The ubiquitin-26S proteasome system and autophagy relay proteome homeostasis regulation during silique development.

Functional studies of the ubiquitin-26S proteasome system (UPS) have demonstrated that virtually all aspects of the plant's life involve UPS-mediated turnover of abnormal or short-lived proteins. However, the role of the UPS during development, including in seeds and fruits, remains to be determined in detail, although mutants of several of its core elements are known to be embryonically lethal. Unfortunately, early termination of embryogenesis limits the possibility to characterize the activities of the UPS in reproductive organs. Given both the economic and the societal impact of reproductive production, such studies are indispensable. Here, we systematically compared expression of multiple 26S proteasome subunits along with the dynamics of proteasome activity and total protein ubiquitylation in seedlings, developing siliques, and embryos of Arabidopsis thaliana. Since autophagy plays the second largest role in maintaining proteome stability, we parallelly studied three rate-limiting enzymes that are involved in autophagy flux. Our experiments unexpectedly discovered that, in contrast to the activities in seedlings, both protein and transcript levels of six selected 26S proteasome subunits gradually decline in immature siliques or embryos toward maturation while the autophagy flux rises despite the nutrient-rich condition. We also discovered a reciprocal turnover pathway between the proteasome and autophagy. While the autophagy flux is suppressed in seedlings by UPS-mediated degradation of its three key enzymes, transcriptional reprogramming dampens this process in siliques, which in turn stimulates a bulk autophagic degradation of proteasomes. Collectively, our study of the developmental changes of the UPS and autophagy activities suggests that they relay the proteome homeostasis regulation in early silique and/or seed development, highlighting their interactions during development.

To Kill or to Be Killed: How Does the Battle between the UPS and Autophagy Maintain the Intracellular Homeostasis in Eukaryotes?

The ubiquitin-26S proteasome system and autophagy are two major protein degradation machineries encoded in all eukaryotic organisms. While the UPS is responsible for the turnover of short-lived and/or soluble misfolded proteins under normal growth conditions, the autophagy-lysosomal/vacuolar protein degradation machinery is activated under stress conditions to remove long-lived proteins in the forms of aggregates, either soluble or insoluble, in the cytoplasm and damaged organelles. Recent discoveries suggested an integrative function of these two seemly independent systems for maintaining the proteome homeostasis. One such integration is represented by their reciprocal degradation, in which the small 76-amino acid peptide, ubiquitin, plays an important role as the central signaling hub. In this review, we summarized the current knowledge about the activity control of proteasome and autophagosome at their structural organization, biophysical states, and turnover levels from yeast and mammals to plants. Through comprehensive literature studies, we presented puzzling questions that are awaiting to be solved and proposed exciting new research directions that may shed light on the molecular mechanisms underlying the biological function of protein degradation.

Generation of a fertile ask1 mutant uncovers a comprehensive set of SCF-mediated intracellular functions.

Many eukaryotic intracellular processes employ protein ubiquitylation by ubiquitin E3 ligases for functional regulation or protein quality control. In plants, the multi-subunit Skp1-Cullin1-F-box (SCF) complexes compose the largest group of E3 ligases whose specificity is determined by a diverse array of F-box proteins. Although both sequence divergence and polymorphism of F-box genes well support a broad spectrum of SCF functions, experimental evidence is scarce due to the low number of identified SCF substrates. Taking advantage of the bridge role of Skp1 between F-box and Cullin1 in the complex, we systematically analyzed the functional influence of a well-characterized Arabidopsis Skp1-Like1 (ASK1) Ds insertion allele, ask1, in different Arabidopsis accessions. Through 10 generations of backcrossing with Columbia-0 (Col-0), we partially rescued the fertility of this otherwise sterile ask1 allele in Landsberg erecta, thus providing experimental evidence showing the polymorphic roles of SCF complexes. This ask1 mutant produces twisted rosette leaves, a reduced number of petals, fewer viable pollen grains, and larger embryos and seeds compared to Col-0. RNA-Seq-based transcriptome analysis of ask1 uncovered a large spectrum of SCF functions, which is greater than a 10-fold increase compared with previous studies. We also identified its hyposensitive responses to auxin and abscisic acid treatments and enhanced far-red light/phyA-mediated photomorphogenesis. Such diverse roles are consistent with the 20-30% reduction of ubiquitylation events in ask1 estimated by immunoblotting analysis in this work. Collectively, we conclude that ASK1 is a predominant Skp1 protein in Arabidopsis and that the fertile ask1 mutant allowed us to uncover a comprehensive set of SCF functions.

Diversifying Evolution of the Ubiquitin-26S Proteasome System in Brassicaceae and Poaceae.

: Genome amplification and sequence divergence provides raw materials to allow organismal adaptation. This is exemplified by the large expansion of the ubiquitin-26S proteasome system (UPS) in land plants, which primarily rely on intracellular signaling and biochemical metabolism to combat biotic and abiotic stresses. While a handful of functional genomic studies have demonstrated the adaptive role of the UPS in plant growth and development, many UPS members remain unknown. In this work, we applied a comparative genomic study to address the functional divergence of the UPS at a systematic level. We first used a closing-target-trimming annotation approach to identify most, if not all, UPS members in six species from each of two evolutionarily distant plant families, Brassicaceae and Poaceae. To reduce age-related errors, the two groups of species were selected based on their similar chronological order of speciation. Through size comparison, chronological expansion inference, evolutionary selection analyses, duplication mechanism prediction, and functional domain enrichment assays, we discovered significant diversities within the UPS, particularly between members from its three largest ubiquitin ligase gene families, the F-box (FBX), the Really Interesting New Gene (RING), and the Bric-a-Brac/Tramtrack/Broad Complex (BTB) families, between Brassicaceae and Poaceae. Uncovering independent Arabidopsis and Oryza genus-specific subclades of the 26S proteasome subunits from a comprehensive phylogenetic analysis further supported a diversifying evolutionary model of the UPS in these two genera, confirming its role in plant adaptation.

Contrasting Impacts of Ubiquitin Overexpression on Arabidopsis Growth and Development.

In plants, the ubiquitin (Ub)-26S proteasome system (UPS) regulates numerous biological functions by selectively targeting proteins for ubiquitylation and degradation. However, the regulation of Ub itself on plant growth and development remains unclear. To demonstrate a possible impact of Ub supply, as seen in animals and flies, we carefully analyzed the growth and developmental phenotypes of two different poly-Ub (UBQ) gene overexpression plants of Arabidopsis thaliana. One is transformed with hexa-6His-UBQ (designated 6HU), driven by the cauliflower mosaic virus 35S promoter, while the other expresses hexa-6His-TEV-UBQ (designated 6HTU), driven by the endogenous promoter of UBQ10. We discovered that 6HU and 6HTU had contrasting seed yields. Compared to wildtype (WT), the former exhibited a reduced seed yield, while the latter showed an increased seed production that was attributed to enhanced growth vigor and an elevated silique number per plant. However, reduced seed sizes were common in both 6HU and 6HTU. Differences in the activity and size of the 26S proteasome assemblies in the two transgenic plants were also notable in comparison with WT, suggestive of a contributory role of UBQ expression in proteasome assembly and function. Collectively, our findings demonstrated that exogenous expression of recombinant Ub may optimize plant growth and development by influencing the UPS activities via structural variance, expression patterns, and abundance of free Ub supply.

Superconductivity in the High-Entropy Ceramics Ti0.2 Zr0.2 Nb0.2 Mo0.2 Ta0.2 Cx with Possible Nontrivial Band Topology.

Topological superconductors have drawn significant interest from the scientific community due to the accompanying Majorana fermions. Here, the discovery of electronic structure and superconductivity (SC) in high-entropy ceramics Ti0.2 Zr0.2 Nb0.2 Mo0.2 Ta0.2 Cx (x = 1 and 0.8) combined with experiments and first-principles calculations is reported. The Ti0.2 Zr0.2 Nb0.2 Mo0.2 Ta0.2 Cx high-entropy ceramics show bulk type-II SC with Tc ≈ 4.00 K (x = 1) and 2.65 K (x = 0.8), respectively. The specific heat jump (∆C/γTc ) is equal to 1.45 (x = 1) and 1.52 (x = 0.8), close to the expected value of 1.43 for the BCS superconductor in the weak coupling limit. The high-pressure resistance measurements show a robust SC against high physical pressure in Ti0.2 Zr0.2 Nb0.2 Mo0.2 Ta0.2 C, with a slight Tc variation of 0.3 K within 82.5 GPa. Furthermore, the first-principles calculations indicate that the Dirac-like point exists in the electronic band structures of Ti0.2 Zr0.2 Nb0.2 Mo0.2 Ta0.2 C, which is potentially a topological superconductor. The Dirac-like point is mainly contributed by the d orbitals of transition metals M and the p orbitals of C. The high-entropy ceramics provide an excellent platform for the fabrication of novel quantum devices, and the study may spark significant future physics investigations in this intriguing material.

MORF2-mediated plastidial retrograde signaling is involved in stress response and skotomorphogenesis beyond RNA editing.

Retrograde signaling modulates the expression of nuclear genome-encoded organelle proteins to adjust organelle function in response to environmental cues. MULTIPLE ORGANELLAR RNA EDITING FACTOR 2 (MORF2) was initially recognized as a plastidial RNA-editing factor but recently shown to interact with GUN1. Given the central role of GUN1 in chloroplast retrograde signaling and the unviable phenotype of morf2 mutants that is inconsistent with many viable mutants involved in RNA editing, we hypothesized that MORF2 has functions either dosage dependent or beyond RNA editing. Using an inducible Clustered Interspaced Short Palindromic Repeat interference (iCRISPRi) approach, we were able to reduce the MORF2 transcripts in a controlled manner. In addition to MORF2-dosage dependent RNA-editing errors, we discovered that reducing MORF2 by iCRISPRi stimulated the expression of stress responsive genes, triggered plastidial retrograde signaling, repressed ethylene signaling and skotomorphogenesis, and increased accumulation of hydrogen peroxide. These findings along with previous discoveries suggest that MORF2 is an effective regulator involved in plastidial metabolic pathways whose reduction can readily activate multiple retrograde signaling molecules possibly involving reactive oxygen species to adjust plant growth. In addition, our newly developed iCRISPRi approach provided a novel genetic tool for quantitative reverse genetics studies on hub genes in plants.

A straightforward spectral emissivity estimating method based on constructing random rough surfaces.

Spectral emissivity is an essential and sensitive parameter to characterize the radiative capacity of the solid surface in scientific and engineering applications, which would be non-negligibly affected by surface morphology. However, there is a lack of assessment of the effect of roughness on emissivity and a straightforward method for estimating the emissivity of rough surfaces. This paper established an estimating method based on constructing random rough surfaces to predict rough surface (Geometric region) emissivity for metal solids. Based on this method, the emissivity of ideal gray and non-gray body surfaces was calculated and analyzed. The calculated and measured spectral emissivities of GH3044, K465, DD6, and TC4 alloys with different roughness were compared. The results show that the emissivity increases with the roughness degree, and the enhancement effect weakens with the increase of roughness or emissivity due to the existing limit (emissivity ε = 1.0). At the same time, the roughness would not change the overall spectral distribution characteristics but may attenuate the local features of the spectral emissivity. The estimated results are in good agreement with the experimental data for the above alloys' rough surfaces. This study provides a new reliable approach to obtaining the spectral emissivity of rough surfaces. This approach is especially beneficial for measuring objects in extreme environments where emissivity is difficult to obtain. Meanwhile, this study promotes an understanding of surface morphology's effect mechanism on emissivity.

Understanding Bridging Sites and Accelerating Quantum Efficiency for Photocatalytic CO2 Reduction.

We report a novel double-shelled nanoboxes photocatalyst architecture with tailored interfaces that accelerate quantum efficiency for photocatalytic CO2 reduction reaction (CO2RR) via Mo-S bridging bonds sites in Sv-In2S3@2H-MoTe2. The X-ray absorption near-edge structure shows that the formation of Sv-In2S3@2H-MoTe2 adjusts the coordination environment via interface engineering and forms Mo-S polarized sites at the interface. The interfacial dynamics and catalytic behavior are clearly revealed by ultrafast femtosecond transient absorption, time-resolved, and in situ diffuse reflectance-Infrared Fourier transform spectroscopy. A tunable electronic structure through steric interaction of Mo-S bridging bonds induces a 1.7-fold enhancement in Sv-In2S3@2H-MoTe2(5) photogenerated carrier concentration relative to pristine Sv-In2S3. Benefiting from lower carrier transport activation energy, an internal quantum efficiency of 94.01% at 380 nm was used for photocatalytic CO2RR. This study proposes a new strategy to design photocatalyst through bridging sites to adjust the selectivity of photocatalytic CO2RR.

Construction of Mixed Ionic-Electronic Conducting Scaffolds in Zn Powder: A Scalable Route to Dendrite-Free and Flexible Zn Anodes.

Zn powder (Zn-P)-based anodes are considered ideal candidates for Zn-based batteries because they enable a positive synergistic integration of safety and energy density. However, Zn-P-based anodes still experience easy corrosion, uncontrolled dendrite growth, and poor mechanical strength, which restrict their further application. Herein, a mixed ionic-electronic conducting scaffold is introduced into Zn-P to successfully fabricate anti-corrosive, flexible, and dendrite-free Zn anodes using a scalable tape-casting strategy. The as-established scaffold is characterized by robust flexibility, facile scale-up synthesis methodology, and exceptional anti-corrosive characteristics, and it can effectively homogenize the Zn2+ flux during Zn plating/stripping, thus allowing stable Zn cycling. Benefiting from these comprehensive attributes, the as-prepared Zn-P-based anode provides superior electrochemical performance, including long-life cycling stability and high rate capability in practical coin and flexible pouch cells; thus, it holds great potential for developing advanced Zn-ion batteries. The findings of this study provide insights for a promising scalable pathway to fabricate highly efficient and reliable Zn-based anodes and will aid in the realization of advanced flexible energy-storage devices.

Mild synthesis of superadhesive hydrogel electrolyte with low interfacial resistance and enhanced ionic conductivity for flexible zinc ion battery.

Flexible aqueous battery is considered to be one of the most promising energy storage devices for powering flexible electronics. However, inferior interfacial compatibility in electrode-electrolyte interfaces and inefficient ionic channel of electrolytes usually result in potential troubles when applied in practical applications. Herein, we report a mild synthetic route to a sodium lignosulfonate-polyacrylamide hydrogel electrolyte with a high adhesiveness to achieve low electrode-electrolyte interfacial resistance and fast ionic conduction. Comprehensive experiments show that the catechol groups from sodium lignosulfonate demonstrate strong interactions with both cathode and anode materials, and thus greatly reduce the contact resistances across the electrodes. Meanwhile, the existence of sulfonate groups significantly enhances the ionic conductivity of the hydrogel electrolyte. Benefiting from this design, a low ohmic resistance of 3.8 Ω (i.e., 11.4 Ω cm2 ), a low charge transfer resistance of 22.5 Ω (i.e., 67.5 Ω cm2 ), a high ionic conductivity of 31.1 mS cm-1 as well as a 100% capacity retention upon harsh bending deformation can be realized in the flexible zinc ion battery, which are significantly superior to those in the traditional candidates. The present investigation provides new insight into addressing the interfacial issue plaguing flexible energy storage devices.

Boosting zinc ion energy storage capability of inert MnO cathode by defect engineering.

Aqueous zinc ion battery constitutes a safe, stable and promising next-generation energy storage device, but suffers the lack of suitable host compounds for zinc ion storage. Development of a facile way to emerging cathode materials is strongly requested toward superior electrochemical activities and practical applications. Herein, defect engineering, i.e., simultaneous introduction of nitrogen dopant and oxygen vacancy into commercial and low-cost MnO, is proposed as a positive strategy to activate the originally inert phase for kinetically propelling its zinc ion storage capability. Both experimental characterization and theoretical calculations demonstrate that the nitrogen dopant significantly improves the electric conductivity of electrochemical inert MnO. Simultaneously, the oxygen vacancy creates sufficient large inserted channels and available activated adsorption sites for zinc ions storage. These synergistic structural advantages obviously ameliorate the electrochemical performance of inert MnO. Therefore, even without any conductive agent additive, the as-prepared material shows high specific capacity, superb rate capability, prolonged cycling stability and attractive energy density, which are dramatically superior to those of the pristine MnO as well as many other host cathode materials. This work presents fresh insights on the role of defect engineering in the enhancement of the intrinsic electrochemical reactivity of inert cathode, and an effective strategy for scalable fabrication of high-performance cathode for zinc ion battery.

Facile construction of uniform ultramicropores in porous carbon for advanced sodium-ion battery.

Facile fabrication of anode materials with low cost, good rate capability and high capacity is a critical factor towards developing sodium-ion battery for practical applications. Herein, a N, O co-doped porous carbon with uniform ultramicropores (NOPC-UM), is synthesized by an in-situ ultramicro templating strategy, and demonstrated as a high-performance sodium-ion storage material. Key to this strategy is employment of an inherent KCl as untramicro template, which leads to formation of uniform size of ultramicropores and heteroatoms (i.e., N and O) doping after high-temperature pyrolysis. The as-constructed NOPC-UM delivers a large capacity of 305 mAh g-1, accompanying with a 93% specific capacity below 1.00 V, and superior cycling stability about 100% after 4000 cycles. These attractive electrochemical performances endow NOPC-UM with impressive potential use as anode materials of sodium-ion battery.

Facile Synthesis of Core-Shell Structured SiO2@Carbon Composite Nanorods for High-Performance Lithium-Ion Batteries.

Recently, SiO2 has attracted wide attention in lithium-ion batteries owing to its high theoretical capacity and low cost. However, the utilization of SiO2 is impeded by the enormous volume expansion and low electric conductivity. Although constructing SiO2/carbon composite can significantly enhance the electrochemical performance, the skillful preparation of the well-defined SiO2/carbon composite is still a remaining challenge. Here, a facile strategy of in situ coating of polydopamine is applied to synthesis of a series of core-shell structured SiO2@carbon composite nanorods with different thicknesses of carbon shells. The carbon shell uniformly coated on the surface of SiO2 nanorods significantly suppresses the volume expansion to some extent, as well as improves the electric conductivity of SiO2. Therefore, the composite nanorods exhibit a remarkable electrochemical performance as the electrode materials of lithium-ion batteries. For instance, a high and stable reversible capacity at a current density of 100 mA g-1 reaches 690 mAh g-1 and a capacity of 344.9 mAh g-1 can be achieved even at the high current density of 1000 mA g-1. In addition, excellent capacity retention reaches 95% over 100 cycles. These SiO2@carbon composite nanorods with decent electrochemical performances hold great potential for applications in lithium-ion batteries.

Improved ion-diffusion performance by engineering an ordered mesoporous shell in hollow carbon nanospheres.

A new kind of hollow carbon nanosphere with an ordered mesoporous shell structure is prepared and demonstrated to have improved performances in practical application areas involving fast ion transport.

Characterization of the deubiquitination activity and substrate specificity of the chicken ubiquitin-specific protease 1/USP associated factor 1 complex.

Deubiquitinases (DUBs) are essential regulators of intracellular processes involving ubiquitin (Ub) modification. The human DUB ubiquitin-specific protease 1 (hUSP1) interacts with human USP-associated factor 1 (hUAF1), and helps to regulate processes such as DNA damage repair. Previously, we identified a chicken USP1 homologue (chUSP1) during an investigation into the properties of Marek's disease virus (MDV). However, chUSP1's deubiquitination activity, interaction with chUAF1, and substrate specificity remained unknown. In the present study, we expressed and purified both chUAF1 and chUSP1 with or without putative catalytic core mutations using the Bac-to-Bac system, before investigating their deubiquitination activity and kinetics using various substrates. chUSP1 was shown to interact with chUAF1 both in cellular assays in which the two proteins were co-expressed, and in in vitro assays using purified proteins. Heterodimerization with chUAF1 increased the deubiquitination activity of chUSP1 up to 54-fold compared with chUSP1 alone. The chUSP1 mutants C91S, H603A, and D758A reduced the deubiquitination activity of the chUSP1/chUAF1 complex by 10-, 7-, and 33-fold, respectively, while the C91A and H594A chUSP1 mutants eliminated deubiquitination activity of the chUSP1/chUAF1 complex completely. This suggests that C91 and H594, but not D758, are essential for chUSP1 deubiquitination activity, and that a nucleophilic group at position 91 is needed for the deubiquitination reaction. The chUSP1/chUAF1 complex was found to have distinct substrate preferences; efficient hydrolysis of Ub dimers with K11-, K48-, and K63-linkages was seen, with weaker hydrolysis observed with K6-, K27-, and K33-linkages and no hydrolysis seen with a K29-linkage. Furthermore, other Ub-like substrates were disfavored by the complex. No activity was seen with SUMO1-GST, SUMO2- and SUMO3-dimers, ISG15-Rho, FAT10-Rho, or Ufm1-Rho, and only weak activity was observed with NEDD8-Rho. Overall, the data presented here characterize the activity and substrate preferences of chUSP1, and thus may facilitate future studies on its in vivo role.