scholarly journals Novel Virulent and Broad-Host-Range Erwinia amylovora Bacteriophages Reveal a High Degree of Mosaicism and a Relationship to Enterobacteriaceae Phages

2011 ◽  
Vol 77 (17) ◽  
pp. 5945-5954 ◽  
Author(s):  
Yannick Born ◽  
Lars Fieseler ◽  
Janine Marazzi ◽  
Rudi Lurz ◽  
Brion Duffy ◽  
...  
Keyword(s):  
Erwinia Amylovora ◽  
Gene Clusters ◽  
Fruit Production ◽  
Specific Gene ◽  
Broad Host Range ◽  
Tail Fiber ◽  
Content Type ◽  
Production Environments ◽  
Terminal Repeats ◽  
High Degree

ABSTRACTA diverse set of 24 novel phages infecting the fire blight pathogenErwinia amylovorawas isolated from fruit production environments in Switzerland. Based on initial screening, four phages (L1, M7, S6, and Y2) with broad host ranges were selected for detailed characterization and genome sequencing. Phage L1 is a member of thePodoviridae, with a 39.3-kbp genome featuring invariable genome ends with direct terminal repeats. Phage S6, another podovirus, was also found to possess direct terminal repeats but has a larger genome (74.7 kbp), and the virus particle exhibits a complex tail fiber structure. Phages M7 and Y2 both belong to theMyoviridaefamily and feature long, contractile tails and genomes of 84.7 kbp (M7) and 56.6 kbp (Y2), respectively, with direct terminal repeats. The architecture of all four phage genomes is typical for tailed phages, i.e., organized into function-specific gene clusters. All four phages completely lack genes or functions associated with lysogeny control, which correlates well with their broad host ranges and indicates strictly lytic (virulent) lifestyles without the possibility for host lysogenization. Comparative genomics revealed that M7 is similar toE. amylovoravirus ΦEa21-4, whereas L1, S6, and Y2 are unrelated to any otherE. amylovoraphage. Instead, they feature similarities to enterobacterial viruses T7, N4, and ΦEcoM-GJ1. In a series of laboratory experiments, we provide proof of concept that specific two-phage cocktails offer the potential for biocontrol of the pathogen.

scholarly journals Cell Surface Attachment Structures Contribute to Biofilm Formation and Xylem Colonization by Erwinia amylovora

2011 ◽  
Vol 77 (19) ◽  
pp. 7031-7039 ◽  
Author(s):  
Jessica M. Koczan ◽  
Bryan R. Lenneman ◽  
Molly J. McGrath ◽  
George W. Sundin
Keyword(s):  
Biofilm Formation ◽  
Time Course ◽  
Erwinia Amylovora ◽  
Critical Role ◽  
Gene Clusters ◽  
Type I ◽  
Content Type ◽  
Type Iv ◽  
Attachment Structures

ABSTRACTBiofilm formation plays a critical role in the pathogenesis ofErwinia amylovoraand the systemic invasion of plant hosts. The functional role of the exopolysaccharides amylovoran and levan in pathogenesis and biofilm formation has been evaluated. However, the role of biofilm formation, independent of exopolysaccharide production, in pathogenesis and movement within plants has not been studied previously. Evaluation of the role of attachment inE. amylovorabiofilm formation and virulence was examined through the analysis of deletion mutants lacking genes encoding structures postulated to function in attachment to surfaces or in cellular aggregation. The genes and gene clusters studied were selected based onin silicoanalyses. Microscopic analyses and quantitative assays demonstrated that attachment structures such as fimbriae and pili are involved in the attachment ofE. amylovorato surfaces and are necessary for the production of mature biofilms. A time course assay indicated that type I fimbriae function earlier in attachment, while type IV pilus structures appear to function later in attachment. Our results indicate that multiple attachment structures are needed for mature biofilm formation and full virulence and that biofilm formation facilitates entry and is necessary for the buildup of large populations ofE. amylovoracells in xylem tissue.

scholarly journals Engineering of Bacteriophages Y2::dpoL1-C and Y2::luxAB for Efficient Control and Rapid Detection of the Fire Blight Pathogen, Erwinia amylovora

2017 ◽  
Vol 83 (12) ◽  
Author(s):  
Yannick Born ◽  
Lars Fieseler ◽  
Valentin Thöny ◽  
Nadja Leimer ◽  
Brion Duffy ◽  
...  
Keyword(s):  
Host Range ◽  
Fire Blight ◽  
Erwinia Amylovora ◽  
Diagnostic Methods ◽  
Host Cells ◽  
Luciferase Reporter ◽  
Economic Losses ◽  
Broad Host Range ◽  
Synergistic Activity ◽  
Content Type

ABSTRACT Erwinia amylovora is the causative agent of fire blight, a devastating plant disease affecting members of the Rosaceae. Alternatives to antibiotics for control of fire blight symptoms and outbreaks are highly desirable, due to increasing drug resistance and tight regulatory restrictions. Moreover, the available diagnostic methods either lack sensitivity, lack speed, or are unable to discriminate between live and dead bacteria. Owing to their extreme biological specificity, bacteriophages are promising alternatives for both aims. In this study, the virulent broad-host-range E. amylovora virus Y2 was engineered to enhance its killing activity and for use as a luciferase reporter phage, respectively. Toward these aims, a depolymerase gene of E. amylovora virus L1 (dpoL1-C) or a bacterial luxAB fusion was introduced into the genome of Y2 by homologous recombination. The genes were placed downstream of the major capsid protein orf68, under the control of the native promoter. The modifications did not affect viability of infectivity of the recombinant viruses. Phage Y2::dpoL1-C demonstrated synergistic activity between the depolymerase degrading the exopolysaccharide capsule and phage infection, which greatly enhanced bacterial killing. It also significantly reduced the ability of E. amylovora to colonize the surface of detached flowers. The reporter phage Y2::luxAB transduced bacterial luciferase into host cells and induced synthesis of large amounts of a LuxAB luciferase fusion. After the addition of aldehyde substrate, bioluminescence could be readily monitored, and this enabled rapid and specific detection of low numbers of viable bacteria, without enrichment, both in vitro and in plant material. IMPORTANCE Fire blight, caused by Erwinia amylovora, is the major threat to global pome fruit production, with high economic losses every year. Bacteriophages represent promising alternatives to not only control the disease, but also for rapid diagnostics. To enhance biocontrol efficacy, we combined the desired properties of two phages, Y2 (broad host range) and L1 (depolymerase for capsule degradation) in a single recombinant phage. This phage showed enhanced biocontrol and could reduce E. amylovora on flowers. Phage Y2 was also genetically engineered into a luciferase reporter phage, which transduces bacterial bioluminescence into infected cells and allows detection of low numbers of viable target bacteria. The combination of speed, sensitivity, and specificity is superior to previously used diagnostic methods. In conclusion, genetic engineering could improve the properties of phage Y2 toward better killing efficacy and sensitive detection of E. amylovora cells.

scholarly journals Evolution of Chemical Diversity in Echinocandin Lipopeptide Antifungal Metabolites

2015 ◽  
Vol 14 (7) ◽  
pp. 698-718 ◽  
Author(s):  
Qun Yue ◽  
Li Chen ◽  
Xiaoling Zhang ◽  
Kuan Li ◽  
Jingzu Sun ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Incomplete Lineage Sorting ◽  
Gene Clusters ◽  
Antifungal Drugs ◽  
Chemical Diversity ◽  
Specific Gene ◽  
Gene Trees ◽  
Content Type ◽  
Antifungal Metabolites ◽  
Pathway Gene

ABSTRACTThe echinocandins are a class of antifungal drugs that includes caspofungin, micafungin, and anidulafungin. Gene clusters encoding most of the structural complexity of the echinocandins provided a framework for hypotheses about the evolutionary history and chemical logic of echinocandin biosynthesis. Gene orthologs among echinocandin-producing fungi were identified. Pathway genes, including the nonribosomal peptide synthetases (NRPSs), were analyzed phylogenetically to address the hypothesis that these pathways represent descent from a common ancestor. The clusters share cooperative gene contents and linkages among the different strains. Individual pathway genes analyzed in the context of similar genes formed unique echinocandin-exclusive phylogenetic lineages. The echinocandin NRPSs, along with the NRPS from theinpgene cluster inAspergillus nidulansand its orthologs, comprise a novel lineage among fungal NRPSs. NRPS adenylation domains from different species exhibited a one-to-one correspondence between modules and amino acid specificity that is consistent with models of tandem duplication and subfunctionalization. Pathway gene trees and Ascomycota phylogenies are congruent and consistent with the hypothesis that the echinocandin gene clusters have a common origin. The disjunct Eurotiomycete-Leotiomycete distribution appears to be consistent with a scenario of vertical descent accompanied by incomplete lineage sorting and loss of the clusters from most lineages of theAscomycota. We present evidence for a single evolutionary origin of the echinocandin family of gene clusters and a progression of structural diversification in two fungal classes that diverged approximately 290 to 390 million years ago. Lineage-specific gene cluster evolution driven by selection of new chemotypes contributed to diversification of the molecular functionalities.

scholarly journals Plasmid Typing and Resistance Profiling of Escherichia fergusonii and Other Enterobacteriaceae Isolates from South Korean Farm Animals

2011 ◽  
Vol 77 (9) ◽  
pp. 3163-3166 ◽  
Author(s):  
Nabin Rayamajhi ◽  
Seung Bin Cha ◽  
Seung Won Shin ◽  
Byeong Yeal Jung ◽  
Suk-Kyung Lim ◽  
...  
Keyword(s):  
Virulence Genes ◽  
Farm Animals ◽  
Broad Host Range ◽  
Content Type ◽  
Zoonotic Pathogen ◽  
South Korean ◽  
Resistance Determinants ◽  
Broad Host Range Plasmid ◽  
High Degree ◽  
Plasmid Replicons

ABSTRACTIn this study, we focused on determining the distribution and prevalence of major plasmid replicons in β-lactam-resistantEscherichia fergusoniiandEnterobacteriaceaeof animal and human origin. A high degree of plasmid variability and multiple plasmid replicons were observed among the isolates. The IncF and IncI1 replicons were the most prevalent inE. fergusoniiandSalmonella entericaserovar Indiana isolated from swine and poultry in South Korea, respectively. The presence of broad-host-range plasmid replicons such as IncN, IncA/C, IncHI1, and IncHI2 that are associated with important virulence genes and toxins as well as antimicrobial resistance determinants indicates thatE. fergusoniihas the potential to become an important pig pathogen and possible emerging opportunistic zoonotic pathogen.

scholarly journals Genetic Analysis of Capsular Polysaccharide Synthesis Gene Clusters from All Serotypes of Streptococcus suis: Potential Mechanisms for Generation of Capsular Variation

2013 ◽  
Vol 79 (8) ◽  
pp. 2796-2806 ◽  
Author(s):  
Masatoshi Okura ◽  
Daisuke Takamatsu ◽  
Fumito Maruyama ◽  
Takashi Nozawa ◽  
Ichiro Nakagawa ◽  
...  
Keyword(s):  
Capsular Polysaccharide ◽  
Single Gene ◽  
Streptococcus Suis ◽  
Gene Clusters ◽  
Small Scale ◽  
Specific Gene ◽  
Chromosomal Locus ◽  
Content Type ◽  
Comprehensive Information ◽  
Genes Encoding

ABSTRACTStreptococcus suisstrains are classified into 35 serotypes on the basis of the antigenicity of their capsular polysaccharides (CPs). CP synthesis genes are known to be clustered on the chromosome (cpsgene cluster). The entirecpsgene clusters ofS. suishave so far been sequenced in 15 serotypes and found to be located betweenorfZandaroA. In this study, to provide comprehensive information aboutS. suisCPs, we sequenced the entirecpsgene clusters of the remaining serotypes and analyzed the complete set ofS. suiscpsgene clusters. Among the 35cpsgene clusters, 22 were located betweenorfZandaroA, whereas the other 13 were flanked by other gene(s) on the chromosomes, and the chromosomal locus was classified into five patterns. By clustering analysis, the predicted products ofcpsgenes found in the 35 serotypes were assigned into 291 homology groups, and all serotypes possessed a serotype-specific gene, except for serotypes 1, 2, 1/2, and 14. Because of the presence of genes encoding flippase (wzx) and polymerase (wzy), CPs of all serotypes were thought to be synthesized by the Wzx/Wzy pathway. Our data also implied the possibility of the transfer of the entire or partialcpsgene clusters amongS. suisstrains, as well as the influence of spontaneous mutations in a single gene or a few genes on the antigenicity of some serotypes. Accumulation of these gene transfers and small-scale mutations may have generated the antigenic diversity ofS. suisCPs.

scholarly journals Pseudomonas chlororaphisProduces Multiple R-Tailocin Particles That Broaden the Killing Spectrum and Contribute to Persistence in Rhizosphere Communities

2018 ◽  
Vol 84 (18) ◽  
Author(s):  
Robert J. Dorosky ◽  
Leland S. Pierson ◽  
Elizabeth A. Pierson
Keyword(s):  
Genomic Analysis ◽  
Gene Clusters ◽  
Bulk Soil ◽  
Tail Fiber ◽  
Content Type ◽  
Wheat Rhizosphere ◽  
Rhizosphere Microbiome ◽  
Different Types ◽  
Plant Growth Promoting ◽  
Tail Fibers

ABSTRACTR-tailocins are high-molecular-weight bacteriocins resembling bacteriophage tails.Pseudomonas chlororaphis30-84 is a plant growth-promoting rhizobacterial (PGPR) strain that produces two distinct R-tailocin particles with different killing spectra. The two R-tailocins have different evolutionary histories but are released by the same lysis cassette. A previous study showed that both tailocins are important for pairwise competition with susceptible rhizosphere-colonizing strains; however, the broader role of tailocins in competition with the native rhizosphere microbiome was not tested. Genomic analysis of theP. chlororaphis30-84 R-tailocin gene cluster uncovered the presence of three tail fiber genes in the tailocin 2 genetic module that could potentially result in tailocin 2 particles having different tail fibers and thus a wider killing spectrum. In this study, the tail fibers were found to incorporate onto different tailocin 2 particles, each with a distinct killing spectrum. A loss of production of one or both tailocins resulted in decreasedP. chlororaphis30-84 persistence within the wheat rhizosphere when in competition with the native microflora but not bulk soil. The capacity to produce three different versions of a single tailocin, each having one of three different types of tail fibers, is a previously unreported mechanism that leads to a broader R-tailocin killing spectrum. This study also provides evidence for the function of R-tailocins in competition with rhizosphere microbiome communities but not in bulk soil.IMPORTANCEAlthough R-tailocin gene clusters typically encode one tail fiber protein, three tail fiber-resembling genes were identified in association with one of the two sets of R-tailocin genes within the tailocin cluster ofP. chlororaphis30-84 and other sequencedP. chlororaphisstrain genomes. This study confirmed thatP. chlororaphis30-84 not only produces two distinct tailocins, but that one of them is produced with three different types of tail fibers. This is a previously unreported strategy to increase the breadth of strains targeted by an R-tailocin. Our finding that R-tailocins produced by a PGPRPseudomonasstrain enhanced its persistence within the wheat rhizosphere microbiome confirms that R-tailocin production contributes to the population dynamics of rhizobacterial communities.

scholarly journals Virulence genes and previously unexplored gene clusters in four commensal Neisseria spp. isolated from the human throat expand the neisserial gene repertoire

2020 ◽  
Vol 6 (9) ◽  
Author(s):  
Alan Calder ◽  
Chukwuma Jude Menkiti ◽  
Aylin Çağdaş ◽  
Jefferson Lisboa Santos ◽  
Ricarda Streich ◽  
...  
Keyword(s):  
Type Species ◽  
Gene Clusters ◽  
Secretion System ◽  
Specific Gene ◽  
Gene Repertoire ◽  
Type Vi Secretion System ◽  
Content Type ◽  
Link Type ◽  
Type Iv ◽  
System A

Commensal non-pathogenic Neisseria spp. live within the human host alongside the pathogenic Neisseria meningitidis and Neisseria gonorrhoeae and due to natural competence, horizontal gene transfer within the genus is possible and has been observed. Four distinct Neisseria spp. isolates taken from the throats of two human volunteers have been assessed here using a combination of microbiological and bioinformatics techniques. Three of the isolates have been identified as Neisseria subflava biovar perflava and one as Neisseria cinerea . Specific gene clusters have been identified within these commensal isolate genome sequences that are believed to encode a Type VI Secretion System, a newly identified CRISPR system, a Type IV Secretion System unlike that in other Neisseria spp., a hemin transporter, and a haem acquisition and utilization system. This investigation is the first to investigate these systems in either the non-pathogenic or pathogenic Neisseria spp. In addition, the N. subflava biovar perflava possess previously unreported capsule loci and sequences have been identified in all four isolates that are similar to genes seen within the pathogens that are associated with virulence. These data from the four commensal isolates provide further evidence for a Neisseria spp. gene pool and highlight the presence of systems within the commensals with functions still to be explored.

scholarly journals The Serratia marcescens Siderophore Serratiochelin Is Necessary for Full Virulence during Bloodstream Infection

2020 ◽  
Vol 88 (8) ◽  
Author(s):  
Danelle R. Weakland ◽  
Sara N. Smith ◽  
Bailey Bell ◽  
Ashootosh Tripathi ◽  
Harry L. T. Mobley
Keyword(s):  
Serratia Marcescens ◽  
Bloodstream Infection ◽  
Iron Acquisition ◽  
Gene Clusters ◽  
Clinical Isolates ◽  
Wild Type ◽  
Serratia Plymuthica ◽  
Content Type ◽  
Cas Assay ◽  
Essential Nutrient

ABSTRACT Serratia marcescens is a bacterium frequently found in the environment, but over the last several decades it has evolved into a concerning clinical pathogen, causing fatal bacteremia. To establish such infections, pathogens require specific nutrients; one very limited but essential nutrient is iron. We sought to characterize the iron acquisition systems in S. marcescens isolate UMH9, which was recovered from a clinical bloodstream infection. Using RNA sequencing (RNA-seq), we identified two predicted siderophore gene clusters (cbs and sch) that were regulated by iron. Mutants were constructed to delete each iron acquisition locus individually and in conjunction, generating both single and double mutants for the putative siderophore systems. Mutants lacking the sch gene cluster lost their iron-chelating ability as quantified by the chrome azurol S (CAS) assay, whereas the cbs mutant retained wild-type activity. Mass spectrometry-based analysis identified the chelating siderophore to be serratiochelin, a siderophore previously identified in Serratia plymuthica. Serratiochelin-producing mutants also displayed a decreased growth rate under iron-limited conditions created by dipyridyl added to LB medium. Additionally, mutants lacking serratiochelin were significantly outcompeted during cochallenge with wild-type UMH9 in the kidneys and spleen after inoculation via the tail vein in a bacteremia mouse model. This result was further confirmed by an independent challenge, suggesting that serratiochelin is required for full S. marcescens pathogenesis in the bloodstream. Nine other clinical isolates have at least 90% protein identity to the UMH9 serratiochelin system; therefore, our results are broadly applicable to emerging clinical isolates of S. marcescens causing bacteremia.

scholarly journals Proteogenomic Insights into the Physiology of Marine, Sulfate-Reducing, Filamentous Desulfonema limicola and Desulfonema magnum

2021 ◽  
Vol 31 (1) ◽  
pp. 36-56
Author(s):  
Vanessa Schnaars ◽  
Lars Wöhlbrand ◽  
Sabine Scheve ◽  
Christina Hinrichs ◽  
Richard Reinhardt ◽  
...  
Keyword(s):  
Energy Metabolism ◽  
Gene Clusters ◽  
Transport Systems ◽  
Natural Habitats ◽  
Sulfate Reducing ◽  
Type Iv ◽  
Aromatic Compound Degradation ◽  
High Degree ◽  
Reducing Bacteria ◽  
Gliding Movement

The genus Desulfonema belongs to the deltaproteobacterial family Desulfobacteraceae and comprises marine, sulfate-reducing bacteria that form filaments and move by gliding. This study reports on the complete, manually annotated genomes of Dn. limicola 5ac10T (6.91 Mbp; 6,207 CDS) and Dn. magnum 4be13T (8.03 Mbp; 9,970 CDS), integrated with substrate-specific proteome profiles (8 vs. 11). The richness in mobile genetic elements is shared with other Desulfobacteraceae members, corroborating horizontal gene transfer as major driver in shaping the genomes of this family. The catabolic networks of Dn. limicola and Dn. magnum have the following general characteristics: 98 versus 145 genes assigned (having genomic shares of 1.7 vs. 2.2%), 92.5 versus 89.7% proteomic coverage, and scattered gene clusters for substrate degradation and energy metabolism. The Dn. magnum typifying capacity for aromatic compound degradation (e.g., p-cresol, 3-phenylpropionate) requires 48 genes organized in operon-like structures (87.7% proteomic coverage; no homologs in Dn. limicola). The protein complements for aliphatic compound degradation, central pathways, and energy metabolism are highly similar between both genomes and were identified to a large extent (69–96%). The differential protein profiles revealed a high degree of substrate-specificity for peripheral reaction sequences (forming central intermediates), agreeing with the high number of sensory/regulatory proteins predicted for both strains. By contrast, central pathways and modules of the energy metabolism were constitutively formed under the tested substrate conditions. In accord with their natural habitats that are subject to fluctuating changes of physicochemical parameters, both Desulfonema strains are well equipped to cope with various stress conditions. Next to superoxide dismutase and catalase also desulfoferredoxin and rubredoxin oxidoreductase are formed to counter exposure to molecular oxygen. A variety of proteases and chaperones were detected that function in maintaining cellular homeostasis upon heat or cold shock. Furthermore, glycine betaine/proline betaine transport systems can respond to hyperosmotic stress. Gliding movement probably relies on twitching motility via type-IV pili or adventurous motility. Taken together, this proteogenomic study demonstrates the adaptability of Dn. limicola and Dn. magnum to its dynamic habitats by means of flexible catabolism and extensive stress response capacities.

scholarly journals Greater fit and a greater gap

2019 ◽  
Vol 26 (4) ◽  
pp. 561-594
Author(s):  
Steven A. Brieger ◽  
Dirk De Clercq ◽  
Jolanda Hessels ◽  
Christian Pfeifer
Keyword(s):  
Life Satisfaction ◽  
Institutional Environment ◽  
Entrepreneurial Activity ◽  
Worker Rights ◽  
Content Type ◽  
Person Environment Fit ◽  
High Power Distance ◽  
High Degree ◽  
The Impact ◽  
Low Uncertainty

Purpose The purpose of this paper is to understand how national institutional environments contribute to differences in life satisfaction between entrepreneurs and employees. Design/methodology/approach Leveraging person–environment fit and institutional theories and using a sample of more than 70,000 entrepreneurs and employees from 43 countries, the study investigates how the impact of entrepreneurial activity on life satisfaction differs in various environmental contexts. An entrepreneur’s life satisfaction arguably should increase when a high degree of compatibility or fit exists between his or her choice to be an entrepreneur and the informal and formal institutional environment. Findings The study finds that differences in life satisfaction between entrepreneurs and employees are larger in countries with high power distance, low uncertainty avoidance, extant entrepreneurship policies, low commercial profit taxes and low worker rights. Originality/value This study sheds new light on how entrepreneurial activity affects life satisfaction, contingent on the informal and formal institutions in a country that support entrepreneurship by its residents.

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