Dissertations / Theses: 'Pseudomonas – Genetics'

1

Haubold, Bernhard. "The population genetics of fluorescent pseudomonas." Thesis, University of Oxford, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.390493.

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Gifford, Danna R. "Population genetics of rifampicin-resistant Pseudomonas aeruginosa." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:044b9258-4f10-4e77-9ff6-aa4035cec33b.

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Antibiotic resistance is generally associated with a cost in terms of reduced competitive fitness in the absence of antibiotics. Despite this 'cost of resistance', the cessation of antibiotic treatment does not result in significant reductions in the prevalence of resistance. The maintenance of resistance, in spite of the costs, has been attributed to the rarity of reversion mutations, relative to compensatory mutations at other loci in the genome. However, the large size of bacteria populations, and the potential for migration, suggest that reversion mutations should occasionally be introduced to resistant populations. In this thesis, I show that additional mechanisms can prevent fixation of reversion mutations even if they do occur. Using an experimental evolution approach, with rifampicin resistance in Pseudomonas aeruginosa as a model system, I measured the costs of resistance in several environments and followed the adaptive dynamics of resistant populations where a sensitive lineage had invaded by migration. The results suggest that several additional mechanisms contribute to the maintenance of antibiotic resistance. Most rifampicin resistance mutations are not unconditionally costly in all environments, suggesting that migration between environments could maintain a resistant reservoir population. In environments where resistance is initially costly, the fixation of a revertant is not guaranteed, even if introduced through migration. Revertant fixation was impeded or prevented by clonal interference from adaptation in the resistant strain. Revertants that did successfully replace the resistant strain were forced to adapt to do so. Contrary to assumptions in the existing literature, fitness in the resistant strains was not recovered by general compensatory mutations, but instead by adaptive mutations specific to the environment. The data challenge several assumptions about the maintenance of antibiotic resistance: that resistance mutations are always costly, that the rarity of back mutations prevents the reversion of resistance, and that resistant strains recover fitness by compensatory mutations.

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3

Hughes, M. A. "Transfer RNA genes in Pseudomonas aeruginosa." Thesis, University of Liverpool, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.370854.

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4

Allen, Rebecca Louise. "A study of gene expression in Pseudomonas." Thesis, University of Leicester, 1989. http://hdl.handle.net/2381/35185.

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An inherent problem in the study of the genetics of the interesting and potentially commercially useful properties of the pseudomonads is that of gene expression, since many of the genes encoding these properties are not well expressed in an E.coli background. The evidence available at the present time indicates that some Pseudomonas genes may possess different promoter sequences not recognised by E.coli RNA polymerase. An in vitro coupled transcription/translation system based on P.putida has been developed. A comparison of E.coli and broad host range plasmid DNA in this and the equivalent E. coli system showed that although cloned E. coli and vector polypeptides were synthesised in both systems, there was a difference in the polypeptide products directed by broad host range plasmid DNA in the two systems. In particular RSF1010 directed the synthesis of a 73kD polypeptide uniquely in the P.putida system. This was shown to be a polypeptide involved in mobilisation of the plasmid. A broad host rsmge proraoter-probe vector based on RSFlOlO was constructed and used for the shotgun cloning of P.putida promoters. A small subset of fragments which were active as promoters in P.putida but exhibited much lower activity in E.coli were isolated, sequenced and analysed with respect to concensus E. coli and nitrogen-regulated promoter sequences. These isolated DNA fragments may represent promoters which have sequences specifically recognised by Pseudomonas RNA polymerase. An analysis of published Pseudomonas chromosomally-encoded promoters revealed putative Pseudomonas-specific concensus regions.

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5

Moulton, Paul Jonathan. "The molecular genetics of Pseudomonas syringae pv. pisi." Thesis, University of the West of England, Bristol, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.278900.

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6

林嘉敏 and Ka-man Amy Lam. "Characterization and heterologous expression of a dehalogenase gene from pseudomonas putida STRAIN A." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1999. http://hub.hku.hk/bib/B31221099.

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7

Wong, Chi-fat, and 黃志發. "Genome sequencing and comparative genomic analysis of Pseudomonas mendocina DLHK." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2012. http://hdl.handle.net/10722/197162.

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Nitrogen oxides are targeted as important gas pollutants to be eliminated. Biological removal of nitrogen oxides, like the use of bio-trickling reactor, is gaining popularity over conventional methods. A bacterium isolated from a bio-trickling reactor showing high performance in removing nitrogen oxides was identified to be Pseudomonas mendocina. The genome of this isolate was sequenced using 454 pyrosequencing technology to a high level of completeness with 33 contigs and N50 contig length of 273 kbp. The genome was annotated by Prokaryotic Genome Automatic Annotaion Pipeline (PGAAP)and the strain was named P. mendocina DLHK. Examination of P. mendocina DLHK genome annotation found nitrate reductase but not nitrite reductase, nitric oxide reductase and nitrous oxide reductase. Novel genes or pathways might be available in P. mendocina DLHK contributingits denitrification function in the bio-trickling reactor. To better understand the evolution of Pseudomonas, a comprehensive comparative study was performed. Genomes of the Pseudomonasgenus were reannotated. Core genes were extracted to construct a phylogenomic tree using supermatrix approach. Effectiveness of using single phylogenetic marker in constructing phylogeny of Pseudomonas was evaluated using rpoB gene marker. Both methods generated phylogenetic trees of very similar topology, suggesting that rpoB gene can be a very effective marker in the rapid construction of Pseudomonas phylogeny.It is surprising to note that Azotobacter vinelandii DJ was included in the large clade of Pseudomonas and have the closest relationship with P. stutzeri in both phylogenetic trees, providing evidence that this species should be reclassified into the genus Pseudomonas. Cluster of Orthologous Groups (COG)category distribution of all pseudomonads were analysed for physiological significance. The large amount of gene categorised into the COG for amino acid metabolism and transcription may imply the importance for these 2 functions on the survival of pseudomonads. It is again surprising to note the COG distribution pattern of A. vinelandii DJ is different from other pseudomonads, especially to its closest phylogenetic neighbour P. stutzeri. Horizontal gene transfer events inpseudomonads were investigated because of its importance in prokaryotic evolution. The high congruence of the phylogemonic tree to most core genes suggests that the phylogenomic tree is a good piece of evidence describing the evolution of pseudomonads. It is a bit surprising to observe that quite a number of core genes may have exhibited horizontal gene transfer which show incongruence of the gene tree to the core genes. The impact of horizontal gene transfer events on the functionality and evolution of pseudomonads remains to be investigated.
published_or_final_version
Biological Sciences
Master
Master of Philosophy

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8

Malik, A. N. "Genetic studies with Pseudomonas syringae pathovar pisi." Thesis, University of Greenwich, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.354390.

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9

Chung, Yiu-kay Wilson, and 鍾堯基. "Identification of the regulatory element of dehalogenase IVa of Burkholderia cepacia MBA4." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2003. http://hub.hku.hk/bib/B29517291.

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10

Roush, Wendy A. "Pyrimidine Genes in Pseudomonas Species." Thesis, University of North Texas, 2003. https://digital.library.unt.edu/ark:/67531/metadc4395/.

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This thesis is a comparative study of gene arrangements in Pseudomonas species, and is organized into three major sections. The first section compares gene arrangements for different pathways in Pseudomonas aeruginosa PAO1 to determine if the gene arrangements are similar to previous studies. It also serves as a reference for pyrimidine gene arrangements in P. aeruginosa. The second part compares the physical, and genetic maps of P. aeruginosa PAO1 with the genome sequence. The final section compares pyrimidine gene arrangements in three species of Pseudomonas. Pyrimidine biosynthesis and salvage genes will be aligned for P. aeruginosa PAO1, P. putida KT2440, and P. syringae DC3000. The whole study will gives insight into gene patterns in Pseudomonas, with a focus on pyrimidine genes.

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11

Jackson, Benjamin. "Molecular genetics of #alpha# pinene metabolism in Pseudomonas fluorescens." Thesis, Imperial College London, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.343598.

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12

Ochsner, Urs Arnold. "Genetics and biochemistry of Pseudomonas aeruginosa rhamnolipid biosurfactant synthesis /." [S.l.] : [s.n.], 1993. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=10401.

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13

Jenner, Carol Elizabeth. "The genetics of avirulence of Pseudomonas syringae pv. phaseolicola." Thesis, Imperial College London, 1990. http://hdl.handle.net/10044/1/46367.

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14

Turner, Keith Holte. "Bistability in Pseudomonas aeruginosa." Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10159.

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The opportunistic pathogen P. aeruginosa is a leading cause of hospital-accquired infections, and is also the primary cause of morbidity and mortality in patients with cystic fibrosis (CF). In this thesis, I describe the identification and characterization of a novel LysR-type transcription regulator (LTTR) of P. aeruginosa named BexR. I show that BexR exhibits reversible ON/OFF bistable expression, which leads to the bistable expression of several genes including one encoding a virulence factor. I present results suggesting that this bistable expression depends on positive feedback of BexR. This work illuminates the simplicity with which a transcription regulatory network can exhibit a complex behavior and generate phenotypic diversity in a clonal population.

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15

Yuen, Hiu-fung, and 阮曉峰. "A study of the catabolite repression of the dehalogenase IVa gene of Burkholderia cepacia MBA4." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2004. http://hub.hku.hk/bib/B30682113.

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16

Kellett, Louise Elizabeth. "The molecular biology of xylanolytic enzymes from Pseudomonas fluorescens subsp. cellulosa." Thesis, University of Newcastle Upon Tyne, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.315636.

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17

Norman, Richard Albert. "Signal transduction in the regulation of operon expression in Pseudomonas aeruginosa." Thesis, University College London (University of London), 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.298366.

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18

Amin, M. K. A. "The ecology and genetics of Pseudomonas bacteriophage in freshwater systems." Thesis, Cardiff University, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.381224.

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19

Anson, J. G. "The genetics and biochemistry of aniline degradation by Pseudomonas CIT1." Thesis, Cranfield University, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.356197.

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20

Kahn, Sophie Georgina. "Molecular characterisation of genes essential for adaptive evolution in Pseudomonas fluorescens SBW25." Thesis, University of Oxford, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.299792.

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21

Diggle, Stephen Paul. "Quorum sensing and the regulation of virulence gene expression in Pseudomonas aeruginosa." Thesis, University of Nottingham, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.368347.

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22

Elamri, Nuria Ali. "Strain diversity and identification of Pseudomonas syringae pv. maculicola and related pathovars." Thesis, University of the West of England, Bristol, 2001. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.365189.

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23

Thomas, Andrew Wyn. "Analysis of a mobile genetic element from Pseudomonas putida which encodes dehalogenase functions." Thesis, Cardiff University, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.313707.

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24

Liljestrand, Laura Gail. "Discovery and Characterization of Two Tn5 Generated pyrA Mutants in Pseudomonas putida and the Generation of Hfr Strains." Thesis, University of North Texas, 1994. https://digital.library.unt.edu/ark:/67531/metadc277935/.

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A pyrA mutation in Pseudomonas putida was isolated using transposon mutagenesis for the first time. Transposon Tn5 was used to inactivate the pyrA gene for carbamoylphosphate synthetase in these mutants. Accordingly, these mutants were defective in pyrimidine and arginine biosynthesis. The suicide vector, pM075, from Pseudomonas aeruginosa, was used to introduce the transposon into the cells. Tn5 was subsequently used to supply homology so that the plasmid pM075 could be introduced in its entirety into the Pseudomonas putida chromosome at the locus of the Tn5 insertion in the pyrA gene. Consequently, these strains exhibited high frequency of recombination and were capable of chromosome mobilization.

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25

Armbruster, Steven C. (Steven Christopher). "Characterization of the OCT Plasmid-Encoded Mercury Resistance Genetic Locus in Pseudomonas putida." Thesis, University of North Texas, 1989. https://digital.library.unt.edu/ark:/67531/metadc500381/.

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A 17.1 Kb genetic element encoding for mercury resistance (OCT-Hg^r) was shown to translocate from its original location on the OCT plasmid to the resistance plasmid, RPl, in Pseudomonas putida. Analysis of RPl-Hg^r recombinant plasmids revealed that insertion of mercury resistance genes into RPl could occur at a variety of sites, with all recombinants having common EcoRI restriction fragments of 9.4, 3.8, 2.3, and 1.6 Kb, derived from the insertion. Hybridization analysis suggested the existence of extensive homology between this insertion and the prototypic mercury resistance transposon, Tn501, as well as the location of a similar merA sequence. Although the overall size was shown to be quite different from Tn501, striking physical similarities are shared between these two elements.

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26

Wang, Chien-Sao. "Molecular Cloning and Functional Analysis of Transposable Mercury Resistance Genes Encoded by the OCT Plasmid." Thesis, University of North Texas, 1991. https://digital.library.unt.edu/ark:/67531/metadc501216/.

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Translocation of a 17.1 kilobase region of the OCT plasmid encoding mercury resistance (mer) in Pseudomonas putida was shown to occur in a recombination-deficient host with plasmid PP1 serving as a recipient replicon. The frequency of transposition in Pseudomonas was estimated at 10^3 -10 -^2, but undetectable in Escherichia soli. ' DNA comprising all of mr as well as subregions there of were cloned and subjected to DNA sequence analysis. Like other transposons, mer was found to contain inverted repeat sequences at its termini. These were similar to, but not identical to the inverted repeat structures found in the prototypical mercury resistance transposon Tn501 from E. aeruginosa.

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27

Williams, Rachel Jayne. "Studies on the amiB and amiS genes of the amidase operons in Pseudomonas aeruginosa." Thesis, University College London (University of London), 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.362653.

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28

Orvis, Julie Dawn. "An investigation into the specificity of race 3 of Pseudomonas syringae pathovar pisi." Thesis, University of the West of England, Bristol, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.315474.

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29

Atherton, G. T. "The genetics of host specificity and pathogenicity of Pseudomonas syringae pathovar pisi." Thesis, University of the West of England, Bristol, 1987. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.379473.

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30

Mur, Luis Alejandro Jose. "The molecular genetics of race 2 specificity in Pseudomonas syringae pathovar pisi." Thesis, University of the West of England, Bristol, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.303616.

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31

Simpson, Luci N. "Cassette Systems for Creating Intergeneric Hybrid ATCases." Thesis, University of North Texas, 1999. https://digital.library.unt.edu/ark:/67531/metadc2237/.

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Cassette systems for creating intergeneric hybrid ATCases were constructed. An MluI restriction enzyme site was introduced at the carbamoylphosphate binding site within the pyrB genes of both Pseudomonas putida and Escherichia coli. Two hybrids, E. coli pyrB polar domain fused with P. putida pyrB equatorial domain and P. putida pyrB polar domain fused with E. coli pyrB equatorial domain, are possible. The intergeneric E. coli-P. putida hybrid pyrB gene was constructed and found to encode an active ATCase which complemented an E. coli Pyr- strain. These hybrids are useful for kinetic and expression studies of ATCase in E. coli.

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32

Crary, Monica J. "Genetic Variability and its Relationship to Acanthamoeba Pathogenesis." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1343831120.

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33

Burke, Genola. "The molecular identification and evaluation of the effects of cold temperatures on Antarctic Pseudomonas spp." Birmingham, Ala. : University of Alabama at Birmingham, 2009. https://www.mhsl.uab.edu/dt/2009m/burke.pdf.

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34

Luo, Xuebin. "Structural Analysis of the Genes Encoding the Oxalocrotonate Branch of the Pseudomonas putida TOL Plasmid pDKI meta-cleavage Pathway and the Expression of the xy1G Gene Product in Escherichia coli." Thesis, University of North Texas, 1992. https://digital.library.unt.edu/ark:/67531/metadc500659/.

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Three overlapping DNA fragments from the lower operon of Pseudomonas putida TOL plasmid pDK1, covering the xy1IH genes and downstream flanking region, were cloned into pUC19. They include a 2.8 kbp XhoI fragment, a 2.7 kbp PstI fragment and a 2.0 kbp EcoRI-HindIII fragment. They were subjected to DNA sequence analysis. The xy1I (4-oxalocrotonate decarboxylase) and xy1H (4-oxalocrotonate tautomerase) genes were found to possess coding regions of 792 and 189 nucleotides, respectively. A possible transcriptional terminator resembling E. coli rho-independent terminators was identified downstream of the translational stop of xy1H. An additional stem and loop structure was found in the intergenic region between xy1I and xy1H. The individual ORF's of the oxalocrotonate branch (xy1G, xy1I and xy1H) have been cloned into pUC18/19. The expression of the xy1G gene in E. coli was successfully assayed spectrophotometrically.

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35

Tsiamis, George A. "Analysis of an avirulence gene from Pseudomonas syringae pv. phaseolicola that determines cultivar specificity towards phaseolous vulgaris L." Thesis, Imperial College London, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.286887.

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36

Balasubramanian, Deepak. "Pseudomonas Aeruginosa AmpR Transcriptional Regulatory Network." FIU Digital Commons, 2013. http://digitalcommons.fiu.edu/etd/863.

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In Enterobacteriaceae, the transcriptional regulator AmpR, a member of the LysR family, regulates the expression of a chromosomal β-lactamase AmpC. The regulatory repertoire of AmpR is broader in Pseudomonas aeruginosa, an opportunistic pathogen responsible for numerous acute and chronic infections including cystic fibrosis. Previous studies showed that in addition to regulating ampC, P. aeruginosa AmpR regulates the sigma factor AlgT/U and production of some quorum sensing (QS)-regulated virulence factors. In order to better understand the ampR regulon, the transcriptional profiles generated using DNA microarrays and RNA-Seq of the prototypic P. aeruginosa PAO1 strain with its isogenic ampR deletion mutant, PAO∆ampR were analyzed. Transcriptome analysis demonstrates that the AmpR regulon is much more extensive than previously thought influencing the differential expression of over 500 genes. In addition to regulating resistance to β-lactam antibiotics via AmpC, AmpR also regulates non-β-lactam antibiotic resistance by modulating the MexEF-OprN efflux pump. Virulence mechanisms including biofilm formation, QS-regulated acute virulence, and diverse physiological processes such as oxidative stress response, heat-shock response and iron uptake are AmpR-regulated. Real-time PCR and phenotypic assays confirmed the transcriptome data. Further, Caenorhabditis elegans model demonstrates that a functional AmpR is required for full pathogenicity of P. aeruginosa. AmpR, a member of the core genome, also regulates genes in the regions of genome plasticity that are acquired by horizontal gene transfer. The extensive AmpR regulon included other transcriptional regulators and sigma factors, accounting for the extensive AmpR regulon. Gene expression studies demonstrate AmpR-dependent expression of the QS master regulator LasR that controls expression of many virulence factors. Using a chromosomally tagged AmpR, ChIP-Seq studies show direct AmpR binding to the lasR promoter. The data demonstrates that AmpR functions as a global regulator in P. aeruginosa and is a positive regulator of acute virulence while negatively regulating chronic infection phenotypes. In summary, my dissertation sheds light on the complex regulatory circuit in P. aeruginosa to provide a better understanding of the bacterial response to antibiotics and how the organism coordinately regulates a myriad of virulence factors.

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37

Black, Gary William. "The molecular analysis of the genes encoding the enzyme carbon monoxide dehydrogenase from the carboxydobacterium Pseudomonas thermocarboxydovorans strain C2." Thesis, University of Sunderland, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.304649.

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38

Shen, Weiping. "Regulation of Escherichia coli pyrBI Gene Expression in Pseudomonas fluorescens." Thesis, University of North Texas, 1995. https://digital.library.unt.edu/ark:/67531/metadc278188/.

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Pseudomonas fluorescens does not appear to regulate the enzymes of de novo pyrimidine biosynthesis at the level of gene expression. Little or no apparent repression of pyr gene expression is observed upon addition of exogenous pyrimidines to the growth medium. The Escherichia coli pyrBI genes for aspartate transcarbamoylase (ATCase) were sized down and cloned into the broad host range plasmid, pKT230. Upon introduction into a P.fluorescenspyrB mutant strain, ATCase showed repression in response to exogenously fed pyrimidine compounds. Thus, it was possible to bring about changes in pyrimidine nucleotide pool levels and in transcriptional regulation of gene expression at the same time.

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Baker, Ronald F. (Ronald Fredrick). "Nucleotide Sequence Determination, Subcloning, Expression and Characterization of the xy1LT Region of the Pseudomonas putida TOL Plasmid pDK1." Thesis, University of North Texas, 1992. https://digital.library.unt.edu/ark:/67531/metadc278316/.

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The complete nucleotide sequence of the region encoding the DHCDH function of the pDK1 lower operon was determined. DNA analysis has shown the presence of two open reading frames, one gene consisting of 777 nucleotides encoding a polypeptide of 27.85 kDa and another gene of 303 nucleotides encoding a polypeptide of 11.13 kDa. The results of enzymatic expression studies suggest that DHCDH activity is associated only with xy1L. However although the addition of xy1T cell-free extracts to xy1L cell-free extracts does not produce an increase in DHCDH activity, subclones carrying both xy1L and xy1T exhibit 300- 400% more DHCDH activity than subclones carrying only xy1L.

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Gehrig, Stefanie. "Adaptation of Pseudomonas fluorescens SBW25 to the air-liquid interface : a study in evolutionary genetics." Thesis, University of Oxford, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.418805.

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41

Delcau, Michael Asher. "Differentiation of Pseudomonas sp. strain ADP biofilms and planktonic cells using methods in gene expression analysis." Diss., University of Iowa, 2018. https://ir.uiowa.edu/etd/6093.

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Bacterial strain Pseudomonas sp. ADP is capable of degrading atrazine via an enzymatic pathway in six sequential steps to yield carbon dioxide and ammonia. Atrazine is a persistent herbicide that frequently contaminates soil, drinking water, and ground water throughout areas of heavy use in the United States. A biological remediation approach using Pseudomonas sp. APD is considered as an effective, cost-efficient, and environmentally conscious method of decreasing atrazine concentration in areas of high contamination. Each enzyme in the degradation pathway is encoded by a corresponding gene, AtzA-AtzF, and is located on a self-transmissible 108-kb plasmid. Due to their prevalence in nature, and their unique genetic and physical characteristics, biofilms are of great interest in the field of bioremediation. Biofilms exhibit high tolerance for harsh environmental stressors/conditions, prodigious potential for recalcitrant compound entrapment via an extracellular polymeric matrix, quorum sensing, and increased horizontal gene transfer compared to their planktonic counterparts. Despite frequent genetic and chemical analyses performed on atrazine-degrading genes on planktonic cells of strain Pseudomonas sp. APD, the genetics and degradation potential of Pseudomonas sp. ADP biofilms is relatively unexplored. Real-time quantitative PCR was used to differentiate the expression of six genes involved in the process of atrazine degradation. Relative expression experiments revealed no statistically significant difference in the expression of atrazine-degrading genes in Pseudomonas sp. ADP cells grown as biofilms relative to Pseudomonas sp. ADP cells grown as planktonic cells. In biofilms alone, the expression of genes AtzDEF was differentiated via temperature of biofilm growth in cells grown at 25, 30, and 37 degrees. Analytical techniques, including GC-MS and HPLC, were used to elucidate atrazine remediation potential of Pseudomonas sp. ADP biofilms and our previously collected genetic data. Stable decreases in atrazine degradation following a first-order kinetic model have been demonstrated for planktonic cells compared to a complex degradation pattern, including transient increases, observed for corresponding biofilm-mediated cells. This is attributed to the unique structure of the biofilm and the potential of atrazine to be entrapped in the substances of the extracellular polymeric matrix and subsequently released into the effluent. Overall, the biodegradation efficiency was higher for Pseudomonas sp. ADP biofilm-mediated cells compared to their planktonic counterparts. A novel methodology of using confocal microscopy and in situ reverse transcription was proposed for optimization to visualize the expression of atrazine-degrading genes in fixed Pseudomonas sp. ADP biofilms. The sugar composition of Pseudomonas sp. ADP was evaluated using fluorescent lectin binding analysis and was determined to exhibit a prominent level of diversity and dependent upon growth medium. The results from these experiments will play a role in application of biofilms grown in bioreactors for atrazine remediation throughout areas of persistent and high contamination throughout the US. The new step in methodology development of an in situ visual gene expression technique can be extended to bioremediation of alternate recalcitrant compounds. The results may also be aid progress in alternate biofilm-related studies in medicine & human health, metallurgy, and engineering.

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42

Marcangione, Luigi. "Isolation of a Pseudomonas aeruginosa PAOI gene involved in 3-hydroxybutyrate catabolism." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape2/PQDD_0031/MQ64403.pdf.

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43

McGuffie, Bryan A. "A sigma factor and anti-sigma factor that control swarming motility and biofilm formation in Pseudomonas aeruginosa." Thesis, Harvard University, 2015. http://nrs.harvard.edu/urn-3:HUL.InstRepos:17467530.

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Pseudomonas aeruginosa is an environmental bacterium and opportunistic human pathogen of major clinical significance. It is the principal cause of morbidity and mortality in patients with cystic fibrosis (CF) and a leading cause of nosocomial infections. Although the organism is unicellular, P. aeruginosa exhibits two forms of multicellular behaviors when associated with a surface under the right conditions: swarming motility and biofilm formation. Swarming motility is a multicellular cooperative form of flagella-dependent surface motility, while biofilm formation produces a sessile community of bacteria enclosed by a self-produced extracellular polymeric matrix. P. aeruginosa is thought to grow as a biofilm in the lungs of CF patients and the growth of P. aeruginosa biofilms on indwelling medical devices, such as endotracheal tubes and catheters, is a significant source of nosocomial infection. By growing as a biofilm, P. aeruginosa resists clearance by the immune system and increases its resistance to antimicrobial therapy. In this thesis, I describe the characterization of a sigma factor and anti-sigma factor implicated in P. aeruginosa virulence and cell envelope stress that control the expression of a novel regulator of swarming motility and biofilm formation. In addition, I describe work done to investigate the role of a post-translational regulator of flagellar motility that has been described in other bacteria, but has not been studied extensively P. aeruginosa. In bacteria, RNA polymerase (RNAP) requires sigma factors for promoter-specific transcription initiation. sigma factors guide RNAP to promoters by recognizing conserved DNA sequences within the promoter called the -10 and -35 elements. Most bacteria encode a primary sigma factor and several alternative sigma factors, each of which recognizes different promoter -10 and -35 sequences. By modulating the activity of alternative sigma factors, bacteria can rapidly alter their transcriptional program in response to changes in growth, morphological development, and environmental conditions. The extracytoplasmic function (ECF) sigma factors are the largest and most diverse group of bacterial sigma factors. The gene encoding an ECF sigma factor is often cotranscribed with its own negative regulator, called an anti-sigma factor, which directly binds to and inhibits its partner sigma factor until the appropriate extracytoplasmic signal stimulates sigma factor release and expression of the sigma factor’s regulon. In this thesis, I describe the characterization of the P. aeruginosa ECF sigma factor PA2896 and its cognate anti-sigma factor PA2895. Using immunoprecipitation, we show that the ECF sigma factor PA2896 and RNAP co-purify in vivo. Utilizing DNA microarrays, we identify the genes that constitute the PA2895 and PA2896 regulon and infer the putative -10 and -35 consensus sequences recognized by PA2896. Genetic analysis revealed a subset of genes within the PA2896 regulon that share the putative promoter consensus sequence are positively regulated by the ECF sigma factor PA2896 and negatively regulated by the anti-sigma factor PA2895. Using a bacterial two-hybrid assay, we show that PA2895 directly interacts with PA2896. We present evidence that increased expression of the PA2896 regulon in ∆PA2895 mutants cells leads to the inhibition of swarming motility and enhanced biofilm formation. We further show that one gene in the PA2896 regulon, PA1494, is necessary and sufficient for the inhibition of swarming motility and promotion of biofilm formation. Thus we report the discovery of a system that may respond to a stress signal by activating PA2896-dependent expression of PA1494 to inhibit swarming motility and promote the formation of a protective biofilm. In many bacteria, swarming motility and biofilm formation are controlled by the second messenger c-di-GMP. In P. aeruginosa, elevated intracellular c-di-GMP generally results in the inhibition of flagellar-dependent swarming motility and enhanced biofilm formation. In some species of bacteria, c-di-GMP-mediated repression of flagellar motility is achieved by repressing the expression of the flagellar genes. However, flagellar gene expression in P. aeruginosa does not appear to be influenced by elevated c-di-GMP, suggesting c-di-GMP controls flagellar motility post transcriptionally in this bacterium. Mechanisms by which c-di-GMP controls flagellar function post translationally have been described in both Gram-negative and Gram-positive bacteria, however the mechanism in P. aeruginosa remains unclear. Gram-negative bacteria appear to utilize a “flagellar brake” to control flagellar function in response to c-di-GMP. P. aeruginosa encodes a homolog of this brake and in this thesis I present evidence that this homolog is involved in controlling flagellar function in P. aeruginosa. Together, the characterization of PA2895 and PA2896, the identification of PA1494 as a novel regulator of swarming motility and biofilm formation, and evidence of a functional flagellar brake in P. aeruginosa advance our understanding of how this bacterium controls the transition from motile cell to sessile biofilm.
Medical Sciences

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44

Wubbolts, Marcel Gerhardus. "Xylene and alkane mono-oxygenases from Pseudomonas putida genetics, regulated expression and utilization in the synthesis of optically active synthons /." [S.l. : [Groningen : s.n.] ; University Library Groningen] [Host], 1994. http://irs.ub.rug.nl/ppn/29797291X.

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45

Poulter, Melinda D. "Structural Analysis of the TOL pDK1 xylGFJQK Region and Partial Characterization of the xylF and xylG Gene Products." Thesis, University of North Texas, 1999. https://digital.library.unt.edu/ark:/67531/metadc2270/.

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TOL plasmids encode enzymes responsible for utilization of toluene and related aromatic compounds by Pseudomonas putida, ultimately converting them to central metabolic intermediates. The nucleotide sequence for the 5.6 kb xylGFJQK region of the pDK1 TOL meta operon was determined. DNA sequence analysis revealed the presence of five open reading frames corresponding to xylG (1458 bp), xylF (846 bp), xylJ (783 bp), xylQ (936 bp) and xylK (1047 bp), encoding predicted protein products of 51.6, 31.3, 27.8, 32.8, and 36.6 kDa in size, respectively. The average G+C content of the xylLTEGFJQK region was 65.7%, somewhat higher than the 58.9% seen in the immediately upstream xylXYZ region and substantially more than the 50% G+C content reported for the upper TOL operon of this plasmid. Homology comparisons were made with genes and proteins of related catabolic plasmids. The dmpCDEFG and pWWO xylGFJQK regions exhibit consistently high levels of nucleotide and amino acid homology to pDK1 xylGFJQK throughout the entire region. In contrast, although the nucleotide sequence homology of the Acinetobacter atdCDE region to xylGFJ is high, the homology of atdFG to xylQK is markedly less. Such radical changes in homology between corresponding regions of different operons, combined with variable base and codon usage patterns within and between operons, provides additional support for the idea that the upper and lower operons encoding enzymes of aromatic pathways have evolved independently of one another and that these operons have continued to exchange genetic material with homologous expression units through a series of recombination events. Recombinant plasmids were constructed for individual expression of each of the xylGFJQK genes. HMSD (XylG) and HMSH (XylF) were partially purified and characterized with respect to substrate specificity and kinetic mechanism. Evidence was obtained suggesting that the HMSD reaction occurs via a steady state ordered mechanism or a random mechanism where binding of the first substrate effects the enzyme's affinity for the second substrate.

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46

Hares, Douglas R. (Douglas Ryan). "Physical and Functional Characterization of the xy1XYZ Region From TOL Plasmid pDK1 and its Associated Downstream Regulatory Elements." Thesis, University of North Texas, 1998. https://digital.library.unt.edu/ark:/67531/metadc278036/.

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The nucleotide sequence for the pDKl TOL plasmid region encoding toluate-1,2-dioxygenase (Xy1XYZ, TO) was determined. TO is the first enzyme in the meta-cleavage operon, responsible for the conversion of toluates and benzoates to their carboxy-substituted diols. DNA sequence analysis revealed the presence of three open reading frames (ORF). The three ORFs correspond to xylX (1353 bp), xylY (486 bp) and xylZ (1008 bp), encoding predicted protein products of 51370 Da, 19368 Da and 36256 Da, respectively.

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47

Licio, Daniela Carolina Pinto e. "Isolamento de bactérias produtoras de polihidroxialcanoatos e caracterização molecular de sua PHA sintase." Universidade de São Paulo, 2011. http://www.teses.usp.br/teses/disponiveis/87/87131/tde-09022012-105548/.

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Um total de 1.520 bactérias isoladas a partir de amostras de lodo de esgoto doméstico e de solo de área preservada foi avaliado para a produção de polihidroxialcanoatos (PHA) com os corantes lipofílicos Nile Red A e Sudan Black B, permitindo a detecção de 261 isolados. Ensaios de produção de PHA revelaram isolados produtores de P3HB apresentando valores superiores à linhagem Burkholderia sacchari LFM101 e valores de produção de PHAMCL superiores à linhagem Pseudomonas sp. LFM046, além de 6 isolados produtores da mistura de P3HB e PHAMCL. Os primers RECF1/RECR permitiram a detecção específica do gene phaC do tipo I de três bactérias produtoras de P3HB, e os primers P613F/P613R detectaram genes phaC do tipo I em bactérias produtoras da mistura de polímeros. Um fragmento de DNA de 4 kpb de uma biblioteca genômica do isolado RMP1058BII, produtor da mistura de P3HB e PHAMCL, foi detectado utilizando os primers P613F/P613R, e a expressão desse fragmento de DNA uma linhagem de Pseudomonas mutada no gene phaC levou à produção de pequena quantidade de P3HB.
A total of 1520 isolates from domestic sewage sludge or soil of preserved area were evaluated in regards of PHA production using the lipophilic Nile Red A or Sudan Black B dyes, allowing the detection of 261 isolates. PHA production experiments revealed P3HB producing isolates at higher amounts than the strain Burkholderia sacchari LFM101 and PHAMCL production rates higher than those presented by the strain Pseudomonas sp. LFM046, besides 6 isolates producing P3HB and PHAMCL mixtures. The RECF1/RECR primers allowed the specific type I phaC genes detection in three P3HB producing bacteria and the P613F/P613R primers detected type I phaC genes in the polymer mixture producing isolates. A 4 kbp DNA fragment from a genomic library of the isolate RMP1058BII was detected using the P613F/P613R primers. This DNA fragment expression in a Pseudomonas strain mutated in phaC gene leaded to the production of small amounts of P3HB.

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Kugelberg, Elisabeth. "Mechanisms of adaptive mutations in bacteria /." Stockholm, 2005. http://diss.kib.ki.se/2005/91-7140-446-5/.

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49

Cai, Rongman. "New hypotheses about the origin of Pseudomonas syringae crop pathogens." Diss., Virginia Tech, 2012. http://hdl.handle.net/10919/37806.

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Pseudomonas syringae is a common foliar plant pathogenic bacterium that causes diseases on many crop plants. We hypothesized that todayâ s highly virulent P. syringae crop pathogens with narrow host range might have evolved after the advent of agriculture from ancestral P. syringae strains with wide host range that were adapted to mixed plant communities. The model tomato and Arabidopsis pathogen P. syringae pv. tomato (Pto) DC3000 and its close relatives isolated from crop plants were thus selected to unravel basic principles of host range evolution by applying molecular evolutionary analysis and comparative genomics approaches. Phylogenetic analysis was combined with host range tests to reconstruct the host range of the most recent common ancestor of all analyzed strains isolated from crop plants. Even though reconstruction of host range of the most recent common ancestor of all analyzed strains was not conclusive, support for this hypothesis was found in some sub-groups of strains. The focus of my studies then turned to Pto T1, which was found to represent the most common P. syringae lineage causing bacterial speck disease on tomato world-wide. Five genomes were sequenced and compared to each other. Identical genotypes were found in North America and Europe suggesting frequent pathogen movement between these continents. Moreover, the type III-secreted effector gene hopM1 was found to be under strong selection for loss of function and non-synonymous mutations in the fliC gene allowed to identify a region that triggers plant immunity. Finally, Pto T1 was compared to closely related bacteria isolated from snow pack and surface water in the French Alps. Recombination between alpine strains and crop strains was inferred and virulence gene repertoires of alpine strains and crop strains were found to overlap. Alpine strains cause disease on tomato and have relatively wider host ranges than Pto T1. The conclusion from these studies is that Pto T1 and other crop pathogens may have evolved from ancestors similar to the characterized environmental strains isolated in the French Alps by adapting their effector repertoire to individual crops becoming more virulent on these crops but losing virulence on other plants.
Ph. D.

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50

Liu, Haiyan 1966. "Attenuation of Escherichia Coli Aspartate Transcarbamoylase Expressed in Pseudomonas Aeruginosa Mutant and Wild Type Strains." Thesis, University of North Texas, 1994. https://digital.library.unt.edu/ark:/67531/metadc279106/.

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No apparent repression of pyr gene expression in Pseudomonas aeruginosa is observed upon addition of exogenous pyrimidines to the growth medium. Upon introduction of the subcloned Escherichia coli pyrBI genes for aspartate transcarbamoylase (ATCase) into a P. aeruginosa pyrB mutant strain, repression was observed in response to exogenously fed pyrimidine compounds. The results proved that it is possible to bring about changes in pyrimidine nucleotide pool levels and changes in transcriptional regulation of gene expression as a result. Thus, the lack of regulatory control in P. aeruginosa pyr gene expression is not due to an inability to take up and incorporate pyrimidine compounds into metabolic pools, or to an inability of the RNA polymerase to respond to regulatory sequences in the DNA but is probably due to a lack of specific regulatory signals in the promoter of the genes themselves.

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Dissertations / Theses on the topic 'Pseudomonas – Genetics'

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