Microalgae realizes self N-doped biochar for heavy metal polluted sediment remediation.

Heavy metal contamination in sediment has become a significant global environmental challenge. Numerous studies have demonstrated the effectiveness of modified biochar to solve heavy metal contamination in sediment. However, the modification process with complex methods and expensive modifiers prevented its large-scale application. In this study, an N self-doped biochar was obtained by pyrolysis of Spirulina sp. (SBC). Meanwhile, the K2CO3 impregnation method was utilized to prepare Spirulina sp. biochar (KSBC), which demonstrated a higher specific surface area (874 m2/g) and richer O, N functional groups. The adsorption capacity of KSBC550-120 for Cu (Ⅱ), Zn (Ⅱ), and Cd (Ⅱ) was 57.9 ± 0.3 mg/g, 43.6 ± 0.7 mg/g, and 63.9 ± 0.6 mg/g, respectively. The adsorption process is primarily governed by chemical processes, mainly through ion exchange, surface complexation, dissolution-precipitation, electrostatic interactions, adsorption-reduction, and cation-π interactions. Moreover, utilizing KSBC550-120 for mixing or capping effectively reduced heavy metal concentrations in both the overlying and pore water of the sediments. 1.0 wt% KSBC550-120 with capping treatment significantly reduced the release of heavy metals from the sediment by 80.3-91.9%. This study provides effective theoretical support for re-utilizing waste algal residues and remediation of the heavy metal-contaminated river and lake sediments using microalgae biochar.

Carbon Doping Regulates Charge Transfer Paths via a Type-II to S-Scheme Transformation to Improve Photocatalytic Performance.

Designing S-scheme heterojunctions with enhanced interfacial interaction is an effective strategy for promoting the separation of photocarriers while maintaining strong photoredox capabilities. However, precisely tailoring the interfacial charge transport pathways between two contacted semiconductors remains a significant challenge due to the similar band alignment in type-II and S-scheme heterostructures. Herein, we report a facile and low-cost carbon doping strategy to smartly tune the charge transfer pathway via a type-II to S-scheme transformation for efficient photocatalytic H2 evolution and H2O2 synthesis. Density functional theory calculations combined with in situ XPS studies demonstrate that the Fermi level of MoO2 shifts from being higher than that of C3N4 to being lower after carbon doping, which drives the inversion of the internal electric field (IEF) direction between MoO2 and C3N4, thus enabling a transition from type-II MoO2/C3N4 heterojunctions to S-scheme C-MoO2/C3N4 heterojunctions. As a result, the optimal S-scheme C-MoO2/C3N4 heterojunctions exhibit a high H2 evolution rate of 16.2 mmol g-1 h-1 and a H2O2 production rate of 877 µmol g-1 h-1, notably surpassing those of the original C3N4 and type-II MoO2/C3N4 heterojunctions. This work provides valuable insights into the fabrication of C3N4 heterostructures and the control of electron migration pathways, thereby creating new possibilities for photocatalysis and optoelectronics applications.

The role of TIR domain-containing proteins in bacterial defense against phages.

Toll/interleukin-1 receptor (TIR) domain-containing proteins play a critical role in immune responses in diverse organisms, but their function in bacterial systems remains to be fully elucidated. This study, focusing on Escherichia coli, addresses how TIR domain-containing proteins contribute to bacterial immunity against phage attack. Through an exhaustive survey of all E. coli genomes available in the NCBI database and testing of 32 representatives of the 90% of the identified TIR domain-containing proteins, we found that a significant proportion (37.5%) exhibit antiphage activities. These defense systems recognize a variety of phage components, thus providing a sophisticated mechanism for pathogen detection and defense. This study not only highlights the robustness of TIR systems in bacterial immunity, but also draws an intriguing parallel to the diversity seen in mammalian Toll-like receptors (TLRs), enriching our understanding of innate immune mechanisms across life forms and underscoring the evolutionary significance of these defense strategies in prokaryotes.

Sustainable Remediation of Soil and Water Utilizing Arbuscular Mycorrhizal Fungi: A Review.

Phytoremediation is recognized as an environmentally friendly technique. However, the low biomass production, high time consumption, and exposure to combined toxic stress from contaminated media weaken the potential of phytoremediation. As a class of plant-beneficial microorganisms, arbuscular mycorrhizal fungi (AMF) can promote plant nutrient uptake, improve plant habitats, and regulate abiotic stresses, and the utilization of AMF to enhance phytoremediation is considered to be an effective way to enhance the remediation efficiency. In this paper, we searched 520 papers published during the period 2000-2023 on the topic of AMF-assisted phytoremediation from the Web of Science core collection database. We analyzed the author co-authorship, country, and keyword co-occurrence clustering by VOSviewer. We summarized the advances in research and proposed prospective studies on AMF-assisted phytoremediation. The bibliometric analyses showed that heavy metal, soil, stress tolerance, and growth promotion were the research hotspots. AMF-plant symbiosis has been used in water and soil in different scenarios for the remediation of heavy metal pollution and organic pollution, among others. The potential mechanisms of pollutant removal in which AMF are directly involved through hyphal exudate binding and stabilization, accumulation in their structures, and nutrient exchange with the host plant are highlighted. In addition, the tolerance strategies of AMF through influencing the subcellular distribution of contaminants as well as chemical form shifts, activation of plant defenses, and induction of differential gene expression in plants are presented. We proposed that future research should screen anaerobic-tolerant AMF strains, examine bacterial interactions with AMF, and utilize AMF for combined pollutant removal to accelerate practical applications.

Understanding the factors of wearable devices among the patients with thyroid cancer: A modified UTAUT2 model.

Wearable devices hold promising prospects on a global scale, including in China. Thyroid cancer prevalence is notably high in China.This purpose of this researchwas to provide an updated theoretical model for assessing Chinese thyroid cancer patients' intentions towards wearable devices, based on the UTAUT2 framework, and to ascertain the factors that have an impact on these intents. A cross-sectional study with an institutional focus wasconducted from January 20, 2023, to June 30, 2023, at several general hospitals in China. Five hundred participants were recruited to identify predictors of wearable device use.The questionnaire survey about patients' intentionswas collected using a face-to-face method, employing a random sampling technique for patient selection. Four hundred sixty-nine individuals (93.8%) had the intention to use wearable devices. The intentions were highly impacted by performance expectancy (PE), effort expectancy (EE), social influence (SI), hedonic motivation (HM), price value (PV) and habit (HA). Usage intention (UI)was a statistically predictor of Usage behavior (UB). The facilitating condition(FC) was not significant. Gender positively moderated the relationship between EE and UI. Income positively moderated the relationship between all variables and UI.Overall, the utilization of wearable devices among patients diagnosed with thyroid cancer has demonstrated considerable potential. This study offers a series of suggestions for digital health developers,healthcare decision-makers,doctors and patients.

The urinary microbiota composition and functionality of calcium oxalate stone formers.

Background: Accumulated evidences indicate that dysbiosis of the urinary microbiota is associated with kidney stone formation. In the present study, we aimed to investigate the urinary microbiota composition and functionality of patients with calcium oxalate stones and compare it with those of healthy individuals. Method: We collected bladder urine samples from 68 adult patients with calcium oxalate stones and 54 age-matched healthy controls by transurethral catheterization. 16S rRNA gene and shotgun sequencing were utilized to characterize the urinary microbiota and functionality associated with calcium oxalate stones. Results: After further exclusion, a total of 100 subjects was finally included and analyzed. The diversity of the urinary microbiota in calcium oxalate stone patients was not significantly different from that of healthy controls. However, the urinary microbiota structure of calcium oxalate stone formers significantly differed from that of healthy controls (PERMANOVA, r = 0.026, P = 0.019). Differential representation of bacteria (e.g., Bifidobacterium) and several enriched functional pathways (e.g., threonine biosynthesis) were identified in the urine of calcium oxalate stone patients. Conclusion: Our results showed significantly different urinary microbiota structure and several enriched functional pathways in calcium oxalate stone patients, which provide new insight into the pathogenesis of calcium oxalate stones.

LINC00606 promotes glioblastoma progression through sponge miR-486-3p and interaction with ATP11B.

BACKGROUND: LncRNAs regulate tumorigenesis and development in a variety of cancers. We substantiate for the first time that LINC00606 is considerably expressed in glioblastoma (GBM) patient specimens and is linked with adverse prognosis. This suggests that LINC00606 may have the potential to regulate glioma genesis and progression, and that the biological functions and molecular mechanisms of LINC00606 in GBM remain largely unknown. METHODS: The expression of LINC00606 and ATP11B in glioma and normal brain tissues was evaluated by qPCR, and the biological functions of the LINC00606/miR-486-3p/TCF12/ATP11B axis in GBM were verified through a series of in vitro and in vivo experiments. The molecular mechanism of LINC00606 was elucidated by immunoblotting, FISH, RNA pulldown, CHIP-qPCR, and a dual-luciferase reporter assay. RESULTS: We demonstrated that LINC00606 promotes glioma cell proliferation, clonal expansion and migration, while reducing apoptosis levels. Mechanistically, on the one hand, LINC00606 can sponge miR-486-3p; the target gene TCF12 of miR-486-3p affects the transcriptional initiation of LINC00606, PTEN and KLLN. On the other hand, it can also regulate the PI3K/AKT signaling pathway to mediate glioma cell proliferation, migration and apoptosis by binding to ATP11B protein. CONCLUSIONS: Overall, the LINC00606/miR-486-3p/TCF12/ATP11B axis is involved in the regulation of GBM progression and plays a role in tumor regulation at transcriptional and post-transcriptional levels primarily through LINC00606 sponging miR-486-3p and targeted binding to ATP11B. Therefore, our research on the regulatory network LINC00606 could be a novel therapeutic strategy for the treatment of GBM.

Benchmarking the Intrinsic Activity of Transition Metal Oxides for the Oxygen Evolution Reaction with Advanced Nanoelectrodes.

The intrinsic activity assessment of transition metal oxides (TMOs) as key electrocatalysts for the oxygen evolution reaction (OER) has not been standardized due to uncertainties regarding their structure and composition, difficulties in accurately measuring their electrochemically active surface area (ECSA), and deficiencies in mass-transfer (MT) rates in conventional measurements. To address these issues, we utilized an electrodeposition-thermal annealing method to precisely synthesize single-particle TMOs with well-defined structure and composition. Concurrently, we engineered low roughness, spherical surfaces for individual particles, enabling precise measurement of their ECSA. Furthermore, by constructing a conductor-core semiconductor-shell structure, we evaluated the inherent OER activity of perovskite-type semiconductor materials, broadening the scope beyond just conductive TMOs. Finally, using single-particle nanoelectrode technique, we systematically measured individual TMO particles of various sizes for OER, overcoming MT limitations seen in conventional approaches. These improvements have led us to propose a precise and reliable approach to evaluating the intrinsic activity of TMOs, not only validating the accuracy of theoretical calculations but also revealing a strong correlation of OER activity on the melting point of TMOs. This discovery holds significant importance for future high-throughput material research and applications, offering valuable insights in electrocatalysis.

The effects of co-existing acridine on adsorption-desorption behavior of carbazole in soils: Co-sorption and mechanism insight.

Carbazole (CBZ) and acridine (ACR) are polycyclic aromatic nitrogen heterocycles (PANHs) widely found in combined contaminated soils, while investigations on organic-organic interactions have been very limited. In this study, batch experiments were carried out on five soils with different properties, taking CBZ as a representative of PANHs and ACR as a co-existing contaminant. The adsorption isotherms of CBZ (50-1000 µg/L) were nonlinear. Soil organic matter (SOM) and cation exchange capacity (CEC) showed positive correlations with CBZ adsorption-desorption coefficients. The adsorption mechanisms of CBZ involved hydrogen bonding, π-π interaction, and cation-π bonding. Different concentrations of ACR had varying effects on CBZ. The adsorption of CBZ was inhibited with 250 µg/L ACR. The cooperative adsorption was observed on three soils with increasing ACR concentration (1000 µg/L) and led to more pronounced nonlinear isotherms. The S-shaped isotherms of ACR indicated that ACR was adsorbed to the soil surface in a perpendicular configuration. New adsorption sites were created allowing for increased CBZ adsorption through π-π interaction with ACR. Therefore, variations in soil properties and potential impacts of co-existing contaminants should be well considered when assessing the combined pollution of site soil. This will contribute to a more accurate estimation of environmental and health risks.

Optimizing Electronic Density at Active W Sites for Boosting Photocatalytic H2 Evolution.

It is highly desirable but challenging to optimize the electronic structure of an active site to realize moderate active site-Hads bond energies for boosting photocatalytic H2 evolution. Herein, an interfacial engineering strategy is developed to simultaneously concentrate hydrogen species and accelerate the combination of an Hads intermediate to generate free H2 by constructing W-WC-W2C (WCC) cocatalysts. Systematic investigations reveal that hybridizing with W2C creates electron-rich W active sites and effectively induces the downshift of the d-band center of W in WC. Consequently, the strong W-Hads bonds on the surface of WC are weakened, thus promoting the desorption of Hads to rapidly produce free H2. The optimized 40-WCC/CdS photocatalyst exhibits a high hydrogen evolution rate of 63.6 mmol g-1 h-1 under visible light (≥420 nm) with an apparent quantum efficiency of 39.5% at 425 nm monochromatic light, which is about 40-fold of the pristine CdS. This work offers insights into the design of cocatalyst for high-efficiency photocatalytic H2 production.

Enhanced d-π overlap in a graphene supported Ni/PtNi heterojunction for efficient seawater hydrogen evolution.

d-π overlap, which represents overlap between metal-d and graphene-π orbitals to facilitate electron transfer, has rarely been reported. Ni/PtNi-G2 exhibits exceptional performance in seawater hydrogen evolution due to the electron-rich surface on Pt resulting from enhanced d-π overlap and subsequent electron transfer from graphene and Ni to Pt.

The effects of Cu-phenanthrene co-contamination on adsorption-desorption behaviors of phenanthrene in soils.

Polycyclic aromatic hydrocarbons (PAHs) are persistent organic pollutants in the environment, which are teratogenic, carcinogenic, and mutagenic. Co-contamination of PAHs and heavy metal commonly exists in soil. In this study, 20 types of soils with different properties in China were collected and comprehensively characterized. Phenanthrene (Phe) and Cu (II) were selected as representatives of PAHs and heavy metals, respectively. The adsorption-desorption behaviors of Phe under Phe contamination and Cu (II)-Phe co-contamination in 20 types of soils were studied. The adsorption-desorption behaviors of Phe in 20 types of soils varied greatly, and adsorption of Phe in the soils followed both linear partitioning and nonlinear surface adsorption. Soil organic matter (SOM) plays an important role in the adsorption-desorption behavior of Phe. When the concentrations of Phe were >50 µg/L, soft carbon (SC) fraction of SOM not black carbon (BC) contributed more to the adsorption of Phe. Soil dissolved organic matter (DOM), especially fulvic acid and humic acid fractions, contributes to the adsorption of Phe. Under the effect of Cu (II) (60 mg/L in solution), the adsorption capacity of soil for Phe increased, which possibly resulted from lowered pH, the existence of the cation-π bonding and the "bonding bridge" effect. The systematic investigation of adsorption-desorption behaviors of Phe in soils under heavy metal-PAHs co-contamination will provide a scientific basis for the calculation of soil environmental capacity in the future.

The different outcomes in the elderly with subclinical hypothyroidism diagnosed by age-specific and non-age-specific TSH reference intervals: a prospectively observational study protocol.

Introduction: Subclinical hypothyroidism (SCH) is a common endocrine disorder characterized by elevated thyroid-stimulating hormone (TSH) levels and normal free thyroxine (FT4) levels. The overdiagnosis and overtreatment of SCH in elderly patients have become concerns as TSH levels naturally increase with age. Studies have shown that many elderly patients with SCH can recover without treatment, and the administration of levothyroxine (L-T4) does not improve their prognosis. Therefore, It is necessary to establish age-specific reference ranges for TSH in elderly individuals to aid in clinical decision-making and prevent overdiagnosis. Methods: This is a multicenter prospective study that focuses on Chinese elderly patients with SCH who have TSH levels below 10 mU/L. After obtaining the informed consent of the patients, their initial diagnosis information will be registered, and they will be asked to fill out questionnaires such as the Montreal Cognitive Assessment-Basic (MoCA-B), Hamilton Depression Scale (HAMD), Hypothyroidism Symptom Questionnaire (SRQ), frail scale(FRAIL), fatigue scale, and EQ-5D. In addition, thyroid function tests, blood lipid analysis, carotid artery ultrasound, and thyroid ultrasound examinations will be conducted. Patients will also be grouped according to FT4 levels, the changes in FT4 and its relationship with TSH can also be described. For patients over 80 years old, a decrease in FT4 will be used as an endpoint event, while for patients between 60-80 years old, TSH levels greater than or equal to 10mIU/L or a decline in FT4 will be used as the endpoint event. The TSH reference intervals of the general and elderly populations will be used to calculate medical costs associated with multiple follow-ups of patients, and a social-economic analysis will also be conducted. Discussion: This study will prospectively observe elderly patients with SCH who are screened using both age-specific and non-age-specific TSH reference ranges for the elderly population. We will compare the results of elderly patients diagnosed with SCH using different reference ranges and analyze their association with FT4 to identify meaningful SCH patients and reduce over diagnosis and over treatment of elderly SCH. Ethics: The Medical Science Research Ethics Committee of the First Affiliated Hospital of China Medical University approved this study (ID: AF-SOP-07-1.1-01). The results will be published in an open-access journal. Clinical trial registration: https://www.chictr.org.cn/, identifier ChiCTR2300070831.

The Relationship between Thyrotropin Serum Concentrations and Thyroid Carcinoma.

Thyroid Stimulating Hormone (TSH) is a hormone secreted by the pituitary gland and plays a role in regulating the production and secretion of thyroid hormones by the thyroid gland. This precise feedback loop is essential for maintaining a harmonious balance of thyroid hormones in the body, which are vital for numerous physiological processes. Consequently, TSH serves as a significant marker in assessing thyroid function, and deviations from normal TSH levels may indicate the presence of a thyroid disorder. Thyroid cancer (TC) is the malignant tumor within the endocrine system. In recent years, numerous experts have dedicated their efforts to discovering efficacious biomarkers for TC. These biomarkers aim to improve the accurate identification of tumors with a poor prognosis, as well as facilitate active monitoring of tumors with a more favorable prognosis. The role of TSH in the thyroid gland underscores its potential influence on the occurrence and progression of TC, which has garnered attention in the scientific community. However, due to the limited scope of clinical research and the dearth of high-quality foundational studies, the precise impact of TSH on TC remains unclear. Consequently, we present a comprehensive review of this subject, aiming to offer a valuable reference for future research endeavors.

Biodegradation of di(2-ethylhexyl) phthalate by a new bacterial consortium.

Di(2-ethylhexyl) phthalate (DEHP) with continuous high concentration was used as the sole carbon and energy source to isolate a new bacterial consortium (K1) from agricultural soil covered with plastic film for a long time. Unclassified Comamonadaceae, Achromobacter, and Pseudomonas in K1 were identified as major genera of the consortium by high-throughput sequencing, and unclassified Commanadaceae was first reported to be related to DEHP degradation. Response surface method (RSM) showed that the optimum conditions for K1 to degrade DEHP were 31.4 °C, pH 7.3, and a concentration of 420 mg L-1. K1 maintains normal cell viability and stable DEHP degradation efficiency in the range of 10-3000 mg L-1 DEHP concentration, which is superior to existing research. The biodegradation of DEHP followed first-order kinetics when the initial concentration of DEHP was between 100 and 3,000 mg L-1. GC-MS analysis of different treatment groups showed that DEHP was degraded by the consortium group through the de-esterification pathway, and treatment effect was significantly better than that of the single bacteria treatment group. The subsequent substrate utilization experiment further confirmed that K1 could quickly mineralize DEHP. In addition, K1 has high degradation capacity for the most common phthalate acid esters in the environment.

Genome-wide analysis of the WRKY genes and their important roles during cold stress in white clover.

Background: White clover (Trifolium repens L) is a high-quality forage grass with a high protein content, but it is vulnerable to cold stress, which can negatively affect its growth and development. WRKY transcription factor is a family of plant transcription factors found mainly in higher plants and plays an important role in plant growth, development, and stress response. Although WRKY transcription factors have been studied extensively in other plants, it has been less studied in white clover. Methods and Results: In the present research, we have performed a genome-wide analysis of the WRKY gene family of white clover, in total, there were 145 members of WRKY transcription factors identified in white clover. The characterization of the TrWRKY genes was detailed, including conserved motif analysis, phylogenetic analysis, and gene duplication analysis, which have provided a better understanding of the structure and evolution of the TrWRKY genes in white clover. Meanwhile, the genetic regulation network (GRN) containing TrWRKY genes was reconstructed, and Gene Ontology (GO) annotation analysis of these function genes showed they contributed to regulation of transcription process, response to wounding, and phosphorylay signal transduction system, all of which were important processes in response to abiotic stress. To determine the TrWRKY genes function under cold stress, the RNA-seq dataset was analyzed; most of TrWRKY genes were highly upregulated in response to cold stress, particularly in the early stages of cold stress. These results were validated by qRT-PCR experiment, implying they are involved in various gene regulation pathways in response to cold stress. Conclusion: The results of this study provide insights that will be useful for further functional analyses of TrWRKY genes in response to biotic or abiotic stresses in white clover. These findings are likely to be useful for further research on the functions of TrWRKY genes and their role in response to cold stress, which is important to understand the molecular mechanism of cold tolerance in white clover and improve its cold tolerance.

Evolutions of dissolved organic matter and disinfection by-products formation in source water during UV-LED (275 nm)/chlorine process.

Ultraviolet light-emitting diode (UV-LED) is a promising option for the traditional low-pressure UV lamp, but the evolutions of DOM composition, the formation of disinfection by-products (DBPs) and their toxicity need further study in raw water during UV-LED/chlorine process. In UV-LED (275 nm)/chlorine process, two-dimensional correlation spectroscopy (2DCOS) analysis on synchronous fluorescence and UV-vis spectra indicated the protein-like fractions responded faster than the humic-like components, the reactive sequence of peaks for DOM followed the order: 340 nm→240 nm→410 nm→205 nm→290 nm. Compared to chlorination for 30 mins, the UV-LED/chlorine process enhanced the degradation efficiency of three fluorescent components (humic-like, tryptophan-like, tyrosine-like) by 5.1%-46.1%, and the formation of carbonaceous DBPs (C-DBPs) significantly reduced by 43.8% while the formation of nitrogenous DBPs (N-DBPs) increased by 27.3%. The concentrations of C-DBPs increased by 17.8% whereas that of N-DBPs reduced by 30.4% in 24 h post-chlorination. The concentrations of brominated DBPs increased by 17.2% during UV-LED/chlorine process, and further increased by 18.5% in 24 h post-chlorination. According to the results of principal component analysis, the non-fluorescent components of DOM might be important precursors in the formation of haloketones, haloacetonitriles and halonitromethanes during UV-LED/chlorine process. Unlike chlorine treatment, the reaction of DOM in UV-LED/chlorine treatment generated fewer unknown DBPs. Compared with chlorination, the cytotoxicity of C-DBPs reduced but the cytotoxicity of both N-DBPs and Br-DBPs increased during UV-LED/chlorine process. Dichloroacetonitrile had the highest cytotoxicity, followed by monobromoacetic acid, bromochloroacetonitrile and trichloroacetic acid during 30 mins of UV-LED/chlorine process. Therefore, besides N-DBPs, the more toxic Br-DBPs formation in bromide-containing water is also not negligible in the practical applications of UV-LED (275 nm)/chlorine process.

T4 bacteriophage nanoparticles engineered through CRISPR provide a versatile platform for rapid development of flu mucosal vaccines.

Vaccines that trigger mucosal immune responses at the entry portals of pathogens are highly desired. Here, we showed that antigen-decorated nanoparticle generated through CRISPR engineering of T4 bacteriophage can serve as a universal platform for the rapid development of mucosal vaccines. Insertion of Flu viral M2e into phage T4 genome through fusion to Soc (Small Outer Capsid protein) generated a recombinant phage, and the Soc-M2e proteins self-assembled onto phage capsids to form 3M2e-T4 nanoparticles during propagation of T4 in E. coli. Intranasal administration of 3M2e-T4 nanoparticles maintains antigen persistence in the lungs, resulting in increased uptake and presentation by antigen-presenting cells. M2e-specific secretory IgA, effector (TEM), central (TCM), and tissue-resident memory CD4+ T cells (TRM) were efficiently induced in the local mucosal sites, which mediated protections against divergent influenza viruses. Our studies demonstrated the mechanisms of immune protection following 3M2e-T4 nanoparticles vaccination and provide a versatile T4 platform that can be customized to rapidly develop mucosal vaccines against future emerging epidemics.

Landscape of New Nuclease-Containing Antiphage Systems in Escherichia coli and the Counterdefense Roles of Bacteriophage T4 Genome Modifications.

Many phages, such as T4, protect their genomes against the nucleases of bacterial restriction-modification (R-M) and CRISPR-Cas systems through covalent modification of their genomes. Recent studies have revealed many novel nuclease-containing antiphage systems, raising the question of the role of phage genome modifications in countering these systems. Here, by focusing on phage T4 and its host Escherichia coli, we depicted the landscape of the new nuclease-containing systems in E. coli and demonstrated the roles of T4 genome modifications in countering these systems. Our analysis identified at least 17 nuclease-containing defense systems in E. coli, with type III Druantia being the most abundant system, followed by Zorya, Septu, Gabija, AVAST type 4, and qatABCD. Of these, 8 nuclease-containing systems were found to be active against phage T4 infection. During T4 replication in E. coli, 5-hydroxymethyl dCTP is incorporated into the newly synthesized DNA instead of dCTP. The 5-hydroxymethylcytosines (hmCs) are further modified by glycosylation to form glucosyl-5-hydroxymethylcytosine (ghmC). Our data showed that the ghmC modification of the T4 genome abolished the defense activities of Gabija, Shedu, Restriction-like, type III Druantia, and qatABCD systems. The anti-phage T4 activities of the last two systems can also be counteracted by hmC modification. Interestingly, the Restriction-like system specifically restricts phage T4 containing an hmC-modified genome. The ghmC modification cannot abolish the anti-phage T4 activities of Septu, SspBCDE, and mzaABCDE, although it reduces their efficiency. Our study reveals the multidimensional defense strategies of E. coli nuclease-containing systems and the complex roles of T4 genomic modification in countering these defense systems. IMPORTANCE Cleavage of foreign DNA is a well-known mechanism used by bacteria to protect themselves from phage infections. Two well-known bacterial defense systems, R-M and CRISPR-Cas, both contain nucleases that cleave the phage genomes through specific mechanisms. However, phages have evolved different strategies to modify their genomes to prevent cleavage. Recent studies have revealed many novel nuclease-containing antiphage systems from various bacteria and archaea. However, no studies have systematically investigated the nuclease-containing antiphage systems of a specific bacterial species. In addition, the role of phage genome modifications in countering these systems remains unknown. Here, by focusing on phage T4 and its host Escherichia coli, we depicted the landscape of the new nuclease-containing systems in E. coli using all 2,289 genomes available in NCBI. Our studies reveal the multidimensional defense strategies of E. coli nuclease-containing systems and the complex roles of genomic modification of phage T4 in countering these defense systems.