Projects

PSEUDOMONAS SYSTEMS BIOLOGY Appropriated (D)   Accession Number: 423000

Publications (Clicking on the reprint icon will take you to the publication reprint.)

CrcZ and CrcX regulate carbon utilization in Pseudomonas syringae pathovar tomato strain DC3000 - (Peer Reviewed Journal)

Filiatrault, M.J., Stodghill, P., Wilson, J.M., Butcher, B.G., Chen, H., Meyers, C.R., Cartinhour, S.W. 2013. CrcZ and CrcX regulate carbon utilization in Pseudomonas syringae pathovar tomato strain DC3000. RNA Biology. 10(2):243-253.

Substrate and target sequence lengths influence RecTEPsy recombineering efficiency in Pseudomonas syringae - (Peer Reviewed Journal) - (23-Oct-12)

Genome-wide identification of transcriptional start sites in the plant pathogen Pseudomonas syringae pv. tomato str. DC3000 - (Peer Reviewed Journal)

Filiatrault, M.J., Stodghill, P., Myers, C.R., Bronstein, P.A., Butcher, B.G., Lam, H., Grills, G., Schweitzer, P., Wang, W., Schneider, D.J., Cartinhour, S.W. 2011. Genome-wide identification of transcriptional start sites in the plant pathogen Pseudomonas syringae pv. tomato str. DC3000. PLoS One. 6(12). Available: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0029335.

HOPX1 Ea (Eop3) in Erwinia Amylovora functions as an avirulence gene in apple and is regulated by HRPL - (Peer Reviewed Journal)

Bocsanczy, A., Schneider, D.J., Declerck, G.A., Cartinhour, S.W., Beer, S.V. 2011. HOPX1 Ea (Eop3) in Erwinia Amylovora functions as an avirulence gene in apple and is regulated by HRPL. Journal of Bacteriology. 194:553-560.

An ECF sigma factor mediated cell surface signaling system in Pseudomonas syringae pv. tomato DC3000 regulates gene expression in response to heterologous siderophores - (Peer Reviewed Journal)

Swingle, B.M., Markel, E.J., Maciak, C.L., Butcher, B., Myers, C., Stodghill, P., Cartinhour, S.W., Bao, Z. 2011. An ECF sigma factor mediated cell surface signaling system in Pseudomonas syringae pv. tomato DC3000 regulates gene expression in response to heterologous siderophores. Journal of Bacteriology. 193:5775-5783.

The small RNA transcriptome of Pseudomonas syringae pathovar tomato DC3000 - (Abstract Only)

Filiatrault, M.J., Moll, S., Bao, Z., Maciak, C.L., Chen, H., Myers, C.R., Stodghill, P., Cartinhour, S.W. 2011. The small RNA transcriptome of Pseudomonas syringae pathovar tomato DC3000. International Conference on Pseudomonas syringae Pathovars. 13:20.

Characterization of the Fur regulon in Pseudomonas syringae pv. tomato DC3000 - (Peer Reviewed Journal)

Butcher, B.G., Bronstein, P., Myers, C., Stodghill, P., Bolton, J.J., Markel, E.J., Filiatrault, M.J., Swingle, B.M., Gaballa, A., Helmann, J.D., Schneider, D.J., Cartinhour, S.W. 2011. Characterization of the Fur regulon in Pseudomonas syringae pv. tomato DC3000. Journal of Bacteriology. 193(18):4598-4611. Available: http://www.ncbi.nlm.nih.gov/pubmed/21784947.

Global survey of Fur binding refines the iron responsive regulon of Pseudomonas syringae - (Abstract Only)

Bronstein, P., Butcher, B.G., Myers, C.R., Stodghill, P., Swingle, B.M., Cartinhour, S.W. 2010. Global survey of Fur binding refines the iron responsive regulon of Pseudomonas syringae [abstract]. p. 31.

Construction of an rsmX co-variance model and identification of five rsmX-like ncRNAs in Pseudomonas syringae pv. tomato DC3000 - (Peer Reviewed Journal)

Moll, S., Schneider, D.J., Stodghill, P., Myers, C.R., Cartinhour, S.W., Filiatrault, M.J. 2010. Construction of an rsmX co-variance model and identification of five rsmX-like ncRNAs in Pseudomonas syringae pv. tomato DC3000. RNA Biology. 7(5):1-10.

Analyzing the transcriptome of Pseudomonas syringae using high-throughput sequencing methodologies - (Abstract Only)

Filiatrault, M.J., Bronstein, P., Stodghill, P., Moll, S., Schneider, D.J., Cartinhour, S.W. 2010. Analyzing the transcriptome of Pseudomonas syringae using high-throughput sequencing methodologies. Meeting Abstract. p. 31.

Recombineering using RecET from Pseudomonas syringae - (Abstract Only)

Swingle, B.M., Bao, Z., Markel, E.J., Cartinhour, S.W. 2010. Recombineering using RecET from Pseudomonas syringae. Molecular Genetics of Bacteria and Phage. 61/34.

Oligonucleotide recombination: a hidden treasure - (Peer Reviewed Journal)

Swingle, B.M., Markel, E.J., Cartinhour, S.W. 2010. Oligonucleotide recombination: a hidden treasure. Bioengineered Bugs. 1(4):1-4.

Transcriptome analysis of Pseudomonas syringae identifies new genes, ncRNAs, and antisense activity - (Peer Reviewed Journal)

Filiatrault, M.J., Stodghill, P., Bronstein, P., Moll, S., Lindeberg, M., Grills, G., Schweitzer, P., Wang, W., Schroth, G., Luo, S., Khrebtukova, I., Thannhauser, T.W., Yang, Y., Butcher, B.G., Cartinhour, S.W., Schneider, D.J. 2010. Transcriptome analysis of Pseudomonas syringae identifies new genes, ncRNAs, and antisense activity. Journal of Bacteriology. 192(9):2359-2372.

Complete genome sequence of the plant pathogen Erwinia amylovora strain ATCC 49946 - (Peer Reviewed Journal)

Sebaihia, M., Bocsanczy, A.M., Biehl, B.S., Quail, M.A., Perna, N.T., Glasner, J.D., Declerck, G.A., Cartinhour, S.W., Schneider, D.J., Bentley, S.D., Parkhill, J., Beer, S.V. 2010. Complete genome sequence of the plant pathogen Erwinia amylovora strain ATCC 49946. Journal of Bacteriology. 192(7):2020-2021.

Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs - (Peer Reviewed Journal)

Oliver, H.F., Orsi, R.H., Ponnala, L., Keich, U., Wang, W., Sun, Q., Cartinhour, S.W., Filiatrault, M.J., Wiedmann, M., Boor, K.J. 2009. Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs. Biomed Central (BMC) Genomics. 10:641.

Oligonucleotide recombination in bacteria - (Abstract Only)

Swingle, B.M., Costantino, N., Court, D., Bubunenko, M.G., Cartinhour, S.W. 2009. Oligonucleotide recombination in bacteria. [abstract}. 17:28.

Oligo Recombination in Gram Negative Bacteria - (Abstract Only)

Swingle, B.M., Cartinhour, S.W., Court, D. 2009. Oligo Recombination in Gram Negative Bacteria. Molecular Genetics of Bacteria and Phage. p. 166.

Iron concentration limits growth rate and the expression of virulence factors in hrp-inducing minimal medium with Pseudomonas syringae - (Peer Reviewed Journal)

Kim, B., Park, J., Park, T., Bronstein, P., Schneider, D.J., Cartinhour, S.W., Shuler, M.L. 2009. Iron concentration limits growth rate and the expression of virulence factors in hrp-inducing minimal medium with Pseudomonas syringae. Applied and Environmental Microbiology. 25(9):2720-2726.

Investigating the role of two iron-regulated small RNAs of Pseudomonas syringae - (Abstract Only)

Bronstein, P., Filiatrault, M.J., Stodghill, P., Schneider, D.J., Cartinhour, S.W. 2009. Investigating the role of two iron-regulated small RNAs of Pseudomonas syringae. American Society for Microbiology. p. 20.

High-throughput identification of transcriptional start sites in Pseudomonas syringae - (Abstract Only)

Filiatrault, M.J., Stodghill, P., Wang, W., Schweitzer, P., Grills, G., Cartinhour, S.W., Schneider, D.J. 2009. High-throughput identification of transcriptional start sites in Pseudomonas syringae. American Society for Microbiology. p. 251.

Global transcriptional responses of Pseudomonas syringae DC3000 to changes in iron bioavailability in vitro - (Peer Reviewed Journal)

Bronstein, P., Filiatrault, M.J., Myers, C., Rutzke, M., Schneider, D.J., Cartinhour, S.W. 2008. Global transcriptional responses of Pseudomonas syringae DC3000 to changes in iron bioavailability in vitro. BMC Microbiology. 8:209.

Characterization of the PvdS-regulated promoter motif in Pseudomonas syringae pv. tomato DC3000 reveals regulon members and insights regarding PvdS function in other pseudomonads - (Peer Reviewed Journal)

Swingle, B.M., Thete, D., Moll, M., Myers, C., Schneider, D.J., Cartinhour, S.W. 2008. Characterization of the PvdS-regulated promoter motif in Pseudomonas syringae pv. tomato DC3000 reveals regulon members and insights regarding PvdS function in other pseudomonads. Molecular Microbiology. 68(4):871-889.

Identification and Characterization of iron-responsive regulatory elements in Pseudomonas syringae pv tomato DC3000 - (Abstract Only)

Bronstein, P., Filiatrault, M.J., Cartinhour, S.W. 2008. Identification and Characterization of iron-responsive regulatory elements in Pseudomonas syringae pv tomato DC3000. American Society for Microbiology Meeting.

Characterization of two small RNAs of Pseudomonas syringae DC3000 - (Abstract Only)

Filiatrault, M.J., Bronstein, P., Stodghill, P., Cartinhour, S.W. 2008. Characterization of two small RNAs of Pseudomonas syringae DC3000. American Society for Microbiology Meeting.

Extracytoplasmic Function (ECF) Sigma Factor Gene Regulation in Pseudomonas syringae: Integrated Molecular and Computational Characterization of PvdS-Regulated Promoters - (Abstract Only)

Swingle, B.M., Thete,, D., Moll, M., Myers,, C., Schneider, D.J., Cartinhour, S.W. 2007. Extracytoplasmic Function (ECF) Sigma Factor Gene Regulation in Pseudomonas syringae: Integrated Molecular and Computational Characterization of PvdS-Regulated Promoters. Molecular Genetics of Bacteria and Phage. p. 262.

Pyoverdine and beyond: PvdS dependent gene regulation in Pseudomonas syringae - (Abstract Only)

Swingle, B.M., Thete,, D., Moll, M., Myers,, C., Schneider, D.J., Cartinhour, S.W. Pyoverdine and beyond: PvdS dependent gene regulation in Pseudomonas syringae. American Society for Microbiology Conference. 159A:p. 90.

Shotgun Sequencing of the Pseudomonas syringae DC3000 Transcriptome - (Abstract Only)

Filiatrault, M.J., Bronstein, P., Stodghill, P., Declerck, G.A., Schneider, D.J., Cartinhour, S.W. 2007. Shotgun Sequencing of the Pseudomonas syringae DC3000 Transcriptome. American Society for Microbiology Conference. p. 20.

Global transcriptional responses of Pseudomonas syringae DC3000 to changes in iron bioavailability in vitro - (Abstract Only)

Bronstein, P., Filiatrault, M.J., Kim, B., Moll, M., Rutzke, M., Shuler, M., Schneider, D.J., Cartinhour, S.W. 2007. Global transcriptional responses of Pseudomonas syringae DC3000 to changes in iron bioavailability in vitro. American Society for Microbiology. p. 20.

Closing the circle on the discovery of genes encoding Hrp regulon members and type III secretion system effectors in the genomes of three model Pseudomonas syringae strains - (Review Article)

Lindeberg, M., Cartinhour, S.W., Myers, C., Schechter, L., Schneider, D.J., Collmer, A. 2006. Closing the circle on the discovery of genes encoding Hrp regulon members and type III secretion system effectors in the genomes of three model Pseudomonas syringae strains. Molecular Plant-Microbe Interactions. 19(11):1151-1158.

Bioinformatics-enabled identification of the HrpL regulon and type III secretion system effector proteins of Pseudomonas syringae pv. phaseolicola 1448A - (Peer Reviewed Journal)

Vencato, M., Tian, F., Alfano, J.R., Buell, C., Cartinhour, S.W., Declerck, G.A., Guttman, D.S., Stavrinides, J., Joardar, V., Lindeberg, M., Bronstein, P., Mansfield, J.W., Myers, C.R., Collmer, A., Schneider, D.J. 2006. Bioinformatics-enabled identification of the HrpL regulon and type III secretion system effector proteins of Pseudomonas syringae pv. phaseolicola 1448A. Molecular Plant-Microbe Interactions. 19(11):1193-1206.

WHOLE-GENOME EXPRESSION PROFILING DEFINES THE HRPL REGULON OF PSEUDOMONAS SYRINGAE PV. TOMATO DC3000, ALLOWS DE NOVO RECONSTRUCTION OF THE HRP CIS ELEMENT, AND IDENTIFIES NOVEL CO-REGULATED GENES - (Peer Reviewed Journal)

Fereirra, A.O., Myers, C.R., Gordon, J., Martin, G.B., Vencato, M., Collmer, A., Wehling, M.D., Alfano, J.R., Moreno-Hagelsieb, G., Lamboy, W.F., Declerck, G.A., Schneider, D.J., Cartinhour, S.W. 2006. Whole-genome expression profiling defines the hrpl regulon of pseudomonas syringae pv. tomato dc3000, allows de novo reconstruction of the hrp cis element, and identifies novel co-regulated genes. Molecular Plant-Microbe Interactions. 19(11):1167-1179.

IDENTIFICATION OF TWIN-ARGININE TRANSLOCATION SYSTEM IN PSEUDOMONAS SYRINGAE AND ITS CONTRIBUTION TO PATHOGENICITY AND FITNESS - (Peer Reviewed Journal)

Bronstein, P., Marrichi, M., Cartinhour, S.W., Schneider, D.J., Delisa, M.P. 2005. Identification of twin-arginine translocation system in pseudomonas syringae and its contribution to pathogenicity and fitness. Journal of Bacteriology. 187(24):8450-8461.

WHOLE GENOME SEQUENCE ANALYSIS OF PSEUDOMONAS SYRINGAE PV. PHASEOLICOLA 1448A REVEALS DIVERGENCE AMONG PATHOVARS IN GENES INVOLVED IN VIRULENCE AND TRANSPOSITION - (Peer Reviewed Journal)

Joardar, V., Lindeberg, M., Jackson, R.W., Fraser, C.M., Chatterjee, A.K., Cartinhour, S.W., Schneider, D.J., Mansfield, J., Collmer, A., Buell, C.R. 2005. Whole genome sequence analysis of pseudomonas syringae pv. phaseolicola 1448a reveals divergence among pathovars in genes involved in virulence and transposition. Journal of Bacteriology. 187:6488-6498.

COMPLETE GENOME SEQUENCE OF THE PLANT COMMENSAL PSEUDOMONAS FLUORESCENS PF-5: INSIGHTS INTO THE BIOLOGICAL CONTROL OF PLANT DISEASE - (Peer Reviewed Journal)

Paulsen, I.T., Press, C.M., Ravel, J., Kobayashi, D.Y., Myers, G., Mavrodi, D.V., Deboy, R.T., Seshadri, R., Ren, Q., Madupu, R., Dodson, R.J., Durkin, A.S., Brinkac, L.M., Daugherty, S.C., Sullivan, S.A., Rosovitz, M.J., Gwinn, M.L., Zhou, L., Schneider, D.J., Cartinhour, S.W., Nelson, W.C., Weidman, J., Watkins, K., Tran, K., Khouri, H., Pierson, E.A., Pierson, L.S., Thomashow, L.S., Loper, J.E. 2005. Complete genome sequence of the plant commensal pseudomonas fluorescens pf-5: insights into the biological control of plant disease. Nature Biotechnology. 23:873-878.

THE COMPLETE GENOME SEQUENCE OF THE ARABIDOPSIS AND TOMATO PATHOGEN PSEUDOMONAS SYRINGAE PV. TOMATODC3000 - (Peer Reviewed Journal)

BUELL, C.R., JOARDAR, V., D'ASCENZO, M., DEGN, W.L., RAMOS, A.R., ALFANO, J.R., CARTINHOUR, S.W., DELANEY, T.P., LAZAROWITZ, S.G., MARTIN, G.B., SCHNEIDER, D.J., COLLMER, A. THE COMPLETE GENOME SEQUENCE OF THE ARABIDOPSIS AND TOMATO PATHOGEN PSEUDOMONAS SYRINGAE PV. TOMATODC3000. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES. 2003. v. 100(18). p. 10181-10186.

A GRAPH-THEORETIC APPROACH TO COMPARING AND INTEGRATING GENETIC, PHYSICAL AND SEQUENCE-BASED MAPS - (Peer Reviewed Journal)

YAP, I.V., SCHNEIDER, D.J., KLEINBERG, J., MATTHEWS, D.E., CARTINHOUR, S.W., MCCOUCH, S.R. A GRAPH-THEORETIC APPROACH TO COMPARING AND INTEGRATING GENETIC, PHYSICAL AND SEQUENCE-BASED MAPS. GENETICS. 2003. V. 165. P. 2235-2247.

DEVELOPMENT AND MAPPING OF 2240 NEW SSR MARKERS FOR RICE (ORYZA SATIVA L.) - (Peer Reviewed Journal)

MCCOUCH, S.R., TEYTELMAN, L., XU, Y., LOBOS, K.B., CLARE, K., WALTON, M., FU, B., MAGHIRANG, R., LI, Z., XING, Y., ZHANG, Q., KONO, I., YANO, M., FJELLSTROM, R.G., DECLERCK, G.A., CARTINHOUR, S.W., SCHNEIDER, D.J., WARE, D., STEIN, L. DEVELOPMENT AND MAPPING OF 2240 NEW SSR MARKERS FOR RICE (ORYZA SATIVA L.). DNA Research 9:199-207. 2002.

DEVELOPMENT OF 2,240 NEW SSR MARKERS FOR RICE (ORYZA SATIVA) - (Peer Reviewed Journal)

MCCOUGH, S.R., TEYTELMAN, L., KONO, I., YANO, M., FJELLSTROM, R.G., DECLERCK, G.A., SCHNEIDER, D.J., CARTINHOUR, S.W., WARE, D., STEIN, L. DEVELOPMENT OF 2,240 NEW SSR MARKERS FOR RICE (ORYZA SATIVA). GENOME RESEARCH. 2002.

GRAMENE: DEVELOPMENT AND INTEGRATION OF TRAIT AND GENE ONTOLOGIES FOR RICE - (Peer Reviewed Journal)

JAISWAL, P., WARE, D., ZHAO, W., SCHMIDT, S., PAN, X., CLARK, K., TEYTELMAN, L., CARTINHOUR, S.W., STEIN, L., MCCOUCH, S. GRAMENE: DEVELOPMENT AND INTEGRATION OF TRAIT AND GENE ONTOLOGIES FOR RICE. COMPARATIVE AND FUNCTIONAL GENOMICS. 2002. v. 3(2). p. 132-136.

GENOME-WIDE IDENTIFICATION OF PSEUDOMONAS SYRINGAE PV. TOMATO DC3000 PROMOTERS CONTROLLED BY THE HRPL ALTERNATIVE SIGMA FACTOR - (Peer Reviewed Journal)

FOUTS, D.E., BALDO, A.M., CARTINHOUR, S.W., LAZAROWITZ, S.G., MARTIN, G.B., REHM, A.H., SCHNEIDER, D.J., VAN DIJK, K., TANG, X., COLLMER, A. GENOME-WIDE IDENTIFICATION OF PSEUDOMONAS SYRINGAE PV. TOMATO DC3000 PROMOTERS CONTROLLED BY THE HRPL ALTERNATIVE SIGMA FACTOR. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES. 2002. v. 99(4). p. 2275-2280.

GRAMENE: A RESOURCE FOR COMPARATIVE GRASS GENOMICS - (Peer Reviewed Journal)

WARE, D., JAISWAL, P., CHANG, K., CLARK, K., TEYTELMAN, L., SCHMIDT, S., ZHAO, W., CARTINHOUR, S.W., MCCOUCH, S., STEIN, L. GRAMENE: A RESOURCE FOR COMPARATIVE GRASS GENOMICS. NUCLEIC ACIDS RESEARCH. 2002. v. 30(1). p. 103-105.

A HIGH-THROUGHPUT AFLP-BASED METHOD FOR CONSTRUCTING INTEGRATED GENETIC AND PHYSICAL MAPS: PROGRESS TOWARD A SORGHUM GENOME MAP - (Peer Reviewed Journal)

Klein, P.E., Klein, R.R., Cartinhour, S.W., Ulanch, P.E., Dong, J., Obert, J.A., Morishige, D.T., Schlueter, S.D., Childs, K.L., Ale, M. 2000. A high-throughput AFLP-based method for constructing integrated genetic and physical maps: Progress toward a sorghum genome map. Genome Research. 10:789-807.