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At least 1,261 records · Page 70

Knocksideways in plants: an inducible system for in planta visualization of protein interactions

Understanding protein-protein interactions (PPIs) is key to unlocking the secrets of various cellular processes. While many tools have been developed to detect PPIs, such as the yeast two-hybrid assay, bimolecular fluorescence complementation, and affinity purification, there is great demand for additional methods to complement existing ones. As all approaches have limitations, evidence from at least two independent assays is required to validate PPIs. In a Breakthrough Report, Joanna Winkler and colleagues present here a promising method, named “knocksideways in plants” (KSP), for inducible visualization of PPIs in planta.

59 BASIC BIOLOGICAL SCIENCES↗

Modeling temporal and hormonal regulation of plant transcriptional response to wounding

Plants respond to wounding stress by changing gene expression patterns and inducing the production of hormones including jasmonic acid. This wounding transcriptional response activates specialized metabolism pathways such as the glucosinolate pathways in Arabidopsis thaliana. While the regulatory factors and sequences controlling a subset of wound-response genes are known, it remains unclear how wound response is regulated globally. Here, we how these responses are regulated by incorporating putative cis-regulatory elements, known transcription factor binding sites, in vitro DNA affinity purification sequencing, and DNase I hypersensitive sites to predict genes with different wound-response patterns using machine learning. We observed that regulatory sites and regions of open chromatin differed between genes upregulated at early and late wounding time-points as well as between genes induced by jasmonic acid and those not induced. Expanding on what we currently know, we identified cis-elements that improved model predictions of expression clusters over known binding sites. Using a combination of genome editing, in vitro DNA-binding assays, and transient expression assays using native and mutated cis-regulatory elements, we experimentally validated four of the predicted elements, three of which were not previously known to function in wound-response regulation. Our study provides a global model predictive of wound response and identifies new regulatory sequences important for wounding without requiring prior knowledge of the transcriptional regulators.

59 BASIC BIOLOGICAL SCIENCES↗

GTP binding by Arabidopsis extra-large G protein 2 is not essential for its functions

The extra-large guanosine-5'-triphosphate (GTP)-binding protein 2, XLG2, is an unconventional Gα subunit of the Arabidopsis (Arabidopsis thaliana) heterotrimeric GTP-binding protein complex with a major role in plant defense. In vitro biochemical analyses and molecular dynamic simulations show that affinity of XLG2 for GTP is two orders of magnitude lower than that of the conventional Gα, AtGPA1. Here we tested the physiological relevance of GTP binding by XLG2. We generated an XLG2(T476N) variant with abolished GTP binding, as confirmed by in vitro GTPγS binding assay. Yeast three-hybrid, bimolecular fluorescence complementation, and split firefly-luciferase complementation assays revealed that the nucleotide-depleted XLG2(T476N) retained wild-type XLG2-like interactions with the Gβγ dimer and defense-related receptor-like kinases. Both wild-type and nucleotide-depleted XLG2(T476N) restored the defense responses against Fusarium oxysporum and Pseudomonas syringae compromised in the xlg2 xlg3 double mutant. Additionally, XLG2(T476N) was fully functional restoring stomatal density, root growth, and sensitivity to NaCl, but failed to complement impaired germination and vernalization-induced flowering. We conclude that XLG2 is able to function in a GTP-independent manner and discuss its possible mechanisms of action.

Plant Sciences↗

Plant SWEETs: from sugar transport to plant–pathogen interaction and more unexpected physiological roles

Abstract Sugars Will Eventually be Exported Transporters (SWEETs) have important roles in numerous physiological mechanisms where sugar efflux is critical, including phloem loading, nectar secretion, seed nutrient filling, among other less expected functions. They mediate low affinity and high capacity transport, and in angiosperms this family is composed by 20 paralogs on average. As SWEETs facilitate the efflux of sugars, they are highly susceptible to hijacking by pathogens, making them central players in plant–pathogen interaction. For instance, several species from the Xanthomonas genus are able to upregulate the transcription of SWEET transporters in rice (Oryza sativa), upon the secretion of transcription-activator-like effectors. Other pathogens, such as Botrytis cinerea or Erysiphe necator, are also capable of increasing SWEET expression. However, the opposite behavior has been observed in some cases, as overexpression of the tonoplast AtSWEET2 during Pythium irregulare infection restricted sugar availability to the pathogen, rendering plants more resistant. Therefore, a clear-cut role for SWEET transporters during plant–pathogen interactions has so far been difficult to define, as the metabolic signatures and their regulatory nodes, which decide the susceptibility or resistance responses, remain poorly understood. This fuels the still ongoing scientific question: what roles can SWEETs play during plant–pathogen interaction? Likewise, the roles of SWEET transporters in response to abiotic stresses are little understood. Here, in addition to their relevance in biotic stress, we also provide a small glimpse of SWEETs importance during plant abiotic stress, and briefly debate their importance in the particular case of grapevine (Vitis vinifera) due to its socioeconomic impact.

Breia, Richard↗

The small protein SbtC is a functional component of the CO 2 concentrating mechanism in Synechocystis sp. PCC 6803

Oxygenic phototrophs fix CO 2 via the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), which shows relatively low CO 2 affinity and specificity. To circumvent low and fluctuating CO 2 concentrations in aquatic systems, cyanobacteria and algae have evolved sophisticated inorganic carbon (Ci) concentrating mechanisms (CCMs). Bicarbonate transporters such as SbtA play a crucial role in the cyanobacterial CCM and hence display multiple layers of tight regulation. Control of sbtA gene expression and corresponding transporter activity involves the PII-like protein SbtB, whose gene is frequently co-transcribed with sbtA. A previously non-annotated gene located upstream of the sbtAB operon in the model Synechocystis sp. PCC 6803 encodes the small protein SbtC, composed of 80 amino acids. Presence of SbtC was confirmed by immunoblotting of the sbtC-coding sequence fused to a Flag-tag. Similar to sbtAB , transcription of the sbtC locus is induced by low CO 2 availability; however, it is controlled independently. Mutation of the sbtC locus in a wild-type background produced only a mild phenotype, even under low CO 2 , but impaired diurnal growth resembled that of the mutant ΔsbtB . Biochemical analysis indicated a trimeric SbtABC complex in the membrane. Bicarbonate leakage from cells was strongly elevated when either sbtB or sbtC was deleted from recombinant Synechocystis strains harboring only SbtA as single Ci uptake system. Here, our results provide evidence that SbtC contributes to the formation of the SbtAB complex, thereby regulating bicarbonate exchange at the cytoplasmic membrane. Well-conserved SbtC-like proteins encoded in the neighborhood of sbtAB exist in many cyanobacterial genomes, pointing toward an important role in the cyanobacterial CCM.

Walke, Peter [Univ. of Rostock (Germany)] (ORCID:0↗

Construction, characterization and crystal structure of a fluorescent single-chain Fv chimera

In vitro display technologies based on phage and yeast have a successful history of selecting single-chain variable fragment (scFv) antibodies against various targets. However, single-chain antibodies are often unstable and poorly expressed in Escherichia coli. Here, we explore the feasibility of converting scFv antibodies to an intrinsically fluorescent format by inserting the monomeric, stable fluorescent protein named thermal green, between the light- and heavy-chain variable regions. Our results show that the scTGP format maintains the affinity and specificity of the antibodies, improves expression levels, allows one-step fluorescent assay for detection of binding and is a suitable reagent for epitope binning. We also report the crystal structure of an scTGP construct that recognizes phosphorylated tyrosine on FcεR1 receptor of the allergy pathway.

59 BASIC BIOLOGICAL SCIENCES↗

Bioinformatics and 3D Structural Analysis of the Coronavirus Main Protease Active Site Diversity

Coronaviruses (Coronaviridae) such as SARS‐CoV‐2 (severe acute respiratory syndrome coronavirus) and MERS‐CoV (Middle East respiratory syndrome coronavirus) have been the source of recent outbreaks and global health concerns. While vaccines have been essential for controlling the SARS‐CoV‐2 (COVID‐19) pandemic, it is uncertain whether they will be effective against future coronavirus strains. Therefore, identification or design of a broad‐spectrum drug that targets highly conserved regions of the main protease of multiple coronavirus strains is essential in the long term. As part of a virtual summer research experience with the RCSB PDB, bioinformatics tools were employed to predict and construct 3D models of the coronavirus main protease (MPro) using SARS‐CoV‐2 as the template, with a focus on mutational trends and active sites. This study focused on the active sites of MPro, a cysteine protease essential for viral assembly and replication. Sequence alignments and structure modeling of MPro structures has identified conserved regions across multiple coronavirus strains. Inhibition of MPro halts coronavirus replication, making it an ideal drug target, and studies of MPro may foster and accelerate the discovery of high affinity broad‐spectrum drugs.

Wu Wu, Amy↗

Selection and development of aptamers for pyoverdine

The rhizosphere is a small region surrounding plant roots that is enriched in biochemicals from root exudates and populated with fungi, nematode, and bacteria. Interaction of rhizosphere organisms with plants is mainly promoted by exudates from the roots. Root exudates contain biochemicals that come from primary and secondary metabolisms of plants. These biochemicals attract microbes, which influence plant nutrition. The rhizosphere bacteria (microbiome) are vital to plant nutrient uptake and influence biotic and abiotic stress and pathogenesis. Pseudomonas is a genus of gammaproteobacteria known for its ubiquitous presence in natural habitats and its striking ecological, metabolic, and biochemical diversity. Within the genus, members of the Pseudomonas fluorescens group are common inhabitants of soil and plant surfaces, and certain strains function in the biological control of plant disease, protecting plants from infection by soilborne and aerial plant pathogens. The soil bacterium Pseudomonas protegens Pf-5 (also known as Pseudomonas fluorescensPf-5) is a well-characterized biological strain, which is distinguished by its prolific production of the secondary metabolite, pyoverdine. Knowledge of the distribution of P. fluorescens secretory activity around plant roots is very important for understanding the interaction between P. fluorescens and plants and can be achieved by real time tracking of pyoverdine. To achieve the capability of real-time tracking in soil, we have used a structure-switching SELEX strategy to select high affinity ssDNA and 2’ F-Y-RNA aptamers with specificity for pyoverdine over other siderophores. Pyoverdines from various strains possess a conserved chromophore along with strain-specific peptide chain. Some of the isolated aptamers bind to chromophore of pyoverdine. These will identify pyoverdines from a variety of pseudomonads. Identification of aptamers that selectively bind the peptide portion of pyoverdine Pf-5 is underway. The identified aptamers that are broadly and narrowly specific for pyoverdines or Pf-5 will be optimized for integration into an electrochemical biosensor to track, in real time, P fluorescens activity and other pseudomonads in and around the rhizosphere.

59 BASIC BIOLOGICAL SCIENCES↗

Preservation of erniettomorph fossils in clay-rich siliciclastic deposits from the Ediacaran Wood Canyon Formation, Nevada

Three-dimensionally preserved Ediacaran fossils occur globally within sandstone beds. Sandy siliciclastic deposits of the Ediacaran Wood Canyon Formation (WCF) in the Montgomery Mountains, Nevada, contain two fossil morphologies with similar shapes and sizes: one exhibits mm-scale ridges and a distinct lower boundary and the other is devoid of these diagnostic features. We interpret these as taphomorphs of erniettomorphs, soft-bodied organisms with uncertain taxonomic affinities. We explore the cast-and-mould preservation of both taphomorphs by petrography, Raman spectroscopy, X-ray fluorescence microprobe and X-ray diffraction. All fossils and the surrounding sedimentary matrix contain quartz grains, iron-rich chlorite and muscovite. The ridged fossils contain about 70% larger quartz grains compared to the ridgeless taphomorph, indicating a lower abundance of clay minerals in the ridged fossil. Chlorite and muscovite likely originated from smectite and kaolinite precursors that underwent lower greenschist facies metamorphism. Kaolinite and smectite are inferred to have been abundant in sediments around the ridged fossil, which enabled the preservation of a continuous, distinct, clay- and kerogen-rich bottom boundary. The prevalence of quartz in the ridged fossils of the WCF and in erniettomorphs from other localities also suggests a role for this mineral in three-dimensional preservation of erniettomorphs in sandstone and siltstone deposits.

58 GEOSCIENCES↗

Molecular mechanism for the interaction between human CPSF30 and hFip1

Most eukaryotic pre-mRNAs must undergo 3'-end cleavage and polyadenylation prior to their export from the nucleus. A large number of proteins in several complexes participate in this 3'-end processing, including cleavage and polyadenylation specificity factor (CPSF) in mammals. The CPSF30 subunit contains five CCCH zinc fingers (ZFs), with ZF2–ZF3 being required for the recognition of the AAUAAA poly(A) signal. ZF4–ZF5 recruits the hFip1 subunit of CPSF, although the details of this interaction have not been characterized. Here we report the crystal structure of human CPSF30 ZF4–ZF5 in complex with residues 161–200 of hFip1 at 1.9 Å resolution, illuminating the molecular basis for their interaction. Unexpectedly, the structure reveals one hFip1 molecule binding to each ZF4 and ZF5, with a conserved mode of interaction. Our mutagenesis studies confirm that the CPSF30–hFip1 complex has 1:2 stoichiometry in vitro. Mutation of each binding site in CPSF30 still allows one copy of hFip1 to bind, while mutation of both sites abrogates binding. Our fluorescence polarization binding assays show that ZF4 has higher affinity for hFip1, with a K d of 1.8 nM. We also demonstrate that two copies of the catalytic module of poly(A) polymerase (PAP) are recruited by the CPSF30–hFip1 complex in vitro, and both hFip1 binding sites in CPSF30 can support polyadenylation.

59 BASIC BIOLOGICAL SCIENCES↗

Structural and biochemical analyses of the nuclear IκBζ protein in complex with the NF-κB p50 homodimer

As part of the efforts to understand nuclear IκB function in NF-κB-dependent gene expression, we report an X-ray crystal structure of the IκBζ ankyrin repeat domain in complex with the dimerization domain of the NF-κB p50 homodimer. IκBζ possesses an N-terminal α helix that conveys domain folding stability. Affinity and specificity of the complex depend on a small portion of p50 at the nuclear localization signal. The model suggests that only one p50 subunit supports binding with IκBζ, and biochemical experiments confirm that IκBζ associates with DNA-bound NF-κB p50:RelA heterodimers. Comparisons of IκBζ:p50 and p50:κB DNA complex crystallographic models indicate that structural rearrangement is necessary for ternary complex formation of IκBζ and p50 with DNA.

Cell Biology↗

Emission properties of a hybrid metallized diamond(001) photocathode

The spectral emission characteristics of a proof-of-concept hybrid metallized diamond(001) photocathode are presented. The quantum efficiency (QE) is shown to be determined by the photoinjection efficiency across the ohmic contact at the back metallized face, whereas the mean transverse energy (MTE) of the photoemitted electrons is consistent with an (optical)phonon-assisted and momentum-resonant Franck-Condon mechanism [Franck-Condon electron emission from polar semiconductor photocathodes, Phys. Rev. Appl. 23, 054065 (2025)] following electron drift transport to the untreated diamond(001) front emission face. Emission is observed from both the lower and upper conduction bands of diamond with positive and negative electron affinity, respectively. A potential route to the realization of a red-visible photocathode based on this concept with a sub-50 meV MTE and a QE greater than 0.1% is discussed.

Density of states↗

Injection mechanisms in a III -nitride light-emitting diode as seen by self-emissive electron microscopy

Here, we report on the investigation of an electrically biased high efficiency green III-nitride light-emitting diode (LED) by electron emission microscopy (EEM) using a low-energy electron microscope (LEEM). The surface of the LED was activated to negative electron affinity via deposition of a submonolayer of Cs. With the illumination column of the LEEM turned off, upon electrical injection of the LED, we directly image the hot electrons generated by eeh Auger-Meitner nonradiative processes that diffuse through the top p-Ga N layer and emit out the surface of the biased LED. By determining the source of emitted electrons using complementary electron emission spectroscopy measurements, EEM allows us to effectively map the carrier density within the LED. Using EEM, we observed nonelectron emitting regions with a density of approximately 3 × 10 8 cm -2 , identified as V-shaped defects (V-defects). This is confirmed through the corresponding dark spots of panchromatic cathodoluminescence measurements of the same sample and by plan-view transmission electron microscopy. The absence of electron emission at the sidewall of the V-defects can be attributed to several factors, including reduced carrier density in the sidewall quantum wells due to carriers traveling fast through the semipolar sidewalls before being injected into the planar quantum wells, the reduced population of hot electrons surviving diffusion through the thicker p-GaN filling in the V-defect before emission onto vacuum, and a smaller Auger-Meitner coefficient for the low In content semipolar sidewall quantum wells. The stronger electron emission observed at the ridges of most V-defects compared to the planar quantum well regions indicates larger local injected carrier densities, confirming that V-defect sidewalls allow for strong lateral carrier injection when compared to the weaker vertical injection away from the V-defect as evidenced by the weaker electron emission intensity away from the V-defects.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Franck-Condon electron emission from polar semiconductor photocathodes

An analytical formulation of (optical-)phonon-mediated and momentum-resonant Franck-Condon emission of photoexcited electrons from polar semiconductors is shown to be very consistent with (i) the observed emission properties of a cesiated Ga⁢As⁢(001) photocathode at 808 nm [J. Phys. D: Appl. Phys. 54, 205301 (2021)] and (ii) the measured spectral emission properties of a Ga⁢N(0001) photocathode from just below its bandgap energy to 5 eV. The theoretical analysis in the parabolic band approximation predicts the form of both the quantum efficiency and mean transverse energy of photoemission as a function of the photocathode’s electron affinity and the electron temperature in the vicinity of its emission face. The good agreement between theory and experimental data also suggests that sub-10-nm rms surface roughness effects are not significant for polar semiconductor photocathodes.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Spectral emission properties of a nitrogen-doped diamond (001) photocathode: Hot electron transport and transverse momentum filtering

The electron emission properties of a single-crystal nitrogen-doped diamond(001) photocathode inserted in a 10 kV DC photoelectron gun are determined using a tunable (235–410 nm) ultraviolet laser radiation source for photoemission from both the back nitrogen-doped substrate face and the front homoepitaxially grown and undoped diamond crystal face. Here, the measured spectral trends of the mean transverse energy and quantum efficiency of the emitted electrons are both anomalous and nonmonotonic, but are shown to be consistent with (i) the known physics of electron photoexcitation from the nitrogen substitution states into the conduction bands of diamond, (ii) the energy position and dispersion characteristics of the conduction bands of diamond in the (001) emission direction, (iii) the effective electron affinity of the crystal faces, (iv) the strong electron-(optical)phonon coupling in diamond, and (v) the associated hot electron transport dynamics under energy equipartition with the optical phonons. Notably, the observed hot electron emission is shown to be restricted parallel to the photocathode surface by the low transverse effective masses of the emitting band states—a transverse momentum filtering effect.

36 MATERIALS SCIENCE↗

Trap-assisted Auger-Meitner recombination in GaN p-i-n diodes

Most properties of semiconductor devices are dominated by shallow impurities. However, deep defects often play an important role, for instance, in recombination processes or high field transport. While a variety of techniques are available to assess the density and energy levels of impurities, other properties, such as the recombination mechanisms of the defects, escape observation. We report on the direct measurement of hot electrons generated by trap-assisted Auger-Meitner recombination (TAAR) in GaN p-i-n diodes. By performing electron emission spectroscopy (EES) on diodes with surfaces activated to negative electron affinity by cesium, we observe the expected overflow electrons of p-i-n diodes under low current injection. However, when operating the devices at higher current densities, as low as ∼25 A/c⁢m 2 , we measure the emission of high-energy electrons. At variance with the observed hot electrons in light-emitting diodes (LEDs) using EES, the hot electrons generated in p-i-n diodes at our tested currents cannot be from eeh Auger-Meitner recombination due to the diodes' significantly lower carrier densities compared to those in LEDs. During our measurements, we observe the emission of accumulated electrons with energies ∼0.42 eV, ∼0.99 eV, ∼1.43 eV, and ∼2.32 eV above the conduction-band minimum (CBM) at various bias conditions, suggesting the existence of conduction-band features in GaN at these energies where electrons can be long-lived, such as satellite-valley minima and inflection points. We also measure incompletely relaxed hot electrons approaching energies 1.97 ± 0.13 eV and 2.94 ± 0.13 eV above the CBM, as the diodes are biased to high currents, suggesting at least some of the TAAR partaking defects have an energy level ≳1.97 eV and ≳2.94 eV away from either the conduction or valence band edges. Additionally, at our highest operating currents, we measure hot electrons with energies 3.28 ± 0.13 eV above the CBM, providing direct evidence of TAAR processes involving shallow impurities. This unexpected observation of TAAR in GaN p-i-n diodes spotlights the importance of further studies of defects in GaN and the necessity to incorporate the multi-phonon emission, radiative, and TAAR capture steps of defect-assisted recombination cycles into device modeling. Furthermore, this experiment demonstrates the applicability of the simplest semiconductor structures, p-i-n diodes, as a test bed to study the rich recombination physics of semiconductor materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Nonaffine Strains Control Ductility of Metallic Glasses

The origin of limited plasticity in metallic glasses is elusive, with no apparent link to their atomic structure. In this study, we propose that the response of the glassy structure to applied stress, not the original structure itself, provides a gauge to predict the degree of plasticity. We carried out high-energy x-ray diffraction on various bulk metallic glasses (BMGs) under uniaxial compression within the elastic limit and evaluated the anisotropic pair distribution function. We show that the extent of local deviation from the affine (uniform) deformation in the elastic regime is strongly correlated with the plastic behavior of BMGs beyond yield, across chemical compositions and sample history. The results suggest that the propensity for collective local atomic rearrangements under stress promotes plasticity.

3-dimensional systems↗

Numerical Evidence for a Haagerup Conformal Field Theory

We numerically study an anyon chain based on the Haagerup fusion category and find evidence that it leads in the long-distance limit to a conformal field theory whose central charge is ~2. Fusion categories generalize the concept of finite group symmetries to noninvertible symmetry operations, and the Haagerup fusion category is the simplest one which comes from neither finite groups nor affine Lie algebras. As such, ours is the first example of conformal field theories which have truly exotic generalized symmetries. Basically the same result was independently obtained in the preceding Letter [Phys. Rev. Lett. 128, 231602 (2022)].

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗