keyword
MENU ▼
Read by QxMD icon Read
search

Rhodobacter

keyword
https://www.readbyqxmd.com/read/28196888/sulfide-responsive-transcriptional-repressor-sqrr-functions-as-a-master-regulator-of-sulfide-dependent-photosynthesis
#1
Takayuki Shimizu, Jiangchuan Shen, Mingxu Fang, Yixiang Zhang, Koichi Hori, Jonathan C Trinidad, Carl E Bauer, David P Giedroc, Shinji Masuda
Sulfide was used as an electron donor early in the evolution of photosynthesis, with many extant photosynthetic bacteria still capable of using sulfur compounds such as hydrogen sulfide (H2S) as a photosynthetic electron donor. Although enzymes involved in H2S oxidation have been characterized, mechanisms of regulation of sulfide-dependent photosynthesis have not been elucidated. In this study, we have identified a sulfide-responsive transcriptional repressor, SqrR, that functions as a master regulator of sulfide-dependent gene expression in the purple photosynthetic bacterium Rhodobacter capsulatus SqrR has three cysteine residues, two of which, C41 and C107, are conserved in SqrR homologs from other bacteria...
February 14, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28177317/structure-of-methylobacterium-extorquens-malyl-coa-lyase-coa-substrate-binding-correlates-with-domain-shift
#2
Javier M González, Ricardo Marti-Arbona, Julian C H Chen, Clifford J Unkefer
Malyl-CoA lyase (MCL) is an Mg(2+)-dependent enzyme that catalyzes the reversible cleavage of (2S)-4-malyl-CoA to yield acetyl-CoA and glyoxylate. MCL enzymes, which are found in a variety of bacteria, are members of the citrate lyase-like family and are involved in the assimilation of one- and two-carbon compounds. Here, the 1.56 Å resolution X-ray crystal structure of MCL from Methylobacterium extorquens AM1 with bound Mg(2+) is presented. Structural alignment with the closely related Rhodobacter sphaeroides malyl-CoA lyase complexed with Mg(2+), oxalate and CoA allows a detailed analysis of the domain motion of the enzyme caused by substrate binding...
February 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28170236/protonation-and-sulfido-versus-oxo-ligation-changes-at-the-molybdenum-cofactor-in-xanthine-dehydrogenase-xdh-variants-studied-by-x-ray-absorption-spectroscopy
#3
Stefan Reschke, Stefan Mebs, Kajsa G V Sigfridsson-Clauss, Ramona Kositzki, Silke Leimkühler, Michael Haumann
Enzymes of the xanthine oxidase family are among the best characterized mononuclear molybdenum enzymes. Open questions about their mechanism of transfer of an oxygen atom to the substrate remain. The enzymes share a molybdenum cofactor (Moco) with the metal ion binding a molybdopterin (MPT) molecule via its dithiolene function and terminal sulfur and oxygen groups. For xanthine dehydrogenase (XDH) from the bacterium Rhodobacter capsulatus, we used X-ray absorption spectroscopy to determine the Mo site structure, its changes in a pH range of 5-10, and the influence of amino acids (Glu730 and Gln179) close to Moco in wild-type (WT), Q179A, and E730A variants, complemented by enzyme kinetics and quantum chemical studies...
February 7, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28167213/metagenomics-approach-to-the-study-of-the-gut-microbiome-structure-and-function-in-zebrafish-danio-rerio-fed-with-gluten-formulated-diet
#4
Hyunmin Koo, Joseph A Hakim, Mickie L Powell, Ranjit Kumar, Peter G Eipers, Casey D Morrow, Michael Crowley, Elliot J Lefkowitz, Stephen A Watts, Asim K Bej
In this study, we report the gut microbial composition and predictive functional profiles of zebrafish, Danio rerio, fed with a control formulated diet (CFD), and a gluten formulated diet (GFD) using metagenomics approach and bioinformatics tools. The microbial communities of the GFD-fed D. rerio displayed heightened abundances of Legionellales, Rhizobiaceae, and Rhodobacter, as compared to the CFD-fed counterparts. Predicted metagenomics of microbial communities (PICRUSt) in GFD-fed D. rerio showed KEGG functional categories corresponding to bile secretion, secondary bile acid biosynthesis, and the metabolism of glycine, serine, and threonine...
February 3, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28118511/lysine-acetylation-regulates-the-function-of-the-global-anaerobic-transcription-factor-fnrl-in-rhodobacter-sphaeroides
#5
Wei Wei, Tong Liu, Xinfeng Li, Ruofan Wang, Wei Zhao, Guoping Zhao, Shimin Zhao, Zhihua Zhou
The metabolism of the purple non-sulfur bacterium Rhodobacter sphaeroides is versatile and it can grow under various conditions. Here, we report evidence that the anaerobic photosynthetic metabolism of R. sphaeroides is regulated by protein lysine acetylation. Using a proteomic approach, 59 acetylated peptides were detected. Among them is the global anaerobic transcription factor FnrL, which regulates the biosynthetic pathway of tetrapyrroles and synthesis of the photosynthetic apparatus. Lysine 223 of FnrL was identified as acetylated...
January 24, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28063363/tracking-bio-hydrogen-mediated-production-of-commodity-chemicals-from-carbon-dioxide-and-renewable-electricity
#6
Sebastià Puig, Ramon Ganigué, Pau Batlle-Vilanova, M Dolors Balaguer, Lluís Bañeras, Jesús Colprim
This study reveals that reduction of carbon dioxide (CO2) to commodity chemicals can be functionally compartmentalized in bioelectrochemical systems. In the present example, a syntrophic consortium composed by H2-producers (Rhodobacter sp.) in the biofilm is combined with carboxidotrophic Clostridium species, mainly found in the bulk liquid. The performance of these H2-mediated electricity-driven systems could be tracked by the activity of a biological H2 sensory protein identified at cathode potentials between -0...
March 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28063359/photofermentative-production-of-hydrogen-and-poly-%C3%AE-hydroxybutyrate-from-dark-fermentation-products
#7
Vincenzo Luongo, Anish Ghimire, Luigi Frunzo, Massimiliano Fabbricino, Giuseppe d'Antonio, Francesco Pirozzi, Giovanni Esposito
The aim of this work is to investigate the hydrogen and poly-β-hydroxybutyrate (PHB) production during the photofermentative treatment of the effluent from a dark fermentation reactor fed with the organic fraction of municipal solid waste. Two different inocula, an adapted culture of Rhodobacter sphaeroides AV1b and a mixed consortium of purple non sulphur bacteria have been investigated under the same operational conditions. Different hydrogen productivities of 364 and 559NmL H2 L(-1) were observed for the Rhodobacter sphaeroides and the mixed culture consortium tests, respectively: the consortium of PNSB resulted 1...
March 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28054547/augmenting-light-coverage-for-photosynthesis-through-yfp-enhanced-charge-separation-at-the-rhodobacter-sphaeroides-reaction-centre
#8
Katie J Grayson, Kaitlyn M Faries, Xia Huang, Pu Qian, Preston Dilbeck, Elizabeth C Martin, Andrew Hitchcock, Cvetelin Vasilev, Jonathan M Yuen, Dariusz M Niedzwiedzki, Graham J Leggett, Dewey Holten, Christine Kirmaier, C Neil Hunter
Photosynthesis uses a limited range of the solar spectrum, so enhancing spectral coverage could improve the efficiency of light capture. Here, we show that a hybrid reaction centre (RC)/yellow fluorescent protein (YFP) complex accelerates photosynthetic growth in the bacterium Rhodobacter sphaeroides. The structure of the RC/YFP-light-harvesting 1 (LH1) complex shows the position of YFP attachment to the RC-H subunit, on the cytoplasmic side of the RC complex. Fluorescence lifetime microscopy of whole cells and ultrafast transient absorption spectroscopy of purified RC/YFP complexes show that the YFP-RC intermolecular distance and spectral overlap between the emission of YFP and the visible-region (QX) absorption bands of the RC allow energy transfer via a Förster mechanism, with an efficiency of 40±10%...
January 5, 2017: Nature Communications
https://www.readbyqxmd.com/read/28032998/pathways-of-transmembrane-electron-transfer-in-cytochrome-bc-complexes-dielectric-heterogeneity-and-interheme-coulombic-interactions
#9
S Bhaduri, V Stadnytskyi, S D Zakharov, S Saif Hasan, Ł Bujnowicz, M Sarewicz, S Savikhin, A Osyczka, W A Cramer
The intramembrane cytochrome bc1 complex of the photosynthetic bacterium Rhodobacter capsulatus and the cytochrome b6f complex, which functions in oxygenic photosynthesis, utilize two pairs of b-hemes in a symmetric dimer to accomplish proton-coupled electron transfer. The transmembrane electron transfer pathway in each complex was identified through the novel use of heme Soret band excitonic circular dichroism (CD) spectra, for which the responsible heme-heme interactions were determined from crystal structures...
February 9, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28011238/effect-of-light-dark-cycles-on-hydrogen-and-poly-%C3%AE-hydroxybutyrate-production-by-a-photoheterotrophic-culture-and-rhodobacter-capsulatus-using-a-dark-fermentation-effluent-as-substrate
#10
Virginia Montiel Corona, Sylvie Le Borgne, Sergio Revah, Marcia Morales
A Rhodobacter capsulatus strain and a photoheterotrophic culture (IZT) were cultivated to produce hydrogen under different light-dark cycles. A dark fermentation effluent (DFE) was used as substrate. It was found that IZT culture had an average cumulative hydrogen production (Paccum H2) of 1300±43mLH2L(-1) under continuous illumination and light-dark cycles of 30 or 60min. In contrast, R. capsulatus reduced its Paccum H2 by 20% under 30:30min light-dark cycles, but tripled its poly-β-hydroxybutyrate (PHB) content (308±2mgPHB gdw(-1)) compared to continuous illumination...
February 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28005286/cover-image-volume-114-number-2-february-2017
#11
Matt S A Wecker, Stephen E Beaton, Robert A Chado, Maria L Ghirardi
The cover image, by Maria L. Ghirardi et al., is based on the Article Development of a Rhodobacter capsulatus self-reporting model system for optimizing light-dependent, [FeFe]-hydrogenase-driven H2 production, DOI: 10.1002/bit.26076.
February 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28000019/long-term-biological-hydrogen-production-by-agar-immobilized-rhodobacter-capsulatus-in-a-sequential-batch-photobioreactor
#12
Kamal Elkahlout, Siamak Alipour, Inci Eroglu, Ufuk Gunduz, Meral Yucel
In this study, agar immobilization technique was employed for biological hydrogen production using Rhodobacter capsulatus DSM 1710 (wild type) and YO3 (hup-mutant) strains in sequential batch process. Different agar and glutamate concentrations were tested with defined nutrient medium. Agar concentration 4% (w/v) and 4 mM glutamate were selected for bacterial immobilization in terms of rate and longevity of hydrogen production. Acetate concentration was increased from 40 to 60-100 and 60 mM gave best results with both bacterial strains immobilized in 4% (w/v) agar...
December 20, 2016: Bioprocess and Biosystems Engineering
https://www.readbyqxmd.com/read/27992646/divalent-cations-increase-dna-repair-activities-of-bacterial-6-4-photolyases
#13
Hongju Ma, Fan Zhang, Elisabeth Ignatz, Martin Suehnel, Peng Xue, Patrick Scheerer, LarsOliver Essen, Norbert Krauß, Tilman Lamparter
The (6-4) photolyases of the FeS-BCP group can be considered as the most ancient type among the large family of cryptochrome and photolyase flavoproteins. In contrast to other photolyases they contain an Fe-S cluster of unknown function, a DMRL chromophore, an interdomain loop which could interact with DNA, and a long C-terminal extension. We compared DNA repair and photoreduction of two members of the FeS-BCP family, Agrobacterium fabrum PhrB and Rhodobacter sphaeroides RsCryB, with a eukaryotic (6-4) photolyase from Ostreococcus, OsCPF, and a member of the class III CPD photolyases, PhrA from A...
December 19, 2016: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/27989806/engineering-electron-metabolism-to-increase-ethanol-production-in-clostridium-thermocellum
#14
Jonathan Lo, Daniel G Olson, Sean Jean-Loup Murphy, Liang Tian, Shuen Hon, Anthony Lanahan, Adam M Guss, Lee R Lynd
The NfnAB (NADH-dependent reduced ferredoxin: NADP(+) oxidoreductase) and Rnf (ion-translocating reduced ferredoxin: NAD(+) oxidoreductase) complexes are thought to catalyze electron transfer between reduced ferredoxin and NAD(P)(+). Efficient electron flux is critical for engineering fuel production pathways, but little is known about the relative importance of these enzymes in vivo. In this study we investigate the importance of the NfnAB and Rnf complexes in Clostridium thermocellum for growth on cellobiose and Avicel using gene deletion, enzyme assays, and fermentation product analysis...
January 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/27956523/the-master-regulators-of-the-fla1-and-fla2-flagella-of-rhodobacter-sphaeroides-control-the-expression-of-their-cognate-chey-proteins
#15
José Hernandez-Valle, Clelia Domenzain, Javier de la Mora, Sebastian Poggio, Georges Dreyfus, Laura Camarena
: Rhodobacter sphaeroides is a α-proteobacterium that has two complete sets of flagellar genes. The fla1 set was acquired by horizontal transfer from an ancestral γ-proteobacterium and is the only set of flagellar genes that is expressed during growth under standard laboratory conditions. The products of these genes assemble a single, subpolar flagellum. In the absence of the Fla1 flagellum, a gain-of-function mutation in the histidine kinase CckA turns on the expression of the fla2 flagellar genes through the response regulator CtrA...
December 12, 2016: Journal of Bacteriology
https://www.readbyqxmd.com/read/27928941/molecular-dynamics-analysis-of-the-structural-and-dynamic-properties-of-the-functionally-enhanced-hepta-variant-of-mouse-5-aminolevulinate-synthase
#16
Insung Na, Shelly DeForte, Bosko M Stojanovski, Gloria C Ferreira, Vladimir N Uversky
Heme biosynthesis, a complex, multistage, and tightly controlled process, starts with 5-aminolevulinate (ALA) production, which, in metazoa and certain bacteria, is a reaction catalyzed by 5-aminolevulinate synthase (ALAS), a pyridoxal 5'-phosphate (PLP)-dependent enzyme. Functional aberrations in ALAS are associated with several human diseases. ALAS can adopt open and closed conformations, with segmental rearrangements of a C-terminal, 16-amino acid loop and an α-helix regulating accessibility to the ALAS active site...
December 8, 2016: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/27910898/hydrogen-overproducing-nitrogenases-obtained-by-random-mutagenesis-and-high-throughput-screening
#17
Emma Barahona, Emilio Jiménez-Vicente, Luis M Rubio
When produced biologically, especially by photosynthetic organisms, hydrogen gas (H2) is arguably the cleanest fuel available. An important limitation to the discovery or synthesis of better H2-producing enzymes is the absence of methods for the high-throughput screening of H2 production in biological systems. Here, we re-engineered the natural H2 sensing system of Rhodobacter capsulatus to direct the emission of LacZ-dependent fluorescence in response to nitrogenase-produced H2. A lacZ gene was placed under the control of the hupA H2-inducible promoter in a strain lacking the uptake hydrogenase and the nifH nitrogenase gene...
December 2, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27902845/cloning-and-heterologous-expression-of-chlorophyll-a-synthase-in-rhodobacter-sphaeroides
#18
Emre M Ipekoğlu, Koray Göçmen, Mehmet T Öz, Muazzez Gürgan, Meral Yücel
Rhodobacter sphaeroides is a purple non-sulfur bacterium which photoheterotrophically produces hydrogen from organic acids under anaerobic conditions. A gene coding for putative chlorophyll a synthase (chlG) from cyanobacterium Prochlorococcus marinus was amplified by nested polymerase chain reaction and cloned into an inducible-expression plasmid which was subsequently transferred to R. sphaeroides for heterologous expression. Induced expression of chlG in R. sphaeroides led to changes in light absorption spectrum within 400-700 nm...
November 30, 2016: Journal of Basic Microbiology
https://www.readbyqxmd.com/read/27900689/novel-tools-for-the-functional-expression-of-metagenomic-dna
#19
Nadine Katzke, Andreas Knapp, Anita Loeschcke, Thomas Drepper, Karl-Erich Jaeger
Functional expression of genes from metagenomic libraries is limited by various factors including inefficient transcription and/or translation of target genes as well as improper folding and assembly of the corresponding proteins caused by the lack of appropriate chaperones and cofactors. It is now well accepted that the use of different expression hosts of distinct phylogeny and physiology can dramatically increase the rate of success. In the following chapter, we therefore describe tools and protocols allowing for the comparative heterologous expression of genes in five bacterial expression hosts, namely Escherichia coli, Pseudomonas putida, Bacillus subtilis, Burkholderia glumae, and Rhodobacter capsulatus...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27871369/co2-reduction-and-organic-compounds-production-by-photosynthetic-bacteria-with-surface-displayed-carbonic-anhydrase-and-inducible-expression-of-phosphoenolpyruvate-carboxylase
#20
Ju-Yong Park, Yang-Hoon Kim, Jiho Min
In Rhodobacter sphaeroides, carbonic anhydrase (CA; EC 4.2.1.1) is a zinc-containing metalloenzyme that catalyzes the reversible hydration of CO2 to HCO3(-) while phosphoenolpyruvate carboxylase (PEPC; 4.1.1.31), an enzyme involved in the carbon metabolism that catalyzed the fixation of CO2 to PEP, is a key factor for biological fixation of CO2 and enhances the production of organic compounds. In this study, the recombinant R. sphaeroides with highly-expressed CA was developed based on a surface displayed system of CA (pJY-OmpCA) on the outer membrane of R...
January 2017: Enzyme and Microbial Technology
keyword
keyword
58629
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"