Characterization of LysB4, an endolysin from the Bacillus cereus-infecting bacteriophage B4

<p>Abstract</p> <p>Background</p> <p><it>Bacillus cereus </it>is a foodborne pathogen that causes emetic or diarrheal types of food poisoning. The incidence of <it>B. cereus </it>food poisoning has been gradually increasing over the past few years, therefore, biocontrol agents effective against <it>B. cereus </it>need to be developed. Endolysins are phage-encoded bacterial peptidoglycan hydrolases and have received considerable attention as promising antibacterial agents.</p> <p>Results</p> <p>The endolysin from <it>B. cereus </it>phage B4, designated LysB4, was identified and characterized. <it>In silico </it>analysis revealed that this endolysin had the VanY domain at the N terminus as the catalytic domain, and the SH3_5 domain at the C terminus that appears to be the cell wall binding domain. Biochemical characterization of LysB4 enzymatic activity showed that it had optimal peptidoglycan hydrolase activity at pH 8.0-10.0 and 50°C. The lytic activity was dependent on divalent metal ions, especially Zn²⁺. The antimicrobial spectrum was relatively broad because LysB4 lysed Gram-positive bacteria such as <it>B. cereus, Bacillus subtilis </it>and <it>Listeria monocytogenes </it>and some Gram-negative bacteria when treated with EDTA. LC-MS analysis of the cell wall cleavage products showed that LysB4 was an <smcaps>L</smcaps>-alanoyl-<smcaps>D</smcaps>-glutamate endopeptidase, making LysB4 the first characterized endopeptidase of this type to target <it>B. cereus</it>.</p> <p>Conclusions</p> <p>LysB4 is believed to be the first reported <smcaps>L</smcaps>-alanoyl-<smcaps>D</smcaps>-glutamate endopeptidase from <it>B. cereus</it>-infecting bacteriophages. The properties of LysB4 showed that this endolysin has strong lytic activity against a broad range of pathogenic bacteria, which makes LysB4 a good candidate as a biocontrol agent against <it>B. cereus </it>and other pathogenic bacteria.</p

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It is crucial to provide forest fire risk forecast information to minimize forest fire-related losses. In this research, forecast models of forest fire risk at a mid-range (with lead times up to 7 days) scale were developed considering past, present and future conditions (i.e., forest fire risk, drought, and weather) through random forest machine learning over South Korea. The models were developed using weather forecast data from the Global Data Assessment and Prediction System, historical and current Fire Risk Index (FRI) information, and environmental factors (i.e., elevation, forest fire hazard index, and drought index). Three schemes were examined: scheme 1 using historical values of FRI and drought index, scheme 2 using historical values of FRI only, and scheme 3 using the temporal patterns of FRI and drought index. The models showed high accuracy (Pearson correlation coefficient &gt;0.8, relative root mean square error &lt;10%), regardless of the lead times, resulting in a good agreement with actual forest fire events. The use of the historical FRI itself as an input variable rather than the trend of the historical FRI produced more accurate results, regardless of the drought index used

The Auxiliary Role of the Amidase Domain in Cell Wall Binding and Exolytic Activity of Staphylococcal Phage Endolysins

In response to increasing concern over antibiotic-resistant Staphylococcus aureus, the development of novel antimicrobials has been called for, with bacteriophage endolysins having received considerable attention as alternatives to antibiotics. Most staphylococcal phage endolysins have a modular structure consisting of an N-terminal cysteine, histidine-dependent amidohydrolases/peptidase domain (CHAP), a central amidase domain, and a C-terminal cell wall binding domain (CBD). Despite extensive studies using truncated staphylococcal endolysins, the precise function of the amidase domain has not been determined. Here, a functional analysis of each domain of two S. aureus phage endolysins (LysSA12 and LysSA97) revealed that the CHAP domain conferred the main catalytic activity, while the central amidase domain showed no enzymatic activity in degrading the intact S. aureus cell wall. However, the amidase-lacking endolysins had reduced hydrolytic activity compared to the full-length endolysins. Comparison of the binding affinities of fusion proteins consisting of the green fluorescent protein (GFP) with CBD and GFP with the amidase domain and CBD revealed that the major function of the amidase domain was to enhance the binding affinity of CBD, resulting in higher lytic activity of endolysin. These results suggest an auxiliary binding role of the amidase domain of staphylococcal endolysins, which can be useful information for designing effective antimicrobial and diagnostic agents against S. aureus

Simultaneous Control of Staphylococcus aureus and Bacillus cereus Using a Hybrid Endolysin LysB4EAD-LysSA11

Bacteriophage endolysins have attracted attention as promising alternatives to antibiotics, and their modular structure facilitates endolysin engineering to develop novel endolysins with enhanced versatility. Here, we constructed hybrid proteins consisting of two different endolysins for simultaneous control of two critical foodborne pathogens, Staphylococcus aureus and Bacillus cereus. The full-length or enzymatically active domain (EAD) of LysB4, an endolysin from the B. cereus-infecting phage B4, was fused to LysSA11, an endolysin of the S. aureus-infecting phage SA11, via a helical linker in both orientations. The hybrid proteins maintained the lytic activity of their parental endolysins against both S. aureus and B. cereus, but they showed an extended antimicrobial spectrum. Among them, the EAD of LysB4 fused with LysSA11 (LysB4EAD-LyaSA11) showed significantly increased thermal stability compared to its parental endolysins. LysB4EAD-LysSA11 exhibited high lytic activity at pH 8.0&ndash;9.0 against S. aureus and at pH 5.0&ndash;10.0 against B. cereus, but the lytic activity of the protein decreased in the presence of NaCl. In boiled rice, treatment with 3.0 &micro;M of LysB4EAD-LysSA11 reduced the number of S. aureus and B. cereus to undetectable levels within 2 h and also showed superior antimicrobial activity to LyB4EAD and LysSA11 in combination. These results suggest that LysB4EAD-LysSA11 could be a potent antimicrobial agent for simultaneous control of S. aureus and B. cereus

Clostridium perfringens Virulent Bacteriophage CPS2 and Its Thermostable Endolysin LysCPS2

Clostridium perfringens is one of the most common causes of food-borne illness. The increasing prevalence of multidrug-resistant bacteria requires the development of alternatives to typical antimicrobial treatments. Here, we isolated and characterized a C. perfringens-specific virulent bacteriophage CPS2 from chicken feces. The CPS2 phage contains a 17,961 bp double-stranded DNA genome with 25 putative ORFs, and belongs to the Picovirinae, subfamily of Podoviridae. Bioinformatic analysis of the CPS2 genome revealed a putative endolysin, LysCPS2, which is homologous to the endolysin of Clostridium phage phiZP2 and phiCP7R. The enzyme showed strong lytic activity against C. perfringens with optimum conditions at pH 7.5–10, 25–65 °C, and over a broad range of NaCl concentrations. Interestingly, LysCPS2 was found to be highly thermostable, with up to 30% of its lytic activity remaining after 10 min of incubation at 95 °C. The cell wall binding domain in the C-terminal region of LysCPS2 showed a binding spectrum specific to C. perfringens strains. This is the first report to characterize highly thermostable endolysin isolated from virulent C. perfringens bacteriophage. The enzyme can be used as an alternative biocontrol and detection agent against C. perfringens

The Auxiliary Role of the Amidase Domain in Cell Wall Binding and Exolytic Activity of Staphylococcal Phage Endolysins

In response to increasing concern over antibiotic-resistant Staphylococcus aureus, the development of novel antimicrobials has been called for, with bacteriophage endolysins having received considerable attention as alternatives to antibiotics. Most staphylococcal phage endolysins have a modular structure consisting of an N-terminal cysteine, histidine-dependent amidohydrolases/peptidase domain (CHAP), a central amidase domain, and a C-terminal cell wall binding domain (CBD). Despite extensive studies using truncated staphylococcal endolysins, the precise function of the amidase domain has not been determined. Here, a functional analysis of each domain of two S. aureus phage endolysins (LysSA12 and LysSA97) revealed that the CHAP domain conferred the main catalytic activity, while the central amidase domain showed no enzymatic activity in degrading the intact S. aureus cell wall. However, the amidase-lacking endolysins had reduced hydrolytic activity compared to the full-length endolysins. Comparison of the binding affinities of fusion proteins consisting of the green fluorescent protein (GFP) with CBD and GFP with the amidase domain and CBD revealed that the major function of the amidase domain was to enhance the binding affinity of CBD, resulting in higher lytic activity of endolysin. These results suggest an auxiliary binding role of the amidase domain of staphylococcal endolysins, which can be useful information for designing effective antimicrobial and diagnostic agents against S. aureus

Satellite-based Drought Forecasting: Research Trends, Challenges, and Future Directions

Drought forecasting is crucial to minimize the damage to food security and water resources caused by drought. Satellite-based drought research has been conducted since 1980s, which includes drought monitoring, assessment, and prediction. Unlike numerous studies on drought monitoring and assessment for the past few decades, satellite-based drought forecasting has gained popularity in recent years. For successful drought forecasting, it is necessary to carefully identify the relationships between drought factors and drought conditions by drought type and lead time. This paper aims to provide an overview of recent research trends and challenges for satellite-based drought forecasts focusing on lead times. Based on the recent literature survey during the past decade, the satellite-based drought forecasting studies were divided into three groups by lead time (i.e., short-term, sub-seasonal, and seasonal) and reviewed with the characteristics of the predictors (i.e., drought factors) and predictands (i.e., drought indices). Then, three major challenges-difficulty in model generalization, model resolution and feature selection, and saturation of forecasting skill improvement-were discussed, which led to provide several future research directions of satellite-based drought forecasting

Characterization and Genome Analysis of Staphylococcus aureus Podovirus CSA13 and Its Anti-Biofilm Capacity

Staphylococcus aureus is one of the notable human pathogens that can be easily encountered in both dietary and clinical surroundings. Among various countermeasures, bacteriophage therapy is recognized as an alternative method for resolving the issue of antibiotic resistance. In the current study, bacteriophage CSA13 was isolated from a chicken, and subsequently, its morphology, physiology, and genomics were characterized. This Podoviridae phage displayed an extended host inhibition effect of up to 23 hours of persistence. Its broad host spectrum included methicillin susceptible S. aureus (MSSA), methicillin resistant S. aureus (MRSA), local S. aureus isolates, as well as non-aureus staphylococci strains. Moreover, phage CSA13 could successfully remove over 78% and 93% of MSSA and MRSA biofilms in an experimental setting, respectively. Genomic analysis revealed a 17,034 bp chromosome containing 18 predicted open reading frames (ORFs) without tRNAs, representing a typical chromosomal structure of the staphylococcal Podoviridae family. The results presented here suggest that phage CSA13 can be applicable as an effective biocontrol agent against S. aureus

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Leaf area index (LAI) provides valuable information necessary forsustainable and effective management of forests. Although global high resolution LAI data are provided by European Space Agency using Sentinel 2 satellite images, they have not been evaluated for various forest ecosystems in South Korea. In this study, we proposed a LAI estimation model combining machine learning and the PROSAIL radiative transfer model using Sentinel-2 satellite data over a local forest area in South Korea. LAI-2200C was used to measure in situ LAI data. The proposed model-estimated LAI was compared to the existing Sentinel-2 LAI product. The results showed that the proposed model outperformed the existing Sentinel-2 LAI product, yielding a difference of bias ~ 0.97 and a difference of root-meansquare-error ~ 0.81 on average, respectively, which improved the underestimation of the existing product. The proposed LAI estimation model provided promising results, implying its use for effective LAI estimation over forests in South Korea