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Caroline S Harwood - One of the best experts on this subject based on the ideXlab platform.
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a disjointed pathway for malonate degradation by Rhodopseudomonas palustris
Applied and Environmental Microbiology, 2020Co-Authors: Zhaobao Wang, Caroline S Harwood, Bo Liang, Jianming YangAbstract:The purple nonsulfur phototrophic bacterium Rhodopseudomonas palustris strain CGA009 uses the three-carbon dicarboxylic acid malonate as a sole carbon source under phototrophic conditions. However, this bacterium grows extremely slowly on this compound and does not have operons for the two pathways for malonate degradation that have been described in other bacteria. Many bacteria grow on a spectrum of carbon sources, some of which are classified as “poor” growth substrates because they support slow growth rates. This trait is rarely addressed in the literature, but slow growth is potentially useful in biotechnological applications where it is imperative for bacteria to divert cellular resources to value-added products rather than to growth. This prompted us to explore the genetic and physiological basis for the slow growth of R. palustris with malonate as a carbon source. There are two unlinked genes annotated as encoding a malonyl-CoA synthetase (MatB) and a malonyl-CoA decarboxylase (MatA) in the genome of R. palustris, which we verified as having the predicted functions. Additionally, two tripartite ATP-independent periplasmic transporters (TRAP systems) encoded by rpa2047-2049 and rpa2541-2543 were needed for optimal growth on malonate. Most of these genes were expressed constitutively during growth on several carbon sources, including malonate. Our data indicate that R. palustris uses a piecemeal approach to growing on malonate. The data also raise the possibility that this bacterium will evolve to use malonate efficiently if confronted with an appropriate selection pressure. Importance There is interest in understanding how bacteria metabolize malonate because this three-carbon dicarboxylic acid can serve as a building block in bioengineering applications to generate useful compounds that have an odd number of carbons. We found that the phototrophic bacterium Rhodopseudomonas palustris grows extremely slowly on malonate. We identified two enzymes and two TRAP transporters involved in the uptake and metabolism of malonate, but some of these elements are apparently not very efficient. R. palustris cells growing with malonate have the potential to be excellent biocatalysts because cells would be able to divert cellular resources to the production of value-added compounds instead of to support rapid growth. In addition, our results suggest that R. palustris is a candidate for directed evolution studies to improve growth on malonate and to observe the kinds of genetic adaptations that occur to make a metabolic pathway operate more efficiently.
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Essential Genome of the Metabolically Versatile Alphaproteobacterium Rhodopseudomonas palustris
Journal of Bacteriology, 2015Co-Authors: Kieran B. Pechter, Larry A. Gallagher, Harley Pyles, Colin Manoil, Caroline S HarwoodAbstract:ABSTRACT Rhodopseudomonas palustris is an alphaproteobacterium that has served as a model organism for studies of photophosphorylation, regulation of nitrogen fixation, production of hydrogen as a biofuel, and anaerobic degradation of aromatic compounds. This bacterium is able to transition between anaerobic photoautotrophic growth, anaerobic photoheterotrophic growth, and aerobic heterotrophic growth. As a starting point to explore the genetic basis for the metabolic versatility of R. palustris, we used transposon mutagenesis and Tn-seq to identify 552 genes as essential for viability in cells growing aerobically on semirich medium. Of these, 323 have essential gene homologs in the alphaproteobacterium Caulobacter crescentus, and 187 have essential gene homologs in Escherichia coli. There were 24 R. palustris genes that were essential for viability under aerobic growth conditions that have low sequence identity but are likely to be functionally homologous to essential E. coli genes. As expected, certain functional categories of essential genes were highly conserved among the three organisms, including translation, ribosome structure and biogenesis, secretion, and lipid metabolism. R. palustris cells divide by budding in which a sessile cell gives rise to a motile swarmer cell. Conserved cell cycle genes required for this developmental process were essential in both C. crescentus and R. palustris. Our results suggest that despite vast differences in lifestyles, members of the alphaproteobacteria have a common set of essential genes that is specific to this group and distinct from that of gammaproteobacteria like E. coli. IMPORTANCE Essential genes in bacteria and other organisms are those absolutely required for viability. Rhodopseudomonas palustris has served as a model organism for studies of anaerobic aromatic compound degradation, hydrogen gas production, nitrogen fixation, and photosynthesis. We used the technique of Tn-seq to determine the essential genes of R. palustris grown under heterotrophic aerobic conditions. The transposon library generated in this study will be useful for future studies to identify R. palustris genes essential for viability under specialized growth conditions and also for survival under conditions of stress.
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Hydrogen Production by Photoreactive Nanoporous Latex Coatings of Nongrowing Rhodopseudomonas palustris CGA009
Biotechnology Progress, 2008Co-Authors: Jimmy L. Gosse, Caroline S Harwood, Brian J. Engel, Federico E. Rey, L. E. Scriven, Michael C. FlickingerAbstract:Nonuniform light distribution is a fundamental limitation to biological hydrogen production by phototrophic bacteria. Numerous light distribution designs and culture conditions have been developed to reduce self-shading and nonuniform reactivity within bioreactors. In this study, highly concentrated (2.0 x 108 CFU/muL formulation) nongrowing Rhodopseudomonas palustris CGA009 were immobilized in thin, nanoporous, latex coatings. The coatings were used to study hydrogen production in an argon atmosphere as a function of coating composition, thickness, and light intensity. These coatings can be generated aerobically or anaerobically and are more reactive than an equivalent number of suspended or settled cells. Rhodopseudomonas palustris latex coatings remained active after hydrated storage for greater than 3 months in the dark and over 1 year when stored at -80 degrees C. The initial hydrogen production rate of the microphotobioreactors containing 6.25 cm2, 58.4 mum thick Rps. palustris latex coatings illuminated by 34.1 PAR mumol photons m-2 s-1 was 6.3 mmol H2 m-2 h-1 and had a final yield of 0.55 mol H2 m-2 in 120 h. A dispersible latex blend has been developed for direct comparison of the specific activity of settled, suspended, and immobilized Rps. palustris.
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Final report: 'Rhodopseudomonas palustris' genome workshop to be held in Spring of 2001
2002Co-Authors: Caroline S HarwoodAbstract: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.
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Rhodopseudomonas palustris genome project. Final report
2000Co-Authors: Caroline S HarwoodAbstract: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.
Lan Wang - One of the best experts on this subject based on the ideXlab platform.
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reduction of selenite to red elemental selenium by Rhodopseudomonas palustris strain n
PLOS ONE, 2014Co-Authors: Na Liu, Weixin Jing, Jinhua Fan, Longyan Zhang, Xiaofeng Zhang, Zhaoming Zhang, Lan WangAbstract:The trace metal selenium is in demand for health supplements to human and animal nutrition. We studied the reduction of selenite (SeO3−2) to red elemental selenium by Rhodopseudomonas palustris strain N. This strain was cultured in a medium containing SeO3−2 and the particles obtained from cultures were analyzed using transmission electron microscopy (TEM), energy dispersive microanalysis (EDX) and X ray diffraction analysis (XRD). Our results showed the strain N could reduce SeO3−2 to red elemental selenium. The diameters of particles were 80–200 nm. The bacteria exhibited significant tolerance to SeO3−2 up to 8.0 m mol/L concentration with an EC50 value of 2.4 m mol/L. After 9 d of cultivation, the presence of SeO32− up to 1.0 m mol/L resulted in 99.9% reduction of selenite, whereas 82.0% (p<0.05), 31.7% (p<0.05) and 2.4% (p<0.05) reduction of SeO3−2 was observed at 2.0, 4.0 and 8.0 m mol/L SeO32− concentrations, respectively. This study indicated that red elemental selenium was synthesized by green technology using Rhodopseudomonas palustris strain N. This strain also indicated a high tolerance to SeO3−2. The finding of this work will contribute to the application of selenium to human health.
E. I. Kompantseva - One of the best experts on this subject based on the ideXlab platform.
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Isolation and purification of malate dehydrogenase isoforms from phototrophic purple bacteria Rhodobacter sphaeroides and Rhodopseudomonas palustris
Biology Bulletin, 2008Co-Authors: A. T. Eprintsev, M. A. Klimova, K. D. Shikhalieva, E. I. KompantsevaAbstract:A five-step procedure was used to obtain electrophoretically pure preparations of malate dehydrogenase (EC 1.1.1.37) from Rhodobacter sphaeroides and Rhodopseudomonas palustris . The procedure included extraction, ammonium sulfate fractionation, gel filtration, and ion exchange and gel permeation chromatography. The enzyme was found to exist in two isoforms, dimeric and tetrameric, formed by the oligomerization of identical subunits. The isoforms are assumed to be involved in different metabolic processes.
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Regulation of carbon flows in the tricarboxylic acid cycle-glyoxylate bypass system in Rhodopseudomonas palustris under different growth conditions
Microbiology, 2008Co-Authors: A. T. Eprintsev, M. I. Falaleeva, M. A. Klimova, E. I. KompantsevaAbstract:The functional roles of the malate dehydrogenase (MDH) tetrameric and dimeric isoforms in the metabolism of the purple nonsulfur phototrophic bacterium Rhodopseudomonas palustris , strain f-8pt was studied with the use of specific inhibitors. It was shown that the enzyme tetrameric form allows the functioning of the glyoxylate cycle and the dimeric form provides for the operation of the tricarboxylic acid cycle.
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Physicochemical properties of malate dehydrogenase from the bacterium Rhodopseudomonas palustris strain f8pt.
Biochemistry, 2006Co-Authors: Alexander T. Eprintsev, M. I. Falaleeva, M. A. Klimova, E. I. KompantsevaAbstract:Electrophoretically homogenous isoforms of malate dehydrogenase with different quaternary structure were prepared from Rhodopseudomonas palustris strain f8pt cultured photolithoheterotrophically on malate and acetate. By selective inhibition of the tricarboxylic acid cycle or glyoxylate cycle, it was shown that the dimeric isoform of the enzyme is responsible for Krebs cycle functioning and the tetrameric isoform is involved in functioning of the glyoxylate cycle.
Jianming Yang - One of the best experts on this subject based on the ideXlab platform.
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a disjointed pathway for malonate degradation by Rhodopseudomonas palustris
Applied and Environmental Microbiology, 2020Co-Authors: Zhaobao Wang, Caroline S Harwood, Bo Liang, Jianming YangAbstract:The purple nonsulfur phototrophic bacterium Rhodopseudomonas palustris strain CGA009 uses the three-carbon dicarboxylic acid malonate as a sole carbon source under phototrophic conditions. However, this bacterium grows extremely slowly on this compound and does not have operons for the two pathways for malonate degradation that have been described in other bacteria. Many bacteria grow on a spectrum of carbon sources, some of which are classified as “poor” growth substrates because they support slow growth rates. This trait is rarely addressed in the literature, but slow growth is potentially useful in biotechnological applications where it is imperative for bacteria to divert cellular resources to value-added products rather than to growth. This prompted us to explore the genetic and physiological basis for the slow growth of R. palustris with malonate as a carbon source. There are two unlinked genes annotated as encoding a malonyl-CoA synthetase (MatB) and a malonyl-CoA decarboxylase (MatA) in the genome of R. palustris, which we verified as having the predicted functions. Additionally, two tripartite ATP-independent periplasmic transporters (TRAP systems) encoded by rpa2047-2049 and rpa2541-2543 were needed for optimal growth on malonate. Most of these genes were expressed constitutively during growth on several carbon sources, including malonate. Our data indicate that R. palustris uses a piecemeal approach to growing on malonate. The data also raise the possibility that this bacterium will evolve to use malonate efficiently if confronted with an appropriate selection pressure. Importance There is interest in understanding how bacteria metabolize malonate because this three-carbon dicarboxylic acid can serve as a building block in bioengineering applications to generate useful compounds that have an odd number of carbons. We found that the phototrophic bacterium Rhodopseudomonas palustris grows extremely slowly on malonate. We identified two enzymes and two TRAP transporters involved in the uptake and metabolism of malonate, but some of these elements are apparently not very efficient. R. palustris cells growing with malonate have the potential to be excellent biocatalysts because cells would be able to divert cellular resources to the production of value-added compounds instead of to support rapid growth. In addition, our results suggest that R. palustris is a candidate for directed evolution studies to improve growth on malonate and to observe the kinds of genetic adaptations that occur to make a metabolic pathway operate more efficiently.
Luetlok Wong - One of the best experts on this subject based on the ideXlab platform.
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cytochrome p450 enzymes from the metabolically diverse bacterium Rhodopseudomonas palustris
Biochemical and Biophysical Research Communications, 2006Co-Authors: Stephen G Bell, Nicola Hoskins, Domenico Caprotti, Zihe Rao, Luetlok WongAbstract:Four (CYP195A2, CYP199A2, CYP203A1, and CYP153A5) of the seven P450 enzymes, and palustrisredoxin A, a ferredoxin associated with CYP199A2, from the metabolically diverse bacterium Rhodopseudomonas palustris have been expressed and purified. A range of substituted benzenes, phenols, benzaldehydes, and benzoic acids was shown to bind to the four P450 enzymes. Monooxygenase activity of CYP199A2 was reconstituted with palustrisredoxin A and putidaredoxin reductase of the P450cam system from Pseudomonas putida. We found that 4-ethylbenzoate and 4-methoxybenzoate were oxidized to single products, and 4-methoxybenzoate was demethylated to form 4-hydroxybenzoate. Crystals of substrate-free CYP199A2 which diffracted to approximately 2.0A have been obtained.