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Rhodopseudomonas palustris genome project. Final report

Description: Rhodopseudomonas palustris is a common soil and water bacterium that makes its living by converting sunlight to cellular energy and by absorbing atmospheric carbon dioxide and converting it to biomass. This microbe can also degrade and recycle components of the woody tissues of plants, wood being the most abundant polymer on earth. Because of its intimate involvement in carbon management and recycling, R. palustris was selected by the DOE Carbon Management Program to have its genome sequenced by the Joint Genome Institute (JGI). This award provided funds for the preparation of R. palustris genomic DNA which was then supplied to the JGI in sufficient amounts to enable the complete sequencing of the R. palustris genome. The PI also supplied the JGI with technical information about the molecular biology of R. palustris.
Date: November 22, 2000
Creator: Harwood, Caroline S.
Partner: UNT Libraries Government Documents Department

Regulation of Alternative Sigma Factors During Oxidative and Ph Stresses in the Phototroph Rhodopseudomonas Palustris

Description: Rhodopseudomonas palustris is a metabolically versatile phototrophic α-proteobacterium. The organism experiences a wide range of stresses in its environment and during metabolism. The oxidative an pH stresses of four ECF (extracytoplasmic function) σ-factors are investigated. Three of these, σ0550, σ1813, and σ1819 show responses to light-generated singlet oxygen and respiration-generated superoxide reactive oxygen species (ROS). The EcfG homolog, σ4225, shows a high response to superoxide and acid stress. Two proteins, one containing the EcfG regulatory sequence, and an alternative exported catalase, KatE, are presented to be regulated by σ4225. Transcripts of both genes show similar responses to oxidative stress compared to σ4225, indicating it is the EcfG-like σ-factor homolog and controls the global stress response in R. palustris.
Date: August 2014
Creator: Perry, Leslie M.
Partner: UNT Libraries

SPECTROSCOPIC INVESTIGATION OF THE INHIBITORY EFFECT OF FATTYACIDS ON PHOTOSYNTHETIC SYSTEMS

Description: Fatty acids have a reversible inhibitory effect on respiration and on photosynthetic action. They investigated the influence of octanoic acid on the photosynthetic bacteria Rhodopseudomonas spheroids R-26. From the spectroscopic data they conclude that a less efficient energy transfer and decoupling of the light harvesting pigment system from the energy converting reaction center is responsible for the inhibitory effect.
Date: May 1, 1971
Creator: Steffea, Hans & Calvin, Melvin.
Partner: UNT Libraries Government Documents Department

Final report: 'Rhodopseudomonas palustris' genome workshop to be held in Spring of 2001

Description: The ''Rhodopseudomonas palustris'' genome workshop took place in Iowa City on April 6-8, 2001. The purpose of the meeting was to instruct members of the annotation working group in approaches to accomplishing the 'human' phase of the 'R. palustris' genome annotation. A partial draft of a paper describing the 'Rhodopseudomonas palustris' genome has been written and a full version of the paper should be ready for submission by the end of the summer 2002.
Date: June 5, 2002
Creator: Harwood, Caroline S.
Partner: UNT Libraries Government Documents Department

Nonphotochemical Hole-Burning Studies of Energy Transfer Dynamics in Antenna Complexes of Photosynthetic Bacteria

Description: This thesis contains the candidate's original work on excitonic structure and energy transfer dynamics of two bacterial antenna complexes as studied using spectral hole-burning spectroscopy. The general introduction is divided into two chapters (1 and 2). Chapter 1 provides background material on photosynthesis and bacterial antenna complexes with emphasis on the two bacterial antenna systems related to the thesis research. Chapter 2 reviews the underlying principles and mechanism of persistent nonphotochemical hole-burning (NPHB) spectroscopy. Relevant energy transfer theories are also discussed. Chapters 3 and 4 are papers by the candidate that have been published. Chapter 3 describes the application of NPHB spectroscopy to the Fenna-Matthews-Olson (FMO) complex from the green sulfur bacterium Prosthecochloris aestuarii; emphasis is on determination of the low energy vibrational structure that is important for understanding the energy transfer process associated within three lowest energy Qy-states of the complex. The results are compared with those obtained earlier on the FMO complex from Chlorobium tepidum. In Chapter 4, the energy transfer dynamics of the B800 molecules of intact LH2 and B800-deficient LH2 complexes of the purple bacterium Rhodopseudomonas acidophila are compared. New insights on the additional decay channel of the B800 ring of bacteriochlorophyll a (BChl a) molecules are provided. General conclusions are given in Chapter 5.
Date: August 1, 2002
Creator: Matsuzaki, Satoshi
Partner: UNT Libraries Government Documents Department

Nonphotochemical Hole-Burning Studies of Energy Transfer Dynamics in Antenna Complexes of Photosynthetic Bacteria

Description: This thesis contains the candidate's original work on excitonic structure and energy transfer dynamics of two bacterial antenna complexes as studied using spectral hole-burning spectroscopy. The general introduction is divided into two chapters (1 and 2). Chapter 1 provides background material on photosynthesis and bacterial antenna complexes with emphasis on the two bacterial antenna systems related to the thesis research. Chapter 2 reviews the underlying principles and mechanism of persistent nonphotochemical hole-burning (NPHB) spectroscopy. Relevant energy transfer theories are also discussed. Chapters 3 and 4 are papers by the candidate that have been published. Chapter 3 describes the application of NPHB spectroscopy to the Fenna-Matthews-Olson (FMO) complex from the green sulfur bacterium Prosthecochloris aestuarii; emphasis is on determination of the low energy vibrational structure that is important for understanding the energy transfer process associated within three lowest energy Q{sub y}-states of the complex. The results are compared with those obtained earlier on the FMO complex from Chlorobium tepidum. In Chapter 4, the energy transfer dynamics of the B800 molecules of intact LH2 and B800-deficient LH2 complexes of the purple bacterium Rhodopseudomonas acidophila are compared. New insights on the additional decay channel of the B800 ring of bacteriochlorophyll{sub a} (BChl{sub a}) molecules are provided. General conclusions are given in Chapter 5. A version of the hole spectrum simulation program written by the candidate for the FMO complex study (Chapter 3) is included as an appendix. The references for each chapter are given at the end of each chapter.
Date: June 27, 2002
Creator: Matsuzaki, Satoshi
Partner: UNT Libraries Government Documents Department

Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation

Description: A pilot-scale field test system with an inner loop nested within an outer loop was constructed for in situ U(VI) bioremediation at a US Department of Energy site, Oak Ridge, TN. The outer loop was used for hydrological protection of the inner loop where ethanol was injected for biostimulation of microorganisms for U(VI) reduction/immobilization. After 2 years of biostimulation with ethanol, U(VI) levels were reduced to below drinking water standard (<30 {micro}gl{sup -1}) in the inner loop monitoring wells. To elucidate the microbial community structure and functions under in situ uranium bioremediation conditions, we used a comprehensive functional gene array (GeoChip) to examine the microbial functional gene composition of the sediment samples collected from both inner and outer loop wells. Our study results showed that distinct microbial communities were established in the inner loop wells. Also, higher microbial functional gene number, diversity and abundance were observed in the inner loop wells than the outer loop wells. In addition, metal-reducing bacteria, such as Desulfovibrio, Geobacter, Anaeromyxobacter and Shewanella, and other bacteria, for example, Rhodopseudomonas and Pseudomonas, are highly abundant in the inner loop wells. Finally, the richness and abundance of microbial functional genes were highly correlated with the mean travel time of groundwater from the inner loop injection well, pH and sulfate concentration in groundwater. These results suggest that the indigenous microbial communities can be successfully stimulated for U bioremediation in the groundwater ecosystem, and their structure and performance can be manipulated or optimized by adjusting geochemical and hydrological conditions.
Date: February 15, 2010
Creator: Xu, M.; Wu, W.-M.; Wu, L.; He, Z.; Van Nostrand, J.D.; Deng, Y. et al.
Partner: UNT Libraries Government Documents Department

Global Regulatory Pathways in the Alphaproteobacteria

Description: A major goal for microbiologists in the twenty-first century is to develop an understanding of the microbial cell in all its complexity. In addition to understanding the function of individual gene products we need to focus on how the cell regulates gene expression at a global level to respond to different environmental parameters. Development of genomic technologies such as complete genome sequencing, proteomics, and global comparisons of mRNA expression patterns allows us to begin to address this issue. This proposal focuses on a number of phylogenetically related bacteria that are involved in environmentally important processes such as carbon sequestration and bioremediation. Genome sequencing projects of a number of these bacteria have revealed the presence of a small family of regulatory genes found thus far only in the alpha-proteobacteria. These genes encode proteins that are related to the global regulatory protein RosR in Rhizobium etli, which is involved in determining nodulation competitiveness in this bacterium. Our goal is to examine the function of the proteins encoded by this gene family in several of the bacteria containing homologs to RosR. We will construct gene disruption mutations in a number of these bacteria and characterize the resulting mutant strains using two-dimensional gel electrophoresis and genetic and biochemical techniques. We will thus determine if the other proteins also function as global regulators of gene expression. Using proteomics methods we will identify the specific proteins whose expression varies depending on the presence or absence of the RosR homolog. Over fifty loci regulated by RosR have been identified in R. etli using transposon mutagenesis; this will serve as out benchmark to which we will compare the other regulons. We expect to identify genes regulated by RosR homologs in several bacterial species, including, but not limited to Rhodopseudomonas palustris and Sphingomonas aromaticivorans. In this way we will ...
Date: April 27, 2007
Partner: UNT Libraries Government Documents Department

Identification and characterization of transcription networks in environmentally significant species

Description: Understanding the regulation of gene expression, transcription regulation in particular, is one of the grand challenges of molecular biology. Transcription regulation is arguably the most important foundation of cellular function, since it exerts the most fundamental control of the abundance of virtually all of a cell's functional macromolecules. Nevertheless, this process, perhaps because of its difficulty, has been the subject of only a limited number of genomic level analyses. We have undertaken bioinformatics projects to address this issue by developing (1) a cross-species comparison method (i.e. phylogenetic footprinting) for the identification of transcription factor binding sites, (2) a Bayesian clustering method to identify regulons, (3) an improved scanning algorithm that uses a position weight matrix and several related species sequence data to locate transcription factor binding sites, and (4) a method to predict cognate binding sites for transcription factors of unknown specificity. These bioinformatics methods were developed using the model proteobacterium Escherichia coli, with further applications to the genomes of environmentally significant microbes (Rhodopseudomonas palustris, Shewanella oneidensis) in later years of the grant.
Date: November 30, 2005
Creator: Lawrence, Charles E. & McCue, Lee Ann
Partner: UNT Libraries Government Documents Department

Phylogenetic Analysis of Shewanella Strains by DNA Relatedness Derived from Whole Genome Microarray DNA-DNA Hybridization and Comparison with Other Methods

Description: Phylogenetic analyses were done for the Shewanella strains isolated from Baltic Sea (38 strains), US DOE Hanford Uranium bioremediation site [Hanford Reach of the Columbia River (HRCR), 11 strains], Pacific Ocean and Hawaiian sediments (8 strains), and strains from other resources (16 strains) with three out group strains, Rhodopseudomonas palustris, Clostridium cellulolyticum, and Thermoanaerobacter ethanolicus X514, using DNA relatedness derived from WCGA-based DNA-DNA hybridizations, sequence similarities of 16S rRNA gene and gyrB gene, and sequence similarities of 6 loci of Shewanella genome selected from a shared gene list of the Shewanella strains with whole genome sequenced based on the average nucleotide identity of them (ANI). The phylogenetic trees based on 16S rRNA and gyrB gene sequences, and DNA relatedness derived from WCGA hybridizations of the tested Shewanella strains share exactly the same sub-clusters with very few exceptions, in which the strains were basically grouped by species. However, the phylogenetic analysis based on DNA relatedness derived from WCGA hybridizations dramatically increased the differentiation resolution at species and strains level within Shewanella genus. When the tree based on DNA relatedness derived from WCGA hybridizations was compared to the tree based on the combined sequences of the selected functional genes (6 loci), we found that the resolutions of both methods are similar, but the clustering of the tree based on DNA relatedness derived from WMGA hybridizations was clearer. These results indicate that WCGA-based DNA-DNA hybridization is an idea alternative of conventional DNA-DNA hybridization methods and it is superior to the phylogenetics methods based on sequence similarities of single genes. Detailed analysis is being performed for the re-classification of the strains examined.
Date: May 17, 2010
Creator: Wu, Liyou; Yi, T. Y.; Van Nostrand, Joy & Zhou, Jizhong
Partner: UNT Libraries Government Documents Department

Biological solar cell

Description: Recent reports have demonstrated the possibility of employing photoactive, biological membrane components in photoelectrochemical cells. Present studies in our laboratories have led to the attachment of a much simpler biological complex, the bacterial photosynthetic reaction center isolated from Rhodopseudomonas sphaeroides, directly onto a SnO/sub 2/ semiconductor electrode. Light-induced photovoltages (70mV) and photocurrents (0.5 ..mu..A/cm/sup 2/) not attributable to Dember effects have been observed in photoelectrochemical cells employing reaction-center-coated, SnO/sub 2/ working electrodes. Such reaction-center electrodes may serve as model systems for future organic photovoltaic devices.
Date: April 1, 1980
Creator: Seibert, M. & Janzen, A.F.
Partner: UNT Libraries Government Documents Department

Isolated photochemical reaction centers from bacteriochlorophyll b - containing organisms

Description: Optical, ESR and pulsed laser spectroscopic examination of isolated bacteriochlorophyll (BChl) b-containing reaction centers (RCs) demonstrates that their composition (1 P960 : 2 bacteriopheophytin (BPh) b : 2 cyt c 558 : 2 cyt c 553 : BChl/BPh = 2) and their mechanism for charge separation are very similar to those in BChl a-containing RCs; however, P960/sup +/, the oxidized form of the primary electron donor, is apparently not a symmetrical dimer of BChl b. The ''primary'' electron acceptor (X) is a quinone-iron complex, and I, the intermediary electron carrier between P960 and X, is BPh which interact(s) strongly with one or more of the other components in the RC. Comparison of the optical spectra of isolated RCs of the BChl b-containing bacteria, Rhodopseudomonas viridis and Thiocapsa pfennigii, with those of their intact cells shows that the BPh in the RC is not generated during the isolation procedure.
Date: January 1, 1977
Creator: Thornber, J.P.; Dutton, P.L.; Fajer, J.; Parson, W.W.; Prince, R.C.; Tiede, D.M. et al.
Partner: UNT Libraries Government Documents Department

Annual progress report, December 1, 1979-November 30, 1980

Description: Structure and function in photosynthetic membranes and their components continue to be studied, principally with Rhodopseudomonas sphaeroides. We have discovered how to remove bacteriochlorophyll (bchl) from a specific binding site in the antenna pigment-protein complex B850, and to replace the bchl without denaturing the complex. This has never before been achieved for any photosynthetic chlorophyllprotein complex. It opens a substantial vista of experiments designed to elucidate the nature of the binding site. Our analyses of the B850 and B875 complexes cast doubt on the accepted ratios of bchl components, carotenoids and protein and hence on models based on these ratios. We have shown that Rp. sphaeroides contains a specific second quinone (Q/sub b/) in contact with the primary photochemical electron acceptor (Q/sub a/) and distinct from the molecules of a larger pool of quinone. We have resolved conflicting reports about the polypeptide composition of reaction centers from Rhodopseudomonas viridis. We have new data on the orientation, relative to the photosynthetic membrane, of cytochrome 552 in Rp. viridis and of the shifting component of carotenoid in Rp. sphaeroides. We have constructed and are using a new circular dichroism spectrometer.
Date: January 1, 1980
Creator: Clayton, R.K.
Partner: UNT Libraries Government Documents Department

Orientation of the hemes of high potential cytochromes relative to photosynthetic membranes, as shown by the linear dichroism of oriented preparations

Description: The orientations of high potential cytochromes with respect to photosynthetic membranes was investigated in spinach chloroplasts and in Rhodopseudomonas viridis. The general approach consists of detection with polarized light of photoinduced absorbance changes related to the oxidation of the cytochromes. The orientation of cytochrome c/sub 558/ was measured at room temperature in chromatophores and whole cells of Rp. viridis, oriented on glass slides and in a magnetic field respectively. The orientation of cytochrome b/sub 559/ of green plants was detected at 77K in magnetically oriented chloroplasts. In both cases the dichroic ratio for the ..cap alpha.. band shows that the heme plane makes an angle greater than 35/sup 0/ with the membrane plane. Moreover, the dichroic ratio is not constant throughout the ..cap alpha.. and ..beta.. bands, for both cytochrome c/sub 558/ and b/sub 559/. Linear dichroism spectra of oriented pure horse heart cytochrome c and cytochrome c/sub 2/ of Rhodopseudomonas sphaeroides in stretched polyvinyl alcohol films show that the variations of the dichroic ratio in the ..cap alpha.. and ..beta.. bands can be explained by the occurrence of x and y polarized transitions absorbing at slightly different wavelengths.
Date: January 1, 1979
Creator: Vermeglio, A.; Breton, J.; Barouch, Y. & Clayton, R.K.
Partner: UNT Libraries Government Documents Department

Engineering aspects of hydrogen production from photosynthetic bacteria

Description: Certain photosynthetic bacteria (PSB), for example, Rhodopseudomonas capsulata, evolve hydrogen when placed in an anaerobic environment with light and a suitable organic substrate. An engineering effort to use such bacteria for large-scale hydrogen production from sunlight is described. A system to produce 28,000 m/sup 3//day (1 x 10/sup 6/ ft/sup 3//day) of hydrogen has been designed on a conceptual level and includes hydrogen cleanup, substrate storage, and waste disposal. The most critical component in the design is the solar bacterial reactor. Several designs were developed and analyzed. A large covered pond concept appears most attractive. Cost estimates for the designs show favorable economics.
Date: February 1, 1982
Creator: Herlevich, A. & Karpuk, M.
Partner: UNT Libraries Government Documents Department

Improved hydrogen photoproduction from photosynthetic bacteria and green algae

Description: Photosynthetic bacteria evolve hydrogen at much higher rates than do other classes of photosynthetic microorganisms. In addition, they tolerate harsh environments, grow rapidly, and utilize both visible and near infrared light in photosynthesis. They do not split water, but this does not necessarily eliminate their potential use in future applied systems. They are easily manipulated genetically, and thus might be modified to metabolize common biomass waste materials in place of expensive defined organic substrates. Furthermore, the potential for increasing hydrogen photoproduction via genetic techniques is promising. Strains that partially degrade cellulose, have high photoproduction rates, or contain very large amounts of the enzymes associated with hydrogen metabolism have been isolated. Green algae also produce hydrogen but are capable of using water as a substrate. For example, C. reinhardi can evolve hydrogen and oxygen at a molar ratio approaching 2:1. Based upon effect of dichlorophenyl dimethylurea (a specific inhibitor of photosystem II, PSII) on hydrogen photoproduction in the wild type strain and upon results obtained with PSII mutants, one can demonstrate that water is the major source of electrons for hydrogen production. The potential efficiency of in vivo coupling between hydrogenase and the photosynthetic electron transport system is high. Up to 76% of the reductants generated by the electron transport system can be channeled directly to the enzyme for in vivo hydrogen production. Rates exceeding 170 ..mu..moles of H/sub 2/ mg Chl/sup -1/ hr/sup -1/ have been observed.
Date: January 1, 1979
Creator: Weaver, P.F.; Lien, S. & Seibert, M.
Partner: UNT Libraries Government Documents Department

Biological solar cells

Description: Recent reports have demonstrated the possibility of employing photoactive, biological membrane components in photoelectrochemical cells. Such systems have produced small photovoltages and photocurrents. Present studies in our laboratories have led to the attachment of a much simpler biological complex, the bacterial photosynthetic reaction center isolated from Rhodopseudomonas sphaeroides, directly onto an SnO/sub 2/ electrode. The light-induced primary charge separation processes which occur across the reaction center macromolecule have been coupled to the electrode, and in a two-electrode configuration photovoltages as high as 70 mV and photocurrents as high as 0.5 ..mu..A/cm/sup 2/ have been observed in an external circuit. The phenomena are not due to biological Dember effects. Such reaction center electrodes may be the forerunner of future biological solar cells or may serve as model systems for future organic photovoltaic devices.
Date: November 1, 1979
Creator: Seibert, M. & Janzen, A. F.
Partner: UNT Libraries Government Documents Department

(Organization and regulation of the genes for nitrogen fixation in Rhodopseudomonas capsulata)

Description: In prior support periods we identified, cloned and sequenced three genes involved in the regulation of nif gene expression in Rhodobacter capsulatus. These were called nifRI, nifR2 and nifR4; they turn out to be homologue of the ntrC, ntrB and ntrA genes of enterobacteria. We subsequently found that mutations in an additional gene, nifR5. render R. capsulatus nif genes constitutive with respect to ammonia. The nifR5 gene was shown to be similar to glnB of enteric bacteria, encoding the regulatory protein PII, and furthering the intersection of the glutamine synthetase adenylylation cascade with the control of nif gene transcription. In pursuit of the mechanism of 0{sub 2} control of nif gene expression, we constructed and analyzed the topology of a small plasmid in R. capsulatus as a function of 0{sub 2} concentration. We also cloned and obtained partial sequence data for two genes encoding the B subunit of DNA gyrase. The nucleotide sequence of the rpoB gene encoding RNA polymerase was nearly completed. A method for isolation of genes expressed differentially, developed for cyanobacteria, was applied successfully to R. capsulatus. Several genes that depend on nifR4 for their transcription were isolated. A transcription start site for a nifA gene was identified and the promoter sequence was analyzed. A physical map of the R calsulatus SB1003 chromosome was prepared, based on pulsed-field electrophoresis of XbaI and AseI fragments and hybridization with a gridded cosmid library, using a device that permits 864 cosmids to be hybridized at one time with a labeled chromosomal fragment.
Date: January 1, 1991
Partner: UNT Libraries Government Documents Department