Hammer, Sarah K., and José L. Avalos. “
Uncovering the role of branched-chain amino acid transaminases in Saccharomyces cerevisiae isobutanol biosynthesis”.
Metabolic Engineering (2017): , -. Web.
Publisher's VersionAbstractAbstract Isobutanol and other branched-chain higher alcohols (BCHAs) are promising advanced biofuels derived from the degradation of branched-chain amino acids (BCAAs). The yeast Saccharomyces cerevisiae is a particularly attractive host for the production of \BCHAs\ due to its high tolerance to alcohols and prevalent use in the bioethanol industry. Degradation of \BCAAs\ begins with transamination reactions, catalyzed by branched-chain amino acid transaminases (BCATs) located in the mitochondria (Bat1p) and cytosol (Bat2p). However, the roles that these transaminases play in isobutanol production remain poorly understood and obscured by conflicting reports in the literature. In this work, we elucidate the influence of \BCATs\ on isobutanol production in two genetic backgrounds (CEN.PK2-1C and BY4741). In the process, we uncover and characterize two competing isobutanol pathways, which can be manipulated by overexpressing or deleting \BAT1\ or BAT2, and adding or removing valine from the fermentation media. We show that deletion of \BAT1\ alone increases isobutanol production by 14.2-fold over wild type strains in media lacking valine, and examine how interactions between valine and the regulatory protein Ilv6p affect isobutanol production. Compartmentalizing the five-gene isobutanol biosynthetic pathway in mitochondria of \BAT1\ deletion strains results in an additional 2.1-fold increase in isobutanol production in the absence of valine. While valine inhibits isobutanol production, it boosts 2-methyl-1-butanol production. This work clarifies the role of transamination activity in \BCHA\ biosynthesis, and develops valuable strategies and strains for future optimization of isobutanol production.
Hammer, Sarah K., and José L. Avalos. “
Harnessing yeast organelles for metabolic engineering”.
Nature Chemical Biology (2017): , 823–832. Web.
Publisher's VersionAbstractEach subcellular compartment in yeast offers a unique physiochemical environment and metabolite, enzyme, and cofactor composition. While yeast metabolic engineering has focused on assembling pathways in the cell cytosol, there is growing interest in embracing subcellular compartmentalization. Beyond harnessing distinct organelle properties, physical separation of organelles from the cytosol has the potential to eliminate metabolic crosstalk and enhance compartmentalized pathway efficiency. In this Perspective we review the state of the art in yeast subcellular engineering, highlighting the benefits of targeting biosynthetic pathways to subcellular compartments, including mitochondria, peroxisomes, the ER and/or Golgi, vacuoles, and the cell wall, in different yeast species. We compare the performances of strains developed with subcellular engineering to those of native producers or yeast strains previously engineered with cytosolic pathways. We also identify important challenges that lie ahead, which need to be addressed for organelle engineering to become as mainstream as cytosolic engineering in academia and industry.
Adesina, Oluwakemi, et al. “
Embracing Biological Solutions to the Sustainable Energy Challenge”.
Chem 21 (2017): ,
2, 1, 20 - 51. Web.
Publisher's VersionAbstractSummary Biological solutions hold unique advantages to address challenges in sustainable energy. Living organisms have evolved for billions of years to solve problems in catalysis, material synthesis, carbon fixation, and energy capture and storage, including not only photosynthesis but also older metabolisms that rely on metal oxidation and reduction. These capabilities offer solutions to problems in sustainable energy, including the safe use of nuclear power, the construction and recycling of batteries, the extraction and processing of rare earth elements, and the carbon-neutral or even carbon-negative synthesis of hydrocarbon fuels. Biological self-repair, self-assembly, and self-replication offer the ability to deploy these capabilities on a global scale, and evolution can be harnessed to accelerate engineering. In this review, we discuss the opportunities for applied biology to contribute to the sustainable energy landscape, the challenges faced, and cutting-edge bioengineering that draws inspiration from fundamental research into biophysics, metabolism, catalysis, and systems biology.
Zhang, Yanfei, and José L. Avalos. “
Traditional and novel tools to probe the mitochondrial metabolism in health and disease”.
Wiley Interdisciplinary Reviews: Systems Biology and Medicine 92 (2017). Web.
Publisher's VersionAbstractMitochondrial metabolism links energy production to other essential cellular processes such as signaling, cellular differentiation, and apoptosis. In addition to producing adenosine triphosphate (ATP) as an energy source, mitochondria are responsible for the synthesis of a myriad of important metabolites and cofactors such as tetrahydrofolate, α-ketoacids, steroids, aminolevulinic acid, biotin, lipoic acid, acetyl-CoA, iron-sulfur clusters, heme, and ubiquinone. Furthermore, mitochondria and their metabolism have been implicated in aging and several human diseases, including inherited mitochondrial disorders, cardiac dysfunction, heart failure, neurodegenerative diseases, diabetes, and cancer. Therefore, there is great interest in understanding mitochondrial metabolism and the complex relationship it has with other cellular processes. A large number of studies on mitochondrial metabolism have been conducted in the last 50 years, taking a broad range of approaches. In this review, we summarize and discuss the most commonly used tools that have been used to study different aspects of the metabolism of mitochondria: ranging from dyes that monitor changes in the mitochondrial membrane potential and pharmacological tools to study respiration or ATP synthesis, to more modern tools such as genetically encoded biosensors and trans-omic approaches enabled by recent advances in mass spectrometry, computation, and other technologies. These tools have allowed the large number of studies that have shaped our current understanding of mitochondrial metabolism. WIREs Syst Biol Med 2017, 9:e1373. doi: 10.1002/wsbm.1373For further resources related to this article, please visit the WIREs website.