More Like this

1. Interpreting metabolic complexity via isotope-assisted metabolic flux analysis

   https://doi.org/10.1016/j.tibs.2023.02.001  

   Moiz, Bilal; Sriram, Ganesh; Clyne, Alisa Morss (June 2023, Trends in Biochemical Sciences)
2. Hierarchical Harmonization of Atom-Resolved Metabolic Reactions across Metabolic Databases

   https://doi.org/10.3390/metabo11070431  

   Jin, Huan; Moseley, Hunter N. (July 2021, Metabolites)

   null (Ed.)

   Metabolic models have been proven to be useful tools in system biology and have been successfully applied to various research fields in a wide range of organisms. A relatively complete metabolic network is a prerequisite for deriving reliable metabolic models. The first step in constructing metabolic network is to harmonize compounds and reactions across different metabolic databases. However, effectively integrating data from various sources still remains a big challenge. Incomplete and inconsistent atomistic details in compound representations across databases is a very important limiting factor. Here, we optimized a subgraph isomorphism detection algorithm to validate generic compound pairs. Moreover, we defined a set of harmonization relationship types between compounds to deal with inconsistent chemical details while successfully capturing atom-level characteristics, enabling a more complete enabling compound harmonization across metabolic databases. In total, 15,704 compound pairs across KEGG (Kyoto Encyclopedia of Genes and Genomes) and MetaCyc databases were detected. Furthermore, utilizing the classification of compound pairs and EC (Enzyme Commission) numbers of reactions, we established hierarchical relationships between metabolic reactions, enabling the harmonization of 3856 reaction pairs. In addition, we created and used atom-specific identifiers to evaluate the consistency of atom mappings within and between harmonized reactions, detecting some consistency issues between the reaction and compound descriptions in these metabolic databases. 

   more » « less
3. Metabolic scaling as an emergent outcome of variation in metabolic rate

   https://doi.org/10.1098/rstb.2022.0495  

   Naug, Dhruba (February 2024, Philosophical Transactions of the Royal Society B: Biological Sciences)

   The allometric scaling of metabolic rate and what drives it are major questions in biology with a long history. Since the metabolic rate at any level of biological organization is an emergent property of its lower-level constituents, it is an outcome of the intrinsic heterogeneity among these units and the interactions among them. However, the influence of lower-level heterogeneity on system-level metabolic rate is difficult to investigate, given the tightly integrated body plan of unitary organisms. In this context, social insects such as honeybees can serve as important model systems because unlike unitary organisms, these superorganisms can be taken apart and reassembled in different configurations to study metabolic rate and its various drivers at different levels of organization. This commentary discusses the background of such an approach and how combining it with artificial selection to generate heterogeneity in metabolic rate with an analytical framework to parse out the different mechanisms that contribute to the effects of heterogeneity can contribute to the various models of metabolic scaling. Finally, the absence of the typical allometric scaling relationship among different species of honeybees is discussed as an important prospect for deciphering the role of top-down ecological factors on metabolic scaling. This article is part of the theme issue ‘The evolutionary significance of variation in metabolic rates’. 

   more » « less
4. Can Sex-Specific Metabolic Rates Provide Insight into Patterns of Metabolic Scaling?

   https://doi.org/10.1093/icb/icac135  

   Somjee, Ummat; Shankar, Anusha; Falk, Jay J (August 2022, Integrative and Comparative Biology)

   Abstract Females and males can exhibit striking differences in body size, relative trait size, physiology, and behavior. As a consequence, the sexes can have very different rates of whole-body energy use, or converge on similar rates through different physiological mechanisms. Yet many studies that measure the relationship between metabolic rate and body size only pay attention to a single sex (more often males), or do not distinguish between sexes. We present four reasons why explicit attention to energy-use between the sexes can yield insight into the physiological mechanisms that shape broader patterns of metabolic scaling in nature. First, the sexes often differ considerably in their relative investment in reproduction, which shapes much of life-history and rates of energy use. Second, males and females share a majority of their genome but may experience different selective pressures. Sex-specific energy profiles can reveal how the energetic needs of individuals are met despite the challenge of within-species genetic constraints. Third, sexual selection often pushes growth and behavior to physiological extremes. Exaggerated sexually selected traits are often most prominent in one sex, can comprise up to 50% of body mass, and thus provide opportunities to uncover energetic constraints of trait growth and maintenance. Finally, sex-differences in behavior such as mating-displays, long-distance dispersal, and courtship can lead to drastically different energy allocation among the sexes; the physiology to support this behavior can shape patterns of metabolic scaling. The mechanisms underlying metabolic scaling in females, males, and hermaphroditic animals can provide opportunities to develop testable predictions that enhance our understanding of energetic scaling patterns in nature. 

   more » « less
5. Bacterial microcompartments: catalysis-enhancing metabolic modules for next generation metabolic and biomedical engineering

   https://doi.org/10.1186/s12915-019-0691-z  

   Kirst, Henning; Kerfeld, Cheryl A. (December 2019, BMC Biology)