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DOE OSTI2025

ReVise: A Human-AI Interface for Incremental Algorithmic Recourse

The recent adoption of artificial intelligence in socio-technical systems raises concerns about the black-box nature of the resulting decisions in fields such as hiring, finance, admissions, etc. If data subjects—such as job applicants, loan applicants, and students—receive an unfavorable outcome, they may be interested in algorithmic recourse, which involves updating certain features to yield a more favorable result when re-evaluated by algorithmic decision-making. Unfortunately, when individuals do not fully understand the incremental steps needed to change their circumstances, they risk following misguided paths that can lead to significant, long-term adverse consequences. Existing recourse approaches focus exclusively on the final recourse goal but neglect the possible incremental steps to reach the goal with real-life constraints, user preferences, and model artifacts. To address this gap, we formulate a visual analytic workflow for incremental recourse planning in collaboration with AI/ML experts and contribute an interactive visualization interface that helps data subjects efficiently navigate the recourse alternatives and make an informed decision. We also present one of the many usage scenarios, developed during exploratory feedback sessions with twelve graduate students using a real-world dataset, which demonstrates that our approach can be instrumental for data subjects in choosing a suitable recourse path.

algorithmic recourse↗

DOE OSTI2016

Highly-defective nanocrystals of ZnS formed via dissimilatory bacterial sulfate reduction: A comparative study with their abiogenic analogues

The physicochemical properties of a (nano)mineral are strongly affected by its formation processes, and thus, may indicate the (nano)mineral’s formation environment and mechanism. This correlation, although relevant to a myriad of geological, environmental, and material-science processes, has not yet been fully appreciated and systematically explored. In this study, using the Zn–S system, we demonstrate that biological and abiotic processes at similar experimental conditions can produce distinctive particle size, morphology, and crystal structure in the formed ZnS. Specifically, bacterial sulfate reduction led to the formation of highly-defective nanocrystals of mixed sphalerite and wurtzite in a range of ~4–12 nm. By comparison, the abiotic procedures of titration- or diffusion-controlled precipitation resulted in the formation of polycrystalline aggregates that contained randomly-oriented, ultrafine crystals below ~2–3 nm. The poor crystallinity in the abiogenic samples, regardless of the sulfide addition rates, reveals an overall nucleation-dominated, crystal growth-restricted pathway for the formation of ZnS from low-temperature aqueous solutions. The difficulty in the ZnS crystallization likely stems from the intrinsic surface instability of the ZnS growth units (i.e., in the form of nanoclusters) resulting from the dipole–dipole interactions of the unit with surrounding water molecules. In the biogenic samples, the ZnS crystallinity was significantly improved, indicating that the presence of bacterial metabolites somehow promoted the crystallization process. With evidence for the enlarged {1 1 1} planes in the biogenic nanocrystals, we attribute this enhancement mainly to the selective interaction of the bacterial metabolites with polar faces of the ZnS growth units, which might have effectively screened the dipole moments in the growth units and enabled their crystallographic assembly. By revealing the intrinsic difficulty and specific pathways for the ZnS crystallization, we also present viable explanations for the exclusive occurrence of structural defects in {1 1 1} planes of the biogenic nanocrystals. The findings of our study provide insight into the origin and fate of metal sulfide nanoparticles in the environment, and have implications for biomineralization, bioremediation of metal-contaminated sites, and bacterial production of functional nanomaterials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

Is it possible to discover a dark matter particle with an accelerator?

The paper contains description of the main properties of the galactic dark matter (DM) particles, available approaches for detection of DM, main features of direct DM detection, ways to estimate prospects for the DM detection, the first collider search for a DM candidate within an Effective Field Theory, complete review of ATLAS results of the DM candidate search with LHC RUN I, and less complete review of “exotic” dark particle searches with other accelerators and not only. From these considerations it follows that one is unable to prove, especially model-independently, a discovery of a DM particle with an accelerator, or collider. One can only obtain evidence on existence of a weakly interacting neutral particle, which could be, or could not be the DM candidate. The current LHC DM search program uses only the missing transverse energy signature. Non-observation of any excess above Standard Model expectations forces the LHC experiments to enter into the same fighting for the best exclusion curve, in which (almost) all direct and indirect DM search experiments permanently take place. But this fighting has very little (almost nothing) to do with a real possibility of discovering a DM particle. The true DM particles possess an exclusive galactic signature—annual modulation of a signal, which is accessible today only for direct DM detection experiments. There is no way for it with a collider, or accelerator. Therefore to prove the DM nature of a collider-discovered candidate one must find the candidate in a direct DM experiment and demonstrate the galactic signature for the candidate. Furthermore, being observed, the DM particle must be implemented into a modern theoretical framework. The best candidate is the supersymmetry, which looks today inevitable for coherent interpretation of all available DM data.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

The congenital APOA1 K107del mutation disrupts the lipid-free conformation of monomeric APOA1 and impairs oligomerization

Apolipoprotein A-I (APOA1) oligomerization is thought to be essential for high-density lipoprotein (HDL) formation and metabolism. Naturally occurring mutations can disrupt normal APOA1 folding and self-association, leading to dysfunctional HDL formation and cardiovascular disease. The congenital APOA1 variant p.K131del (APOA1 K107del ) has been associated with cardiovascular pathologies such as low HDL-cholesterol levels and aortic amyloidosis, and multiple studies indicate structural changes in APOA1 conformation underlie associated dysfunction. In the current study, we confirmed that APOA1 K107del exhibits no notable defect in lipid-binding. However, using polyacrylamide gel electrophoresis (PAGE) and size-exclusion chromatography (SEC), we found that loss of lysine 107 resulted in a remarkable shift in the distribution of APOA1 oligomers with a much higher proportion of monomers present in APOA1 K107del compared to wild-type APOA1. Further investigation using quantitative cross-linking revealed a major disruption of interactions in helical regions reported to participate in domain swaps necessary for proper self-association. This structural disruption appears to impair N- and C-termini interactions and dynamics that lead to non-specific aggregation. In conclusion, these findings support the hypothesis that lysine 107 is critical for proper folding and self-association of lipid-free APOA1 which could impact HDL biogenesis.

APOA1 (p.K131del)↗

DOE OSTI2023

Probing proton cross-shell excitations through the two-neutron removal from 38 Ca

Bound states of the neutron-deficient, near-dripline nucleus 36 Ca were populated in two-neutron removal from the ground state of 38 Ca, a direct reaction sensitive to the single-particle configurations and couplings of the removed neutrons in the projectile wave function. Final-state exclusive cross sections for the formation of 36 Ca and the corresponding longitudinal momentum distributions, both determined through the combination of particle and γ-ray spectroscopy, are compared to predictions combining eikonal reaction theory and shell-model two-nucleon amplitudes from the USDB, USDC, and ZBM2 effective interactions. The final-state cross-section ratio σ($2$$^{+}_{1}$) / σ (0 + ) shows particular sensitivity and is approximately reproduced only with the two-nucleon amplitudes from the ZBM2 effective interaction that includes proton cross-shell excitations into the pf shell. Characterizing the proton pf-shell occupancy locally and schematically, an increase of the sd – pf shell gap by 250 keV yields an improved description of this cross-section ratio and simultaneously enables a reproduction of the B(E2;$0$$^{+}_{1}$ → $2$$^{+}_{1}$) excitation strength of 36 Ca. Furthermore, this highlights an important aspect if a new shell-model effective interaction for the region was to be developed on the quest to model the neutron-deficient Ca isotopes and surrounding nuclei whose structure is impacted by proton cross-shell excitations.

20 ≤ A ≤ 38↗

DOE OSTI2024

Specific iron binding to natural sphingomyelin membrane induced by non-specific co-solutes

Sphingomyelin (SPM), a crucial phospholipid in the myelin sheath, plays a vital role in insulating nerve fibers. We hypothesize that iron ions selectively bind to the phosphatidylcholine (PC) template within the SPM membrane under near-physiological conditions, resulting in disruptions to membrane organization. These interactions could potentially contribute to the degradation of the myelin sheath, thereby playing a role in the development of neurodegenerative diseases. We utilized synchrotron-based X-ray spectroscopy and diffraction techniques to study the interaction of iron ions with a bovine spinal-cord SPM monolayer (ML) at the liquid-vapor interface under physiological conditions. The SPM ML serves as a model system, representing localized patches of lipids within a more complex membrane structure. The experiments assessed iron binding to the SPM membrane both in the presence of salts and with additional evaluation of the effects of various ion species on membrane behavior. Grazing incidence X-ray diffraction was employed to analyze the impact of iron binding on the structural integrity of the SPM membrane. Furthermore, our results demonstrate that iron ions in dilute solution selectively bind to the PC template of the SPM membrane exclusively at near-physiological salt concentrations (e.g., NaCl, KCl, KI, or CaCl 2 ) and are pH-dependent. In-significant binding was detected in the absence of these salts or at near-neutral pH with salts. The surface adsorption of iron ions is correlated with salt concentration, reaching saturation at physiological levels. In contrast, multivalent ions such as La 3+ and Ca 2+ do not bind to SPM under similar conditions. Notably, iron binding to the SPM membrane disrupts its in-plane organization, suggesting that these interactions may compromise membrane integrity and contribute to myelin sheath damage associated with neurological disorders.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Strong Electronic and Magnetic Coupling in M 4 (M = Ni, Cu) Clusters via Direct Orbital Interactions between Low-Coordinate Metal Centers

In this report we present an extensive study of tetranuclear transition-metal cluster compounds M 4 (NP t Bu 3 ) 4 and [M 4 (NP t Bu 3 ) 4 ][B(C 6 F 5 ) 4 ] (M = Ni, Cu; t Bu = tert -butyl), which feature low-coordinate metal centers and direct metal-metal orbital overlap. X-ray diffraction, electrochemical, magnetic, spectroscopic, and computational analysis elucidate the nature of the bonding interactions in these clusters and the impact of these interactions on the electronic and magnetic properties. Direct orbital overlap results in strongly coupled, large-spin ground states in the [Ni 4 (NP t Bu 3 ) 4 ] +/0 clusters and fully delocalized, spin-correlated electrons. Correlated electronic structure calculations confirm the presence of ferromagnetic ground states that arise from direct exchange between magnetic orbitals, and, in the case of the neutral cluster, itinerant electron magnetism similar to that in metallic ferromagnets. The cationic nickel cluster also possesses large magnetic anisotropy exemplified by a large, positive axial zero-field splitting parameter of D = +7.95 or +9.2 cm -1 , as determined by magnetometry or electron paramagnetic resonance spectroscopy, respectively. The [Ni 4 (NP t Bu 3 ) 4 ] + cluster is also the first molecule with easy-plane magnetic anisotropy to exhibit zero-field slow magnetic relaxation, and under a small applied field, it exhibits relaxation exclusively through an Orbach mechanism with a spin relaxation barrier of 16 cm -1 . The S = 1 / 2 complex [Cu 4 (NP t Bu 3 ) 4 ] + exhibits slow magnetic relaxation via a Raman process on the millisecond time scale, supporting the presence of slow relaxation via an Orbach process in the nickel analogue. Overall, this work highlights the unique electronic and magnetic properties that can be realized in metal clusters featuring direct metal-metal orbital interactions between low-coordinate metal centers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Streptococcus pneumoniae HtrA is a dynamic and monomeric virulence factor capable of forming larger oligomeric complexes

Abstract High‐temperature requirement A (HtrA) proteases are a conserved family of serine proteases central to protein quality control and bacterial virulence. While Gram‐negative and human HtrAs are structurally well studied, Gram‐positive homologs remain essentially uncharacterized. Here, we present the first integrated structural and mechanistic analysis of a Gram‐positive HtrA, from Streptococcus pneumoniae , a virulence factor essential for adhesion and infection in vivo. Proteomic profiling of an htrA knockout and cleavage assays demonstrate that S. pneumoniae HtrA is required for protein quality control, with the PDZ domain mediating substrate recognition. Biochemically, S. pneumoniae HtrA exists exclusively as a monomer in solution, a striking divergence from canonical trimeric HtrAs that we show is shared with other Gram‐positive homologs. NMR analyses reveal that the monomer dynamically samples open and closed conformations, while cryo‐EM of a catalytic mutant identifies a hexamer stabilized by a unique LoopA–PDZ interaction. Together, these findings define S. pneumoniae HtrA as a dynamic monomer with interdomain coupling between its protease and PDZ domains, establishing Gram‐positive HtrAs as a mechanistically divergent subgroup within the HtrA family.

Lee, Eunjeong [Department of Biochemistry and Mole↗

DOE OSTI2020

Effects of canopy midstory management and fuel moisture on wildfire behavior

Abstract Increasing trends in wildfire severity can partly be attributed to fire exclusion in the past century which led to higher fuel accumulation. Mechanical thinning and prescribed burns are effective techniques to manage fuel loads and to establish a higher degree of control over future fire risk, while restoring fire prone landscapes to their natural states of succession. However, given the complexity of interactions between fine scale fuel heterogeneity and wind, it is difficult to assess the success of thinning operations and prescribed burns. The present work addresses this issue systematically by simulating a simple fire line and propagating through a vegetative environment where the midstory has been cleared in different degrees, leading to a canopy with almost no midstory, another with a sparse midstory and another with a dense midstory. The simulations are conducted for these three canopies under two different conditions, where the fuel moisture is high and where it is low. These six sets of simulations show widely different fire behavior, in terms of fire intensity, spread rate and consumption. To understand the physical mechanisms that lead to these differences, detailed analyses are conducted to look at wind patterns, mean flow and turbulent fluxes of momentum and energy. The analyses also lead to improved understanding of processes leading to high intensity crowning behavior in presence of a dense midstory. Moreover, this work highlights the importance of considering fine scale fuel heterogeneity, seasonality, wind effects and the associated fire-canopy-atmosphere interactions while considering prescribed burns and forest management operations.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Variational Self-Consistent Theory for Beam-Loaded Cavities

A new variational theory is presented for beam loading in microwave cavities. The beam{field interaction is formulated as a dynamical interaction whose stationarity according to Hamilton’s principle will naturally lead to steady-state solutions that indicate how a cavity’s resonant frequency, Q and optimal coupling coefficient will detune as a result of the beam loading. A driven cavity Lagrangian is derived from first principles, including the effects of cavity wall losses, input power and beam interaction. The general formulation is applied to a typical klystron input cavity to predict the appropriate detuning parameters required to maximize the gain (or modulation depth) in the average Lorentz factor boost, (Δ γ). Numerical examples are presented, showing agreement with the general detuning trends previously observed in the literature. The developed formulation carries several advantages for beam-loaded cavity structures. It provides a self-consistent model for the dynamical (nonlinear) beam{field interaction, a procedure for maximizing gain under beam-loading conditions, and a useful set of parameters to guide cavity-shape optimization during the design of beam-loaded systems. Enhanced clarity of the physical picture underlying the problem seems to be gained using this approach, allowing straightforward inclusion or exclusion of different field configurations in the calculation and expressing the final results in terms of measurable quantities. Two field configurations are discussed for the klystron input cavity, using finite magnetic confinement or no confinement at all. Formulating the problem in a language that is directly accessible to the powerful techniques found in Hamiltonian dynamics and canonical transformations may potentially carry an additional advantage in terms of analytical computational gains, under suitable conditions

43 PARTICLE ACCELERATORS↗

DOE OSTI2025

First Joint Oscillation Analysis of Super-Kamiokande Atmospheric and T2K Accelerator Neutrino Data

The Super-Kamiokande and T2K Collaborations present a joint measurement of neutrino oscillation parameters from their atmospheric and beam neutrino data. It uses a common interaction model for events overlapping in neutrino energy and correlated detector systematic uncertainties between the two datasets, which are found to be compatible. Using 3244.4 days of atmospheric data and a beam exposure of 19.7⁢(16.3) × 10 20 protons on target in (anti)neutrino mode, the analysis finds a 1.9⁢𝜎 exclusion of 𝐶⁢𝑃 conservation (defined as 𝐽 𝐶⁢𝑃 = 0) and a 1.2⁢𝜎 exclusion of the inverted mass ordering.

Neutrino detection↗

NASA NTRS1986

On ion acceleration in interplanetary quasi-perpendicular shock waves

The kinematic and pitch angle scattering constraints for multiple shock encounters to occur are investigated. The results suggest that (1) large particle anisotropies and a large number of shock encounters are not mutually exclusive and (2) solar wind ions are not directly injected into the nearly perpendicular interplanetary shock acceleration process. Also, the average number of shock encounters required to accelerate an ion between two energies is calculated. The results are consistent with the shock geometry dependence observed in interplanetary shock spike and corotating interaction region associated energetic ion events.

Pesses, M. E.↗

DOE OSTI2018

Direct Determination of Hydroxymethyl Conformations of Plant Cell Wall Cellulose Using 1 H Polarization Transfer Solid-State NMR

In contrast to the well-studied crystalline cellulose of microbial and animal origins, cellulose in plant cell walls is disordered due to its interactions with matrix polysaccharides. Plant cell wall (PCW) is an undisputed source of sustainable global energy; therefore, it is important to determine the molecular structure of PCW cellulose. The most reactive component of cellulose is the exocyclic hydroxymethyl group: when it adopts the tg conformation, it stabilizes intrachain and interchain hydrogen bonding, while gt and gg conformations destabilize the hydrogen-bonding network. So far, information about the hydroxymethyl conformation in cellulose has been exclusively obtained from 13 C chemical shifts of monosaccharides and oligosaccharides, which do not reflect the environment of cellulose in plant cell walls. Here, we use solid-state Nuclear Magnetic Resonance (ssNMR) spectroscopy to measure the hydroxymethyl torsion angle of cellulose in two model plants, by detecting distance-dependent polarization transfer between H4 and H6 protons in 2D 13 C– 13 C correlation spectra. We show that the interior crystalline portion of cellulose microfibrils in Brachypodium and Arabidopsis cell walls exhibits H4–H6 polarization transfer curves that are indicative of a tg conformation, whereas surface cellulose chains exhibit slower H4–H6 polarization transfer that is best fit to the gt conformation. Joint constraints by the H4–H6 polarization transfer curves and 13 C chemical shifts indicate that it is unlikely for interior cellulose to have a significant population of the gt and gg conformation mixed with the tg conformation, while surface cellulose may adopt a small percentage of the gg conformation. These results provide new constraints to the structure and matrix interactions of cellulose in plant cell walls, and represent the first direct determination of a torsion angle in an important noncrystalline carbohydrate polymer.

09 BIOMASS FUELS↗

DOE OSTI2018

Probing lattice dynamics and electron-phonon coupling in the topological nodal-line semimetal ZrSiS

Topological materials provide an exclusive platform to study the dynamics of relativistic particles in table-top experiments and offer the possibility of wide-scale technological applications. ZrSiS is a newly discovered topological nodal-line semimetal and has drawn enormous interests. In this paper, we have investigated the lattice dynamics and electron-phonon interaction in single-crystalline ZrSiS using Raman spectroscopy. Polarization and angle-resolved Raman data have been analyzed using crystal symmetries and theoretically calculated atomic vibrational patterns along with phonon dispersion spectra. Wavelength- and temperature-dependent measurements show the complex interplay of electron and phonon degrees of freedom, resulting in resonant phonon and quasielastic electron scattering through interband transition. Our high-pressure Raman studies reveal vibrational anomalies, which are the signature of structural phase transitions. Further investigations through high-pressure synchrotron x-ray diffraction clearly show pressure-induced structural transitions and coexistence of multiple phases, which also indicate possible electronic topological transitions in ZrSiS. Lastly, this study not only provides the fundamental information on the phonon subsystem, but also sheds some light in understanding the topological nodal-line phase in ZrSiS and other isostructural systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2023

Enhanced Urea Oxidation Electrocatalytic Activity by Synergistic Cobalt and Nickel Mixed Oxides

In this study, exploring reactive and selective Ni-based electrocatalysts for the urea oxidation reaction (UOR) is crucial for developing urea-related energy conversion technologies. Herein, synergistic interactions in Ni/Co mixed oxides/hydroxides enhanced the UOR with low onset potential, fast reaction kinetics, and good selectivity against oxygen evolution reaction (OER). Our electrochemical measurements and theoretical calculations signified the collaborative interaction of Ni/Co mixed oxide/hydroxide heterostructures to enhance UOR activity. Our results showed that Ni 3+ species, formed at high anodic potential, produced a high anodic current primarily from unwanted OER. Instead, the Ni/Co heterostructures with dominant Ni 2+ and Co 3+ species remained stable at low anodic potential and exhibited anodic current exclusively attributed to UOR. This work highlights the importance of tuning valence charges for designing high-performance and selective UOR electrocatalysts to benefit the environmental remediation of urea runoff and enable urea electrolysis for hydrogen production by replacing conventional OER with UOR at the anode.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Viruses of Nitrogen-Fixing Mesorhizobium Bacteria in Globally Distributed Chickpea Root Nodules

Legume nodules are specialized environments on plant roots that are induced and dominated by nitrogen-fixing bacteria. Bacteriophages (phages) in these nodules could potentially provide top-down controls on the population size and, therefore, the function of nitrogen-fixing symbionts. Here we sought to characterize the diversity and biogeographical patterns of phages that infect nitrogen-fixing Mesorhizobium symbionts isolated from root nodules, leveraging 266 genomes of Mesorhizobium isolated from nodules and 648 nodule metagenomes collected from three species of chickpea plants ( Cicer spp.) under different agricultural management practices, spanning eight countries on five continents. We identified 106 phage populations (viral operational taxonomic units [vOTUs]) in Mesorhizobium draft genomes, 37% of which were confirmed as likely prophages. These vOTUs were detected in 64% of the Mesorhizobium-dominated nodule metagenomes and 58% of the Mesorhizobium isolates. Per metagenome, 1 to 16 putative Mesorhizobium vOTUs were detected, with more than half of the nodules containing only one such vOTU. The majority of vOTUs were detected exclusively in Ethiopia, followed by India and Morocco, with the lowest richness of putative Mesorhizobium phages in countries that applied industrial Mesorhizobium inoculants to crops. Two vOTUs were identified in five or more countries and in nodules dominated by different strains of Mesorhizobium, suggesting infection of diverse Mesorhizobium hosts and long-term interactions. Beta-diversity of these Mesorhizobium phage assemblages was significantly correlated with the dominant Mesorhizobium strain, but not with measured environmental parameters. Our findings indicate that nitrogen-fixing nodules in chickpea plants can contain distinct viral assemblages, with potential impacts on the nodule microbiome that bear further exploration.

Microbiology↗

DOE OSTI2021

Binding of Campylobacter jejuni FliW Adjacent to the CsrA RNA-Binding Pockets Modulates CsrA Regulatory Activity

Campylobacter jejuni CsrA is an mRNA-binding, post-transcriptional regulator that controls many metabolic- and virulence-related characteristics of this important pathogen. In contrast to E. coli CsrA, whose activity is modulated by binding to small non-coding RNAs (sRNAs), C. jejuni CsrA activity is controlled by binding to the CsrA antagonist FliW. In this study, we identified the FliW binding site on CsrA. Deletion of the C-terminus of C. jejuni CsrA, which is extended relative to sRNA-binding CsrA proteins, abrogated FliW binding. Bacterial two-hybrid experiments were used to assess the interaction of FliW with wild-type CsrA and mutants thereof, in which every amino acid was individually mutated. Two CsrA mutations (V51A and N55A) resulted in a significant decrease in FliW binding. The V51A and N55A mutants also showed a decrease in CsrA-FliW complex formation, as assessed by size-exclusion chromatography and surface plasmon resonance. These residues were highly conserved in bacterial species containing CsrA orthologs whose activities are predicted to be regulated by FliW. The location of FliW binding was immediately adjacent to the two RNA-binding sites of the CsrA homodimer, suggesting the model that FliW binding to CsrA modulates its ability to bind to its mRNA targets either by steric hindrance, electrostatic repulsion, or by altering the overall structure of the RNA-binding sites.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Phylogenetic and amino acid conservation analyses of bacterial l-aspartate-α-decarboxylase and of its zymogen-maturation protein reveal a putative interaction domain

Background: All organisms must synthesize the enzymatic cofactor coenzyme A (CoA) from the precursor pantothenate. Most bacteria can synthesize pantothenate de novo by the condensation of pantoate and β-alanine. The synthesis of β-alanine is catalyzed by l-aspartate-α-decarboxylase (PanD), a pyruvoyl enzyme that is initially synthesized as a zymogen (pro-PanD). Active PanD is generated by self-cleavage of pro-PanD at Gly24-Ser25 creating the activesite pyruvoyl moiety. In Salmonella enterica, this cleavage requires PanM, an acetyl-CoA sensor related to the Gcn5-like N-acetyltransferases. PanM does not acetylate pro-PanD, but the recent publication of the three-dimensional crystal structure of the PanM homologue PanZ in complex with the PanD zymogen of Escherichia coli provides validation to our predictions and provides a framework in which to further examine the cleavage mechanism. In contrast, PanD from bacteria lacking PanM efficiently cleaved in the absence of PanM in vivo. Results: Using phylogenetic analyses combined with in vivo phenotypic investigations, we showed that two classes of bacterial l-aspartate-α-decarboxylases exist. This classification is based on their posttranslational activation by self-cleavage of its zymogen. Class I l-aspartate-α-decarboxylase zymogens require the acetyl-CoA sensor PanM to be cleaved into active PanD. This class is found exclusively in the Gammaproteobacteria. Class II l-aspartate-αdecarboxylase zymogens self cleave efficiently in the absence of PanM, and are found in a wide number of bacterial phyla. Several members of the Euryarchaeota and Crenarchaeota also contain Class II l-aspartate-α-decarboxylases. Phylogenetic and amino acid conservation analyses of PanM revealed a conserved region of PanM distinct from conserved regions found in related Gcn5-related acetyltransferase enzymes (Pfam00583). This conserved region represents a putative domain for interactions with l-aspartate-α-decarboxylase zymogens. This work may inform future biochemical and structural studies of pro-PanD-PanM interactions. Conclusions: Experimental results indicate that S. enterica and C. glutamicum l-aspartate-α-decarboxylases represent two different classes of homologues of these enzymes. Class I homologues require PanM for activation, while Class II self cleave in the absence of PanM. Computer modeling of conserved amino acids using structure coordinates of PanM and l-aspartate-α-decarboxylase available in the protein data bank (RCSB PDB) revealed a putative site of interactions, which may help generate models to help understand the molecular details of the self-cleavage mechanism of l-aspartate-α-decarboxylases.

Aspartate decarboxylase↗