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Abstract Supercoiled flagellar filaments function as mechanical propellers within the bacterial flagellum complex, playing a crucial role in motility. Flagellin, the building block of the filament, features a conserved inner D0/D1 core domain across different bacterial species. In contrast, approximately half of the flagellins possess additional, highly divergent outer domain(s), suggesting varied functional potential. In this study, we report atomic structures of flagellar filaments from three distinct bacterial species: Cupriavidus gilardii, Stenotrophomonas maltophilia, and Geovibrio thiophilus. Our findings reveal that the flagella from the facultative anaerobic G. thiophilus possesses a significantly more negatively charged surface, potentially enabling adhesion to positively charged minerals. Furthermore, we analyze all AlphaFold predicted structures for annotated bacterial flagellins, categorizing the flagellin outer domains into 682 structural clusters. This classification provides insights into the prevalence and experimental verification of these outer domains. Remarkably, two of the flagellar structures reported herein belong to a distinct cluster, indicating additional opportunities on the study of the functional diversity of flagellar outer domains. Our findings underscore the complexity of bacterial flagellins and open up possibilities for future studies into their varied roles beyond motility.

Abstract Type IV pili (T4P) represent one of the most common varieties of surface appendages in archaea. These filaments, assembled from small pilin proteins, can be many microns long and serve diverse functions, including adhesion, biofilm formation, motility, and intercellular communication. Here, we determine atomic structures of two distinct adhesive T4P from Saccharolobus islandicus via cryo-electron microscopy (cryo-EM). Unexpectedly, both pili were assembled from the same pilin polypeptide but under different growth conditions. One filament, denoted mono-pilus, conforms to canonical archaeal T4P structures where all subunits are equivalent, whereas in the other filament, the tri-pilus, the same polypeptide exists in three different conformations. The three conformations in the tri-pilus are very different from the single conformation found in the mono-pilus, and involve different orientations of the outer immunoglobulin-like domains, mediated by a very flexible linker. Remarkably, the outer domains rotate nearly 180° between the mono- and tri-pilus conformations. Both forms of pili require the same ATPase and TadC-like membrane pore for assembly, indicating that the same secretion system can produce structurally very different filaments. Our results show that the structures of archaeal T4P appear to be less constrained and rigid than those of the homologous archaeal flagellar filaments that serve as helical propellers.

Abstract Acinetobacters pose a significant threat to human health, especially those with weakened immune systems. Type IV pili of acinetobacters play crucial roles in virulence and antibiotic resistance. Single-stranded RNA bacteriophages target the bacterial retractile pili, including type IV. Our study delves into the interaction between Acinetobacter phage AP205 and type IV pili. Using cryo-electron microscopy, we solve structures of the AP205 virion with an asymmetric dimer of maturation proteins, the native Acinetobacter type IV pili bearing a distinct post-translational pilin cleavage, and the pili-bound AP205 showing its maturation proteins adapted to pilin modifications, allowing each phage to bind to one or two pili. Leveraging these results, we develop a 20-kilodalton AP205-derived protein scaffold targeting type IV pili in situ, with potential for research and diagnostics.

It is well acknowledged to all that an active equalization strategy can overcome the inconsistency of lithium-ion cell's voltage and state of charge (SOC) in series-connected lithium-ion battery (LIB) pack in the electric vehicle application. In this regard, a novel dual threshold trigger mechanism based active equalization strategy (DTTM-based AES) is proposed to overcome the inherent inconsistency of cells and to improve the equalization efficiency for a series-connected LIB pack. First, a modified dual-layer inductor equalization circuit is constructed to make it possible for the energy transfer path optimization. Next, based on the designed dual threshold trigger mechanism provoked by battery voltage and SOC, an active equalization strategy is proposed, each single cell's SOC in the battery packs is estimated using the extended Kalman particle filter algorithm. Besides, on the basis of the modified equalization circuit, the improved particle swarm optimization is adopted to optimize the energy transfer path with aiming to reduce the equalization time. Lastly, the simulation and experimental results are provided to validate the proposed DTTM-based AES.

Broken soft and low permeability (BSLP) coal reservoirs are widely distributed in China. However, due to its soft and broken structure and low permeability, the conventional vertical/horizontal well direct fracturing technology is not ideal for the enhancement of BSLP coal seams and the surface development of coalbed methane (CBM). The efficient development of CBM in BSLP coal reservoirs has been an important technical bottleneck restricting the large-scale development of CBM industry and the efficient treatment of coal mine gas control in China. Based on the systematic analysis of the characteristics of BSLP coal reservoirs and the problems existing in the surface development of CBM, the current technological progress in the enhancement of BSLP coal reservoirs and surface development of CBM were reviewed by taking horizontal well as the base well type and focusing on three different technical directions: indirect fracturing, stress relief and consolidation before fracturing. The CBM development technologies of indirect fracturing, including roof indirect fracturing, gangue indirect fracturing and hard coal stratification indirect fracturing were summarized. The stress release CBM development technologies using different stress release methods, such as hydraulic jet cavitation, gas dynamic cavitation, mechanical + hydraulic + induced instability coupling cavitation and hydraulic slit, were reviewed. Furthermore, the CBM development technology of first consolidation and then fracturing of BSLP coal reservoirs induced by microorganisms was also summarized. The exploration of indirect fracturing technology has accumulated a lot of engineering practice, and has achieved a good effect on enhancing the BSLP coal reservoirs in areas with suitable geological conditions. The exploration of new technology for enhancing BSLP coal reservoir represented by stress release has also made great progress, and has entered the stage of engineering tests and verification. According to the characteristics of BSLP coal reservoir and the new development principle, the horizontal well stress release technology has greater potential for reservoir reconstruction and better effect for CBM development. Based on the horizontal well stress release method, the development trend of BSLP coal reservoir enhancement and surface CBM development technology was forecasted in three aspects: expanding the stress release range, improving the development effect of CBM and achieving the co-production of coal and CBM. It is expected to provide reference for improving the stimulation effect of BSLP coal reservoir and increasing the production of CBM well in China.

Abstract A contractile sheath and rigid tube assembly is a widespread apparatus used by bacteriophages, tailocins, and the bacterial type VI secretion system to penetrate cell membranes. In this mechanism, contraction of an external sheath powers the motion of an inner tube through the membrane. The structure, energetics, and mechanism of the machinery imply rigidity and straightness. The contractile tail of Agrobacterium tumefaciens bacteriophage Milano is flexible and bent to varying degrees, which sets it apart from other contractile tail-like systems. Here, we report structures of the Milano tail including the sheath-tube complex, baseplate, and putative receptor-binding proteins. The flexible-to-rigid transformation of the Milano tail upon contraction can be explained by unique electrostatic properties of the tail tube and sheath. All components of the Milano tail, including sheath subunits, are crosslinked by disulfides, some of which must be reduced for contraction to occur. The putative receptor-binding complex of Milano contains a tailspike, a tail fiber, and at least two small proteins that form a garland around the distal ends of the tailspikes and tail fibers. Despite being flagellotropic, Milano lacks thread-like tail filaments that can wrap around the flagellum, and is thus likely to employ a different binding mechanism.

Abstract Large gaps exist in our understanding of how bacteriophages, the most abundant biological entities on Earth, assemble and function. The structure of the “neck” region, where the DNA-filled capsid is connected to the host-recognizing tail remains poorly understood. We describe cryo-EM structures of the neck, the neck-capsid and neck-tail junctions, and capsid of the Agrobacterium phage Milano. The Milano neck 1 protein connects the 12-fold symmetrical neck to a 5-fold vertex of the icosahedral capsid. Comparison of Milano neck 1 homologs leads to four proposed classes, likely evolved from the simplest one in siphophages to more complex ones in myo- and podophages. Milano neck is surrounded by the atypical collar, which covalently crosslinks the tail sheath to neck 1. The Milano capsid is decorated with three types of proteins, a minor capsid protein (mCP) and two linking proteins crosslinking the mCP to the major capsid protein. The extensive network of disulfide bonds within and between neck, collar, capsid and tail provides an exceptional structural stability to Milano.

Understanding the genetic basis of salt resistance in crops is crucial for agricultural productivity. This study investigates the phenotypic and genetic basis of salt stress response in rice (Oryza sativa L.), focusing on germination and seedling traits. Under salt stress conditions, significant differences were observed in seed germination and seedling traits between parental LH99 (Indica rice LuHui 99) and SN265 (japonica rice ShenNong 265). Transgressive segregation was evident within the RIL population, indicating complex genetic interactions. Nine QTLs were detected at germination and seedling stages under salt stress, namely qSGE5 and qSGE7 for seed germination energy (SGE); qSGP7 for seed germination percentage (SGP); qSSH7, qSSH9-1, and qSSH9-2 for seeding height (SSH); qSRN6 for root number (SRN); and qSDW6 and qSDW9 for dry weight (SDW). Among them, qSSH9-1 and qSDW9 were localized in the same interval, derived from the salt-resistant parent SN265. PCA revealed distinct trait patterns under salt stress, captured by six PCs explaining 81.12% of the total variance. PC composite scores were used to localize a QTL associated with early salt resistance in rice qESC9, which was located in the same interval as qSSH9-1 and qSDW9, and was subsequently unified under the name qESC9, an important QTL for early-growth salt tolerance in rice. Correlation analysis also confirmed a relationship between alleles of qESC9 and the resistance to salt, underscoring the critical role this locus plays in the determination of overall salt tolerance in rice. Physiological analyses of extreme phenotype lines highlighted the importance of ion exclusion mechanisms in salt-resistant lines, while salt-susceptible lines exhibited elevated oxidative stress and impaired antioxidant defense, contributing to cellular damage. This comprehensive analysis sheds light on the genetic and physiological mechanisms underlying salt stress response in rice, providing valuable insights for breeding programs aimed at enhancing salt resistance in rice.

Off-road machinery is one of the significant contributors to air pollution due to its large quantity. In this study, a deep learning model was developed to predict the transient engine emissions of CO, NO, NO2, and NOx, which are the main pollutants emitted by off-road machinery. A portable emission measurement system (PEMS) was used to measure the exhaust emission features of four types of construction machinery. The raw PEMS data were preprocessed using data compensation, local linear regression, and normalization to ensure that the data could handle transient conditions. The proposed model utilizes the preprocessing PEMS data to estimate the CO, NO, NO2, and NOx emissions from off-road machinery using a recurrent neural network (RNN) based on a long short-term memory (LSTM) model. The experimental results show that the proposed method can effectively predict the emissions from off-road construction machinery under transient conditions and can be applied to controlling the emissions from off-road construction machinery.

Bacteria can exchange DNA through extracellular appendages (‘mating pili’) in a process known as conjugation. Here, Beltran et al. determine atomic structures by cryo-electron microscopy of a bacterial conjugative pilus and two archaeal pili, showing that the archaeal pili are homologous to bacterial mating pili.

Different active powders were incorporated into TiC particle (TiCp) preforms of TiCp/manganese steel matrix composites to enhance the TiC/steel interfacial bonding. The effect of the active powders on bending strength and toughness of the composites was investgated. The composites were fabricated using a squeeze casting infiltration method, with a TiCp volume fraction of 50%. The active powders were mixed powders of Fe and tungsten carbide (WC), Ni and WC, and Ni and Si, respectively. Energy dispersive spectrometer (EDS) and transmission electron microscopy (TEM) were employed to analyze the interfacial microstructure of the composites. The results show that the addition of WCp results in the formation of a (W, Ti)C layer around TiCps, thereby strengthening the interfacial bonding. Conversely, the addition of Fe powder leads to the presence of significant glass-phase material at the interface, which is prone to cracking. Consequently, the composite with active Ni+WC exhibits notably higher bending strength (680.3 MPa) and impact toughness (7.7 J cm ^−2 ) compared to the composite with active Fe+WC (574.3 MPa and 2.6 J cm ^−2 ), with increases of 18.5% and 196.2%, respectively. Furthermore, the composite with active Ni+Si demonstrates the highest bending strength (886.7 MPa) and good toughness (4.3 J cm ^−2 ), which are 54.4% and 65.4% higher than those of the Fe+WC active composite, respectively, and its strength is 30.3% greater than that of the Ni+WC active composite. This improvement is attributed to enhanced wettability between TiCp and the matrix.

Titanium carbide particles (TiCp) is one of the most commonly used ceramic particles in ceramic- particle-reinforced metal matrix composites. The study prepared TiCp/Cr8Mo2VSi composites using the squeeze casting technique and investigated the effects of different TiCp volume fractions on the mechanical properties, including bending strength and impact toughness. Additionally, the study added tungsten carbide particles (WCp) powder to the preform to examine its effect on the mechanical properties of the composites. The study found that as the volume fraction of TiCp increased, the bending strength of the composites decreased gradually. The highest bending strength of 642.7 MPa was observed at 35% volume fraction. The impact toughness showed a small change, approximately 1.7 J cm ^−2 . Upon the addition of WCp powder (with a mass fraction of 5.0 wt% and TiCp volume fraction of 50%), the bending strength and impact toughness of the composites were 375.2 MPa and 2.1 J cm ^−2 , respectively. Compared to the composites without WCp powder (105.4 MPa, 1.7 J cm ^−2 ), the addition of WCp powder resulted in a 256.0% increase in bending strength and a 23.5% increase in impact toughness.

RNA modifications are important regulators of RNA biology. Here we report N1-methyladenosine (m1A) enrichment on 22-nucleotide tRNA fragments and its effect on gene-silencing. Higher level of m1A in bladder cancer is accompanied by gene dysregulation in unfolded protein response.

It has been suggested that the outer domains of bacterial flagellins are not needed for motility. Here, the authors show that flagellar filament outer domains from some bacteria have unique structures which can alter the motility of the bacteria.

While early genetic and low-resolution structural observations suggested that extracellular conductive filaments on metal-reducing organisms such as Geobacter were composed of type IV pili, it has now been established that bacterial c-type cytochromes can polymerize to form extracellular filaments capable of long-range electron transport. Atomic structures exist for two such cytochrome filaments, formed from the hexaheme cytochrome OmcS and the tetraheme cytochrome OmcE. Due to the highly conserved heme packing within the central OmcS and OmcE cores, and shared pattern of heme coordination between subunits, it has been suggested that these polymers have a common origin. We have now used cryo-electron microscopy (cryo-EM) to determine the structure of a third extracellular filament, formed from the Geobacter sulfurreducens octaheme cytochrome, OmcZ. In contrast to the linear heme chains in OmcS and OmcE from the same organism, the packing of hemes, heme:heme angles, and between-subunit heme coordination is quite different in OmcZ. A branched heme arrangement within OmcZ leads to a highly surface exposed heme in every subunit, which may account for the formation of conductive biofilm networks, and explain the higher measured conductivity of OmcZ filaments. This new structural evidence suggests that conductive cytochrome polymers arose independently on more than one occasion from different ancestral multiheme proteins.

Abstract Background Dysfunction of mesenchymal stem cells (MSCs) is recognized as critical to the pathogenesis of glucocorticoid-induced osteoporosis (GIO), suggesting the potential of MSC-targeting interventions for this disorder. As the miR-133a has been shown to play an important role in bone metabolism, we hypothesized that miR-133a may also be involved in GIO. Methods In the in vitro study, we examined the effect of miR-133a antagomir on DEX-treated MSCs, including proliferation, apoptosis, osteoblast, and adipocyte differentiation, then, we explored the mechanism of these effects of miR-133a silencing through measuring the phosphorylation of ERK1/2 and its regulator FGFR1 via western blot and qRT-PCR. In the in vivo study, we developed a GIO rat model by injecting methylprednisolone and modulated the miR-133a expression in the femur by intramedullary injection of the miR-133a antagomir, and then micro-CT analyses and histological staining of the femurs were used to investigate the effect of miR-133a silencing on bone loss of the GIO rats. Results qRT-PCR analysis indicated that glucocorticoid induced high miR-133a expression in MSCs and animal models. The in vitro study showed that miR-133a antagomir significantly promoted cell proliferation, viability, and osteoblast differentiation and inhibited adipocyte differentiation in DEX-treated MSCs. Furthermore, the expression of p-ERK1/2 and FGFR1 in DEX-treated MSCs was also upregulated by miR-133a antagomir. Then we investigated the effect of miR-133a silencing on the bone architecture of GIO models, micro-CT analysis showed that miR-133a antagomir attenuated the loss of bone mass and improved the trabecular and cortical parameters induced by methylprednisolone. Histological study showed that miR-133a silencing simultaneously increased bone formation and decreased marrow fat accumulation in GIO rats. Conclusions Our findings suggested that miR-133a is strongly associated with GIO and similar disorders induced by glucocorticoids in MSCs. Silencing miR-133a resulted in positive effects on GC-treated MSCs and on bone loss in GIO animal models. Moreover, the FGFR1-MAPK/ERK signaling may be involved in the protective effect of miR-133a silencing.

Peptide-based filamentous assemblies are successfully used for generation of structurally ordered materials, but their de novo design and structural characterization is challenging. Here, the authors provide a strategy for the design of self-assembling peptide nanotubes based on modifications of an arginine clasp interaction motif, and report the cryo-EM structures of seven designed nanotubes.

Archaeal type IV pili (T4P) mediate adhesion to surfaces and are receptors for hyperthermophilic archaeal viruses. Here, the authors present the cryo-EM structures of two archaeal T4P from Pyrobaculum arsenaticum and Saccharolobus solfataricus and discuss evolutionary relationships between bacterial T4P, archaeal T4P and archaeal flagellar filaments.

Malate dehydrogenase (MDH) is widely present in nature and regulates plant growth and development, as well as playing essential roles, especially in abiotic stress responses. Nevertheless, there is no comprehensive knowledge to date on MDH family members in rice. In this study, a total of 12 MDH members in rice were identified through genome-wide analysis and divided into three groups on the basis of their phylogenetic relationship and protein-conserved motifs. Evolutionary analysis showed that MDH proteins from rice, maize and wheat shared a close phylogenetic relationship, and the MDH family was conserved in the long-term process of domestication. We identified two segmental duplication events involving four genes, which could be the major force driving the expansion of the OsMDH family. The expression profile, cis-regulatory elements and qRT-PCR results of these genes revealed that a few OsMDH showed high tissue specificity, almost all of which had stress response elements in the promoter region, and ten MDH members were significantly induced by salt stress. Through gene-based association analysis, we found a significant correlation between salt tolerance at the seedling stage and the genetic variation of OsMDH8.1 and OsMDH12.1. Additionally, we found that the polymorphism in the promoter region of OsMDH8.1 might be related to the salt tolerance of rice. This study aimed to provide valuable information on the functional study of the rice MDH gene family related to salt stress response and revealed that OsMDH8.1 might be an important gene for the cultivar improvement of salt tolerance in rice.

Summary: Intracellular protein filaments are ubiquitous for cellular functions, but forming bona fide biomimetic intracellular filaments of small molecules in living cells remains elusive. Here, we report the in situ formation of self-limiting intracellular filaments of a small peptide via enzymatic morphological transition of a phosphorylated and trimethylated heterochiral tetrapeptide. Enzymatic dephosphorylation reduces repulsive intermolecular electrostatic interactions and converts the peptidic nanoparticles into filaments, which exhibit distinct types of cross-β structures with either C7 or C2 symmetries, with the hydrophilic C-terminal residues at the periphery of the helix. Macromolecular crowding promotes the peptide filaments to form bundles, which extend from the plasma membrane to nuclear membrane and hardly interact with endogenous components, including cytoskeletons. Stereochemistry and post-translational modification (PTM) of peptides are critical for generating the intracellular bundles. This work may offer a way to gain lost functions or to provide molecular insights for understanding normal and aberrant intracellular filaments.

Only a few archaeal filamentous viruses have been structurally characterized. Here the authors describe the membrane-enveloped Sulfolobus filamentous virus 1 that infects Sulfolobus shibatae and present its 3.7 Å resolution cryo-EM structure, which reveals that major coat proteins are structurally conserved among archaeal filamentous viruses.

The disease causing L253P mutation in the actin-binding domain (ABD) of β-III-spectrin drastically increases actin-binding affinity. Here, the authors present the cryo-EM structure of F-actin complexed with the ABD mutant and double electron–electron resonance measurements show how the mutation affects the ABD conformational state.

Bacterial flagellar filaments are composed almost entirely of a single protein—flagellin—which can switch between different supercoiled states in a highly cooperative manner. Here the authors present near-atomic resolution cryo-EM structures of nine flagellar filaments, and begin to shed light on the molecular basis of filament switching.

KDM4 histone demethylases target specific chromatin regions by a mechanism that is not fully characterised. Here, the authors identify trimethyl-lysine histone-binding preferences for closely related KDM4 double tudor domains and use structural and biochemical information to examine the molecular details of this interaction.

Uropathogenic E. coli (UPEC), which cause urinary tract infections (UTI), utilize type 1 pili, a chaperone usher pathway (CUP) pilus, to cause UTI and colonize the gut. The pilus rod, comprised of repeating FimA subunits, provides a structural scaffold for displaying the tip adhesin, FimH. We solved the 4.2 Å resolution structure of the type 1 pilus rod using cryo-electron microscopy. Residues forming the interactive surfaces that determine the mechanical properties of the rod were maintained by selection based on a global alignment of fimA sequences. We identified mutations that did not alter pilus production in vitro but reduced the force required to unwind the rod. UPEC expressing these mutant pili were significantly attenuated in bladder infection and intestinal colonization in mice. This study elucidates an unappreciated functional role for the molecular spring-like property of type 1 pilus rods in host-pathogen interactions and carries important implications for other pilus-mediated diseases.

CalE6 from Micromonospora echinospora is a (pyridoxal 5′ phosphate) PLP-dependent methionine γ-lyase involved in the biosynthesis of calicheamicins. We report the crystal structure of a CalE6 2-(N-morpholino)ethanesulfonic acid complex showing ligand-induced rotation of Tyr100, which stacks with PLP, resembling the corresponding tyrosine rotation of true catalytic intermediates of CalE6 homologs. Elastic network modeling and crystallographic ensemble refinement reveal mobility of the N-terminal loop, which involves both tetrameric assembly and PLP binding. Modeling and comparative structural analysis of PLP-dependent enzymes involved in Cys/Met metabolism shine light on the functional implications of the intrinsic dynamic properties of CalE6 in catalysis and holoenzyme maturation.

Fracture healing is a multifaceted process that requires various phases and intercellular interactions. In recent years, investigations have been conducted to assess the feasibility of utilizing exosomes, small extracellular vesicles (EVs), to enhance and accelerate the healing process. Exosomes serve as a cargo transport platform, facilitating intercellular communication, promoting the presentation of antigens to dendritic cells, and stimulating angiogenesis. Exosomes have a special structure that gives them a special function, especially in the healing process of bone injuries. This article provides an overview of cellular and molecular processes associated with bone fracture healing, as well as a survey of existing exosome research in this context. We also discuss the potential use of exosomes in fracture healing, as well as the obstacles that must be overcome to make this a viable clinical practice. [ABSTRACT FROM AUTHOR]

Flagellar motility has independently arisen three times during evolution: in bacteria, archaea, and eukaryotes. In prokaryotes, the supercoiled flagellar filaments are composed largely of a single protein, bacterial or archaeal flagellin, although these two proteins are not homologous, while in eukaryotes, the flagellum contains hundreds of proteins. Archaeal flagellin and archaeal type IV pilin are homologous, but how archaeal flagellar filaments (AFFs) and archaeal type IV pili (AT4Ps) diverged is not understood, in part, due to the paucity of structures for AFFs and AT4Ps. Despite having similar structures, AFFs supercoil, while AT4Ps do not, and supercoiling is essential for the function of AFFs. We used cryo-electron microscopy to determine the atomic structure of two additional AT4Ps and reanalyzed previous structures. We find that all AFFs have a prominent 10-strand packing, while AT4Ps show a striking structural diversity in their subunit packing. A clear distinction between all AFF and all AT4P structures involves the extension of the N-terminal α-helix with polar residues in the AFFs. Additionally, we characterize a flagellar- like AT4P from Pyrobaculum calidifontis with filament and subunit structure similar to that of AFFs which can be viewed as an evolutionary link, showing how the structural diversity of AT4Ps likely allowed for an AT4P to evolve into a supercoiling AFF. [ABSTRACT FROM AUTHOR]