scholarly journals Tailed Lytic Bacteriophages of Soft Rot Pectobacteriaceae

2021 ◽  
Vol 9 (9) ◽  
pp. 1819
Author(s):  
Konstantin A. Miroshnikov ◽  
Peter V. Evseev ◽  
Anna A. Lukianova ◽  
Alexander N. Ignatov
Keyword(s):  
Molecular Mechanisms ◽  
Soft Rot ◽  
Genomic Databases ◽  
Control Applications ◽  
Taxonomic Distribution ◽  
Bacterial Diseases ◽  
Receptor Recognition ◽  
Bacterial Viruses ◽  
Resistant Mutants

The study of the ecological and evolutionary traits of Soft Rot Pectobacteriaceae (SRP) comprising genera Pectobacterium and Dickeya often involves bacterial viruses (bacteriophages). Bacteriophages are considered to be a prospective tool for the ecologically safe and highly specific protection of plants and harvests from bacterial diseases. Information concerning bacteriophages has been growing rapidly in recent years, and this has included new genomics-based principles of taxonomic distribution. In this review, we summarise the data on phages infecting Pectobacterium and Dickeya that are available in publications and genomic databases. The analysis highlights not only major genomic properties that assign phages to taxonomic families and genera, but also the features that make them potentially suitable for phage control applications. Specifically, there is a discussion of the molecular mechanisms of receptor recognition by the phages and problems concerning the evolution of phage-resistant mutants.

scholarly journals Unlocking the Potential of 46 New Bacteriophages for Biocontrol of Dickeya Solani

Viruses ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 621 ◽  
Author(s):  
Alexander Carstens ◽  
Amaru Djurhuus ◽  
Witold Kot ◽  
Deborah Jacobs-Sera ◽  
Graham Hatfull ◽  
...  
Keyword(s):  
Soft Rot ◽  
Potato Production ◽  
Storage Conditions ◽  
Bacterial Diseases ◽  
Modern Agriculture ◽  
Production Pipeline ◽  
Global Demand ◽  
Phage Cocktail ◽  
Dickeya Solani ◽  
Sustainability Standards

Modern agriculture is expected to face an increasing global demand for food while also needing to comply with higher sustainability standards. Therefore, control of crop pathogens requires new, green alternatives to current methods. Potatoes are susceptible to several bacterial diseases, with infections by soft rot Enterobacteriaceae (SRE) being a significant contributor to the major annual losses. As there are currently no efficient ways of combating SRE, we sought to develop an approach that could easily be incorporated into the potato production pipeline. To this end, 46 phages infecting the emerging potato pathogen Dickeya solani were isolated and thoroughly characterized. The 46 isolated phages were grouped into three different groups based on DNA similarity, representing two distinct clusters and a singleton. One cluster showed similarity to phages previously used to successfully treat soft rot in potatoes, whereas the remaining phages were novel and showed only very limited similarity to previously isolated phages. We selected six diverse phages in order to create the hereto most complex phage cocktail against SRE. The cocktail was applied in a proof-of-principle experiment to treat soft rot in potatoes under simulated storage conditions. We show that the phage cocktail was able to significantly reduce the incidence of soft rot as well as disease severity after 5 days of storage post-infection with Dickeya solani. This confirms results from previous studies that phages represent promising biocontrol agents against SRE infection in potato.

Activity and Phylogenetics of the Broadly Occurring Family of Microbial Nep1-Like Proteins

2019 ◽  
Vol 57 (1) ◽  
pp. 367-386 ◽  
Author(s):  
Michael F. Seidl ◽  
Guido Van den Ackerveken
Keyword(s):  
Arabidopsis Thaliana ◽  
Plant Species ◽  
Historical Perspective ◽  
Plasma Membranes ◽  
Molecular Mechanisms ◽  
Plant Immunity ◽  
Taxonomic Distribution ◽  
Outer Leaflet ◽  
Molecular Patterns ◽  
Shed Light

Necrosis- and ethylene-inducing peptide 1 (Nep1)-like proteins (NLP) have an extremely broad taxonomic distribution; they occur in bacteria, fungi, and oomycetes. NLPs come in two forms, those that are cytotoxic to eudicot plants and those that are noncytotoxic. Cytotoxic NLPs bind to glycosyl inositol phosphoryl ceramide (GIPC) sphingolipids that are abundant in the outer leaflet of plant plasma membranes. Binding allows the NLP to become cytolytic in eudicots but not monocots. The function of noncytotoxic NLPs remains enigmatic, but the expansion of NLP genes in oomycete genomes suggests they are important. Several plant species have evolved the capacity to recognize NLPs as molecular patterns and trigger plant immunity, e.g., Arabidopsis thaliana detects nlp peptides via the receptor-like protein RLP23. In this review, we provide a historical perspective from discovery to understanding of molecular mechanisms and describe the latest developments in the NLP field to shed light on these fascinating microbial proteins.

scholarly journals The Iturin-like Lipopeptides Are Essential Components in the Biological Control Arsenal of Bacillus subtilis Against Bacterial Diseases of Cucurbits

2011 ◽  
Vol 24 (12) ◽  
pp. 1540-1552 ◽  
Author(s):  
Houda Zeriouh ◽  
Diego Romero ◽  
Laura García-Gutiérrez ◽  
Francisco M. Cazorla ◽  
Antonio de Vicente ◽  
...  
Keyword(s):  
Biological Control ◽  
Antibacterial Activity ◽  
Bacillus Subtilis ◽  
Xanthomonas Campestris ◽  
Soft Rot ◽  
Bacterial Diseases ◽  
Chromatography Analysis ◽  
Essential Components ◽  
Bacillus Spp

The antibacterial potential of four strains of Bacillus subtilis, UMAF6614, UMAF6619, UMAF6639, and UMAF8561, previously selected on the basis of their antifungal activity and efficacy against cucurbit powdery mildew, was examined. Among these strains, UMAF6614 and UMAF6639 showed the highest antibacterial activity in vitro, especially against Xanthomonas campestris pv. cucurbitae and Pectobacterium carotovorum subsp. carotovorum. These strains produced the three families of lipopeptide antibiotics known in Bacillus spp.: surfactins, iturins, and fengycins. Using thin-layer chromatography analysis and direct bioautography, the antibacterial activity could be associated with iturin lipopeptides. This result was confirmed by mutagenesis analysis using lipopeptide-defective mutants. The antibacterial activity was practically abolished in iturin-deficient mutants, whereas the fengycin mutants retained certain inhibitory capabilities. Analyses by fluorescence and transmission electron microscopy revealed the cytotoxic effect of these compounds at the bacterial plasma membrane level. Finally, biological control assays on detached melon leaves demonstrated the ability of UMAF6614 and UMAF6639 to suppress bacterial leaf spot and soft rot; accordingly, the biocontrol activity was practically abolished in mutants deficient in iturin biosynthesis. Taken together, our results highlight the potential of these B. subtilis strains as biocontrol agents against fungal and bacterial diseases of cucurbits and the versatility of iturins as antifungal and antibacterial compounds.

scholarly journals Structural basis for receptor recognition by the novel coronavirus from Wuhan

2020 ◽  
Author(s):  
Jian Shang ◽  
Gang Ye ◽  
Ke Shi ◽  
Yushun Wan ◽  
Chuming Luo ◽  
...  
Keyword(s):  
Binding Affinity ◽  
Structural Changes ◽  
Molecular Mechanisms ◽  
Intervention Strategies ◽  
Structural Basis ◽  
The Novel ◽  
Recognition Mechanism ◽  
Future Evolution ◽  
Receptor Recognition ◽  
Novel Coronavirus

Abstract A novel SARS-like coronavirus (2019-nCoV) recently emerged from Wuhan, China and is quickly spreading in humans. A key to tackling this epidemic is to understand the virus’s receptor recognition mechanism, which regulates its infection, pathogenesis, and host range. 2019-nCoV and SARS-CoV recognize the same host receptor ACE2. Here we determined the crystal structure of 2019-nCoV receptor-binding domain (RBD) (engineered to facilitate crystallization) in complex of human ACE2.Compared with SARS-CoV, an ACE2-binding ridge in 2019-nCoV RBD takes more compact conformations, causing structural changes at the RBD/ACE2 interface. Adaptive to these structural changes, several mutations in 2019-nCoV RBD enhance ACE2- binding affinity, contributing to the high infectivity of 2019-CoV. These mutations also reveal the molecular mechanisms of the animal-to-human transmission of 2019-nCoV. Alarmingly, a single N439R mutation in 2019-nCoV RBD further enhances its ACE2- binding affinity, indicating possible future evolution of 2019-nCoV in humans. This study sheds light on the epidemiology and evolution of 2019-nCoV, and provides guidance for intervention strategies targeting receptor recognition by 2019-nCoV.

scholarly journals Genome-wide identification and expression analysis of glycine-rich protein genes in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

2019 ◽  
Author(s):  
Xiaonan Lu ◽  
Ming Gao ◽  
Yaxiong Cheng ◽  
Meilan Li ◽  
Xiaoyong XU
Keyword(s):  
Low Temperature ◽  
Chinese Cabbage ◽  
Molecular Mechanisms ◽  
Plant Stress ◽  
Evolutionary Relationship ◽  
Soft Rot ◽  
Biotic And Abiotic Stress ◽  
Motif Analysis ◽  
Abnormal Expression ◽  
Glycine Rich Protein

Abstract Background Plant Glycine-rich proteins, a superfamily with a glycine-rich domain, play an important role in various stress such as low temperature, drought, high salt, and so on. Although the research of GRP genes has been reported in many plants, the GRP gene has seldom reported in Chinese cabbage so far. Research results made a guide to further understand the function of BrGRP genes in Chinese cabbage. Results In this study, a total of 141 glycine-rich protein genes were identified in Chinese cabbage by homology comparative analysis. A further prediction of physical and chemical characteristics revealed that 58.3% of BrGRPs were alkalines, 63.1% of BrGRPs were unstable, and 73.8% were hydrophilic. Conserved domain analysis showed that 110 BrGRPs contained 18 same conserved motifs, and could be classified into five main subclasses which the evolutionary relationship and gene structure may be conserved while the other 31 BrGRPs, including Bra014168 , Bra040002 , etc, may gain new functions or gradually lost gene functions according to the evolution process. These identified BrGRP genes were also located in ten chromosomes and three different subgenomes of Chinese cabbage, and 101 pairs of orthologous GRP genes were found between Chinese cabbage and Arabidopsis. According to the opened transcriptome data, we found that 138 BrGRP genes showed abnormal expression at high temperature, 108 BrGRP genes showed abnormal expression at low temperature, and 74 at drought stress, 47 at soft rot stress, while only 3 and 7 genes at ozone and salt stress, respectively. Further promoter motif analysis found that a large number of stress-related cis-acting elements, such as DRE, MYC, MYB, and ABRE, were identified in their promoter regions, which were in correspondence with previous differential expression. In addition, some BrGRP genes were involved in multiple stresses suggested their broad-spectrum resistance. Conclusion A total of 141 GRP genes were identified in Chinese cabbage, which suggested their potential roles in plant stress response. But the molecular mechanisms by which BrGRP genes respond and resist biotic and abiotic stress remain unclear. These results may provide an important basis for the study of their function in Chinese cabbage.

Бактериозы картофеля в Российской Федерации

2018 ◽  
Author(s):  
A.N. Ignatov ◽  
Yu.S. Panycheva ◽  
M.V. Voronina ◽  
F.S. Dzhalilov
Keyword(s):  
Sugar Beet ◽  
Bacterial Pathogens ◽  
Soft Rot ◽  
Phytopathogenic Fungi ◽  
Control Measures ◽  
Clavibacter Michiganensis ◽  
Accurate Identification ◽  
Bacterial Diseases ◽  
Clavibacter Michiganensis Subsp ◽  
Regions Of Russia

Картофель поражается с заметным экономическим ущербом по меньшей мере 54 видами фитопатогенных грибов, 39 видами вирусов, 19 видами нематод, 3 видами фитоплазм и 11 видами бактерий. Бактериальные патогены вызывают болезни различной этиологии: от мокрой гнили до «зебры чипсов». Примерно 8-12 лет назад появились первые сообщения о проникновении и распространении новых возбудителей бактериозов во всех регионах России, в том числе о заболеваниях, вызываемых бактериями родов Dickeya dianthicola, D. solani и Clavibacter michiganensis subsp. michiganensis. В связи с усилением в России вредоносности бактериальных болезней картофеля, вызываемых различными группами бактерий, необходима точная идентификация патогенов, изучение путей их распространения, сохранения и разработка мер борьбы, ограничивающих распространение и обеспечивающих снижение ущерба от бактериальных болезней. Мы оценили распространение бактериальных патогенов картофеля как на основе собственных данных, так и по опубликованным сообщениям.Potato is affected at least by 54 species of phytopathogenic fungi, 39 viruses, 19 species of nematodes, 3 species of phytoplasmas, and 11 species of bacteria. Bacterial pathogens can cause diseases of different etiology: from "soft rot" to “zebra chips”. About 8-12 years ago, the increased severity of bacterial diseases in regions of Russia was reported, including diseases, caused by bacteria of genus Dickeya and Clavibacter michiganensis subsp. michiganensis. In connection with the increased harmfulness of bacterial diseases of sugar beet in Russia, caused by different groups of bacteria, we need an accurate identification of the pathogens, ways of their distribution, preservation, and search for control measures to limit the spread and reduce the damage from bacterial diseases of potato. We assessed and confirmed the distribution of potato bacterial pathogens based on own data as well as on reported incidence.

scholarly journals Use of a Specific Phage Cocktail for Soft Rot Control on Ware Potatoes: A Case Study

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1095
Author(s):  
Eugenia N. Bugaeva ◽  
Maya V. Voronina ◽  
Dmitry M. Vasiliev ◽  
Anna A. Lukianova ◽  
Nikolay N. Landyshev ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Soft Rot ◽  
Maintenance System ◽  
Specific Phage ◽  
Phage Cocktail ◽  
Complete Lysis ◽  
Bacterial Viruses ◽  
Phage Selection

Using bacteriophages (bacterial viruses) to control pathogenic bacteria is a promising approach in horticulture. However, the application of this strategy in real conditions requires compliance with particular technological and environmental restraints. The presented paper concerns the process of phage selection to create a cocktail that is efficient against the circulating causal agents of potato soft rot. The resulting phage cocktail causes a complete lysis of a mixture of circulating pectobacterial strains in vitro. In the context of being used to treat ware potatoes during off-season storage, the protocol of phage application via the humidity maintenance system was designed. The phage cocktail was shown to reduce the population of Pectobacterium spp. 10–12-fold, achieving a population that was below a symptomatic threshold.

scholarly journals Mitochondrial dysfunctions trigger the calcium signaling-dependent fungal multidrug resistance

2019 ◽  
Vol 117 (3) ◽  
pp. 1711-1721 ◽  
Author(s):  
Yeqi Li ◽  
Yuanwei Zhang ◽  
Chi Zhang ◽  
Hongchen Wang ◽  
Xiaolei Wei ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Multidrug Resistance ◽  
Mitochondrial Dysfunction ◽  
Calcium Signaling ◽  
Molecular Mechanisms ◽  
Expression Profiles ◽  
Drug Binding ◽  
Fitness Cost ◽  
Drug Resistant ◽  
Resistant Mutants

Drug resistance in fungal pathogens has risen steadily over the past decades due to long-term azole therapy or triazole usage in agriculture. Modification of the drug target protein to prevent drug binding is a major recognized route to induce drug resistance. However, mechanisms for nondrug target-induced resistance remain only loosely defined. Here, we explore the molecular mechanisms of multidrug resistance resulted from an efficient adaptation strategy for survival in drug environments in the human pathogen Aspergillus fumigatus. We show that mutants conferring multidrug resistance are linked with mitochondrial dysfunction induced by defects in heme A biosynthesis. Comparison of the gene expression profiles between the drug-resistant mutants and the parental wild-type strain shows that multidrug-resistant transporters, chitin synthases, and calcium-signaling-related genes are significantly up-regulated, while scavenging mitochondrial reactive oxygen species (ROS)-related genes are significantly down-regulated. The up-regulated-expression genes share consensus calcium-dependent serine threonine phosphatase-dependent response elements (the binding sites of calcium-signaling transcription factor CrzA). Accordingly, drug-resistant mutants show enhanced cytosolic Ca2+ transients and persistent nuclear localization of CrzA. In comparison, calcium chelators significantly restore drug susceptibility and increase azole efficacy either in laboratory-derived or in clinic-isolated A. fumigatus strains. Thus, the mitochondrial dysfunction as a fitness cost can trigger calcium signaling and, therefore, globally up-regulate a series of embedding calcineurin-dependent–response-element genes, leading to antifungal resistance. These findings illuminate how fitness cost affects drug resistance and suggest that disruption of calcium signaling might be a promising therapeutic strategy to fight against nondrug target-induced drug resistance.

scholarly journals Вacterial rot of tomatoes when grown in a protected ground

2020 ◽  
Vol 11 (3) ◽  
Author(s):  
V.A. Bohoslavets ◽  
◽  
Yu.V. Kolomiiets ◽  
L.M. Butsenko ◽  
Yu.M. Bohdan ◽  
...  
Keyword(s):  
Soft Rot ◽  
Control Measures ◽  
Effective Control ◽  
Bacterial Cells ◽  
Tomato Plants ◽  
Bacterial Diseases ◽  
Ground Conditions ◽  
Carotovorum Subsp ◽  
Bacterial Rot ◽  
Water Saturated

The specific conditions of the protected ground, the almost constant tomato culture without substitution of the substrate, the elevated temperature and humidity lead to the accumulation of a large number of pathogens of bacterial diseases, which limit the increase in yield of this crop. The aim of the work was to characterize the symptoms, determine the etiology of wet rot of tomatoes for growing in protected ground and propose measures to control the pathogen. The study was conducted by standard microbiological and phytopathological methods. The pathogenic properties of the isolates were studied on vegetative tomato plants using a suspension of bacterial cells with a titer of 107 CFU/ml. It was established that the defeat of tomato plants with soft bacterial rot in closed ground conditions prevails in the second half of the growing season. The development of the disease was 30‒34% for a prevalence of 45%. Diseases of tomato plants in greenhouses in the Kiev region of Ukraine are of bacterial origin, caused by the soft rot pathogen P. carotovorum subsp. carotovorum. Characteristic symptoms of wet tomato rot are discoloration, chlorosis and leaf necrosis, void stems, the appearance of depressed water-saturated areas in the stalk, accompanied by decay of the fetus. Effective control measures can be preventive and agricultural measures

scholarly journals Integrative Analysis to Uncover the Molecular Mechanisms of Caesalpinia sappan L. for Anti-Cancer Activity

2021 ◽  
Vol 16 (11) ◽  
pp. 1934578X2110399
Author(s):  
Bing Liu ◽  
Hao Lian
Keyword(s):  
Molecular Docking ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
The Cancer Genome Atlas ◽  
Network Pharmacology ◽  
Dependent Manner ◽  
Genomic Databases ◽  
Caesalpinia Sappan ◽  
Dose Dependent

Objectives: Caesalpinia Sappan L. is a traditional Chinese medicine with a long history. Recent studies have confirmed that Sappan has an antitumor effect, but its specific mechanism is still unclear. Methods: In this study, we used network pharmacology to predict the target and signal pathway of Sappan. In addition, the Cancer Genome Atlas and cancer cell lines encyclopedia large-scale genomic databases were used to analyze the relationship between different subtypes of Akt. Based on molecular docking technology, the interaction mode between small molecule compounds and protein targets was explored. Finally, we studied the effect of Sappan on Akt protein expression by Western blot in vitro. Results: AKT1 and AKT2 were significantly expressed in breast cancer cells, but they were significantly different from AKT3. Finally, molecular docking analysis showed that (3R,5R)-1,3,4,5-tetrakis(((E)-3-(3,4-dihydroxyphenyl)acryloyl)oxy)cyclohexane-1-carboxylic acid had a very ideal binding mode with Akt. Subsequent experiments showed that Sappan extract could induce apoptosis of HepG2 cells in a dose-dependent manner, and down regulate the phosphorylation level of Akt protein thr308 in a dose-dependent manner. Conclusions: This study provides new ideas for Sappan's anticancer research through the strategy of system pharmacology.

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