Journal: Molecular Plant Pathology

Article Title: Comparative genomics of Spiraeoideae‐infecting Erwinia amylovora strains provides novel insight to genetic diversity and identifies the genetic basis of a low‐virulence strain

doi: 10.1111/mpp.12647

Figure Lengend Snippet: Phylogeny of Spiraeoideae‐infecting (SI) (A), and SI and Rubus‐infecting (RI) (B), Erwinia amylovora strains, inferred from a whole‐genome alignment. The phylogenetic tree was generated based on a merged whole‐genome nucleotide alignment generated by REALPHY. The tree was constructed using the maximum likelihood method with the general time reversible model, and was midpoint rooted. Bootstrap support values are 100% unless indicated. Colours indicate the regions in which the strains were isolated (green, eastern USA; red, western USA and Mexico; blue, Europe).

Article Snippet: Only four genomes of E. amylovora have been deposited in the National Center for Biotechnology Information (NCBI) in the past 8 years.

Techniques: Generated, Construct, Isolation, Western Blot

Journal: Molecular Plant Pathology

Article Title: Comparative genomics of Spiraeoideae‐infecting Erwinia amylovora strains provides novel insight to genetic diversity and identifies the genetic basis of a low‐virulence strain

doi: 10.1111/mpp.12647

Figure Lengend Snippet: Mantel's test of genetic distance by geographical distance. (A) Mantel's test using all strains except those of the ‘Widely Prevalent’ clade. (B) Mantel's test using all 29 Spiraeoideae‐infecting (SI) Erwinia amylovora strains. OR6 is excluded because of a lack of GPS coordinates.

Article Snippet: Only four genomes of E. amylovora have been deposited in the National Center for Biotechnology Information (NCBI) in the past 8 years.

Techniques:

Journal: Molecular Plant Pathology

Article Title: Comparative genomics of Spiraeoideae‐infecting Erwinia amylovora strains provides novel insight to genetic diversity and identifies the genetic basis of a low‐virulence strain

doi: 10.1111/mpp.12647

Figure Lengend Snippet: Recombination between any two Spiraeoideae‐infecting (SI) Erwinia amylovora strains at the genome level. Gene conversion fragments were identified by GENECONV using the nucleotide alignment of the whole‐genome sequences. The percentage was calculated by dividing the size of cumulative gene conversion fragments by the size of the aligned sequences.

Article Snippet: Only four genomes of E. amylovora have been deposited in the National Center for Biotechnology Information (NCBI) in the past 8 years.

Techniques:

Journal: Molecular Plant Pathology

Article Title: Comparative genomics of Spiraeoideae‐infecting Erwinia amylovora strains provides novel insight to genetic diversity and identifies the genetic basis of a low‐virulence strain

doi: 10.1111/mpp.12647

Figure Lengend Snippet: Presence of restriction modification and clustered regularly interspaced short palindromic repeats/CRISPR‐associated protein (CRISPR/Cas) systems in Erwinia amylovora strains

Article Snippet: Only four genomes of E. amylovora have been deposited in the National Center for Biotechnology Information (NCBI) in the past 8 years.

Techniques: Modification, CRISPR, Western Blot

Journal: Molecular Plant Pathology

Article Title: Comparative genomics of Spiraeoideae‐infecting Erwinia amylovora strains provides novel insight to genetic diversity and identifies the genetic basis of a low‐virulence strain

doi: 10.1111/mpp.12647

Figure Lengend Snippet: Virulence variations of Erwinia amylovora strains on immature pear. (A) Quantification of the sizes of the maceration area on immature pear fruits. (B) Virulence phenotypes of representative high‐virulence and low‐virulence strains. Photographs of the pears with maceration symptoms were taken at 8 days post‐inoculation and the sizes of maceration were quantified using ImageJ.

Article Snippet: Only four genomes of E. amylovora have been deposited in the National Center for Biotechnology Information (NCBI) in the past 8 years.

Techniques:

Journal: Molecular Plant Pathology

Article Title: Comparative genomics of Spiraeoideae‐infecting Erwinia amylovora strains provides novel insight to genetic diversity and identifies the genetic basis of a low‐virulence strain

doi: 10.1111/mpp.12647

Figure Lengend Snippet: Virulence variations of Erwinia amylovora strains on immature pear. (A) Virulence of CTBT3‐1, CTBT1‐1, Δhfq of the two strains and Δhfq strains complemented by pCLhfq16R and pCLhfq16H. Photographs were taken at 9 days post‐inoculation. (B) Alignment of the first 54 nucleotides of hfq in CTBT3‐1 and CTBT1‐1, illustrating the single nucleotide polymorphism at nucleotide 47 (amino acid 16).

Article Snippet: Only four genomes of E. amylovora have been deposited in the National Center for Biotechnology Information (NCBI) in the past 8 years.

Techniques:

Journal: Molecular Plant Pathology

Article Title: CsrD regulates amylovoran biosynthesis and virulence in Erwinia amylovora in a novel cyclic‐di‐GMP dependent manner

doi: 10.1111/mpp.13217

Figure Lengend Snippet: (a) The domain architecture of CsrD comprises an N‐terminal GAPES4 periplasmic sensory domain flanked by transmembrane helices. CsrD also comprises GGDEF and EAL motifs (Finn et al., ). Critical residues for each domain are highlighted to denote the variations present in Erwinia amylovora Ea1189 versus Escherichia coli K12 when aligned. (b) Aligned CsrD orthologs from a diverse subset of Enterobacteriaceae species indicate that the EXLXR motif within the EAL domain of CsrD is only conserved in the Glu (E) and Arg (R) residues. The Leu (L) residue was found to be highly variable among the evaluated species. Alignment was conducted using Clustal Omega (Sievers & Higgins, ). (c) A maximum‐likelihood tree (Schmidt et al., ) revealed three distinct lineages within the evaluated CsrD orthologs from various Enterobacteriaceae species. The functionally active PdeC from E . amylovora was used as an out‐group. MEGA v. 7.0 was used as a platform to conduct both analyses (Agbo et al., )

Article Snippet: The E . amylovora Ea1189 and E . coli K12 genome sequences along with annotations were acquired from the National Center for Biotechnology Information (NCBI) (Riley et al., ; Yu et al., ).

Techniques: Residue

Journal: Molecular Plant Pathology

Article Title: CsrD regulates amylovoran biosynthesis and virulence in Erwinia amylovora in a novel cyclic‐di‐GMP dependent manner

doi: 10.1111/mpp.13217

Figure Lengend Snippet: (a) A panel depicting the overall results of pull‐down assays with multiple variations analysed to determine the specifics of CsrD binding to c‐di‐GMP. (i) Biotinylated c‐di‐GMP (100 µM) immobilized to streptavidin beads shows binding to increasing concentrations (0, 0.003, 0.03, 0.3, 1.7 µM) of His‐tagged CsrD. (ii) Binding between 1.7 µM of CsrD and increasing concentrations (0, 5, 25, 50, 100 µM) of biotinylated c‐di‐GMP. (iii) Binding between 1.7 µM CsrD and 100 µM biotinylated c‐di‐GMP with increasing concentrations (0, 5, 25, 50, 100 µM) of unlabelled c‐di‐GMP as a competitor. (iv) Binding between 1.7 µM CsrD and 100 µM of biotinylated c‐di‐GMP with increasing concentrations (0, 5, 25, 50, 100 µM) of GTP as a nonspecific competitor. (b) Binding between truncated and site‐directed substituted versions of E rwinia amylovora CsrD as well as CsrD from Escherichia coli K12 (1.7 µM of all proteins) and biotinylated c‐di‐GMP (100 µM). (c) The dissociation constant ( K D ) for CsrD binding to c‐di‐GMP determined at the half‐maximal binding level (Chambers & Sauer, ). The graph compares the binding level in the form of pixel density from the immunoblot (generated using ImageJ) involving a pull‐down of the interaction between 1.7 µM of CsrD with increasing concentrations of biotinylated c‐di‐GMP (Schneider et al., )

Article Snippet: The E . amylovora Ea1189 and E . coli K12 genome sequences along with annotations were acquired from the National Center for Biotechnology Information (NCBI) (Riley et al., ; Yu et al., ).

Techniques: Binding Assay, Western Blot, Generated

Journal: Molecular Plant Pathology

Article Title: CsrD regulates amylovoran biosynthesis and virulence in Erwinia amylovora in a novel cyclic‐di‐GMP dependent manner

doi: 10.1111/mpp.13217

Figure Lengend Snippet: Bacterial strains, plasmids, and their relevant characteristics

Article Snippet: The E . amylovora Ea1189 and E . coli K12 genome sequences along with annotations were acquired from the National Center for Biotechnology Information (NCBI) (Riley et al., ; Yu et al., ).

Techniques: Plasmid Preparation, Mutagenesis, Expressing, Recombinant, Cloning, Residue, Clone Assay

Journal: iScience

Article Title: On-site applicable diagnostic fluorescent probe for fire blight bacteria

doi: 10.1016/j.isci.2023.106557

Figure Lengend Snippet: Key resources table

Article Snippet: VDRG® E.amylovora Rapid kit , MEDIAN Diagnostics Inc. , Cat. # FB-EAV-11.

Techniques: Virus, Recombinant, Saline, Software

Journal: BMC Genomics

Article Title: Comparative transcriptome analysis of a lowly virulent strain of Erwinia amylovora in shoots of two apple cultivars – susceptible and resistant to fire blight

doi: 10.1186/s12864-017-4251-z

Figure Lengend Snippet: Mean virulence rating of E. amylovora 650 strain used for inoculation of actively growing shoots of three apple cultivars of different susceptibility. Virulence was measured 6 weeks post-inoculation and it is expressed as a percent of the length of a shoot exhibiting necrosis divided by the entire length of shoot. Mean virulence ratings were separated with Tukey’s test at a significance level of P = 0.05. The vertical bars represent standard error

Article Snippet: However, the higher expression of E. amylovora flagellar genes (recognized as PAMP) in Free Redstar can explain why strain 650 cannot effectively attack Free Redstar trees.

Techniques:

Journal: BMC Genomics

Article Title: Comparative transcriptome analysis of a lowly virulent strain of Erwinia amylovora in shoots of two apple cultivars – susceptible and resistant to fire blight

doi: 10.1186/s12864-017-4251-z

Figure Lengend Snippet: Venn diagram representing number of E. amylovora genes a / up- and b / down-regulated in planta comparing to expression of genes of pure bacterial culture grown overnight in TY medium. I – Idared; FR – Free Redstar; 24 h – sample collected 24 h after inoculation; 6d - sample collected 6 days after inoculation

Article Snippet: However, the higher expression of E. amylovora flagellar genes (recognized as PAMP) in Free Redstar can explain why strain 650 cannot effectively attack Free Redstar trees.

Techniques: Expressing

Journal: BMC Genomics

Article Title: Comparative transcriptome analysis of a lowly virulent strain of Erwinia amylovora in shoots of two apple cultivars – susceptible and resistant to fire blight

doi: 10.1186/s12864-017-4251-z

Figure Lengend Snippet: Relative abundance of CDSs assigned to each eggNOG functional categories for commonly a/ 640 down and b/ 698 up-regulated E. amylovora genes in planta . The eggNOG functional categories are as follows: C, energy production and conversion; D, cell cycle control, cell division and chromosome partitioning; E, amino acid transport and metabolism; F, nucleotide transport and metabolism; G, carbohydrate transport and metabolism; H, coenzyme transport and metabolism; I, lipid transport and metabolism; J, translation; K, transcription; L, replication; M, cell wall/membrane/envelope biogenesis; N, cell motility; O, posttranslational modification, protein turnover, chaperones; P, inorganic ion transport and metabolism; Q, secondary metabolites biosynthesis, transport and catabolism; S, function unknown; T, signal transduction mechanisms; U, intracellular trafficking and secretion; V, defence mechanisms. ↑- over-represented; ↓ - under-represented COG categories calculated based on hypergeometric distribution at FDR < 0.05

Article Snippet: However, the higher expression of E. amylovora flagellar genes (recognized as PAMP) in Free Redstar can explain why strain 650 cannot effectively attack Free Redstar trees.

Techniques: Functional Assay, Control, Membrane, Modification, Transduction

Journal: BMC Genomics

Article Title: Comparative transcriptome analysis of a lowly virulent strain of Erwinia amylovora in shoots of two apple cultivars – susceptible and resistant to fire blight

doi: 10.1186/s12864-017-4251-z

Figure Lengend Snippet: Diagram showing the study design. One-year-old, potted apple trees cultivars Idared and Free Redstar grafted on M.26 were inoculated with E. amylovora strain 650 in greenhouse conditions. Inoculation was made on actively growing shoots, with bacterial suspension grown overnight in TY medium. After 24 h and 6 days from the inoculation time total RNA was isolated from inoculated shoots. At each time point, RNA was isolated separately from at least 6 shoots of each apple cultivar. Additionally, RNA was isolated from the pure culture of E. amylovora 650 grown overnight in TY medium. In each time point, RNA was isolated from 3 biological replicates (in case of pure bacterial culture - two biological replicates). The replicates constituted the sample (marked by red circle)

Article Snippet: However, the higher expression of E. amylovora flagellar genes (recognized as PAMP) in Free Redstar can explain why strain 650 cannot effectively attack Free Redstar trees.

Techniques: Suspension, Isolation