Publications

2020
Zhang, Yanfei, et al.Genetically encoded biosensors for branched-chain amino acid metabolism to monitor mitochondrial and cytosolic production of isobutanol and isopentanol in yeast”. bioRxiv (2020): n. pag. Web. Publisher's VersionAbstract
Branched-chain amino acid (BCAA) metabolism can be harnessed to produce many valuable chemicals. Among these, isobutanol, which is derived from valine degradation, has received substantial attention due to its promise as an advanced biofuel. While Saccharomyces cerevisiae is the preferred organism for isobutanol production, the lack of isobutanol biosensors in this organism has limited the ability to screen strains at high throughput. Here, we use a transcriptional regulator of BCAA biosynthesis, Leu3p, to develop the first genetically encoded biosensor for isobutanol production in yeast. Small modifications allowed us to redeploy Leu3p in a second biosensor for isopentanol, another BCAA-derived product of interest. Each biosensor is highly specific to isobutanol or isopentanol, respectively, and was used to engineer metabolic enzymes to increase titers. The isobutanol biosensor was additionally employed to isolate high-producing strains, and guide the construction and enhancement of mitochondrial and cytosolic isobutanol biosynthetic pathways, including in combination with optogenetic actuators to enhance metabolic flux. These biosensors promise to accelerate the development of enzymes and strains for branched-chain higher alcohol production, and offer a blueprint to develop biosensors for other products derived from BCAA metabolism.
Carrasco-López, César, et al.Light-responsive monobodies for dynamic control of customizable protein binding”. bioRxiv (2020): n. pag. Web. Publisher's VersionAbstract
Customizable, high affinity protein-protein interactions, such as those mediated by antibodies and antibody-like molecules, are invaluable to basic and applied research and have become pillars for modern therapeutics. The ability to reversibly control the binding activity of these proteins to their targets on demand would significantly expand their applications in biotechnology, medicine, and research. Here we present, as proof-of-principle, a light-controlled monobody (OptoMB) that works in vitro and in vivo, whose affinity for its SH2-domain target exhibits a 300-fold shift in binding affinity upon illumination. We demonstrate that our αSH2-OptoMB can be used to purify SH2-tagged proteins directly from crude E. coli extract, achieving 99.8% purity and over 40% yield in a single purification step. This OptoMB belongs to a new class of light-sensitive protein binders we call OptoBinders (OptoBNDRs) which, by virtue of their ability to be designed to bind any protein of interest, have the potential to find new powerful applications as light-switchable binders of untagged proteins with high affinity and selectivity, and with the temporal and spatial precision afforded by light.
Hammer, Sarah K., Yanfei Zhang, and José L. Avalos. “Mitochondrial Compartmentalization Confers Specificity to the 2-Ketoacid Recursive Pathway: Increasing Isopentanol Production in Saccharomyces cerevisiae”. ACS Synthetic Biology (2020): n. pag. Web. Publisher's Version
2019
Lane, Stephan, et al.Xylose assimilation enhances the production of isobutanol in engineered Saccharomyces cerevisiae”. Biotechnology and Bioengineering 2019. Web. Publisher's VersionAbstract
Abstract Bioconversion of xylose—the second most abundant sugar in nature—into high-value fuels and chemicals by engineered Saccharomyces cerevisiae has been a long-term goal of the metabolic engineering community. Although most efforts have heavily focused on the production of ethanol by engineered S. cerevisiae, yields and productivities of ethanol produced from xylose have remained inferior as compared with ethanol produced from glucose. However, this entrenched focus on ethanol has concealed the fact that many aspects of xylose metabolism favor the production of nonethanol products. Through reduced overall metabolic flux, a more respiratory nature of consumption, and evading glucose signaling pathways, the bioconversion of xylose can be more amenable to redirecting flux away from ethanol towards the desired target product. In this report, we show that coupling xylose consumption via the oxidoreductive pathway with a mitochondrially-targeted isobutanol biosynthesis pathway leads to enhanced product yields and titers as compared to cultures utilizing glucose or galactose as a carbon source. Through the optimization of culture conditions, we achieve 2.6 g/L of isobutanol in the fed-batch flask and bioreactor fermentations. These results suggest that there may be synergistic benefits of coupling xylose assimilation with the production of nonethanol value-added products.
Gil, Agnieszka A., et al.Optogenetic control of protein binding using light-switchable nanobodies”. bioRxiv 2019: n. pag. Print.
Lalwani, Makoto A., et al.Optogenetic lac operon to control chemical and protein production in Escherichia coli with light”. bioRxiv 2019: n. pag. Print.
Lovelett, Robert, José L. Avalos, and IoannisG. Kevrekidis. “Partial observations and conservation laws: Grey-box modeling in biotechnology and optogenetics”. Industrial & Engineering Chemistry Research (2019): n. pag. Print.
Kuroda, Kouichi, et al.Critical Roles of the Pentose Phosphate Pathway and GLN3 in Isobutanol-Specific Tolerance in Yeast”. Cell Systems (2019): n. pag. Print.
Zhang, Yanfei, et al.Xylose utilization stimulates mitochondrial production of isobutanol and 2-methyl-1-butanol in Saccharomyces cerevisiae”. Biotechnology for Biofuels (2019): n. pag. Print.
Zhao, Evan M., et al.Light-based control of metabolic flux through assembly of synthetic organelles”. Nature Chemical Biology (2019). Web. Publisher's VersionAbstract

To maximize a desired product, metabolic engineers typically express enzymes to high, constant levels. Yet, permanent pathway activation can have undesirable consequences including competition with essential pathways and accumulation of toxic intermediates. Faced with similar challenges, natural metabolic systems compartmentalize enzymes into organelles or post-translationally induce activity under certain conditions. Here we report that optogenetic control can be used to extend compartmentalization and dynamic control to engineered metabolisms in yeast. We describe a suite of optogenetic tools to trigger assembly and disassembly of metabolically active enzyme clusters. Using the deoxyviolacein biosynthesis pathway as a model system, we find that light-switchable clustering can enhance product formation six-fold and product specificity 18-fold by decreasing the concentration of intermediate metabolites and reducing flux through competing pathways. Inducible compartmentalization of enzymes into synthetic organelles can thus be used to control engineered metabolic pathways, limit intermediates and favor the formation of desired products.

2018
Bracha, Dan, et al.Mapping Local and Global Liquid Phase Behavior in Living Cells Using Photo-Oligomerizable Seeds”. Cell 175.6 (2018): , 175, 6, 1467–1480. Web. Publisher's Version
Lalwani, Makoto A., Evan M. Zhao, and José L. Avalos. “Current and future modalities of dynamic control in metabolic engineering”. Current Opinion in Biotechnology (2018). Web. Publisher's VersionAbstract
Metabolic engineering aims to maximize production of valuable compounds using cells as biological catalysts. When incorporating engineered pathways into host organisms, an inherent conflict is presented between maintenance of cellular health and generation of products. This challenge has been addressed through two main modalities of dynamic control: decoupling growth from production via two-phase fermentations and autoregulation of pathways to optimize product formation. However, dynamic control can offer even greater potential for metabolic engineering through open-loop and closed-loop control modalities of the production phase. Here we review recent applications of dynamic control strategies in metabolic engineering. We then explore the potential of integrating biosensors and computer-assisted feedback control as a promising future modality of dynamic control.
Zhao, Evan M., et al.Optogenetic regulation of engineered cellular metabolism for microbial chemical production”. Nature (2018). Web. Publisher's VersionAbstract
The optimization of engineered metabolic pathways requires careful control over the levels and timing of metabolic enzyme expression1,2,3,4. Optogenetic tools are ideal for achieving such precise control, as light can be applied and removed instantly without complex media changes. Here we show that light-controlled transcription can be used to enhance the biosynthesis of valuable products in engineered Saccharomyces cerevisiae. We introduce new optogenetic circuits to shift cells from a light-induced growth phase to a darkness-induced production phase, which allows us to control fermentation with only light. Furthermore, optogenetic control of engineered pathways enables a new mode of bioreactor operation using periodic light pulses to tune enzyme expression during the production phase of fermentation to increase yields. Using these advances, we control the mitochondrial isobutanol pathway to produce up to 8.49 ± 0.31 g l−1 of isobutanol and 2.38 ± 0.06 g l−1 of 2-methyl-1-butanol micro-aerobically from glucose. These results make a compelling case for the application of optogenetics to metabolic engineering for the production of valuable products.
2017
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 VersionAbstract
Abstract 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 VersionAbstract

Each 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 VersionAbstract

Summary 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 VersionAbstract

Mitochondrial 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.

2016
Hammer, Sarah K., and Jose L. Avalos. “Metabolic engineering: Biosensors get the green light”. Nat Chem Biol 2016894-895. Web. Publisher's VersionAbstract

A novel approach recruits the largest prokaryotic family of ligand-induced transcriptional regulators to develop a new class of biosensors in yeast based on transcriptional activation, vastly expanding the repertoire of biosensors that could function in eukaryotic hosts.

2013
Avalos, Jose L., Gerald R. Fink, and Gregory Stephanopoulos. “Compartmentalization of metabolic pathways in yeast mitochondria improves the production of branched-chain alcohols”. Nature Biotechnology 31 (2013): , 31, 335-341. Web. Publisher's VersionAbstract

Efforts to improve the production of a compound of interest in Saccharomyces cerevisiae have mainly involved engineering or overexpression of cytoplasmic enzymes. We show that targeting metabolic pathways to mitochondria can increase production compared with overexpression of the enzymes involved in the same pathways in the cytoplasm. Compartmentalization of the Ehrlich pathway into mitochondria increased isobutanol production by 260%, whereas overexpression of the same pathway in the cytoplasm only improved yields by 10%, compared with a strain overproducing enzymes involved in only the first three steps of the biosynthetic pathway. Subcellular fractionation of engineered strains revealed that targeting the enzymes of the Ehrlich pathway to the mitochondria achieves greater local enzyme concentrations. Other benefits of compartmentalization may include increased availability of intermediates, removing the need to transport intermediates out of the mitochondrion and reducing the loss of intermediates to competing pathways.

2009
Tao, Xiao, et al.Crystal Structure of the Eukaryotic Strong Inward-Rectifier K+ Channel Kir2.2 at 3.1 angstrom Resolution”. Science 326 (2009): , 326, 1668-1674. Web. Publisher's VersionAbstract

Inward-rectifier potassium (K+) channels conduct K+ ions most efficiently in one direction, into the cell. Kir2 channels control the resting membrane voltage in many electrically excitable cells, and heritable mutations cause periodic paralysis and cardiac arrhythmia. We present the crystal structure of Kir2.2 from chicken, which, excluding the unstructured amino and carboxyl termini, is 90% identical to human Kir2.2. Crystals containing rubidium (Rb+), strontium (Sr2+), and europium (Eu3+) reveal binding sites along the ion conduction pathway that are both conductive and inhibitory. The sites correlate with extensive electrophysiological data and provide a structural basis for understanding rectification. The channel's extracellular surface, with large structured turrets and an unusual selectivity filter entryway, might explain the relative insensitivity of eukaryotic inward rectifiers to toxins. These same surface features also suggest a possible approach to the development of inhibitory agents specific to each member of the inward-rectifier K+ channel family.

2006
Hoff, Kevin G., et al.Insights into the sirtuin mechanism from ternary complexes containing NAD(+) and acetylated peptide”. Structure 14 (2006): , 14, 1231-1240. Web. Publisher's VersionAbstract

Sirtuin proteins comprise a unique class of NAD(+)-dependent protein deacetylases. Although several structures of sirtuins have been determined, the mechanism by which NAD(+) cleavage occurs has remained unclear. We report the structures of ternary complexes containing NAD(+) and acetylated peptide bound to the bacterial sirtuin Sir2Tm and to a catalytic mutant (Sir2TM(H116Y)). NAD(+) in these structures binds in a conformation different from that seen in previous structures, exposing the alpha face of the nicotinamide ribose to the carbonyl oxygen of the acetyl lysine substrate. The NAD+ conformation is identical in both structures, suggesting that proper coenzyme orientation is not dependent on contacts with the catalytic histidine. We also present the structure of Sir2TM(H116A) bound to deacteylated peptide and 3'-O-acetyl ADP ribose. Taken together, these structures suggest a mechanism for nicotinamide cleavage in which an invariant phenylalanine plays a central role in promoting formation of the O-alkylamidate reaction intermediate and preventing nicotinamide exchange.

Cosgrove, M. S., et al.The structural basis of sirtuin substrate affinity”. Biochemistry 45 (2006): , 45, 7511-7521. Web. Publisher's VersionAbstract

Sirtuins comprise a family of enzymes that catalyze the deacetylation of acetyllysine side chains in a reaction that consumes NAD+. Although several crystal structures of sirtuins bound to non-native acetyl peptides have been determined, relatively little about how sirtuins discriminate among different substrates is understood. We have carried out a systematic structural and thermodynamic analysis of several peptides bound to a single sirtuin, the Sir2 homologue from Thermatoga maritima (Sir2Tm). We report structures of five different forms of Sir2Tm: two forms bound to the p53 C-terminal tail in the acetylated and unacetylated states, two forms bound to putative acetyl peptide substrates derived from the structured domains of histones H3 and H4, and one form bound to polypropylene glycol (PPG), which resembles the apoenzyme. The structures reveal previously unobserved complementary side chain interactions between Sir2Tm and the first residue N-terminal to the acetyllysine (position-1) and the second residue C-terminal to the acetyllysine (position+2). Isothermal titration calorimetry was used to compare binding constants between wild-type and mutant forms of Sir2Tm and between additional acetyl peptide substrates with substitutions at positions-1 and +2. The results are consistent with a model in which peptide positions-1 and + 2 play a significant role in sirtuin substrate binding. This model provides a framework for identifying sirtuin substrates.

2005
Avalos, J. L., K. M. Bever, and C. Wolberger. “Mechanism of sirtuin inhibition by nicotinamide: Altering the NAD(+) cosubstrate specificity of a Sir2 enzyme”. Molecular Cell 17 (2005): , 17, 855-868. Web. Publisher's VersionAbstract

Sir2 enzymes form a unique class of NAD+-dependent deacetylases required for diverse biological processes, including transcriptional silencing, regulation of apoptosis, fat mobilization, and lifespan regulation. Sir2 activity is regulated by nicotinamide, a noncompetitive inhibitor that promotes a base-exchange reaction at the expense of deacetylation. To elucidate the mechanism of nicotinamide inhibition, we determined ternary complex structures of Sir2 enzymes containing nicotinamide. The structures show that free nicotinamide binds in a conserved pocket that participates in NAD(+) binding and catalysis. Based on our structures, we engineered a mutant that deacetylates peptides by using nicotinic acid adenine dinucleotide (NAAD) as a cosubstrate and is inhibited by nicotinic acid. The characteristics of the altered specificity enzyme establish that Sir2 enzymes contain a single site that participates in catalysis and nicotinamide regulation and provides additional insights into the Sir2 catalytic mechanism.

2004
Avalos, J. L., J. D. Boeke, and C. Wolberger. “Structural basis for the mechanism and regulation of Sir2 enzymes”. Molecular Cell 13 (2004): , 13, 639-648. Web. Publisher's VersionAbstract

Sir2 proteins form a family of NAD(+)-dependent protein deacetylases required for diverse biological processes, including transcriptional silencing, suppression of rDNA recombination, control of p53 activity, regulation of acetyl-CoA synthetase, and aging. Although structures of Sir2 enzymes in the presence and absence of peptide substrate or NAD(+) have been determined, the role of the enzyme in the mechanism of cleacetylation and NAD(+) cleavage is still unclear. Here, we present additional structures of Sir2Af2 in several differently complexed states: in a productive complex with NAD(+), in a nonproductive NAD(+) complex with bound ADP-ribose, and in the unliganded state. We observe a new mode of NAD(+) binding that seems to depend on acetyl-lysine binding, in which the nicotinamide ring of NAD(+) is buried in the highly conserved "C" pocket of the enzyme. We propose a detailed structure-based mechanism for cleacetylation and nicotinamide inhibition of Sir2 consistent with mutagenesis and enzymatic studies.

2002
Avalos, J. L., et al.Structure of a Sir2 enzyme bound to an acetylated p53 peptide”. Molecular Cell 10 (2002): , 10, 523-535. Web. Publisher's VersionAbstract

Sir2 proteins are NAD(+)-dependent protein deacetylases that play key roles in transcriptional regulation, DNA repair, and life span regulation. The structure of an archaeal Sir2 enzyme, Sir2-Af2, bound to an acetylated p53 peptide reveals that the substrate binds in a cleft in the enzyme, forming an enzyme-substrate 0 sheet with two flanking strands in Sir2-Af2. The acetyllysine inserts into a conserved hydrophobic tunnel that contains the active site histidine. Comparison with other structures of Sir2 enzymes suggests that the apoenzyme undergoes a conformational change upon substrate binding. Based on the Sir2-Af2 substrate complex structure, mutations were made in the other A. fulgidus sirtuin, Sir2-Af1, that increased its affinity for the p53 peptide.

2000
Smith, J. S., et al.A phylogenetically conserved NAD(+)-dependent protein deacetylase activity in the Sir2 protein family”. Proceedings of the National Academy of Sciences of the United States of America 97 (2000): , 97, 6658-6663. Web. Publisher's VersionAbstract

The yeast Sir2 protein, required for transcriptional silencing, has an NAD(+)-dependent histone deacetylase (HDA) activity. Yeast extracts contain a NAD(+)-dependent HDA activity that is eliminated in a yeast strain from which SIR2 and its four homologs have been deleted. This HDA activity is also displayed by purified yeast Sir2p and homologous Archaeal, eubacterial, and human proteins, and depends completely on NAD(+) in all species tested. The yeast NPT1 gene, encoding an important NAD(+) synthesis enzyme, is required for rDNA and telomeric silencing and contributes to silencing of the HM loci. Null mutants in this gene have significantly reduced intracellular NAD(+) concentrations and have phenotypes similar to sir2 null mutants. Surprisingly, yeast from which all five SIR2 homologs have been deleted have relatively normal bulk histone acetylation levels. The evolutionary conservation of this regulated activity suggests that the Sir2 protein family represents a set of effector proteins in an evolutionarily conserved signal transduction pathway that monitors cellular energy and redox states.