Biology subjects

Ooka, H.

Publications and source records attributed to Ooka, H..

3 recordsLinked to original sources

bioRxiv2024

Thermodynamics Underpinning the Microbial Community-Level Nitrogen Networks

Nitrogen species often serve as crucial electron donors or acceptors in microbial catabolism, enabling the synthesis of adenosine triphosphate (ATP). Although theoretically any nitrogen redox reactions could be an energy source, it remains unclear why specific reactions are predominantly utilized. This study evaluates energetically superior reactions from 988 theoretically plausible combinations involving 11 nitrogen species, oxygen gas, hydrogen ion, and water. Our analysis of the similarity between this model-based energetically superior network and the actual microbial community-level nitrogen network, reconstructed as a combination of enzymatic reactions, showed increased link overlap rates with thermodynamic weighting on reaction rates. In particular, existing microbial reactions involving solely nitrogen species and additionally oxygen, such as anaerobic ammonia oxidation (ANAMMOX) and complete and partial nitrification, were frequently identified as energetically superior among the examined reactions. The alignment of these reactions with thermodynamically favorable outcomes underscores the critical role of thermodynamics not only in individual metabolic processes but also in shaping the broader network interactions within ecosystems, consequently affecting biodiversity and ecological functions. Significance StatementThis study advances our understanding of how thermodynamics governs energy metabolism at the community level within microbial ecosystems by systematically analyzing 988 potential redox reactions involving inorganic nitrogen species, oxygen gas, hydrogen ion, and water. We uncover that existing microbial reactions, such as anaerobic ammonia oxidation (ANAMMOX) and nitrification, stand out as energetically superior over other examined reactions. The robust alignment between model-predicted energetically favorable reactions and actual microbial nitrogen reactions underscores the predictive power of thermodynamic principles, even in ecological networks. Our findings extend the traditional applications of thermodynamics in biology, highlighting how thermodynamic constraints shape ecological networks and influence biodiversity and ecosystem functions in natural ecosystems.

ecology↗

bioRxiv2023

Diverse Phosphoserine Phosphatases Exhibit Maximum Activity at an Intermediate Binding Affinity in Accord with the Sabatier Principle of Catalysis

A unified framework to rationalize enzymatic activity is essential to understand cellular function and metabolic evolution. Recent studies have shown that the activity of several hydrolases is maximized when the substrate binding affinity (Michaelis-Menten constant: Km) is neither too strong nor too weak. This is because an intermediate Km resolves the trade-off between Km and kcat, in accord with the Sabatier principle of artificial catalysis. However, it remains unclear whether this concept is applicable to enzymes in general, especially for those which catalyze the same reaction but have evolved under different selection pressures due to the phylogeny or physiology of the host organism. Here, we demonstrate that the activity of 10 distinct wild-type phosphoserine phosphatases (PSP) exhibits a maximum at an intermediate binding affinity (Km {approx} 0.5 mM), indicating that they also follow the Sabatier principle. Furthermore, by considering not only Km but also the equilibrium rate constant [Formula] of each enzyme, we have succeeded in rationalizing the PSP activity quantitatively. [Formula] is the rate constant of product release (ES [->] E + P) in the absence of any driving force, and a large [Formula] allows kcat to be increased without increasing Km. Although the traditional Sabatier principle considers only the binding affinity (Km), we show that the additional contribution of [Formula] drastically improves the consistency between experiments and theory. Our expanded framework which quantitatively explains the activity of phylogenetically and physiologically diverse enzymes with respect to their physicochemical parameters may lead to the rational design of highly active enzymes.

biochemistry↗

bioRxiv2023

Universal Design Principle to Enhance Enzymatic Activity using the Substrate Affinity

Design principles to improve enzymatic activity are essential to promote energy-material conversion using biological systems. For more than a century, the Michaelis-Menten equation has provided a fundamental framework of enzymatic activity. However, there is still no concrete guideline on how the parameters should be optimized to enhance enzymatic activity. Here, we demonstrate that tuning the Michaelis-Menten constant (Km) to the substrate concentration (S) maximizes enzymatic activity. This guideline (Km = S) was obtained by applying the Bronsted (Bell)-Evans-Polanyi (BEP) principle of heterogeneous catalysis to the Michaelis-Menten equation, and is robust even with mechanistic deviations such as reverse reactions and inhibition. Furthermore, Km and S are consistent to within an order of magnitude over an experimental dataset of approximately 1000 wild-type enzymes, suggesting that even natural selection follows this principle. The concept of an optimum Km offers the first quantitative guideline towards improving enzymatic activity which can be used for highthroughput enzyme screening.

biochemistry↗