The Chinese pine genome and methylome unveil key features of conifer evolution.

Conifers dominate the world's forest ecosystems and are the most widely planted tree species. Their giant and complex genomes present great challenges for assembling a complete reference genome for evolutionary and genomic studies. We present a 25.4-Gb chromosome-level assembly of Chinese pine (Pinus tabuliformis) and revealed that its genome size is mostly attributable to huge intergenic regions and long introns with high transposable element (TE) content. Large genes with long introns exhibited higher expressions levels. Despite a lack of recent whole-genome duplication, 91.2% of genes were duplicated through dispersed duplication, and expanded gene families are mainly related to stress responses, which may underpin conifers' adaptation, particularly in cold and/or arid conditions. The reproductive regulation network is distinct compared with angiosperms. Slow removal of TEs with high-level methylation may have contributed to genomic expansion. This study provides insights into conifer evolution and resources for advancing research on conifer adaptation and development.

Acute SARS-CoV-2 Infection Impairs Dendritic Cell and T Cell Responses.

The SARS-CoV-2 pandemic has resulted in millions of infections, yet the role of host immune responses in early COVID-19 pathogenesis remains unclear. By investigating 17 acute and 24 convalescent patients, we found that acute SARS-CoV-2 infection resulted in broad immune cell reduction including T, natural killer, monocyte, and dendritic cells (DCs). DCs were significantly reduced with functional impairment, and ratios of conventional DCs to plasmacytoid DCs were increased among acute severe patients. Besides lymphocytopenia, although neutralizing antibodies were rapidly and abundantly generated in patients, there were delayed receptor binding domain (RBD)- and nucleocapsid protein (NP)-specific T cell responses during the first 3 weeks after symptoms onset. Moreover, acute RBD- and NP-specific T cell responses included relatively more CD4 T cells than CD8 T cells. Our findings provided evidence that impaired DCs, together with timely inverted strong antibody but weak CD8 T cell responses, could contribute to acute COVID-19 pathogenesis and have implications for vaccine development.

Highly selective synthesis of surface FeIV=O with nanoscale zero-valent iron and chlorite for efficient oxygen transfer reactions.

High-valent iron-oxo species (FeIV=O) has been a long-sought-after oxygen transfer reagent in biological and catalytic chemistry but suffers from a giant challenge in its gentle and selective synthesis. Herein, we propose a new strategy to synthesize surface FeIV=O (≡FeIV=O) on nanoscale zero-valent iron (nZVI) using chlorite (ClO2-) as the oxidant, which possesses an impressive ≡FeIV=O selectivity of 99%. ≡FeIV=O can be energetically formed from the ferrous (FeII) sites on nZVI through heterolytic Cl-O bond dissociation of ClO2- via a synergistic effect between electron-donating surface ≡FeII and proximal electron-withdrawing H2O, where H2O serves as a hydrogen-bond donor to the terminal O atom of the adsorbed ClO2- thereby prompting the polarization and cleavage of Cl-O bond for the oxidation of ≡FeII toward the final formation of ≡FeIV=O. With methyl phenyl sulfoxide (PMS16O) as the probe molecule, the isotopic labeling experiment manifests an exclusive 18O transfer from Cl18O2- to PMS16O18O mediated by ≡FeIV=18O. We then showcase the versatility of ≡FeIV=O as the oxygen transfer reagent in activating the C-H bond of methane for methanol production and facilitating selective triphenylphosphine oxide synthesis with triphenylphosphine. We believe that this new ≡FeIV=O synthesis strategy possesses great potential to drive oxygen transfer for efficient high-value-added chemical synthesis.

Evolution of the Correlated Genomic Variation Landscape Across a Divergence Continuum in the Genus Castanopsis.

The heterogeneous landscape of genomic variation has been well documented in population genomic studies. However, disentangling the intricate interplay of evolutionary forces influencing the genetic variation landscape over time remains challenging. In this study, we assembled a chromosome-level genome for Castanopsis eyrei and sequenced the whole genomes of 276 individuals from 12 Castanopsis species, spanning a broad divergence continuum. We found highly correlated genomic variation landscapes across these species. Furthermore, variations in genetic diversity and differentiation along the genome were strongly associated with recombination rates and gene density. These results suggest that long-term linked selection and conserved genomic features have contributed to the formation of a common genomic variation landscape. By examining how correlations between population summary statistics change throughout the species divergence continuum, we determined that background selection alone does not fully explain the observed patterns of genomic variation; the effects of recurrent selective sweeps must be considered. We further revealed that extensive gene flow has significantly influenced patterns of genomic variation in Castanopsis species. The estimated admixture proportion correlated positively with recombination rate and negatively with gene density, supporting a scenario of selection against gene flow. Additionally, putative introgression regions exhibited strong signals of positive selection, an enrichment of functional genes, and reduced genetic burdens, indicating that adaptive introgression has played a role in shaping the genomes of hybridizing species. This study provides insights into how different evolutionary forces have interacted in driving the evolution of the genomic variation landscape.

Regulation of phosphoribosyl ubiquitination by a calmodulin-dependent glutamylase.

The bacterial pathogen Legionella pneumophila creates an intracellular niche permissive for its replication by extensively modulating host-cell functions using hundreds of effector proteins delivered by its Dot/Icm secretion system1. Among these, members of the SidE family (SidEs) regulate several cellular processes through a unique phosphoribosyl ubiquitination mechanism that bypasses the canonical ubiquitination machinery2-4. The activity of SidEs is regulated by another Dot/Icm effector known as SidJ5; however, the mechanism of this regulation is not completely understood6,7. Here we demonstrate that SidJ inhibits the activity of SidEs by inducing the covalent attachment of glutamate moieties to SdeA-a member of the SidE family-at E860, one of the catalytic residues that is required for the mono-ADP-ribosyltransferase activity involved in ubiquitin activation2. This inhibition by SidJ is spatially restricted in host cells because its activity requires the eukaryote-specific protein calmodulin (CaM). We solved a structure of SidJ-CaM in complex with AMP and found that the ATP used in this reaction is cleaved at the α-phosphate position by SidJ, which-in the absence of glutamate or modifiable SdeA-undergoes self-AMPylation. Our results reveal a mechanism of regulation in bacterial pathogenicity in which a glutamylation reaction that inhibits the activity of virulence factors is activated by host-factor-dependent acyl-adenylation.

Formic Acid-Intensified Photoreduction of NOx on Iron Minerals Triggers Daytime HONO Formation through Active Hydrogen.

Nitrous acid (HONO) is crucial in atmospheric chemistry as a precursor to morning peak hydroxyl radicals and significantly affects urban air quality by forming secondary pollutants, yet the mechanisms of its daytime formation is not fully understood. This study investigates the role of formic acid (HCOOH), a prevalent electron and proton donor, in the transformation of nitrogen oxides (NOx) and the formation of HONO on photoactive mineral dust. Exploiting hematite (Fe2O3) as an environmental indicator, we demonstrate that HCOOH significantly promotes the photoreduction of NO2 to HONO, while suppressing nitrate accumulation. This occurs through the formation of a surface ≡Fe-OOCH complex, where sunlight activates the C-H bond to generate and transfer active hydrogen, directly converting NO2 to HONO. Additionally, HCOOH can trigger the photolysis of nitrates as predeposited on Fe2O3, further increasing HONO production. These findings show that HCOOH-mediated photochemical reactions on iron minerals may contribute to elevated atmospheric HONO levels, highlighting a crucial pathway with broad effects on atmospheric chemistry and public health.

Occurrence and Exposure Assessment of Lipophilic Shellfish Toxins in the Zhejiang Province, China.

Although lipophilic shellfish toxins (LSTs) pose a significant threat to the health of seafood consumers, their systematic investigation and risk assessment remain scarce. The goals of this study were as follows: (1) analyze LST levels in commercially available shellfish in Zhejiang province, China, and determine factors influencing LST distribution; (2) assess the acute dietary risk of exposure to LSTs for local consumers during the red tide period; (3) explore potential health risks of LSTs in humans; and (4) study the acute risks of simultaneous dietary exposure to LSTs and paralytic shellfish toxins (PSTs). A total of 546 shellfish samples were collected. LSTs were detected in 89 samples (16.3%) at concentrations below the regulatory limits. Mussels were the main shellfish species contaminated with LSTs. Spatial variations were observed in the yessotoxin group. Acute exposure to LSTs based on multiple scenarios was low. The minimum tolerable exposure durations for LSTs calculated using the mean and the 95th percentile of consumption data were 19.7 and 4.9 years, respectively. Our findings showed that Zhejiang province residents are at a low risk of combined exposure to LSTs and PSTs; however, the risk may be higher for children under 6 years of age in the extreme scenario.

The Fast Quantification of Vitamin B12 in Milk Powder by High-Performance Liquid Chromatography-Inductively Coupled Plasma Mass Spectrometry.

This study presents a new technique for determining vitamin B12 in milk powder using high-performance liquid chromatography-inductively coupled plasma mass spectrometry (HPLC-ICP-MS). We used ultrasonics with potassium ferrocyanide and zinc acetate solutions to extract the samples. 59Co was employed as the analytical target for cyanocobalamin. It was separated using a Phenomenex Luna 5 µm C18 (250 × 4.6 mm) chromatographic column with a mobile phase consisting of 1.6 mmol/L EDTA and 0.4 mmol/L KH2PO4 in a 60% v/v methanol solution (pH = 4.0). The sample has an excellent separating degree for free cobalt and cyanocobalamin, and isocratic elution can be finished within 4.0 min. To eliminate the matrix interference due to the presence of milk powder, we applied collision mode (KED). The linear range of cyanocobalamine ranged from 1.0 µg/L to 20 µg/L, with correlation coefficients (r2) of 0.9994. The limit of detection (LOD) was 0.63 µg/kg, and the limit of quantitation (LOQ) was 2.11 µg/kg. The mean recoveries were in the range of 87.4-103.6%. The accuracy and precision of the developed method are well suited for the fast quantification of the trace vitamin B12 in milk powder.

Cu1-Fe Dual Sites for Superior Neutral Ammonia Electrosynthesis from Nitrate.

The electrochemical nitrate reduction reaction (NO3RR) is able to convert nitrate (NO3 -) into reusable ammonia (NH3), offering a green treatment and resource utilization strategy of nitrate wastewater and ammonia synthesis. The conversion of NO3 - to NH3 undergoes water dissociation to generate active hydrogen atoms and nitrogen-containing intermediates hydrogenation tandemly. The two relay processes compete for the same active sites, especially under pH-neutral condition, resulting in the suboptimal efficiency and selectivity in the electrosynthesis of NH3 from NO3 -. Herein, we constructed a Cu1-Fe dual-site catalyst by anchoring Cu single atoms on amorphous iron oxide shell of nanoscale zero-valent iron (nZVI) for the electrochemical NO3RR, achieving an impressive NO3 - removal efficiency of 94.8 % and NH3 selectivity of 99.2 % under neutral pH and nitrate concentration of 50 mg L-1 NO3 --N conditions, greatly surpassing the performance of nZVI counterpart. This superior performance can be attributed to the synergistic effect of enhanced NO3 - adsorption on Fe sites and strengthened water activation on single-atom Cu sites, decreasing the energy barrier for the rate-determining step of *NO-to-*NOH. This work develops a novel strategy of fabricating dual-site catalysts to enhance the electrosynthesis of NH3 from NO3 -, and presents an environmentally sustainable approach for neutral nitrate wastewater treatment.

Genome-Wide Identification and Expression Analysis of Calmodulin-Like Gene Family in Paspalums vaginatium Revealed Their Role in Response to Salt and Cold Stress.

The calmodulin-like (CML) family is an important calcium (Ca2+) sensor in plants and plays a pivotal role in the response to abiotic and biotic stresses. As one of the most salt-tolerant grass species, Paspalums vaginatum is resistant to multiple abiotic stresses, such as salt, cold, and drought. However, investigations of PvCML proteins in P. vaginatum have been limited. Based on the recently published P. vaginatum genome, we identified forty-nine PvCMLs and performed a comprehensive bioinformatics analysis of PvCMLs. The main results showed that the PvCMLs were unevenly distributed on all chromosomes and that the expansion of PvCMLs was shaped by tandem and segmental duplications. In addition, cis-acting element analysis, expression profiles, and qRT-PCR analysis revealed that PvCMLs were involved in the response to salt and cold stress. Most interestingly, we found evidence of a tandem gene cluster that independently evolved in P. vaginatum and may participate in cold resistance. In summary, our work provides important insight into how grass species are resistant to abiotic stresses such as salt and cold and could be the basis of further gene function research on CMLs in P. vaginatum.

Strain-Engineering of Mesoporous Cs3 Bi2 Br9 /BiVO4 S-Scheme Heterojunction for Efficient CO2 Photoreduction.

Slow charge kinetics and unfavorable CO2 adsorption/activation strongly inhibit CO2 photoreduction. In this study, a strain-engineered Cs3 Bi2 Br9 /hierarchically porous BiVO4 (s-CBB/HP-BVO) heterojunction with improved charge separation and tailored CO2 adsorption/activation capability is developed. Density functional theory calculations suggest that the presence of tensile strain in Cs3 Bi2 Br9 can significantly downshift the p-band center of the active Bi atoms, which enhances the adsorption/activation of inert CO2 . Meanwhile, in situ irradiation X-ray photoelectron spectroscopy and electron spin resonance confirm that efficient charge transfer occurs in s-CBB/HP-BVO following an S-scheme with built-in electric field acceleration. Therefore, the well-designed s-CBB/HP-BVO heterojunction exhibits a boosted photocatalytic activity, with a total electron consumption rate of 70.63 µmol g-1 h-1 , and 79.66% selectivity of CO production. Additionally, in situ diffuse reflectance infrared Fourier transform spectroscopy reveals that CO2 photoreduction undergoes a formaldehyde-mediated reaction process. This work provides insight into strain engineering to improve the photocatalytic performance of halide perovskite.

Reversible Stacking of 2D ZnIn2 S4 Atomic Layers for Enhanced Photocatalytic Hydrogen Evolution.

It is technically challenging to reversibly tune the layer number of 2D materials in the solution. Herein, a facile concentration modulation strategy is demonstrated to reversibly tailor the aggregation state of 2D ZnIn2 S4 (ZIS) atomic layers, and they are implemented for effective photocatalytic hydrogen (H2 ) evolution. By adjusting the colloidal concentration of ZIS (ZIS-X, X = 0.09, 0.25, or 3.0 mg mL-1 ), ZIS atomic layers exhibit the significant aggregation of (006) facet stacking in the solution, leading to the bandgap shift from 3.21 to 2.66 eV. The colloidal stacked layers are further assembled into hollow microsphere after freeze-drying the solution into solid powders, which can be redispersed into colloidal solution with reversibility. The photocatalytic hydrogen evolution of ZIS-X colloids is evaluated, and the slightly aggregated ZIS-0.25 displays the enhanced photocatalytic H2 evolution rates (1.11 µmol m-2 h-1 ). The charge-transfer/recombination dynamics are characterized by time-resolved photoluminescence (TRPL) spectroscopy, and ZIS-0.25 displays the longest lifetime (5.55 µs), consistent with the best photocatalytic performance. This work provides a facile, consecutive, and reversible strategy for regulating the photo-electrochemical properties of 2D ZIS, which is beneficial for efficient solar energy conversion.

Genomic vulnerability to climate change in Quercus acutissima, a dominant tree species in East Asian deciduous forests.

Understanding the evolutionary processes that shape the landscape of genetic variation and influence the response of species to future climate change is critical for biodiversity conservation. Here, we sampled 27 populations across the distribution range of a dominant forest tree, Quercus acutissima, in East Asia, and applied genome-wide analyses to track the evolutionary history and predict the fate of populations under future climate. We found two genetic groups (East and West) in Q. acutissima that diverged during Pliocene. We also found a heterogeneous landscape of genomic variation in this species, which may have been shaped by population demography and linked selections. Using genotype-environment association analyses, we identified climate-associated SNPs in a diverse set of genes and functional categories, indicating a model of polygenic adaptation in Q. acutissima. We further estimated three genetic offset metrics to quantify genomic vulnerability of this species to climate change due to the complex interplay between local adaptation and migration. We found that marginal populations are under higher risk of local extinction because of future climate change, and may not be able to track suitable habitats to maintain the gene-environment relationships observed under the current climate. We also detected higher reverse genetic offsets in northern China, indicating that genetic variation currently present in the whole range of Q. acutissima may not adapt to future climate conditions in this area. Overall, this study illustrates how evolutionary processes have shaped the landscape of genomic variation, and provides a comprehensive genome-wide view of climate maladaptation in Q. acutissima.

Oxalate-Promoted SO2 Uptake and Oxidation on Iron Minerals: Implications for Secondary Sulfate Aerosol Formation.

Mineral dust serves as a significant source of sulfate aerosols by mediating heterogeneous sulfur dioxide (SO2) oxidation in the atmosphere. Given that a considerable proportion of small organic acids are deposited onto mineral dust via long-range transportation, understanding their impact on atmospheric SO2 transformation and sulfate formation is of great importance. This study investigates the effect of oxalate on heterogeneous SO2 uptake and oxidation phenomenon by in situ FTIR, theoretical calculation, and continuous stream experiments, exploiting hematite (Fe2O3) as an environmental indicator. The results highlight the critical role of naturally deposited oxalate in mononuclear monodentate coordinating surface Fe atoms of Fe2O3 that enhances the activation of O2 for oxidizing SO2 into sulfate. Meanwhile, oxalate increases the hygroscopicity of Fe2O3, facilitating H2O dissociation into reactive hydroxyl groups and further augmenting the SO2 uptake capacity of Fe2O3. More importantly, other conventional iron minerals, such as goethite and magnetite, as well as authentic iron-containing mineral dust, exhibit similar oxalate-promoted sulfate accumulation behaviors. Our findings suggest that oxalate-assisted SO2 oxidation on iron minerals is one of the important contributors to secondary sulfate aerosols, especially during the nighttime with high relative humidity.

Symmetric three-port laparoscopic Roux-en-Y gastric bypass: a novel technique that is safe, effective, and feasible.

PURPOSE: Single-incision laparoscopic surgery (SILS) has been validated as a safe approach for bariatric surgery. However, as the utilization of SILS in bariatric surgery is still limited by its disadvantages, this study analyzes the outcomes of symmetric three-port laparoscopic Roux-en-Y gastric bypass (STLGB). METHODS: The medical records of patients who underwent STLGB between January 2018 and February 2021 were analyzed retrospectively using an institutional database. The patients were divided into four groups according to their baseline body mass index (BMI). The primary endpoints were operative time, length of stay, complication rate, and weight loss 12 months after surgery. RESULTS: We analyzed the records of 101 patients who underwent STLGB. There was a slight predominance of women (n = 61; 60.4%). The mean operative time was 97.16 ± 38.79 min and the length of stay in the hospital after surgery was 2.79 ± 1.4 days. One patient (0.99%) suffered a gastrojejunal anastomosis leak within 30 days of surgery. There were no significant differences in LOS, complication rate, or cosmetic score among the four groups. The mean BMI reduction was 8.67 kg/m2 and the % total weight loss (%TWL) was 24.37%. Weight loss measured 12 months after surgery was significantly different among the four groups. CONCLUSIONS: STLGB is safe, effective, and feasible for all kinds of patients. It is reproducible with standardization of the procedure.

[Cost-benefit analysis on the intervention of application iron-fortified soy sauce for anemia in Deqing 15-54 years women, Zhejiang].

OBJECTIVE: To make a cost-benefit analysis on anemia intervention with iron-fortified soy sauce in 15-54 years old women. METHODS: The study was conducted in Deqing county, Zhejiang province in 2012-2013. A total 585 women as sampling size were estimated with statistical model and randomly selected by probability proportionate to size sampling. Hemoglobin were measured before intervention and after 15 months. The cost of the intervention project were collected with manpower, communication and other invest. The benefit was estimated with profiling model. RESULTS: After the intervention, the anemia prevalence of sampled women decreased from 31.1% to 21.9%(P<0.01). The major cost of the project was 156 400 RMB, and total benefits result ing from projects were 1 448 485 RMB. The cost-benefit ratio of the project is 1∶9.49. If investing one yuan can produce economic benefits of nearly 9.49 yuan, therefore, the intervention projectis worth to be scaling up. Sensitivity analysis showed the result of this study was stable. CONCLUSION: The intervention can significantly reduce the prevalence of anemia in women, and reduce the economic burden of the diseases. .

[Occurrence and exposure assessment of fumonisins from grains and grain products in Zhejiang Province in 2018-2019].

OBJECTIVE: To monitor fumonisins(FBs) in grains and grain products in Zhejiang and assess the exposure risks of FBs to local residents. METHODS: Liquid chromatography coupled with tandem mass spectrometry method was used to determine the occurrence of FBs in rice, millet, dried noodles, instant noodles, and maize grains, and food frequency questionnaires were used to collect the food consumption data of Zhejiang population. Then, the simple probability distribution model was used to assess the exposure risk. RESULTS: The levels of FBs in rice, millet, dried noodles and instant noodles were relatively low. The occurrence of FB_1, FB_2 and FB_3 in these foods was 0-23.7%, 0-16.7% and 0-5.4%, respectively, and the mean levels were not detected(ND)-22.36, ND-20.63 and ND-7.19 µg/kg correspondingly. However, the levels of FBs in maize grains were relatively high. The occurrence of FB_1, FB_2, and FB_3 in maize grains was 100%, 93.6% and 90.3%, respectively, and the mean levels were 638.99, 103.54 and 59.69 µg/kg correspondingly. In 12.9% of the maize grain samples, the levels of FBs were higher than the standard reference. The residents were at low exposure risk overall. The mean estimated daily intake(EDI) of FBs was far lower than the provisional maximum tolerable daily intake of 2 µg/(kg·BW·d). However, 0.30% of the residents were at high risk. Among people of different ages, the mean EDI of children, adults, and elderly were 0.43, 0.28 and 0.29 µg/(kg·BW·d) respectively, and children were in the highest exposure levels of FBs. Among the tested five foodstuffs, rice and maize grains were the main sources of FBs exposure. CONCLUSION: Except for maize grains, the levels of FBs in grains and grain products were relatively low, and Zhejiang residents were at low FBs exposure risk generally.

Comparison of the effects of two extraction methods on the alveolar ridge preservation of Maxillary Anterior Teeth.

Objective: To compare the effects of high-speed turbodrill root extraction and piezosurgery tooth socket enlargement on the alveolar ridge preservation of maxillary anterior teeth. Methods: Thirty-six clinically eligible patients admitted to the No.2 Hospital of Baoding or the Baoding First Central Hospital from January 2018 to November 2019 were selected and randomly divided into two groups. Group-A were extracted by high-speed turbodrill root extraction, while Group-B were extracted by piezosurgery tooth socket enlargement. After extraction, GBR bone grafting and soft tissue transplantation were performed on the extraction sockets. The extraction time, integrity rate of labial bone plate of the extraction socket, pain-free rate, satisfaction rate, reduction of the height and width of the alveolar ridge, alveolar bone mineral density score, and new bone contour score of the alveolar bone of two groups were compared. Result: Group-B was significantly superior to Group-A in terms of tooth extraction time, pain-free rate, satisfaction rate and reduction of alveolar ridge height at three sites on the palatal side, with a statistically significant difference (p<0.05). Conclusions: Piezosurgery tooth socket enlargement is more worthy of clinical application due to its advantages of less impact on the preservation of the palatal alveolar ridge height of the maxillary anterior teeth, shorter tooth extraction time, postoperative pain-free rate and high final satisfaction rate.

Perovskite Bifunctional Diode with High Photovoltaic and Electroluminescent Performance by Holistic Defect Passivation.

Integration of photovoltaic (PV) and electroluminescent (EL) functions and/or units in one device is attractive for new generation optoelectronic devices but it is challenging to achieve highly comprehensive efficiency. Herein, perovskite solar cells (PSCs) are fabricated, assisted by 3-sulfopropyl methacrylate potassium salt (SPM) additive to tackle this issue. SPMs not only induce large grain size during the film formation but also produce a secondary phase of 2D K2 PbI4 to passivate the grain boundaries (GBs). In addition, its sulfonic acid group and potassium ion can coordinate to lead ion and fill the interstitial defects, respectively. Thus, SPM reduces the defective states and suppresses nonradiative recombination loss. As a result, planar PSC delivers a power conversion efficiency of ≈22%, with a maximum open-circuit voltage (Voc ) of 1.20 V. The Voc is 94% of the radiative Voc limit (1.28 V), higher than the control device (Voc of 1.12 V). In addition, the reciprocity between PV and EL is also correlated to quantify the energy losses and understand the device physics. When operated as a light-emitting diode, the maximum EL external quantum efficiency (EQEEL ) is up to 12.2% (EQEEL of 10.7% under an injection current of short-circuit photocurrent), thus leading to high-performance PV/EL dual functions.

Structural and functional insights into a novel two-component endolysin encoded by a single gene in Enterococcus faecalis phage.

Using bacteriophage-derived endolysins as an alternative strategy for fighting drug-resistant bacteria has recently been garnering renewed interest. However, their application is still hindered by their narrow spectra of activity. In our previous work, we demonstrated that the endolysin LysIME-EF1 possesses efficient bactericidal activity against multiple strains of Enterococcus faecalis (E. faecalis). Herein, we observed an 8 kDa fragment and hypothesized that it contributes to LysIME-EF1 lytic activity. To examine our hypothesis, we determined the structure of LysIME-EF1 at 1.75 Å resolution. LysIME-EF1 exhibits a unique architecture in which one full-length LysIME-EF1 forms a tetramer with three additional C-terminal cell-wall binding domains (CBDs) that correspond to the abovementioned 8 kDa fragment. Furthermore, we identified an internal ribosomal binding site (RBS) and alternative start codon within LysIME-EF1 gene, which are demonstrated to be responsible for the translation of the truncated CBD. To elucidate the molecular mechanism for the lytic activity of LysIME-EF1, we combined mutagenesis, lytic activity assays and in vivo animal infection experiments. The results confirmed that the additional LysIME-EF1 CBDs are important for LysIME-EF1 architecture and its lytic activity. To our knowledge, this is the first determined structure of multimeric endolysin encoded by a single gene in E. faecalis phages. As such, it may provide valuable insights into designing potent endolysins against the opportunistic pathogen E. faecalis.