scholarly journals Functional Annotation Analytics of Rhodopseudomonas palustris Genomes

2011 ◽  
Vol 5 ◽  
pp. BBI.S7316 ◽  
Author(s):  
Shaneka S. Simmons ◽  
Raphael D. Isokpehi ◽  
Shyretha D. Brown ◽  
Donee L. Mcallister ◽  
Charnia C. Hall ◽  
...  
Keyword(s):  
Sugar Content ◽  
Pfam Domain ◽  
Rhodopseudomonas Palustris ◽  
Protein Family ◽  
Hydrogen Gas ◽  
Integrated Analysis ◽  
Limiting Factor ◽  
Genome Sequences ◽  
Functional Annotations ◽  
Metabolic Versatility

Rhodopseudomonas palustris, a nonsulphur purple photosynthetic bacteria, has been extensively investigated for its metabolic versatility including ability to produce hydrogen gas from sunlight and biomass. The availability of the finished genome sequences of six R. palustris strains (BisA53, BisB18, BisB5, CGA009, HaA2 and TIE-1) combined with online bioinformatics software for integrated analysis presents new opportunities to determine the genomic basis of metabolic versatility and ecological lifestyles of the bacteria species. The purpose of this investigation was to compare the functional annotations available for multiple R. palustris genomes to identify annotations that can be further investigated for strain-specific or uniquely shared phenotypic characteristics. A total of 2,355 protein family Pfam domain annotations were clustered based on presence or absence in the six genomes. The clustering process identified groups of functional annotations including those that could be verified as strain-specific or uniquely shared phenotypes. For example, genes encoding water/glycerol transport were present in the genome sequences of strains CGA009 and BisB5, but absent in strains BisA53, BisB18, HaA2 and TIE-1. Protein structural homology modeling predicted that the two orthologous 240 aa R. palustris aquaporins have water-specific transport function. Based on observations in other microbes, the presence of aquaporin in R. palustris strains may improve freeze tolerance in natural conditions of rapid freezing such as nitrogen fixation at low temperatures where access to liquid water is a limiting factor for nitrogenase activation. In the case of adaptive loss of aquaporin genes, strains may be better adapted to survive in conditions of high-sugar content such as fermentation of biomass for biohydrogen production. Finally, web-based resources were developed to allow for interactive, user-defined selection of the relationship between protein family annotations and the R. palustris genomes.

scholarly journals Calvin Cycle Flux, Pathway Constraints, and Substrate Oxidation State Together Determine the H2 Biofuel Yield in Photoheterotrophic Bacteria

mBio ◽  
2011 ◽  
Vol 2 (2) ◽  
Author(s):  
James B. McKinlay ◽  
Caroline S. Harwood
Keyword(s):  
Organic Compounds ◽  
Oxidation State ◽  
Rhodopseudomonas Palustris ◽  
Calvin Cycle ◽  
Substrate Oxidation ◽  
Hydrogen Gas ◽  
Anaerobic Growth ◽  
Anoxygenic Phototrophic Bacteria ◽  
Transportation Fuel ◽  
Content Type

ABSTRACTHydrogen gas (H2) is a possible future transportation fuel that can be produced by anoxygenic phototrophic bacteria via nitrogenase. The electrons for H2are usually derived from organic compounds. Thus, one would expect more H2to be produced when anoxygenic phototrophs are supplied with increasingly reduced (electron-rich) organic compounds. However, the H2yield does not always differ according to the substrate oxidation state. To understand other factors that influence the H2yield, we determined metabolic fluxes inRhodopseudomonas palustrisgrown on13C-labeled fumarate, succinate, acetate, and butyrate (in order from most oxidized to most reduced). The flux maps revealed that the H2yield was influenced by two main factors in addition to substrate oxidation state. The first factor was the route that a substrate took to biosynthetic precursors. For example, succinate took a different route to acetyl-coenzyme A (CoA) than acetate. As a result,R. palustrisgenerated similar amounts of reducing equivalents and similar amounts of H2from both succinate and acetate, even though succinate is more oxidized than acetate. The second factor affecting the H2yield was the amount of Calvin cycle flux competing for electrons. When nitrogenase was active, electrons were diverted away from the Calvin cycle towards H2, but to various extents, depending on the substrate. When Calvin cycle flux was blocked, the H2yield increased during growth on all substrates. In general, this increase in H2yield could be predicted from the initial Calvin cycle flux.IMPORTANCEPhotoheterotrophic bacteria, likeRhodopseudomonas palustris, obtain energy from light and carbon from organic compounds during anaerobic growth. Cells can naturally produce the biofuel H2as a way of disposing of excess electrons. Unexpectedly, feeding cells organic compounds with more electrons does not necessarily result in more H2. Despite repeated observations over the last 40 years, the reasons for this discrepancy have remained unclear. In this paper, we identified two metabolic factors that influence the H2yield, (i) the route taken to make biosynthetic precursors and (ii) the amount of CO2-fixing Calvin cycle flux that competes against H2production for electrons. We show that the H2yield can be improved on all substrates by using a strain that is incapable of Calvin cycle flux. We also contributed quantitative knowledge to the long-standing question of why photoheterotrophs must produce H2or fix CO2even on relatively oxidized substrates.

Integrated analysis of transcriptomic and metabolomic data reveals critical metabolic pathways involved in polyphenol biosynthesis in Nicotiana tabacum under chilling stress

2019 ◽  
Vol 46 (1) ◽  
pp. 30 ◽  
Author(s):  
Peilu Zhou ◽  
Qiyao Li ◽  
Guangliang Liu ◽  
Na Xu ◽  
Yinju Yang ◽  
...  
Keyword(s):  
Nicotiana Tabacum ◽  
Chilling Stress ◽  
Lignin Biosynthesis ◽  
Cinnamyl Alcohol Dehydrogenase ◽  
Integrated Analysis ◽  
Limiting Factor ◽  
Active Metabolites ◽  
Cold Temperatures ◽  
Flight Mass Spectrometry ◽  
Key Steps

Chilling stress increases the amount of polyphenols, especially lignin, which protects tobacco (Nicotiana tabacum L. cv. k326) from chilling stress. To clarify the molecular biosynthesis mechanism of the key representative compounds, specifically lignin, RNA sequencing and ultra-high pressure liquid chromatography coupled to quadrupole-time of flight mass spectrometry technologies were used to construct transcriptomic and metabolomic libraries from the leaves of tobacco plants subjected to normal (25°C) and chilling (4°C) temperature treatments. Transcriptomic libraries from the different samples were sequenced, generating more than 40million raw reads. Among nine samples, metabolomic analysis identified a total of 97 encoding enzymes that function in the key steps of pathways related to polyphenol biosynthesis, where 42 metabolites were also located. An integrated analysis of metabolic and transcriptomic data revealed that most of the intermediate metabolites and enzymes related to lignin biosynthesis were synthesised in the leaves under chilling stress, which suggests that the biosynthesis of lignin plays an important role in the response of tobacco leaves to cold temperatures. In addition, the cold insensitivity of chalcone synthase genes might be considered to be an important rate-limiting factor in the process of precursor substance flow to flavonoid biosynthesis under chilling stress. Furthermore, the upregulated expression of phenylalanine ammonia lyase (PAL), hydroxycinnamoyl transferase (HCT) and cinnamyl-alcohol dehydrogenase (CAD) under chilling stress is the key to an increase in lignin synthesis. This study provides a hypothetical basis for the screening of new active metabolites and the metabolic engineering of polyphenols in tobacco.

scholarly journals CATH: expanding the horizons of structure-based functional annotations for genome sequences

2018 ◽  
Vol 47 (D1) ◽  
pp. D280-D284 ◽  
Author(s):  
Ian Sillitoe ◽  
Natalie Dawson ◽  
Tony E Lewis ◽  
Sayoni Das ◽  
Jonathan G Lees ◽  
...  
Keyword(s):  
Genome Sequences ◽  
Functional Annotations

scholarly journals The climatic rhythm and blooms of cyanobacteria in a tropical reservoir in São Paulo, Brazil

2014 ◽  
Vol 74 (1) ◽  
pp. 72-78 ◽  
Author(s):  
I Ogashawara ◽  
JA Zavattini ◽  
JG Tundisi
Keyword(s):  
Water Quality ◽  
Meteorological Data ◽  
Polar Front ◽  
Sao Paulo ◽  
Cyanobacterial Blooms ◽  
Metropolitan Region ◽  
Integrated Analysis ◽  
Limiting Factor ◽  
São Paulo ◽  
Tropical Reservoir

The present study sought to develop a methodology to analyse water quality based on the concepts and methods of climate and climatology. Accordingly, we attempted to relate hydro- and limnometeorological techniques and methodologies to a rhythmic analysis technique developed within the context of the Brazilian geographical climatology. Our goal was to assess and analyse cyanobacterial blooms, the main index of water quality for the reservoirs of the “Alto Tietê” Basin and, consequently, the Metropolitan Region of São Paulo, an area of high environmental complexity due to its high degree of development and high population density. The meteorological data used were collected by the Institute of Astronomy, Geophysics and Atmospheric Sciences at the University of São Paulo meteorological station, and the limnological data were collected through the Hydrological Monitoring System implemented by SABESP in the Billings and Guarapiranga Reservoirs and the laboratory of the same entity. The rhythmic and integrated analysis showed that the process of cyanobacterial blooms is dependent on a combination of meteorological factors as temperature and wind intensity that may disrupt the stability of the reservoir, providing the conditions necessary for the development of cyanobacteria during the stabilisation process. The pace of the Atlantic Polar Front Entrance during the winter in São Paulo is a limiting factor for the growth of cyanobacteria because of their high frequency, thus maintaining the balance of the reservoir throughout this period. The weather types those could cause a instability in the water column were: Cold Front entrance (66.67%), conflict between masses (22.22%) and the Tropical Instability Line (11.11%). The possibility for prevention and forecasting periods advise when these reservoirs should not be used, mainly with regard to recreational activities.

A STUDY OF THE RELATIVE VALUE OF HONEY AND SUCROSE IN BREAD MANUFACTURE

1930 ◽  
Vol 3 (6) ◽  
pp. 543-559 ◽  
Author(s):  
W. F. Geddes ◽  
C. A. Winkler
Keyword(s):  
Sugar Content ◽  
Gas Production ◽  
Reducing Sugar ◽  
Limiting Factor ◽  
Loaf Volume ◽  
Usual Manner ◽  
Relative Value ◽  
Significant Difference ◽  
Comparison Of The Results ◽  
Baking Industry

Honey was substituted for commercial sucrose in various straight-dough bread baking formulae, the doughs fermented for varying times and proofed and baked in the usual manner. No significant difference in loaf volume, flavor, or other bread characteristics could be detected, indicating that honey possesses no superiority over sucrose but is of equal value when compared on the basis of equivalent sugar content. The baking tests were supplemented by studies on the rate of gas production in doughs and also by determinations of the reducing-sugar content of the doughs at the end of the proof period. Rate of gas production was similar and the reducing-sugar content of the doughs were of the same order. A comparison of the results obtained by the different baking formulae indicate the importance of considering the formula in relation to the apparent fermentation tolerance of a flour. No difference was observed in the rate of gas production in partially buffered yeast-honey and yeast-sucrose suspensions of equivalent sugar content prepared in a manner to simulate conditions in fermenting bread doughs. Studies on the rate of inversion of sucrose by yeast showed that the rate of invertase action exceeds the speed of zymase action and indicate that sucrose inversion is not a limiting factor in the rate of gas production in bread doughs. An extension of the market for honey in the baking industry would seem to lie in the direction of increasing its use in sweet goods where its flavor, higher sweetening power and greater hygroscopicity are particularly advantageous—the last in relation to checking. In bread manufacture these properties do not come into play since the relatively low percentage of sugar used is to a large extent removed by fermentation.

scholarly journals Phototrophic lactate utilization by Rhodopseudomonas palustris is stimulated by co-utilization with additional substrates

2018 ◽  
Author(s):  
Alekhya Govindaraju ◽  
James B McKinlay ◽  
Breah LaSarre
Keyword(s):  
Organic Acids ◽  
Rhodopseudomonas Palustris ◽  
Substrate Utilization ◽  
Carbon Utilization ◽  
Mixed Substrate ◽  
Metabolic Versatility ◽  
Carbon Substrates ◽  
Glycerol Utilization ◽  
Lactate Utilization ◽  
Time Frames

The phototrophic purple nonsulfur bacterium Rhodopseudomonas palustris is known for its metabolic versatility and is of interest for various industrial and environmental applications. Despite decades of research on R. palustris growth under diverse conditions, patterns of R. palustris growth and carbon utilization with mixtures of carbon substrates remain largely unknown. R. palustris readily utilizes most short chain organic acids but cannot readily use lactate as a sole carbon source. Here we investigated the influence of mixed-substrate utilization on phototrophic lactate consumption by R. palustris. We found that lactate was simultaneously utilized with a variety of other organic acids and glycerol in time frames that were insufficient for R. palustris growth on lactate alone. Thus, lactate utilization by R. palustris was expedited by its co-utilization with additional substrates. Separately, experiments using carbon pairs that did not contain lactate revealed acetate-mediated inhibition of glycerol utilization in R. palustris. This inhibition was specific to the acetate-glycerol pair, as R. palustris simultaneously utilized acetate or glycerol when either was paired with succinate or lactate. Overall, our results demonstrate that (i) R. palustris commonly employs simultaneous mixed-substrate utilization, (ii) mixed-substrate utilization expands the spectrum of readily utilized organic acids in this species, and (iii) R. palustris has the capacity to exert carbon catabolite control in a substrate-specific manner.

scholarly journals Modeling the Interplay between Photosynthesis, CO2 Fixation, and the Quinone Pool in a Purple Non-Sulfur Bacterium

2019 ◽  
Author(s):  
Adil Alsiyabi ◽  
Cheryl Immethun ◽  
Rajib Saha
Keyword(s):  
Organic Compounds ◽  
Redox State ◽  
Rhodopseudomonas Palustris ◽  
Tca Cycle ◽  
Metabolic Model ◽  
Hydrogen Gas ◽  
A Genome ◽  
Feed Forward Controller ◽  
Quinone Pool

AbstractRhodopseudomonas palustris CGA009 is a purple non-sulfur bacterium (PNSB) that can fix CO2 and nitrogen or break down organic compounds for its carbon and nitrogen requirements. Light, inorganic, and organic compounds can all be used for its source of energy. Excess electrons produced during its metabolic processes can be exploited to produce hydrogen gas or biodegradable polyesters (polyhydroxybutyrate). A genome-scale metabolic model of the bacterium was reconstructed to study the interactions between photosynthesis, carbon dioxide fixation, and the redox state of the quinone pool. A comparison of model-predicted flux values with published in vivo MFA fluxes resulted in predicted errors of 5-19% across four different growth substrates. The model predicted the presence of an unidentified sink responsible for the oxidation of excess quinols generated by the TCA cycle. Furthermore, light-dependent energy production was found to be highly dependent on the rate of quinol oxidation. Finally, the extent of CO2 fixation was predicted to be dependent on the amount of ATP generated through the electron transport cycle, with excess ATP going toward the energy-demanding CBB pathway. Based on this analysis, it is hypothesized that the quinone redox state acts as a feed-forward controller of the CBB pathway, signaling the amount of ATP available.

scholarly journals Towards sustainable bioplastic production in resource limited environments using the photoferroautotrophic and photoelectroautotrophic bacteriumRhodopseudomonas palustrisTIE-1

2017 ◽  
Author(s):  
Tahina Onina Ranaivoarisoa ◽  
Karthikeyan Rengasamy ◽  
Michael S. Guzman ◽  
Rajesh Singh ◽  
Arpita Bose
Keyword(s):  
Energy Source ◽  
Carbon Source ◽  
Organic Carbon ◽  
Ferrous Iron ◽  
Rhodopseudomonas Palustris ◽  
Electron Source ◽  
Light Energy ◽  
Attractive Alternative ◽  
Metabolic Versatility ◽  
Phb Production

ABSTRACTBioplastics are an attractive alternative to petroleum-derived plastics because of the harmful environmental effects of conventional plastics and the impending fossil fuel crisis. Polyhydroxybutyrate (PHB) is a well-known bioplastic that is produced by several microbes using organic carbon sources. Autotrophic (using carbon dioxide or CO2) PHB production is reported for only a few organisms. Sustainable PHB bioproduction using other autotrophic microbes needs to be explored.Rhodopseudomonas palustris, a metabolically versatile purple non-sulfur bacterium (PNSB) is known to produce PHBs under photoheterotrophic conditions.Rhodopseudomonas palustrisstrain TIE-1 demonstrates extended metabolic versatility by using electron sources such as ferrous iron and poised electrodes for photoautotrophy. Here we report the ability of TIE-1 to produce PHB under photoferroautotrophic (light - energy source, ferrous iron - electron source and CO2- carbon source) and photoelectroautotrophic (light - energy source, poised electrodes - electron source and CO2- carbon source) growth conditions. PHB accumulation was observed both under nitrogen (N2) fixing and non-N2fixing conditions. For comparison, we determined PHB production under chemoheterotrophic, photoheterotrophic and photoautotrophic conditions using hydrogen as the electron donor. Photoferroautotrophic and photoelectroautotrophic PHB production was on par with that observed from organic carbon substrates such as butyrate. PHB production increased during N2fixation under photoheterotrophic conditions but not during photoautotrophic growth. Electron microscopy confirmed that TIE-1 cells accumulate PHBs internally under the conditions that showed highest production. However, gene expression analysis suggests that PHB cycle genes are not differentially regulated despite observable changes in biopolymer production.

scholarly journals Verrucomicrobial methanotrophs: ecophysiology of metabolically versatile acidophiles

2021 ◽  
Author(s):  
Rob A Schmitz ◽  
Stijn H Peeters ◽  
Wouter Versantvoort ◽  
Nunzia Picone ◽  
Arjan Pol ◽  
...  
Keyword(s):  
Current Knowledge ◽  
Ammonium Nitrogen ◽  
Hydrogen Gas ◽  
Nutrient Cycles ◽  
Nitrogen Gas ◽  
Important Group ◽  
The Past ◽  
Metabolic Versatility ◽  
Genomic Analyses ◽  
Physiological And Biochemical

ABSTRACT Methanotrophs are an important group of microorganisms that counteract methane emissions to the atmosphere. Methane-oxidising bacteria of the Alpha- and Gammaproteobacteria have been studied for over a century, while methanotrophs of the phylum Verrucomicrobia are a more recent discovery. Verrucomicrobial methanotrophs are extremophiles that live in very acidic geothermal ecosystems. Currently, more than a dozen strains have been isolated, belonging to the genera Methylacidiphilum and Methylacidimicrobium. Initially, these methanotrophs were thought to be metabolically confined. However, genomic analyses and physiological and biochemical experiments over the past years revealed that verrucomicrobial methanotrophs, as well as proteobacterial methanotrophs, are much more metabolically versatile than previously assumed. Several inorganic gases and other molecules present in acidic geothermal ecosystems can be utilised, such as methane, hydrogen gas, carbon dioxide, ammonium, nitrogen gas and perhaps also hydrogen sulfide. Verrucomicrobial methanotrophs could therefore represent key players in multiple volcanic nutrient cycles and in the mitigation of greenhouse gas emissions from geothermal ecosystems. Here, we summarise the current knowledge on verrucomicrobial methanotrophs with respect to their metabolic versatility and discuss the factors that determine their diversity in their natural environment. In addition, key metabolic, morphological and ecological characteristics of verrucomicrobial and proteobacterial methanotrophs are reviewed.

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