Dynamic substrate preferences and predicted metabolic properties of a simple microbial consortium

Mapping Intimacies ◽

10.1101/053777 ◽

2016 ◽

Cited By ~ 1

Author(s):

Onur Erbilgin ◽

Benjamin P. Bowen ◽

Suzanne M. Kosina ◽

Stefan Jenkins ◽

Rebecca K. Lau ◽

...

Keyword(s):

Species Interactions ◽

Low Complexity ◽

Biomass Composition ◽

Substrate Preferences ◽

Maximal Growth Rate ◽

Substrate Usage ◽

Metabolic Properties ◽

Global Biogeochemical Cycles ◽

Substrate Mixtures ◽

Kinetics Of

AbstractMicroorganisms are typically found as complex microbial communities that altogether govern global biogeochemical cycles. Microbes have developed highly regulated metabolic capabilities to efficiently use available substrates including preferential substrate usage that can result in diauxic shifts. This and other metabolic behaviors have been discovered in studies of microbes in monoculture when grown on low-complexity (e.g.two-component) mixtures of substrates, however, little is known about how species partition environmental substrates through substrate competition in more complex substrate mixtures. Here we use exometabolomic profiling to examine the time-varying substrate depletion from a mixture of 19 amino acids and glucose by twoPseudomonadsand oneBacillusspecies isolated from ground water. We examine if the first substrates depleted result in maximal growth rate, or relate to growth medium or biomass composition and find surprisingly few correlations. Patterns of substrate depletion are modeled, and these models are used to examine if substrate usage preferences and substrate depletion kinetics of three microbial isolates can be used to predict the metabolism of the pooled isolates in co-culture. We find that most of the substrates fit the model predictions, indicating that the microbes are not altering their behaviors for these substrates in the presence of competitors. Glucose and histidine were depleted more slowly than predicted, while proline, glycine, glutamate, lysine, and arginine were all consumed significantly faster; these compounds highlight substrates that could be involved in species-species interactions within the consortium.Author ContributionsOE, TRN conceived and designed the experimentsOE, BPB, SMK, SJ, RL performed the experimentsOE, BPB, SJ, TRN analyzed the dataOE, TRN wrote the manuscriptTRN contributed materials and analysis tools

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Metabolic properties and kinetics of methanogenic granules

Applied Microbiology and Biotechnology ◽

10.1007/bf00164470 ◽

1993 ◽

Vol 39 (6) ◽

pp. 804-811 ◽

Cited By ~ 18

Author(s):

Wei-Min Wu ◽

J�rgen H. Thiele ◽

Mahendra K. Jain ◽

J. Gregory Zeikus

Keyword(s):

Metabolic Properties ◽

Kinetics Of

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Metabolic and functional differences between brain and spinal cord mitochondria underlie different predisposition to pathology

AJP Regulatory Integrative and Comparative Physiology ◽

10.1152/ajpregu.00528.2010 ◽

2011 ◽

Vol 300 (4) ◽

pp. R844-R854 ◽

Cited By ~ 28

Author(s):

Alexander V. Panov ◽

Nataliya Kubalik ◽

Natalia Zinchenko ◽

Daisy M. Ridings ◽

David A. Radoff ◽

...

Keyword(s):

Spinal Cord ◽

Motor Neurons ◽

Calcium Content ◽

Brain Mitochondria ◽

Respiratory Enzymes ◽

Tissue Calcium ◽

Metabolic Properties ◽

Reverse Electron Transport ◽

Substrate Mixtures ◽

Total Tissue

Mitochondrial dysfunctions contribute to neurodegeneration, the locations of which vary among neurodegenerative diseases. To begin to understand what mechanisms may underlie higher vulnerability of the spinal cord motor neurons in amyotrophic lateral sclerosis, compared with brain mitochondria, we studied three major functions of rat brain mitochondria (BM) and spinal cord mitochondria (SCM) mitochondria: oxidative phosphorylation, Ca2+ sequestration, and production of reactive oxygen species (ROS), using a new metabolic paradigm (Panov et al., J. Biol. Chem. 284: 14448–14456, 2009). We present data that SCM share some unique metabolic properties of the BM. However, SCM also have several distinctions from the BM: 1) With the exception of succinate, SCM show significantly lower rates of respiration with all substrates studied; 2) immunoblotting analysis showed that this may be due to 30–40% lower contents of respiratory enzymes and porin; 3) compared with BM, SCM sequestered 40–50% less Ca2+, and the total tissue calcium content was 8 times higher in the spinal cord; 4) normalization for mitochondria from 1 g of tissue showed that BM can sequester several times more Ca2+ than was available in the brain tissue, whereas SCM had the capacity to sequester only 10–20% of the total tissue Ca2+; and 5) with succinate and succinate-containing substrate mixtures, SCM showed significantly higher state 4 respiration than BM and generated more ROS associated with the reverse electron transport. We conclude that SCM have an intrinsically higher risk of oxidative damage and overload with calcium than BM, and thus spinal cord may be more vulnerable under some pathologic conditions. (250)

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Intrinsically disordered linkers control tethered kinases via effective concentration

10.1101/2020.04.04.023713 ◽

2020 ◽

Cited By ~ 1

Author(s):

Mateusz Dyla ◽

Magnus Kjaergaard

Keyword(s):

Effective Concentration ◽

Scaffolding Proteins ◽

Know How ◽

Intrinsically Disordered ◽

Steady State Kinetics ◽

Interaction Domains ◽

Substrate Usage ◽

Kinase Specificity ◽

Complex Architecture ◽

Kinetics Of

AbstractKinase specificity is crucial to the fidelity of signalling pathways, yet many pathways use the same kinases to achieve widely different effects. Specificity arises in part from the enzymatic domain, but also from the physical tethering of kinases to their substrates. Such tethering can occur via protein interaction domains in the kinase or via anchoring and scaffolding proteins, and can drastically increase the kinetics of phosphorylation. However, we do not know how such intra-complex reactions depend on the link between enzyme and substrate. Here we show that the kinetics of tethered kinases follow a Michaelis-Menten like dependence on effective concentration. We find that phosphorylation kinetics scale with the length of the intrinsically disordered linkers that join the enzyme and substrate, but that the scaling differs between substrates. Steady-state kinetics can only partially predict rates of tethered reactions as product release may obscure the rate of phospho-transfer. Our results suggest that changes in signalling complex architecture not only enhance the rates of phosphorylation reactions, but may also alter the relative substrate usage. This suggests a mechanism for how scaffolding proteins can allosterically modify the output from a signalling pathway.

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Intrinsically disordered linkers control tethered kinases via effective concentration

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2006382117 ◽

2020 ◽

Vol 117 (35) ◽

pp. 21413-21419 ◽

Cited By ~ 1

Author(s):

Mateusz Dyla ◽

Magnus Kjaergaard

Keyword(s):

Effective Concentration ◽

Scaffolding Proteins ◽

Signaling Complex ◽

Intrinsically Disordered ◽

Steady State Kinetics ◽

Interaction Domains ◽

Substrate Usage ◽

Kinase Specificity ◽

Complex Architecture ◽

Kinetics Of

Kinase specificity is crucial to the fidelity of signaling pathways, yet many pathways use the same kinases to achieve widely different effects. Specificity arises in part from the enzymatic domain but also from the physical tethering of kinases to their substrates. Such tethering can occur via protein interaction domains in the kinase or via anchoring and scaffolding proteins and can drastically increase the kinetics of phosphorylation. However, we do not know how such intracomplex reactions depend on the link between enzyme and substrate. Here we show that the kinetics of tethered kinases follow a Michaelis–Menten-like dependence on effective concentration. We find that phosphorylation kinetics scale with the length of the intrinsically disordered linkers that join the enzyme and substrate but that the scaling differs between substrates. Steady-state kinetics can only partially predict rates of tethered reactions as product release may obscure the rate of phosphotransfer. Our results suggest that changes in signaling complex architecture not only enhance the rates of phosphorylation reactions but may also alter the relative substrate usage. This suggests a mechanism for how scaffolding proteins can allosterically modify the output from a signaling pathway.

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Electronic energy pooling in organic systems: a cross-disciplinary tutorial review

Canadian Journal of Chemistry ◽

10.1139/cjc-2017-0369 ◽

2017 ◽

Vol 95 (10) ◽

pp. 1025-1040 ◽

Cited By ~ 6

Author(s):

Ronald P. Steer

Keyword(s):

Species Interactions ◽

Solid Phase ◽

Electronic Energy ◽

Excited Singlet ◽

Standard Format ◽

Organic Systems ◽

Energy Pooling ◽

Phase Systems ◽

Exciton Annihilation ◽

Kinetics Of

Electronic energy pooling via excited state (exciton) annihilation, primarily in organic systems, is reviewed in tutorial form. Cross-disciplinary terminologies and references are used and reference is made to the historical origins of the phenomena. Applications in organic photovoltaic and electroluminescent devices are addressed. Particular attention is paid to the kinetics of the processes involved; a standard format for all systems is developed. Within the organic materials framework, all triplet–triplet, triplet–singlet, and singlet–singlet annihilation processes are discussed. Examples from gas, liquid, and solid phase systems, including both homo- and hetero-species interactions, are employed. Particular attention is given to triplet–triplet annihilation processes in which product states other than the lowest excited singlet state are formed.

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Competitive growth kinetics of Sphaerotilus natans and Acinetobacter anitratus

Water Science & Technology ◽

10.2166/wst.2002.0454 ◽

2002 ◽

Vol 46 (1-2) ◽

pp. 45-48 ◽

Cited By ~ 6

Author(s):

E.M. Contreras ◽

L. Giannuzzi ◽

N.E. Zaritzky

Keyword(s):

Growth Kinetics ◽

Mixed Cultures ◽

Biomass Composition ◽

Competitive Growth ◽

Microbial Composition ◽

Sphaerotilus Natans ◽

Analysis Technique ◽

Quantitative Image ◽

Micro Organisms ◽

Kinetics Of

Growth kinetics of Sphaerotilus natans and Acinetobacter anitratus (strain E932) in pure and mixed cultures were analysed. In order to determine mixed cultures biomass composition, a quantitative image analysis technique was developed. Pure culture studies showed that for dilution rates less than 0.188 h−1, the filamentous micro-organism will predominate leading to bulking phenomena. By using the developed technique to determine biomass composition, mixed culture experiments showed that changes in the dilution rate modify the microbial composition of the biomass determining which micro-organisms predominate. The stated equations that predict the predominance of S. natans at low dilution rates agree satisfactorily with the obtained results.

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A generic approach for studying the kinetics of liquid-liquid phase separation under near-native conditions

10.1101/563700 ◽

2019 ◽

Author(s):

Joris van Lindt ◽

Anna Bratek-Skicki ◽

Donya Pakravan ◽

Ludo Van Den Bosch ◽

Dominique Maes ◽

...

Keyword(s):

Phase Separation ◽

Liquid Phase ◽

Cell Biology ◽

Low Complexity ◽

Liquid Phase Separation ◽

Ph Values ◽

Phase Separation Behavior ◽

Kinetics Of ◽

Separation Behavior ◽

Liquid Liquid Phase Separation

Understanding the kinetics and underlying physicochemical forces of liquid-liquid phase separation (LLPS) is of paramount importance in cell biology, requiring reproducible methods for the analysis of often severely aggregation-prone proteins. Frequently applied approaches, such as dilution of the protein from an urea-containing solution or cleavage of its fused solubility tag, however, often lead to very different kinetic behaviors. Here we suggest that at extreme pH values even proteins such as the low-complexity domain (LCD) of hnRNPA2, TDP-43, and NUP-98 can be kept in solution, and then their LLPS can be induced by a jump to native pH, resulting in a system that can be easily controlled. This approach represents a generic method for studying LLPS under near native conditions, providing a platform for studying the phase-separation behavior of diverse proteins.

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Structural and Gasification Kinetic Studies on Co-pyrolysis Chars of Coal and Biomass

10.21203/rs.3.rs-524028/v1 ◽

2021 ◽

Author(s):

Lang Liu ◽

Jingsong Zeng ◽

Qingrui Jiao ◽

Shan Ren ◽

Jian Yang ◽

...

Keyword(s):

Thermogravimetric Analysis ◽

Porous Structure ◽

Kinetic Studies ◽

Activation Energies ◽

Biomass Composition ◽

Pore Model ◽

Gasification Reactivity ◽

Char Gasification ◽

The Relationship ◽

Kinetics Of

Abstract In the present study, the CO2 gasification behaviours of the co-pyrolysis chars with coal and biomass as feedstock were investigated using isothermal thermogravimetric analysis (TGA) at 950–1150 °C. The TGA results demonstrated that the char gasification reactivity was improved at higher biomass composition. In addition, the char characteristics results evaluation revealed that biomass promoted the development of a porous structure and inhibited the formation of graphite-like carbon during the co-pyrolysis of coal and biomass. Moreover, an extended random pore model (eRPM) was proposed to define the char gasification kinetics of coal and biomass. It was found that the activation energies of chars decreased with increasing biomass composition. Lastly, the relationship between the gasification reactivity and char characteristics was evaluated.

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Sulphate-Reducing Microorganisms: the Study of Phylogenetic Community Composition, Metabolic Properties, a Role in Natural and Anthropogenic Ecosystems

Vestnik Volgogradskogo Gosudarstvennogo Universiteta Serija 11 Estestvennye nauki ◽

10.15688/jvolsu11.2018.2.7 ◽

2018 ◽

pp. 42-45

Author(s):

Andrey Brukhanov ◽

Nicolay Pimenov ◽

Tatyana Khizniak

Keyword(s):

Water Column ◽

Black Sea ◽

Sulfate Reducing Bacteria ◽

The Black Sea ◽

Sulfate Reducing ◽

Pure Cultures ◽

Metabolic Properties ◽

Global Biogeochemical Cycles ◽

Biological Methods ◽

Reducing Bacteria

Representatives of sulfate-reducing bacteria are among the oldest microorganisms on Earth and play a key role in the global biogeochemical cycles of carbon and sulfur, especially in marine ecosystems. Using the modern molecular biological methods based on the analysis of genes 16S rRNA and dsrAB the heterogeneous phylogenetic composition of different communities of sulfate-reducing bacteria in the water column and sediments of the Barents, Baltic and Black seas was studied. In particular, we have found representatives of the genera Desulfovibrio,Desulfomicrobium, Desulfotomaculum, Desulfococcus, Desulfosarcina, Desulfobacter. For the first time, pure cultures were obtained and the psychrophilic black sea sulfate-reducing bacteria from the water column and bottom sediments of the Black sea were fully characterized. In particular, we described as a new species of Desulfofrigus euxinos, which has a wider range of used donors and electron acceptors than a typical strain.

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