Salvo JJ, Grindley ND. A simple and efficient procedure for saturation mutagenesis using mixed oligodeoxynucleotides. Gene. 1986;46(2-3):145-52. doi: 10.1016/0378-1119(86)90398-7. PubMed PMID: 3803923.

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Derbyshire KM, Willetts NS. Mobilization of the non-conjugative plasmid RSF1010: a genetic analysis of its origin of transfer. Mol Gen Genet. 1987 Jan;206(1):154-60. doi: 10.1007/BF00326551. PubMed PMID: 3033437.

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Derbyshire KM, Hatfull G, Willetts N. Mobilization of the non-conjugative plasmid RSF1010: a genetic and DNA sequence analysis of the mobilization region. Mol Gen Genet. 1987 Jan;206(1):161-8. doi: 10.1007/BF00326552. PubMed PMID: 3033438.

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Derbyshire KM, Hwang L, Grindley ND. Genetic analysis of the interaction of the insertion sequence IS903 transposase with its terminal inverted repeats. Proc Natl Acad Sci U S A. 1987 Nov;84(22):8049-53. doi: 10.1073/pnas.84.22.8049. PubMed PMID: 2825175; PubMed Central PMCID: PMC299474.

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Derbyshire KM, Kramer M, Grindley ND. Role of instability in the cis action of the insertion sequence IS903 transposase. Proc Natl Acad Sci U S A. 1990 Jun;87(11):4048-52. doi: 10.1073/pnas.87.11.4048. PubMed PMID: 2161528; PubMed Central PMCID: PMC54044.

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Derbyshire KM, Grindley ND. Binding of the IS903 transposase to its inverted repeat in vitro. EMBO J. 1992 Sep;11(9):3449-55. doi: 10.1002/j.1460-2075.1992.tb05424.x. PubMed PMID: 1324175; PubMed Central PMCID: PMC556880.

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Derbyshire KM. An IS903-based vector for transposon mutagenesis and the isolation of gene fusions. Gene. 1995 Nov 7;165(1):143-4. doi: 10.1016/0378-1119(95)00512-5. PubMed PMID: 7489906; NIHMSID:NIHMS451376.

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Derbyshire KM, Grindley ND. Cis preference of the IS903 transposase is mediated by a combination of transposase instability and inefficient translation. Mol Microbiol. 1996 Sep;21(6):1261-72. doi: 10.1111/j.1365-2958.1996.tb02587.x. PubMed PMID: 8898394; NIHMSID:NIHMS451377.

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Tavakoli NP, DeVost J, Derbyshire KM. Defining functional regions of the IS903 transposase. J Mol Biol. 1997 Dec 12;274(4):491-504. doi: 10.1006/jmbi.1997.1410. PubMed PMID: 9417930; NIHMSID:NIHMS451378.

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Parsons LM, Jankowski CS, Derbyshire KM. Conjugal transfer of chromosomal DNA in Mycobacterium smegmatis. Mol Microbiol. 1998 May;28(3):571-82. doi: 10.1046/j.1365-2958.1998.00818.x. PubMed PMID: 9632259.

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Hu WY, Derbyshire KM. Target choice and orientation preference of the insertion sequence IS903. J Bacteriol. 1998 Jun;180(12):3039-48. doi: 10.1128/JB.180.12.3039-3048.1998. PubMed PMID: 9620951; PubMed Central PMCID: PMC107802.

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Tavakoli NP, Derbyshire KM. IS903 transposase mutants that suppress defective inverted repeats. Mol Microbiol. 1999 Feb;31(4):1183-95. doi: 10.1046/j.1365-2958.1999.01260.x. PubMed PMID: 10096085; NIHMSID:NIHMS451380.

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Griffin TJ 4th, Parsons L, Leschziner AE, DeVost J, Derbyshire KM, Grindley ND. In vitro transposition of Tn552: a tool for DNA sequencing and mutagenesis. Nucleic Acids Res. 1999 Oct 1;27(19):3859-65. doi: 10.1093/nar/27.19.3859. PubMed PMID: 10481025; PubMed Central PMCID: PMC148649.

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Thomson VJ, Bhattacharjee MK, Fine DH, Derbyshire KM, Figurski DH. Direct selection of IS903 transposon insertions by use of a broad-host-range vector: isolation of catalase-deficient mutants of Actinobacillus actinomycetemcomitans. J Bacteriol. 1999 Dec;181(23):7298-307. doi: 10.1128/JB.181.23.7298-7307.1999. PubMed PMID: 10572134; PubMed Central PMCID: PMC103693.

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Machowski EE, McAdam RA, Derbyshire KM, Mizrahi V. Construction and application of mycobacterial reporter transposons. Gene. 2000 Jul 25;253(1):67-75. doi: 10.1016/s0378-1119(00)00238-9. PubMed PMID: 10925203; NIHMSID:NIHMS451383.

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Hu WY, Thompson W, Lawrence CE, Derbyshire KM. Anatomy of a preferred target site for the bacterial insertion sequence IS903. J Mol Biol. 2001 Feb 23;306(3):403-16. doi: 10.1006/jmbi.2000.4421. PubMed PMID: 11178901; NIHMSID:NIHMS451384.

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Tavakoli NP, Derbyshire KM. Tipping the balance between replicative and simple transposition. EMBO J. 2001 Jun 1;20(11):2923-30. doi: 10.1093/emboj/20.11.2923. PubMed PMID: 11387225; PubMed Central PMCID: PMC125483.

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Kirby C, Waring A, Griffin TJ, Falkinham JO 3rd, Grindley ND, Derbyshire KM. Cryptic plasmids of Mycobacterium avium: Tn552 to the rescue. Mol Microbiol. 2002 Jan;43(1):173-86. doi: 10.1046/j.1365-2958.2002.02729.x. PubMed PMID: 11849545; NIHMSID:NIHMS451386.

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Wang J, Parsons LM, Derbyshire KM. Unconventional conjugal DNA transfer in mycobacteria. Nat Genet. 2003 May;34(1):80-4. doi: 10.1038/ng1139. PubMed PMID: 12669068; NIHMSID:NIHMS451387.

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Curcio MJ, Derbyshire KM. The outs and ins of transposition: from mu to kangaroo. Nat Rev Mol Cell Biol. 2003 Nov;4(11):865-77. doi: 10.1038/nrm1241. Review. PubMed PMID: 14682279; NIHMSID:NIHMS451388.

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Swingle B, O'Carroll M, Haniford D, Derbyshire KM. The effect of host-encoded nucleoid proteins on transposition: H-NS influences targeting of both IS903 and Tn10. Mol Microbiol. 2004 May;52(4):1055-67. doi: 10.1111/j.1365-2958.2004.04051.x. PubMed PMID: 15130124; NIHMSID:NIHMS451389.

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Wang J, Derbyshire KM. Plasmid DNA transfer in Mycobacterium smegmatis involves novel DNA rearrangements in the recipient, which can be exploited for molecular genetic studies. Mol Microbiol. 2004 Aug;53(4):1233-41. doi: 10.1111/j.1365-2958.2004.04201.x. PubMed PMID: 15306024; NIHMSID:NIHMS451362.

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Flint JL, Kowalski JC, Karnati PK, Derbyshire KM. The RD1 virulence locus of Mycobacterium tuberculosis regulates DNA transfer in Mycobacterium smegmatis. Proc Natl Acad Sci U S A. 2004 Aug 24;101(34):12598-603. doi: 10.1073/pnas.0404892101. Epub 2004 Aug 16. PubMed PMID: 15314236; PubMed Central PMCID: PMC515103.

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Coros AM, Twiss E, Tavakoli NP, Derbyshire KM. Genetic evidence that GTP is required for transposition of IS903 and Tn552 in Escherichia coli. J Bacteriol. 2005 Jul;187(13):4598-606. doi: 10.1128/JB.187.13.4598-4606.2005. PubMed PMID: 15968071; PubMed Central PMCID: PMC1151752.

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Twiss E, Coros AM, Tavakoli NP, Derbyshire KM. Transposition is modulated by a diverse set of host factors in Escherichia coli and is stimulated by nutritional stress. Mol Microbiol. 2005 Sep;57(6):1593-607. doi: 10.1111/j.1365-2958.2005.04794.x. PubMed PMID: 16135227; NIHMSID:NIHMS451359.

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Wardle SJ, O'Carroll M, Derbyshire KM, Haniford DB. The global regulator H-NS acts directly on the transpososome to promote Tn10 transposition. Genes Dev. 2005 Sep 15;19(18):2224-35. doi: 10.1101/gad.1338905. PubMed PMID: 16166383; PubMed Central PMCID: PMC1221892.

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Wang J, Karnati PK, Takacs CM, Kowalski JC, Derbyshire KM. Chromosomal DNA transfer in Mycobacterium smegmatis is mechanistically different from classical Hfr chromosomal DNA transfer. Mol Microbiol. 2005 Oct;58(1):280-8. doi: 10.1111/j.1365-2958.2005.04824.x. PubMed PMID: 16164565; NIHMSID:NIHMS451360.

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Mo Y, Quanquin NM, Vecino WH, Ranganathan UD, Tesfa L, Bourn W, Derbyshire KM, Letvin NL, Jacobs WR Jr, Fennelly GJ. Genetic alteration of Mycobacterium smegmatis to improve mycobacterium-mediated transfer of plasmid DNA into mammalian cells and DNA immunization. Infect Immun. 2007 Oct;75(10):4804-16. doi: 10.1128/IAI.01877-06. Epub 2007 Jul 30. PubMed PMID: 17664267; PubMed Central PMCID: PMC2044538.

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Coros A, DeConno E, Derbyshire KM. IS6110, a Mycobacterium tuberculosis complex-specific insertion sequence, is also present in the genome of Mycobacterium smegmatis, suggestive of lateral gene transfer among mycobacterial species. J Bacteriol. 2008 May;190(9):3408-10. doi: 10.1128/JB.00009-08. Epub 2008 Mar 7. PubMed PMID: 18326566; PubMed Central PMCID: PMC2347380.

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Coros A, Callahan B, Battaglioli E, Derbyshire KM. The specialized secretory apparatus ESX-1 is essential for DNA transfer in Mycobacterium smegmatis. Mol Microbiol. 2008 Aug;69(4):794-808. doi: 10.1111/j.1365-2958.2008.06299.x. Epub 2008 Jun 28. PubMed PMID: 18554329; PubMed Central PMCID: PMC2562793.

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Nguyen KT, Piastro K, Derbyshire KM. LpqM, a mycobacterial lipoprotein-metalloproteinase, is required for conjugal DNA transfer in Mycobacterium smegmatis. J Bacteriol. 2009 Apr;191(8):2721-7. doi: 10.1128/JB.00024-09. Epub 2009 Feb 20. PubMed PMID: 19233923; PubMed Central PMCID: PMC2668431.

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Bitter W, Houben EN, Bottai D, Brodin P, Brown EJ, Cox JS, Derbyshire K, Fortune SM, Gao LY, Liu J, Gey van Pittius NC, Pym AS, Rubin EJ, Sherman DR, Cole ST, Brosch R. Systematic genetic nomenclature for type VII secretion systems. PLoS Pathog. 2009 Oct;5(10):e1000507. doi: 10.1371/journal.ppat.1000507. Epub 2009 Oct 30. PubMed PMID: 19876390; PubMed Central PMCID: PMC2763215.

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Callahan B, Nguyen K, Collins A, Valdes K, Caplow M, Crossman DK, Steyn AJ, Eisele L, Derbyshire KM. Conservation of structure and protein-protein interactions mediated by the secreted mycobacterial proteins EsxA, EsxB, and EspA. J Bacteriol. 2010 Jan;192(1):326-35. doi: 10.1128/JB.01032-09. PubMed PMID: 19854905; PubMed Central PMCID: PMC2798242.

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Nguyen KT, Piastro K, Gray TA, Derbyshire KM. Mycobacterial biofilms facilitate horizontal DNA transfer between strains of Mycobacterium smegmatis. J Bacteriol. 2010 Oct;192(19):5134-42. doi: 10.1128/JB.00650-10. Epub 2010 Jul 30. PubMed PMID: 20675473; PubMed Central PMCID: PMC2944546.

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Javid B, Derbyshire KM. Nanotubes: shaking hands, talking, or sharing?. Front Microbiol. 2011;2:95. doi: 10.3389/fmicb.2011.00095. eCollection 2011. PubMed PMID: 21833333; PubMed Central PMCID: PMC3153053.

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Wirth SE, Krywy JA, Aldridge BB, Fortune SM, Fernandez-Suarez M, Gray TA, Derbyshire KM. Polar assembly and scaffolding proteins of the virulence-associated ESX-1 secretory apparatus in mycobacteria. Mol Microbiol. 2012 Feb;83(3):654-64. doi: 10.1111/j.1365-2958.2011.07958.x. Epub 2012 Jan 11. PubMed PMID: 22233444; PubMed Central PMCID: PMC3277861.

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Gray TA, Palumbo MJ, Derbyshire KM. Draft Genome Sequence of MKD8, a Conjugal Recipient Mycobacterium smegmatis Strain. Genome Announc. 2013 Apr 25;1(2):e0014813. doi: 10.1128/genomeA.00148-13. PubMed PMID: 23618714; PubMed Central PMCID: PMC3636542.

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Gray TA, Krywy JA, Harold J, Palumbo MJ, Derbyshire KM. Distributive conjugal transfer in mycobacteria generates progeny with meiotic-like genome-wide mosaicism, allowing mapping of a mating identity locus. PLoS Biol. 2013 Jul;11(7):e1001602. doi: 10.1371/journal.pbio.1001602. Epub 2013 Jul 9. PubMed PMID: 23874149; PubMed Central PMCID: PMC3706393.

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Derbyshire KM, Gray TA. Distributive Conjugal Transfer: New Insights into Horizontal Gene Transfer and Genetic Exchange in Mycobacteria. Microbiol Spectr. 2014;2(1). doi: 10.1128/microbiolspec.MGM2-0022-2013. PubMed PMID: 25505644; PubMed Central PMCID: PMC4259119.

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Shell SS, Wang J, Lapierre P, Mir M, Chase MR, Pyle MM, Gawande R, Ahmad R, Sarracino DA, Ioerger TR, Fortune SM, Derbyshire KM, Wade JT, Gray TA. Leaderless Transcripts and Small Proteins Are Common Features of the Mycobacterial Translational Landscape. PLoS Genet. 2015 Nov;11(11):e1005641. doi: 10.1371/journal.pgen.1005641. eCollection 2015 Nov. PubMed PMID: 26536359; PubMed Central PMCID: PMC4633059.

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Gray TA, Clark RR, Boucher N, Lapierre P, Smith C, Derbyshire KM. Intercellular communication and conjugation are mediated by ESX secretion systems in mycobacteria. Science. 2016 Oct 21;354(6310):347-350. doi: 10.1126/science.aag0828. PubMed PMID: 27846571; PubMed Central PMCID: PMC8324006.

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Yang Y, Thomas J, Li Y, Vilchèze C, Derbyshire KM, Jacobs WR Jr, Ojha AK. Defining a temporal order of genetic requirements for development of mycobacterial biofilms. Mol Microbiol. 2017 Sep;105(5):794-809. doi: 10.1111/mmi.13734. Epub 2017 Jul 7. PubMed PMID: 28628249; PubMed Central PMCID: PMC5607029.

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Judd J, Boucher N, Van Roey E, Gray TA, Derbyshire KM. Application of Distributive Conjugal DNA Transfer in Mycobacterium smegmatis To Establish a Genome-Wide Synthetic Genetic Array. J Bacteriol. 2017 Oct 15;199(20). doi: 10.1128/JB.00410-17. Print 2017 Oct 15. PubMed PMID: 28784812; PubMed Central PMCID: PMC5637176.

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Gray TA, Derbyshire KM. Blending genomes: distributive conjugal transfer in mycobacteria, a sexier form of HGT. Mol Microbiol. 2018 Jun;108(6):601-613. doi: 10.1111/mmi.13971. Epub 2018 May 11. Review. PubMed PMID: 29669186; PubMed Central PMCID: PMC5997560.

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Clark RR, Judd J, Lasek-Nesselquist E, Montgomery SA, Hoffmann JG, Derbyshire KM, Gray TA. Direct cell-cell contact activates SigM to express the ESX-4 secretion system in Mycobacterium smegmatis. Proc Natl Acad Sci U S A. 2018 Jul 10;115(28):E6595-E6603. doi: 10.1073/pnas.1804227115. Epub 2018 Jun 25. PubMed PMID: 29941598; PubMed Central PMCID: PMC6048512.

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Li Y, Sharma MR, Koripella RK, Yang Y, Kaushal PS, Lin Q, Wade JT, Gray TA, Derbyshire KM, Agrawal RK, Ojha AK. Zinc depletion induces ribosome hibernation in mycobacteria. Proc Natl Acad Sci U S A. 2018 Aug 7;115(32):8191-8196. doi: 10.1073/pnas.1804555115. Epub 2018 Jul 23. PubMed PMID: 30038002; PubMed Central PMCID: PMC6094098.

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Canestrari JG, Lasek-Nesselquist E, Upadhyay A, Rofaeil M, Champion MM, Wade JT, Derbyshire KM, Gray TA. Polycysteine-encoding leaderless short ORFs function as cysteine-responsive attenuators of operonic gene expression in mycobacteria. Mol Microbiol. 2020 Jul;114(1):93-108. doi: 10.1111/mmi.14498. Epub 2020 Apr 9. PubMed PMID: 32181921; PubMed Central PMCID: PMC8764745.