Host plant genetic control of associated fungal and insect species in a Populus hybrid cross
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59 BASIC BIOLOGICAL SCIENCES↗
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Manganese uptake by red maples in response to mineral dissolution rates in soil
Manganese (Mn) is an essential plant micronutrient that influences photosynthesis, ecosystem productivity, and soil carbon storage. Our objective was to quantify how Mn uptake by forest vegetation relates to Mn release into soil solution through mineral dissolution. In this work, a greenhouse pot experiment was conducted to quantify Mn uptake by red maple saplings as a function of mineral solubility to test whether Mn uptake was limited by the supply of Mn to soil solution. Differences in soil microbial community composition between treatments, particularly amongst Mn cycling bacteria and fungi, were also evaluated to assess potential microbial impacts on observed Mn fluxes. Plant Mn uptake was highest in systems supplied with dissolved Mn(II) because it was not kinetically limited by mineral weathering. Mn uptake was also higher in systems supplied with a fast-weathering substrate (shale containing Mn(II)-bearing pyrite) than a slow-weathering substrate (Mn(IV)-oxide). However, vegetation accumulated a decreasing proportion of available Mn with increasing solubility, indicating that uptake was tempered relative to solubility. The presence of bacterial phyla containing known Mn-oxidizing bacteria indicates the potential for Mn-oxidizing bacteria to influence Mn solubility within Mn-oxide and dissolved Mn treatments. A relatively low abundance of these bacteria points to their limited capacity to oxidize and retain Mn in the shale treatments, consistent with substantial Mn leaching. We conclude that Mn uptake was primarily controlled by dissolution rates of Mn-bearing minerals but modified by biological processes. The quantitative framework presented here can guide understanding of how biogeochemical processes control element cycling between plants and soils.
59 BASIC BIOLOGICAL SCIENCES↗
The 21.5-kDa isoform of myelin basic protein has a non-traditional PY-nuclear-localization signal
Highlights: Black-Right-Pointing-Pointer Full-length 21.5-kDa MBP isoform is translocated to the nucleus. Black-Right-Pointing-Pointer We hypothesized that the exon-II-encoded sequence contained the NLS. Black-Right-Pointing-Pointer We mutated this sequence in RFP-tagged constructs and transfected N19-cells. Black-Right-Pointing-Pointer Abolition of two key positively-charged residues resulted in loss of nuclear-trafficking. Black-Right-Pointing-Pointer The 21.5-kDa isoform of classic MBP contains a non-traditional PY-NLS. -- Abstract: The predominant 18.5-kDa classic myelin basic protein (MBP) is mainly responsible for compaction of the myelin sheath in the central nervous system, but is multifunctional, having numerous interactions with Ca{sup 2+}-calmodulin, actin, tubulin, and SH3-domains, and can tether these proteins to a lipid membrane in vitro. The full-length 21.5-kDa MBP isoform has an additional 26 residues encoded by exon-II of the classic gene, which causes it to be trafficked to the nucleus of oligodendrocytes (OLGs). We have performed site-directed mutagenesis of selected residues within this segment in red fluorescent protein (RFP)-tagged constructs, which were then transfected into the immortalized N19-OLG cell line to view protein localization using epifluorescence microscopy. We found that 21.5-kDa MBP contains two non-traditional PY-nuclear-localization signals, and that arginine and lysine residues within these motifs were involved in subcellular trafficking of this protein to the nucleus, where it may have functional roles during myelinogenesis.
60 APPLIED LIFE SCIENCES↗
Rational design of antimicrobial peptides targeting Gram-negative bacteria
Membrane-targeting host antimicrobial peptides (AMPs) can kill or inhibit the growth of Gram-negative bacteria. However, the evolution of resistance among microbes poses a substantial barrier to the long-term utility of the host AMPs. Combining experiment and molecular dynamics simulations, we demonstrate that terminal carboxyl capping enhances both membrane insertion and antibacterial activity of an AMP called P1. Furthermore, we show that a bacterial strain with evolved resistance to this peptide becomes susceptible to P1 variants with either backbone capping or lysine-to-arginine substitutions. Our results suggest that cocktails of closely related AMPs may be useful in overcoming evolved resistance.
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Formation, characterization and modeling of emergent synthetic microbial communities
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59 BASIC BIOLOGICAL SCIENCES↗
Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV
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59 BASIC BIOLOGICAL SCIENCES↗
A Non-Stem-Loop CRISPR RNA Is Processed by Dual Binding Cas6
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Design of compact ultrafast microscopes for single- and multi-shot imaging with MeV electrons
Ultrafast high-energy electron microscopy, taking advantage of strong interaction of electrons with matter while minimizing space charge problems, can be used to address a wide range of grand challenges in basics energy sciences. However, MeV-electron lenses are inherently bulky and expensive, preventing them from acceptance in a broad scientific community. In this article, we report our novel design of a compact, low-cost imaging-lens system for MeV-electrons based on quadrupole multiplets, including triplet, quadruplet and quintuplet, both symmetric and asymmetric. We compare optical performance of quadrupole-based condenser, objective and projector lenses with that of the traditional round-lenses and discuss the strategy for their practical use in constructing MeV-electron microscopes for high spatial and temporal resolution single- and multi-shot imaging. Combining the compound electron-optical system with a photocathode radiofrequency (RF) gun, such a MeV electron microscope can be fit into a smallsized laboratory for ultrafast observations and measurements.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
In vivo subcellular localization of Mal de Rio Cuarto virus (MRCV) non-structural proteins in insect cells reveals their putative functions
The in vivo subcellular localization of Mal de Rio Cuarto virus (MRCV, Fijivirus, Reoviridae) non-structural proteins fused to GFP was analyzed by confocal microscopy. P5-1 showed a cytoplasmic vesicular-like distribution that was lost upon deleting its PDZ binding TKF motif, suggesting that P5-1 interacts with cellular PDZ proteins. P5-2 located at the nucleus and its nuclear import was affected by the deletion of its basic C-termini. P7-1 and P7-2 also entered the nucleus and therefore, along with P5-2, could function as regulators of host gene expression. P6 located in the cytoplasm and in perinuclear cloud-like inclusions, was driven to P9-1 viroplasm-like structures and co-localized with P7-2, P10 and {alpha}-tubulin, suggesting its involvement in viroplasm formation and viral intracellular movement. Finally, P9-2 was N-glycosylated and located at the plasma membrane in association with filopodia-like protrusions containing actin, suggesting a possible role in virus cell-to-cell movement and spread.
60 APPLIED LIFE SCIENCES↗
Substrate Promotes Productive Gas Binding in the α-Ketoglutarate-Dependent Oxygenase FIH
The Fe 2+ /α-ketoglutarate (αKG)-dependent oxygenases use molecular oxygen to conduct a wide variety of reactions with important biological implications, such as DNA base excision repair, histone demethylation, and the cellular hypoxia response. These enzymes follow a sequential mechanism in which O 2 binds and reacts after the primary substrate binds, making those structural factors that promote productive O 2 binding central to their chemistry. A large challenge in this field is to identify strategies that engender productive turnover. Factor inhibiting HIF (FIH) is a Fe 2+ /αKG-dependent oxygenase that forms part of the O 2 sensing machinery in human cells by hydroxylating the C-terminal transactivation domain (CTAD) found within the HIF-1α protein. In this work, the structure of FIH was determined with the O 2 analogue NO bound to Fe, offering the first direct insight into the gas binding geometry in this enzyme. Through a combination of density functional theory calculations, {FeNO} 7 electron paramagnetic resonance spectroscopy, and ultraviolet–visible absorption spectroscopy, we demonstrate that CTAD binding stimulates O 2 reactivity by altering the orientation of the bound gas molecule. Although unliganded FIH binds NO with moderate affinity, the bound gas can adopt either of two orientations with similar stability; upon CTAD binding, NO adopts a single preferred orientation that is appropriate for supporting oxidative decarboxylation. Combined with other studies of related enzymes, our data suggest that substrate-induced reorientation of bound O 2 is the mechanism utilized by the αKG oxygenases to tightly couple O 2 activation to substrate hydroxylation.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Structural and Biophysical Characterization of the Mycobacterium tuberculosis Protein Rv0577, a Protein Associated with Neutral Red Staining of Virulent Tuberculosis Strains and Homologue of the Streptomyces coelicolor Protein KbpA
The 261-residue Mycobacterium tuberculosis protein Rv0577 is a prominent antigen in tuberculosis patients, the responsible component for neutral red staining of virulent strains of M. tuberculosis, a putative component in a methylglyoxal detoxification pathway, and an agonist of toll-like receptor 2. It also has 36% sequence identity to AfsK-binding protein A (KbpA), a component in the complex secondary metabolite pathways in the Streptomycetes genus from which many commercial antibiotics are derived. To gain insight into the biological function of Rv0577 and the family of KpbA kinase regulators, the crystal structure for Rv0577 was determined to a resolution of 1.75 Å (3OXH), binding properties with neutral red and deoxyadenosine (Ado) surveyed, backbone dynamics measured, and thermal stability assayed by CD spectroscopy. The protein is composed of four approximate repeats with an topology arranged radially in consecutive pairs to form two continuous eight-strand -sheets capped on both ends with an -helix. The two -sheets intersect in the center at roughly a right angle and form an asymmetric deep “saddle” on both sides of the protein, saddle one (P11 to A129) and saddle two (L143 to A258), that may serve to bind ligands. NMR chemical shift perturbation experiments show that neutral red binds to Rv0577, further cementing the role of Rv0577 in the neutral red staining of virulent strains of M. tuberculosis. Similar experiments show that adenosine also bind to Rv0577, although less tightly, with estimated dissociation constants of 4.1 ± 0.3 mM for saddle one and > 1 M for saddle two. Heteronuclear steady-state {1H}-15N NOE, T1, and T2 values were generally uniform through-out the sequence with only a few modest pockets of differences suggestive of slightly different motion in loops between -strands in saddle 1. Circular dichroism spectroscopy characterization of the thermal stability of Rv0577 indicated irreversible unfolding upon heating with an estimated melting temperature of 56 °C. While it is not known if Rv0577 has a kinase regulatory role similar to its Streptomyces homolog KbpA, protein kinase and phosphatase signaling help M. tuberculosis adapt to the hostile host environment during infections. Consequently, new anti-tuberculosis drugs targeting Rv0577 may act by interfering with multiple mechanisms; a potential signaling machinery as well as toll-like receptor 2 activation and the methylglyoxal detoxification pathway.
59 BASIC BIOLOGICAL SCIENCES↗
Dynamical and phase behavior of a phospholipid membrane altered by an antimicrobial peptide at low concentration
Here we discuss that the mechanism of action of antimicrobial peptides is traditionally attributed to the formation of pores in the lipid cell membranes of pathogens, which requires a substantial peptide to lipid ratio. However, using incoherent neutron scattering, we show that even at a concentration too low for pore formation, an archetypal antimicrobial peptide, melittin, disrupts the regular phase behavior of the microscopic dynamics in a phospholipid membrane, dimyristoylphosphatidylcholine (DMPC). At the same time, another antimicrobial peptide, alamethicin, does not exert a similar effect on the DMPC microscopic dynamics. The melittin-altered lateral motion of DMPC at physiological temperature no longer resembles the fluid-phase behavior characteristic of functional membranes of the living cells. The disruptive effect demonstrated by melittin even at low concentrations reveals a new mechanism of antimicrobial action relevant in more realistic scenarios, when peptide concentration is not as high as would be required for pore formation, which may facilitate treatment with antimicrobial peptides.
59 BASIC BIOLOGICAL SCIENCES↗
Structural Insight into a Novel Formyltransferase and Evolution to a Nonribosomal Peptide Synthetase Tailoring Domain
Nonribosomal peptide synthetases (NRPSs) increase the chemical diversity of their products by acquiring tailoring domains. Linear gramicidin synthetase starts with a tailoring formylation (F) domain, which likely originated from a sugar formyltransferase (FT) gene. Here, we present studies on an Anoxybacillus kamchatkensis sugar FT representative of the prehorizontal gene transfer FT. Gene cluster analysis reveals that this FT acts on a UDP-sugar in a novel pathway for synthesis of a 7-formamido derivative of CMP-pseudaminic acid. We recapitulate the pathway up to and including the formylation step in vitro, experimentally demonstrating the role of the FT. We also present X-ray crystal structures of the FT alone and with ligands, which unveil contrasts with other structurally characterized sugar FTs and show close structural similarity with the F domain. In conclusion, the structures reveal insights into the adaptations that were needed to co-opt and evolve a sugar FT into a functional and useful NRPS domain.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Crowding-Induced Spatial Organization of Gene Expression in Cell-Sized Vesicles
Cell-free protein synthesis is an important tool for studying gene expression and harnessing it for applications. In cells, gene expression is regulated in part by the spatial organization of transcription and translation. Unfortunately, current cell-free approaches are unable to control the organization of molecular components needed for gene expression, which limits the ability to probe and utilize its effects. In this work, we show, using complementary computational and experimental approaches, that macromolecular crowding can be used to control the spatial organization and translational efficiency of gene expression in cell-sized vesicles. Computer simulations and imaging experiments reveal that, as crowding is increased, DNA plasmids become localized at the inner surface of vesicles. Ribosomes, in contrast, remain uniformly distributed, demonstrating that crowding can be used to differentially organize components of gene expression. We further carried out cell-free protein synthesis reactions in cell-sized vesicles and quantified mRNA and protein abundance. At sufficiently high levels of crowding, we observed localization of mRNA near vesicle surfaces, a decrease in translational efficiency and protein abundance, and anomalous scaling of protein abundance as a function of vesicle size. These results are consistent with high levels of crowding causing altered spatial organization and slower diffusion. Our work demonstrates a straightforward way to control the organization of gene expression in cell-sized vesicles and provides insight into the spatial regulation of gene expression in cells.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Laser Spectroscopic and Theoretical Studies of Encapsulation Complexes of Calix[4]arene
The complexes between the host calix[4]arene (C4A) and various guest molecules such as NH3, N2, CH4, and C2H2 have been investigated via experimental and theoretical methods. The S1-S0 electronic spectra of these guest-host complexes are observed by mass-selected resonant two-photon ionization (R2PI) and laser induced fluorescence (LIF) spectroscopy. The infrared (IR) spectra of the complexes formed in molecular beams are obtained by IR-UV double resonance (IR-UV DR) and IR photodissociation (IRPD) spectroscopy. The supramolecular structures of the complexes are investigated by electronic structure methods (density functional and second order perturbation theory). The current results for the various molecular guests are put in perspective with the previously reported ones for the C4A-Rare Gas (Rg) (Phys. Chem. Chem. Phys. 2007, 126, 141101) and C4A-H2O complexes (J. Phys. Chem. A, 2010, 114, 2967). The electronic spectra of the complexes of C4A with N2, CH4 and C2H2 exhibit red-shifts of similar magnitudes with the ones observed for the C4A-Rg complexes, whereas the complexes of C4A with H2O and NH3 show much larger red-shifts. Most of the IR-UV DR spectra of the complexes, except for C4A-C2H2, show a broad hydrogen bonded OH stretching band with a peak at ~3160 cm-1. The analysis of the experimental results, in agreement with the ones resulted from the electronic structure calculations, suggest that C4A preferentially forms endo-complexes with all the guest species reported in this study. We discuss the similarities and differences of the structures, binding energies and the nature of the interaction between the C4A host and the various guest species. This work was supported by the US Department of Energy, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences & Biosciences. Pacific Northwest National Laboratory is operated by Battelle for the US Department of Energy
08 HYDROGEN↗
Tunable orbital angular momentum in high-harmonic generation
Optical vortices are currently one of the most intensively studied topics in optics. These light beams, which carry orbital angular momentum (OAM), have been successfully utilized in the visible and infrared in a wide variety of applications. Moving to shorter wavelengths may open up completely new research directions in the areas of optical physics and material characterization. Here, we report on the generation of extreme-ultraviolet optical vortices with femtosecond duration carrying a controllable amount of OAM. From a basic physics viewpoint, our results help to resolve key questions such as the conservation of angular momentum in highly nonlinear light–matter interactions, and the disentanglement and independent control of the intrinsic and extrinsic components of the photon’s angular momentum at short-wavelengths. Finally, the methods developed here will allow testing some of the recently proposed concepts such as OAM-induced dichroism, magnetic switching in organic molecules and violation of dipolar selection rules in atoms.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Research Update: Electrical monitoring of cysts using organic electrochemical transistors
Organotypic three-dimensional (3D) cell culture models have the potential to act as surrogate tissues in vitro, both for basic research and for drug discovery/toxicology. 3D cultures maintain not only 3D architecture but also cell-cell and cell extracellular matrix interactions, particularly when grown in cysts or spheroids. Characterization of cell cultures grown in 3D formats, however, provides a significant challenge for cell biologists due to the incompatibility of these structures with commonly found optical or electronic monitoring systems. Electronic impedance spectroscopy is a cell culture monitoring technique with great potential; however, it has not been possible to integrate 3D cultures with commercially available systems to date. Cyst-like 3D cultures are particularly challenging due to their small size and difficulty in manipulation. Herein, we demonstrate isolation of cyst-like 3D cultures by capillarity and subsequent integration with the organic electrochemical transistor for monitoring the integrity of these structures. We show not only that this versatile device can be adapted to the cyst format for measuring resistance and, therefore, the quality of the cysts, but also can be used for quantitative monitoring of the effect of toxic compounds on cells in a 3D format. The ability to quantitatively predict effects of drugs on 3D cultures in vitro has large future potential for the fields of drug discovery and toxicology.
60 APPLIED LIFE SCIENCES↗
Tracking metal ions through a Cu/Ag efflux pump assigns the functional roles of the periplasmic proteins
Copper is an essential nutrient for all aerobic organisms but is toxic in excess. At the host–pathogen interface, macrophages respond to bacterial infection by copper-dependent killing mechanisms, whereas the invading bacteria are thought to counter with an up-regulation of copper transporters and efflux pumps. The tripartite efflux pump CusCBA and its metallochaperone CusF are vital to the detoxification of copper and silver ions in the periplasm of Escherichia coli . However, the mechanism of efflux by this complex, which requires the activation of the inner membrane pump CusA, is poorly understood. In this paper, we use selenomethionine (SeM) active site labels in a series of biological X-ray absorption studies at the selenium, copper, and silver edges to establish a “switch” role for the membrane fusion protein CusB. We determine that metal-bound CusB is required for activation of cuprous ion transfer from CusF directly to a site in the CusA antiporter, showing for the first time (to our knowledge) the in vitro activation of the Cus efflux pump. This metal-binding site of CusA is unlike that observed in the crystal structures of the CusA protein and is composed of one oxygen and two sulfur ligands. Finally, our results suggest that metal transfer occurs between CusF and apo-CusB, and that, when metal-loaded, CusB plays a role in the regulation of metal ion transfer from CusF to CusA in the periplasm.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗