Fukui, S. | Search bioRxiv

bioRxiv2026

Nitrogen metabolic map of Escherichia coli mediated by multi-functional aminotransferases

Nitrogen is a key element of organic molecules essential to all life. Unlike extensively characterized carbon metabolic maps, it remains elusive how assimilated nitrogen flows through metabolic networks. Here we determined the nitrogen metabolic map of Escherichia coli and used it to construct an enzyme-constrained metabolic model that includes multi-functionality of aminotransferase enzymes responsible for nitrogen transfer reactions. We characterized substrate specificities of sixteen E. coli aminotransferase enzymes by evaluating 2,528 reactions, uncovering 56 previously unrecognized activities. The cellular concentrations of these aminotransferase enzymes were quantified and used to estimate their catalytic rates across all enzyme-substrate pairs, leading to improved predictions of nitrogen flows in E. coli. This work advances our fundamental understanding of the nitrogen metabolic map critical for metabolism and growth.

biochemistry↗

bioRxiv2023

Does winterkill explain contrasting demographics of winter-breeding freshwater mussel populations in Ishikari River floodplain?

O_LIEnvironmental conditions bottlenecking species population demographics are less known in cold regions with harsh winters despite of global concerns of declining freshwater mussels (Unionidae). Few studies examined both cold and summer environments in attempts to promote habitat conservation of Unionidae species. C_LIO_LIWe identified the taxonomically confused Unionidae species using phylogenetic analysis with mtDNA (COI region) and tested the hypothesis that winter mortality is the main cause of contrasting population demographics and structures in floodplain lakes in northern Japan. Demographic surveys were conducted in two lakes, which contrasted in recruitment rates, over one year including 4-month ice-covered periods C_LIO_LIAlthough previous studies have identified freshwater mussels as introduced Anemina arcaeformis (Heude 1877) based on morphology, this study confirmed the focal species as potentially native Buldowskia iwakawai (Suzuki, 1939). High winter mortality (30-40%) of adult mussels was found, although the mortality did not significantly differ between the populations with contrasting recruitment. C_LIO_LISurprisingly, the annual mortality was much lower in juveniles (10%) than in gravid and nongravid adult individuals (40-75%). The main inter-population difference was attributed to the higher summer mortality of gravid females, but not juveniles and non-gravid individuals, in the population with low recruitment. C_LIO_LIThese results collectively suggest that summer hypoxia combined with physiological stresses on females in winter is a likely population growth-limiting mechanism. To prevent a chain of adult abundance decreases in winter and high mortality of gravid mussels and newly born juveniles in summer, improvements in summer habitat conditions are necessary, while winter conditions need to be considered simultaneously. Increases in water circulation rates and alleviations of hypoxic conditions is an option for short-term habitat improvement approach. The current study sheds light on the winter-mediated mortality of freshwater mussels in shallow eutrophic floodplain lakes and contributes to improved management strategies for degraded floodplain waterbodies. C_LI

ecology↗