Construction of a large signature-tagged mini-Tn5 transposon library and its application to mutagenesis of Sinorhizobium meliloti

Pobigaylo N, Wetter D, Szymczak S, Schiller U, Kurtz S, Meyer F, Nattkemper TW, Becker A (2006)

Zeitschriftenaufsatz | Veröffentlicht | Englisch
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Pobigaylo, N; Wetter, D; Szymczak, S; Schiller, U; Kurtz, S; Meyer, F; Nattkemper, Tim WilhelmUniBi ; Becker, A
Abstract / Bemerkung
Sinorhizobium meliloti genome sequence determination has provided the basis for different approaches of functional genomics for this symbiotic nitrogen-fixing alpha-proteobacterium. One of these approaches is gene disruption with subsequent analysis of mutant phenotypes. This method is efficient for single genes; however, it is laborious and time-consuming if it is used on a large scale. Here, we used a signature-tagged transposon mutagenesis method that allowed analysis of the survival and competitiveness of many mutants in a single experiment. A novel set of signature tags characterized by similar melting temperatures and G+C contents of the tag sequences was developed. The efficiencies of amplification of all tags were expected to be similar. Thus, no preselection of the tags was necessary to create a library of 412 signature-tagged transposons. To achieve high specificity of tag detection, each transposon was bar coded by two signature tags. In order to generate defined, nonredundant sets of signature-tagged S. meliloti mutants for subsequent experiments, 12,000 mutants were constructed, and insertion sites for more than 5,000 mutants were determined. One set consisting of 378 mutants was used in a validation experiment to identify mutants showing altered growth patterns.
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Pobigaylo N, Wetter D, Szymczak S, et al. Construction of a large signature-tagged mini-Tn5 transposon library and its application to mutagenesis of Sinorhizobium meliloti. APPLIED AND ENVIRONMENTAL MICROBIOLOGY. 2006;72(6):4329-4337.
Pobigaylo, N., Wetter, D., Szymczak, S., Schiller, U., Kurtz, S., Meyer, F., Nattkemper, T. W., et al. (2006). Construction of a large signature-tagged mini-Tn5 transposon library and its application to mutagenesis of Sinorhizobium meliloti. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 72(6), 4329-4337.
Pobigaylo, N, Wetter, D, Szymczak, S, Schiller, U, Kurtz, S, Meyer, F, Nattkemper, Tim Wilhelm, and Becker, A. 2006. “Construction of a large signature-tagged mini-Tn5 transposon library and its application to mutagenesis of Sinorhizobium meliloti”. APPLIED AND ENVIRONMENTAL MICROBIOLOGY 72 (6): 4329-4337.
Pobigaylo, N., Wetter, D., Szymczak, S., Schiller, U., Kurtz, S., Meyer, F., Nattkemper, T. W., and Becker, A. (2006). Construction of a large signature-tagged mini-Tn5 transposon library and its application to mutagenesis of Sinorhizobium meliloti. APPLIED AND ENVIRONMENTAL MICROBIOLOGY 72, 4329-4337.
Pobigaylo, N., et al., 2006. Construction of a large signature-tagged mini-Tn5 transposon library and its application to mutagenesis of Sinorhizobium meliloti. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 72(6), p 4329-4337.
N. Pobigaylo, et al., “Construction of a large signature-tagged mini-Tn5 transposon library and its application to mutagenesis of Sinorhizobium meliloti”, APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol. 72, 2006, pp. 4329-4337.
Pobigaylo, N., Wetter, D., Szymczak, S., Schiller, U., Kurtz, S., Meyer, F., Nattkemper, T.W., Becker, A.: Construction of a large signature-tagged mini-Tn5 transposon library and its application to mutagenesis of Sinorhizobium meliloti. APPLIED AND ENVIRONMENTAL MICROBIOLOGY. 72, 4329-4337 (2006).
Pobigaylo, N, Wetter, D, Szymczak, S, Schiller, U, Kurtz, S, Meyer, F, Nattkemper, Tim Wilhelm, and Becker, A. “Construction of a large signature-tagged mini-Tn5 transposon library and its application to mutagenesis of Sinorhizobium meliloti”. APPLIED AND ENVIRONMENTAL MICROBIOLOGY 72.6 (2006): 4329-4337.

55 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Identification of in vivo Essential Genes of Vibrio vulnificus for Establishment of Wound Infection by Signature-Tagged Mutagenesis.
Yamazaki K, Kashimoto T, Morita M, Kado T, Matsuda K, Yamasaki M, Ueno S., Front Microbiol 10(), 2019
PMID: 30774628
The Nitrate Assimilatory Pathway in Sinorhizobium meliloti: Contribution to NO Production.
Ruiz B, Le Scornet A, Sauviac L, Rémy A, Bruand C, Meilhoc E., Front Microbiol 10(), 2019
PMID: 31333627
Overexpression of the periplasmic nitrate reductase supports anaerobic growth by Ensifer meliloti.
Torres MJ, Avila S, Bedmar EJ, Delgado MJ., FEMS Microbiol Lett 365(7), 2018
PMID: 29462313
An sRNA and Cold Shock Protein Homolog-Based Feedforward Loop Post-transcriptionally Controls Cell Cycle Master Regulator CtrA.
Robledo M, Schlüter JP, Loehr LO, Linne U, Albaum SP, Jiménez-Zurdo JI, Becker A., Front Microbiol 9(), 2018
PMID: 29740411
Comprehensive Functional Analysis of the Enterococcus faecalis Core Genome Using an Ordered, Sequence-Defined Collection of Insertional Mutations in Strain OG1RF.
Dale JL, Beckman KB, Willett JLE, Nilson JL, Palani NP, Baller JA, Hauge A, Gohl DM, Erickson R, Manias DA, Sadowsky MJ, Dunny GM., mSystems 3(5), 2018
PMID: 30225373
Specificity traits consistent with legume-rhizobia coevolution displayed by Ensifer meliloti rhizosphere colonization.
Salas ME, Lozano MJ, López JL, Draghi WO, Serrania J, Torres Tejerizo GA, Albicoro FJ, Nilsson JF, Pistorio M, Del Papa MF, Parisi G, Becker A, Lagares A., Environ Microbiol 19(9), 2017
PMID: 28618121
Construction and pilot screening of a signature-tagged mutant library of Sinorhizobium fredii.
Wang D, Wang YC, Wu LJ, Liu JX, Zhang P, Jiao J, Yan H, Liu T, Tian CF, Chen WX., Arch Microbiol 198(2), 2016
PMID: 26472206
Arabinose and protocatechuate catabolism genes are important for growth of Rhizobium leguminosarum biovar viciae in the pea rhizosphere.
Garcia-Fraile P, Seaman JC, Karunakaran R, Edwards A, Poole PS, Downie JA., Plant Soil 390(1-2), 2015
PMID: 26166901
Anoxic growth of Ensifer meliloti 1021 by N2O-reduction, a potential mitigation strategy.
Bueno E, Mania D, Frostegard Ǻ, Bedmar EJ, Bakken LR, Delgado MJ., Front Microbiol 6(), 2015
PMID: 26074913
Sinorhizobium meliloti Controls Nitric Oxide-Mediated Post-Translational Modification of a Medicago truncatula Nodule Protein.
Blanquet P, Silva L, Catrice O, Bruand C, Carvalho H, Meilhoc E., Mol Plant Microbe Interact 28(12), 2015
PMID: 26422404
RNase E affects the expression of the acyl-homoserine lactone synthase gene sinI in Sinorhizobium meliloti.
Baumgardt K, Charoenpanich P, McIntosh M, Schikora A, Stein E, Thalmann S, Kogel KH, Klug G, Becker A, Evguenieva-Hackenberg E., J Bacteriol 196(7), 2014
PMID: 24488310
The Sinorhizobium meliloti EmrAB efflux system is regulated by flavonoids through a TetR-like regulator (EmrR).
Rossbach S, Kunze K, Albert S, Zehner S, Göttfert M., Mol Plant Microbe Interact 27(4), 2014
PMID: 24224534
Genomic analysis of cyclic-di-GMP-related genes in rhizobial type strains and functional analysis in Rhizobium etli.
Gao S, Romdhane SB, Beullens S, Kaever V, Lambrichts I, Fauvart M, Michiels J., Appl Microbiol Biotechnol 98(10), 2014
PMID: 24728599
Genetic basis for denitrification in Ensifer meliloti.
Torres MJ, Rubia MI, de la Peña TC, Pueyo JJ, Bedmar EJ, Delgado MJ., BMC Microbiol 14(), 2014
PMID: 24888981
Riboregulation in plant-associated α-proteobacteria.
Becker A, Overlöper A, Schlüter JP, Reinkensmeier J, Robledo M, Giegerich R, Narberhaus F, Evguenieva-Hackenberg E., RNA Biol 11(5), 2014
PMID: 25003187
A vapBC-type toxin-antitoxin module of Sinorhizobium meliloti influences symbiotic efficiency and nodule senescence of Medicago sativa.
Lipuma J, Cinege G, Bodogai M, Oláh B, Kiers A, Endre G, Dupont L, Dusha I., Environ Microbiol 16(12), 2014
PMID: 25156344
The DivJ, CbrA and PleC system controls DivK phosphorylation and symbiosis in Sinorhizobium meliloti.
Pini F, Frage B, Ferri L, De Nisco NJ, Mohapatra SS, Taddei L, Fioravanti A, Dewitte F, Galardini M, Brilli M, Villeret V, Bazzicalupo M, Mengoni A, Walker GC, Becker A, Biondi EG., Mol Microbiol 90(1), 2013
PMID: 23909720
ExpR is not required for swarming but promotes sliding in Sinorhizobium meliloti.
Nogales J, Bernabéu-Roda L, Cuéllar V, Soto MJ., J Bacteriol 194(8), 2012
PMID: 22328673
A comparative genomics screen identifies a Sinorhizobium meliloti 1021 sodM-like gene strongly expressed within host plant nodules.
Queiroux C, Washburn BK, Davis OM, Stewart J, Brewer TE, Lyons MR, Jones KM., BMC Microbiol 12(), 2012
PMID: 22587634
Sinorhizobium meliloti sigma factors RpoE1 and RpoE4 are activated in stationary phase in response to sulfite.
Bastiat B, Sauviac L, Picheraux C, Rossignol M, Bruand C., PLoS One 7(11), 2012
PMID: 23226379
Both plant and bacterial nitrate reductases contribute to nitric oxide production in Medicago truncatula nitrogen-fixing nodules.
Horchani F, Prévot M, Boscari A, Evangelisti E, Meilhoc E, Bruand C, Raymond P, Boncompagni E, Aschi-Smiti S, Puppo A, Brouquisse R., Plant Physiol 155(2), 2011
PMID: 21139086
Identification of Mesorhizobium loti genes relevant to symbiosis by using signature-tagged mutants.
Borjigin N, Furukawa K, Shimoda Y, Tabata S, Sato S, Eda S, Minamisawa K, Mitsui H., Microbes Environ 26(2), 2011
PMID: 21502733
The RpiR-like repressor IolR regulates inositol catabolism in Sinorhizobium meliloti.
Kohler PR, Choong EL, Rossbach S., J Bacteriol 193(19), 2011
PMID: 21784930
Strategies for bacterial tagging and gene expression in plant-host colonization studies
Ramos HJO, Yates MG, Pedrosa FO, Souza EM., Soil Biol Biochem 43(8), 2011
PMID: IND44599181
Absence of functional TolC protein causes increased stress response gene expression in Sinorhizobium meliloti.
Santos MR, Cosme AM, Becker JD, Medeiros JM, Mata MF, Moreira LM., BMC Microbiol 10(), 2010
PMID: 20573193
Inositol catabolism, a key pathway in sinorhizobium meliloti for competitive host nodulation.
Kohler PR, Zheng JY, Schoffers E, Rossbach S., Appl Environ Microbiol 76(24), 2010
PMID: 20971862
Role of symbiotic auxotrophy in the Rhizobium-legume symbioses.
Prell J, Bourdès A, Kumar S, Lodwig E, Hosie A, Kinghorn S, White J, Poole P., PLoS One 5(11), 2010
PMID: 21085630
A portal for rhizobial genomes: RhizoGATE integrates a Sinorhizobium meliloti genome annotation update with postgenome data.
Becker A, Barnett MJ, Capela D, Dondrup M, Kamp PB, Krol E, Linke B, Rüberg S, Runte K, Schroeder BK, Weidner S, Yurgel SN, Batut J, Long SR, Pühler A, Goesmann A., J Biotechnol 140(1-2), 2009
PMID: 19103235
The Symbiosis Interactome: a computational approach reveals novel components, functional interactions and modules in Sinorhizobium meliloti.
Rodriguez-Llorente I, Caviedes MA, Dary M, Palomares AJ, Cánovas FM, Peregrín-Alvarez JM., BMC Syst Biol 3(), 2009
PMID: 19531251
RNase J is involved in the 5'-end maturation of 16S rRNA and 23S rRNA in Sinorhizobium meliloti.
Madhugiri R, Evguenieva-Hackenberg E., FEBS Lett 583(14), 2009
PMID: 19540834
Identification of genes relevant to symbiosis and competitiveness in Sinorhizobium meliloti using signature-tagged mutants.
Pobigaylo N, Szymczak S, Nattkemper TW, Becker A., Mol Plant Microbe Interact 21(2), 2008
PMID: 18184066
Efficient computation of absent words in genomic sequences.
Herold J, Kurtz S, Giegerich R., BMC Bioinformatics 9(), 2008
PMID: 18366790
Response of Sinorhizobium meliloti to elevated concentrations of cadmium and zinc.
Rossbach S, Mai DJ, Carter EL, Sauviac L, Capela D, Bruand C, de Bruijn FJ., Appl Environ Microbiol 74(13), 2008
PMID: 18469129
Mutational analysis of the Sinorhizobium meliloti short-chain dehydrogenase/reductase family reveals substantial contribution to symbiosis and catabolic diversity.
Jacob AI, Adham SA, Capstick DS, Clark SR, Spence T, Charles TC., Mol Plant Microbe Interact 21(7), 2008
PMID: 18533838
Construction of signature-tagged mutant library in Mesorhizobium loti as a powerful tool for functional genomics.
Shimoda Y, Mitsui H, Kamimatsuse H, Minamisawa K, Nishiyama E, Ohtsubo Y, Nagata Y, Tsuda M, Shinpo S, Watanabe A, Kohara M, Yamada M, Nakamura Y, Tabata S, Sato S., DNA Res 15(5), 2008
PMID: 18658183
Auxotrophy accounts for nodulation defect of most Sinorhizobium meliloti mutants in the branched-chain amino acid biosynthesis pathway.
de las Nieves Peltzer M, Roques N, Poinsot V, Aguilar OM, Batut J, Capela D., Mol Plant Microbe Interact 21(9), 2008
PMID: 18700827
Sinorhizobium meliloti regulator MucR couples exopolysaccharide synthesis and motility.
Bahlawane C, McIntosh M, Krol E, Becker A., Mol Plant Microbe Interact 21(11), 2008
PMID: 18842098
Genetic and computational identification of a conserved bacterial metabolic module.
Boutte CC, Srinivasan BS, Flannick JA, Novak AF, Martens AT, Batzoglou S, Viollier PH, Crosson S., PLoS Genet 4(12), 2008
PMID: 19096521
Rhizobium-initiated rice growth inhibition caused by nitric oxide accumulation.
Perrine-Walker FM, Gartner E, Hocart CH, Becker A, Rolfe BG., Mol Plant Microbe Interact 20(3), 2007
PMID: 17378431
Genomes of the symbiotic nitrogen-fixing bacteria of legumes.
MacLean AM, Finan TM, Sadowsky MJ., Plant Physiol 144(2), 2007
PMID: 17556525
An integrated approach to functional genomics: construction of a novel reporter gene fusion library for Sinorhizobium meliloti.
Cowie A, Cheng J, Sibley CD, Fong Y, Zaheer R, Patten CL, Morton RM, Golding GB, Finan TM., Appl Environ Microbiol 72(11), 2006
PMID: 16963549

45 References

Daten bereitgestellt von Europe PubMed Central.

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ., Nucleic Acids Res. 25(17), 1997
PMID: 9254694
A dual-genome Symbiosis Chip for coordinate study of signal exchange and development in a prokaryote-host interaction.
Barnett MJ, Toman CJ, Fisher RF, Long SR., Proc. Natl. Acad. Sci. U.S.A. 101(47), 2004
PMID: 15542588
Comprehensive metabolite profiling of Sinorhizobium meliloti using gas chromatography-mass spectrometry.
Barsch A, Patschkowski T, Niehaus K., Funct. Integr. Genomics 4(4), 2004
PMID: 15372312
Global changes in gene expression in Sinorhizobium meliloti 1021 under microoxic and symbiotic conditions.
Becker A, Berges H, Krol E, Bruand C, Ruberg S, Capela D, Lauber E, Meilhoc E, Ampe F, de Bruijn FJ, Fourment J, Francez-Charlot A, Kahn D, Kuster H, Liebe C, Puhler A, Weidner S, Batut J., Mol. Plant Microbe Interact. 17(3), 2004
PMID: 15000396

Analysis of the chromosome sequence of the legume symbiont Sinorhizobium meliloti strain 1021.
Capela D, Barloy-Hubler F, Gouzy J, Bothe G, Ampe F, Batut J, Boistard P, Becker A, Boutry M, Cadieu E, Dreano S, Gloux S, Godrie T, Goffeau A, Kahn D, Kiss E, Lelaure V, Masuy D, Pohl T, Portetelle D, Puhler A, Purnelle B, Ramsperger U, Renard C, Thebault P, Vandenbol M, Weidner S, Galibert F., Proc. Natl. Acad. Sci. U.S.A. 98(17), 2001
PMID: 11481430

In vivo genetic analysis of bacterial virulence.
Chiang SL, Mekalanos JJ, Holden DW., Annu. Rev. Microbiol. 53(), 1999
PMID: 10547688
Lipopolysaccharide mutants of Rhizobium meliloti are not defective in symbiosis.
Clover RH, Kieber J, Signer ER., J. Bacteriol. 171(7), 1989
PMID: 2738026
A global analysis of protein expression profiles in Sinorhizobium meliloti: discovery of new genes for nodule occupancy and stress adaptation.
Djordjevic MA, Chen HC, Natera S, Van Noorden G, Menzel C, Taylor S, Renard C, Geiger O, Weiller GF; Sinorhizobium DNA Sequencing Consortium., Mol. Plant Microbe Interact. 16(6), 2003
PMID: 12795377

The composite genome of the legume symbiont Sinorhizobium meliloti.
Galibert F, Finan TM, Long SR, Puhler A, Abola P, Ampe F, Barloy-Hubler F, Barnett MJ, Becker A, Boistard P, Bothe G, Boutry M, Bowser L, Buhrmester J, Cadieu E, Capela D, Chain P, Cowie A, Davis RW, Dreano S, Federspiel NA, Fisher RF, Gloux S, Godrie T, Goffeau A, Golding B, Gouzy J, Gurjal M, Hernandez-Lucas I, Hong A, Huizar L, Hyman RW, Jones T, Kahn D, Kahn ML, Kalman S, Keating DH, Kiss E, Komp C, Lelaure V, Masuy D, Palm C, Peck MC, Pohl TM, Portetelle D, Purnelle B, Ramsperger U, Surzycki R, Thebault P, Vandenbol M, Vorholter FJ, Weidner S, Wells DH, Wong K, Yeh KC, Batut J., Science 293(5530), 2001
PMID: 11474104
In vivo analysis of the overlapping functions of DnaK and trigger factor.
Genevaux P, Keppel F, Schwager F, Langendijk-Genevaux PS, Hartl FU, Georgopoulos C., EMBO Rep. 5(2), 2004
PMID: 14726952
Simultaneous identification of bacterial virulence genes by negative selection.
Hensel M, Shea JE, Gleeson C, Jones MD, Dalton E, Holden DW., Science 269(5222), 1995
PMID: 7618105
High efficiency transformation of Escherichia coli with plasmids.
Inoue H, Nojima H, Okayama H., Gene 96(1), 1990
PMID: 2265755

Application of high-density array-based signature-tagged mutagenesis to discover novel Yersinia virulence-associated genes.
Karlyshev AV, Oyston PC, Williams K, Clark GC, Titball RW, Winzeler EA, Wren BW., Infect. Immun. 69(12), 2001
PMID: 11705963


Use of signature-tagged mutagenesis in pathogenesis studies.
Mecsas J., Curr. Opin. Microbiol. 5(1), 2002
PMID: 11834366
GenDB--an open source genome annotation system for prokaryote genomes.
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A., Nucleic Acids Res. 31(8), 2003
PMID: 12682369
Constructs for insertional mutagenesis, transcriptional signal localization and gene regulation studies in root nodule and other bacteria.
Reeve WG, Tiwari RP, Worsley PS, Dilworth MJ, Glenn AR, Howieson JG., Microbiology (Reading, Engl.) 145 ( Pt 6)(), 1999
PMID: 10411257
Construction and validation of a Sinorhizobium meliloti whole genome DNA microarray: genome-wide profiling of osmoadaptive gene expression.
Ruberg S, Tian ZX, Krol E, Linke B, Meyer F, Wang Y, Puhler A, Weidner S, Becker A., J. Biotechnol. 106(2-3), 2003
PMID: 14651866

Development of a functional genomics platform for Sinorhizobium meliloti: construction of an ORFeome.
Schroeder BK, House BL, Mortimer MW, Yurgel SN, Maloney SC, Ward KL, Kahn ML., Appl. Environ. Microbiol. 71(10), 2005
PMID: 16204497
Signature-tagged mutagenesis in the identification of virulence genes in pathogens.
Shea JE, Santangelo JD, Feldman RG., Curr. Opin. Microbiol. 3(5), 2000
PMID: 11050441
Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy.
Shoemaker DD, Lashkari DA, Morris D, Mittmann M, Davis RW., Nat. Genet. 14(4), 1996
PMID: 8944025

A cysG mutant strain of Rhizobium etli pleiotropically defective in sulfate and nitrate assimilation.
Tate R, Riccio A, Iaccarino M, Patriarca EJ., J. Bacteriol. 179(23), 1997
PMID: 9393698


Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis.
Winzeler EA, Shoemaker DD, Astromoff A, Liang H, Anderson K, Andre B, Bangham R, Benito R, Boeke JD, Bussey H, Chu AM, Connelly C, Davis K, Dietrich F, Dow SW, El Bakkoury M, Foury F, Friend SH, Gentalen E, Giaever G, Hegemann JH, Jones T, Laub M, Liao H, Liebundguth N, Lockhart DJ, Lucau-Danila A, Lussier M, M'Rabet N, Menard P, Mittmann M, Pai C, Rebischung C, Revuelta JL, Riles L, Roberts CJ, Ross-MacDonald P, Scherens B, Snyder M, Sookhai-Mahadeo S, Storms RK, Veronneau S, Voet M, Volckaert G, Ward TR, Wysocki R, Yen GS, Yu K, Zimmermann K, Philippsen P, Johnston M, Davis RW., Science 285(5429), 1999
PMID: 10436161
Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation.
Yang YH, Dudoit S, Luu P, Lin DM, Peng V, Ngai J, Speed TP., Nucleic Acids Res. 30(4), 2002
PMID: 11842121

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