Ithaca, NY | United States
Main Specialties: Biology
Additional Specialties: Environmental Chemistry; Environmental Biochemistry; Environmental Engineering.
Ludmilla Aristilde is currently an Associate Professor in the Department of Biological and Environmental Engineering at Cornell University. Dr. Aristilde completed a B.S. in Science of Earth Systems at Cornell University and obtained her M.S. in Environmental Engineering and Ph.D. in Molecular Toxicology at the University of California-Berkeley. After Berkeley, she went to Grenoble (France) as a Fulbright Scholar to advance her study of contaminant trapping in environmental matrices. Prior to starting her faculty position at Cornell in 2012, she spent three years as a NSF Postdoctoral Fellow at Princeton University where she studied molecular biology tools to address problems at the interface of environmental chemistry and biological processes.
Primary Affiliation: Cornell University - Ithaca, NY , United States
28PubMed Central Citations
Carbohydr Res, doi: 10.1016/j.carres.2018.12.007
The cellulolytic ability of fungal species is important to both natural and engineered biocycling of plant matter. One essential step is the conversion of cellobiose into glucose catalyzed by beta-glucosidases. Mutagenesis studies have implicated altering the substrate binding pocket to influence the pH-activity profile of this enzyme. However, structural understanding of the pH-affected substrate binding environment is lacking. Here we conducted molecular dynamics simulations of fully hydrated TrBgl2, a beta-glucosidase of Trichoderma reesei, equilibrated at its optimal pH (pH 6) and two unfavorable pHs (pH 5 and pH 7.5). We identified structural arrangement of specific residues that facilitated substrate escape from the catalytic site at pH 5 but locked the bound substrate in an unfavorable orientation at pH 7.5. For comparative analysis, we also performed simulations of a mutated TrBgl2 with previously demonstrated improved catalysis as a function of pH. We captured the responsible conformational changes in the engineered substrate binding pocket.
Front Microbiol. 2018; 9: 2789
Frontiers in Microbiology
Bacillus megaterium is a bacterium of great importance as a plant-beneficial bacterium in agricultural applications and in industrial bioproduction of proteins. Understanding intracellular processing of carbohydrates in this species is crucial to predicting natural carbon utilization as well as informing strategies in metabolic engineering. Here, we applied stable isotope-assisted metabolomics profiling and metabolic flux analysis to elucidate, at high resolution, the connections of the different catabolic routes for carbohydrate metabolism immediately following substrate uptake in B. megaterium QM B1551. We performed multiple 13C tracer experiments to obtain both kinetic and long-term 13C profiling of intracellular metabolites. In addition to the direct phosphorylation of glucose to glucose-6-phosphate (G6P) prior to oxidation to 6-phosphogluconate (6P-gluconate), the labeling data also captured glucose catabolism through the gluconate pathway involving glucose oxidation to gluconate followed by phosphorylation to 6P-gluconate. Our data further confirmed the absence of the Entner–Doudoroff pathway in B. megaterium and showed that subsequent catabolism of 6P-gluconate was instead through the oxidative pentose–phosphate (PP) pathway. Quantitative flux analysis of glucose-grown cells showed equal partition of consumed glucose from G6P to the Embden–Meyerhof–Parnas (EMP) pathway and from G6P to the PP pathway through 6P-gluconate. Growth on fructose alone or xylose alone was consistent with the ability of B. megaterium to use each substrate as a sole source of carbon. However, a detailed 13C mapping during simultaneous feeding of B. megaterium on glucose, fructose, and xylose indicated non-uniform intracellular investment of the different carbohydrate substrates. Flux of glucose-derived carbons dominated the gluconate pathway and the PP pathway, whereas carbon flux from both glucose and fructose populated the EMP pathway; there was no assimilatory flux of xylose-derived carbons. Collectively, our findings provide new quantitative insights on the contribution of the different catabolic routes involved in initiating carbohydrate catabolism in B. megaterium and related Bacillus species.
Clostridial fermentation of cellulose and hemicellulose relies on the cellular physiology controlling the metabolism of the cellulosic hexose sugar (glucose) with respect to the hemicellulosic pentose sugars (xylose and arabinose) and the hemicellulosic hexose sugars (galactose and mannose). Here, liquid chromatography–mass spectrometry and stable isotope tracers in Clostridium acetobutylicum were applied to investigate the metabolic hierarchy of glucose relative to the different hemicellulosic sugars towards two important biofuel precursors, acetyl‐coenzyme A and butyryl‐coenzyme A. The findings revealed constitutive metabolic hierarchies in C. acetobutylicum that facilitate (i) selective investment of hemicellulosic pentoses towards ribonucleotide biosynthesis without substantial investment into biofuel production and (ii) selective contribution of hemicellulosic hexoses through the glycolytic pathway towards biofuel precursors. Long‐term isotopic enrichment demonstrated incorporation of both pentose sugars into pentose‐phosphates and ribonucleotides in the presence of glucose. Kinetic labelling data, however, showed that xylose was not routed towards the biofuel precursors but there was minor contribution from arabinose. Glucose hierarchy over the hemicellulosic hexoses was substrate‐dependent. Kinetic labelling of hexose‐phosphates and triose‐phosphates indicated that mannose was assimilated but not galactose. Labelling of both biofuel precursors confirmed this metabolic preference. These results highlight important metabolic considerations in the accounting of clostridial mixed‐sugar utilization.
Environmental Chemistry Letters
Microcystins are toxic cyclic peptides produced worldwide by cyanobacteria in surface caters. The general structure of microcystin is inherently amenable to metal complexation. However, structural characterization of metal–microcystin complexes is lacking. Here we performed molecular dynamics simulations to obtain structures of aqueous complexes of microcystin–leucine–arginine and microcystin–arginine–arginine with Ca2+, Mg2+, Fe2+, Zn2+, and Cu2+. Results show that complexes with Cu2+ and Zn2+ were the most stable. Shorter metal-O atom distances result in more favorable complexes. For instance, the relatively stronger Zn–microcystin complexes have metal-Ocarboxyl distances of 1.78 Å, whereas the weaker Ca–microcystin complexes have this distance greater than 2.0 Å. Favorable metal complexation is attributed to the conformation of the microcystin peptide cavity that facilitated a specific coordination geometry of carboxyl and keto O atoms around the metal cation. Our findings imply that the cellular and extracellular roles of microcystin with respect to metal chelation are controlled both by the metal species and by the population of microcystin variants.
Ludmilla Aristilde , Stephen M. Galdi , Sabrina E. Kelch , Thalia G. Aoki , Sugar-Influenced Water Diffusion, Interaction, and Retention in Clay Interlayer Nanopores Probed by Theoretical Simulations and Experimental Spectroscopies, Advances in Water Resources (2017), doi: 10.1016/j.advwatres.2017.0
Advances in Water Resources
Environmental Chemistry Letters
Phytochelatins or (γ–glutamyl-cysteine)n-glycine are specialized peptides produced by plants and algae to mitigate toxic metal exposure. Previous experimental studies have reported biological production of these peptides specifically in response to high levels of heavy metals including Cu, Cd, and Zn. Stability constants and structural characterization of metal-phytochelatin complexes are largely lacking. This information is required to gain mechanistic insights on the metal selectivity of phytochelatins. Here we elucidate structural coordination in concert with thermodynamic stability predictions by performing molecular dynamics simulations of a fully hydrated phytochelatin molecule complexed with Ca, Mg, Fe(II), Zn(II), and Cu(II). Our molecular dynamics results predicted the following order for the thermodynamic stability of the different complexes: Zn(II) ≥ Cu(II) ≥ Fe(II) > Mg > Ca. Shorter binding distances and greater coordination from carboxylate and carbonyl O atoms explained the favorable binding energies with Zn(II) and Cu(II) over the other metal cations. Conformational re-arrangement of phytochelatin following metal chelation was captured by monitoring changes in the solvent-accessible volume. Accessibility of solvent molecules to the phytochelatin structure was inversely proportional to the distance between the coordinated ligands and the chelated metal. These new findings demonstrate the influence of the metal-phytochelatin structure on the metal binding thermodynamics and the phytochelatin conformation, both of which are important to evaluating the intracellular role of phytochelatin in mediating algal response to toxic heavy metal exposure.
Charlet L, Baham J, Giraldez JV, Lo W, Aristilde L and Baveye PC (2016) Éloge de la Méthode: A Tribute to Garrison Sposito on the Occasion of His Retirement. Front. Environ. Sci. 4:73. doi: 10.3389/fenvs.2016.00073
Frontiers in Environmental Science
Energy and Environmental Science
Acetogenic bacteria are attracting interest as biocatalysts in the biotechnology industry, since they are able to ferment carbon monoxide (CO)-rich gases. Wild-type strains produce mainly acetate and ethanol, but genetic modifications have already broadened the product portfolio. To enhance the production of intrinsic or heterologous biochemicals, knowledge on the microbial physiology is necessary. This physiology includes two different phases: acidogenesis (growth/acetate production) and solventogenesis (starvation/ethanol production). We operated two sequential, continuous bioreactors with a pure culture of Clostridium ljungdahlii to achieve steady-state conditions in an acetate- and an ethanol-producing stage to spatially separate acidogenesis and solventogenesis. Here, nearly 2000 proteins and their differential abundances between acidogenesis and solventogenesis were identified. In addition, we measured important metabolites. The results showed that nutrient-limited conditions triggered a transition to solventogenesis without altering the differential abundances of enzymes in the central energy metabolism. Our proteomics results revealed that the enzymes for ethanol production (AOR/ADH) were consistently abundant, even during acidogenesis. Based on this work, we developed an overflow model with thermodynamic rather than genetic regulation. The model identifies acetic acid and reduced cofactors as the saturation reactants. When the intracellular concentration of undissociated acetic acid reaches a thermodynamic threshold, C. ljungdahlii will be able to shunt surplus reducing equivalents toward ethanol immediately. This is important during retarded growth, when reducing equivalents can no longer be shunted toward biomass production, while the supply of CO-rich gas is still high. Nutrient availability and pH can be manipulated to achieve the desirable level of solventogenesis during bioprocessing.
Limnology and Oceanography
In natural samples from the New Jersey coast and the Gulf of Alaska, zinc (Zn) and cadmium (Cd) uptake rates by phytoplankton decreased on average about 30% as pH was decreased from 8.5 to 7.9 or 7.7, and the partial pressure of carbon dioxide (PCO2) increased accordingly. The underlying mechanism was explored with the model species, Thalassiosira weissflogii and Emiliania huxleyi, using ethylenediaminetetraacetic acid (EDTA), desferrioxamine B, phytochelatin, and cysteine as complexing agents. Experiments with single complexing agents did not reproduce the effect of pH seen in field samples, ruling out two possible mechanisms: a direct effect on the uptake machinery or down‐regulation of uptake at high PCO2.