Characterization of hns genes from Erwinia amylovora

The small basic histone-like protein H-NS is known for bacteria to attenuate virulence of several animal pathogens. An hns homologue from E. amylovora was identified by complementing an E. coli hns-mutant strain with a cosmid library from E. amylovora. A 1.6 kb EcoRI-fragment complemented the mucoid phenotype and repressed the ss-glucosidase activity of E. coli PD32. The open reading frame encoding an H-NS-like protein of 134 amino acid was later shown to be located on plasmid pEA29 (McGhee and Jones 2000). A chromosomal hns gene was amplified with PCR consensus primers and localized near galU of E. amylovora. E. amylovora mutants were created by insertion of a resistance cassette, and the intact gene was inserted into a high copy number plasmid for constitutive expression. Purified chromosomal H-NS protein preferentially bound to a DNA fragment from the lsc region and bending was predicted for an adjacent fragment with the rlsB-promoter. Levan production was significantly increased by hns mutations. Synthesis of the capsular exopolysaccharide amylovoran and of levan were reduced, when hns from the E. amylovora plasmid was overexpressed. A mutation in chromosomal hns of E. amylovora increased amylovoran synthesis, and both mutations retarded symptom formation on immature pears.     

真菌群体基因组学研究进展

近年来,随着第二代高通量测序技术的出现和发展,测序成本不断降低,完成全基因组测序的真菌物种迅速增加。以大规模测序为基础的群体基因组学,也逐渐应用于解析真菌的群体结构、物种形成、种群分化和位点特异性效应。本文综述了群体基因组学在工业真菌、病原真菌、食用真菌、共生真菌及其在表型性状遗传基础解析中的研究进展,并对其今后的发展方向进行了展望。     

Secretion and regulation Hrp mutants of Erwinia amylovora trigger different responses in apple

The interaction between two Hrp mutants of Erwinia amylovora, the parental virulent strain, and a host plant (Malus sp.) was studied with apple seedlings and apple flowers, using inoculation procedures which reduce the possibility of injury. We showed that one hrp regulatory mutant protected apple tissue against the virulent strain to a greater degree than a secretion mutant. The dynamics of bacterial growth in this interaction indicated that the protection was associated with the inhibition of the multiplication of the virulent strain. The activity of two enzymes involved in plant defence responses, phenylalanine-ammonia lyase and guaiacol peroxidase, increased in leaves treated with the regulatory mutant, but not in the leaves treated with the secretion mutant. The role of regulatory genes of the hrp cluster in this interaction is discussed.     

Potential versus actual contribution of vertical transmission to pathogen fitness

Theory predicts that virulent parasites cannot be maintained at high prevalence if they are only vertically transmitted. However, parasites with high rates of vertical transmission that cause severe reduction in host fitness have been reported. Atkinsonella hypoxylon is a fungal pathogen capable of both vertical and horizontal transmission that drastically reduces its host''s fitness. In contrast with theoretical predictions, field and laboratory observations suggested that the primary mechanism of transmission was vertical. Using randomly amplified polymorphic DNA markers, we investigated the effective contribution of vertical and horizontal transmission to the genetic structure of three natural populations of A. hypoxylon. We found high genotypic diversity and low linkage disequilibrium, indicating that most established genotypes are derived from horizontally transmitted, sexual spores. The low contribution of vertical transmission to the parasite''s fitness despite its high potential might be due to lower establishment of cleistogamous seeds (through which vertical transmission occurs) or lower vigour of vertically transmitted fungal genotypes. Low establishment of vertically infected hosts might explain the persistence of virulent parasites with high apparent vertical transmission. Our results suggest that caution must be taken when using the potential for vertical transmission to make predictions about the evolution of parasite virulence.     

Structure of the sidechain of lipopolysaccharide from Erwinia amylovora T

The sidechain of lipopolysaccharide from Erwinia amylovora T was composed of D-fucose, D-galactose and D-glucose in equimolar proportions. Using NMR spectroscopy, methylation analysis, mass spectrometry, Smith degradation and optical rotation data, the repeat unit was shown to have the following most probable structure: (formula; see text)     

Isolation of a Factor from Apple that Agglutinates Erwinia amylovora

Extracts prepared from apple seeds contain a factor (AF) capable of agglutinating cells of Erwinia amylovora. In drop agglutination tests, AF is more active in agglutinating an avirulent, acapsular strain of E. amylovora than a virulent, capsular strain. AF precipitates in agar plates with a receptor derived from boiled cells of avirulent acapsular strain and, therefore, can be located during fractionation by rocket electrophoresis. AF was heat-stable and had a pH optimum for agglutination near congruent with3.6 pH. The agglutination activity was not affected by the presence of Mg(2+), Ca(2+), or EDTA. AF was separated into two fractions (AF I and AF II) by elution from a Bio-Gel P-100 column. The precipitin and agglutination activities associated with AF II were found to be present in a positively charged molecule which was sensitive to treatment with protease and trypsin and, hence, presumably resides in a protein. The approximate molecular weight of AF II was determined to be 12,600 daltons. Besides precipitating the receptor derived from cells of avirulent acapsular strain, AF II was capable of precipitating extracellular polysaccharide from cultures of virulent capsular strain, sodium polygalacturonate, and carboxymethylcellulose. These three polymers also inhibited the agglutination activity associated with AF II. AF II could be replaced by poly-l-lysines in both the precipitin and agglutination assays. In addition, in antigen absorption experiments, poly-l-lysines were found to remove the receptors for AF II from the boiled extracts of avirulent acapsular strain. Based on these observations, it is proposed that the activity of AF II resides in a highly positively charged protein which causes agglutination of bacterial cells by interacting on a charge-charge basis with negatively charged components on the surface of the bacterial cells.     

Evolutionary insights into genome-wide nucleosome positioning

A new study takes an evolutionary approach to investigate to what extent nucleosome positioning is determined by underlying sequence or by trans-acting factors.     

Functional insights from structural genomics

Structural genomics efforts have produced structural information, either directly or by modeling, for thousands of proteins over the past few years. While many of these proteins have known functions, a large percentage of them have not been characterized at the functional level. The structural information has provided valuable functional insights on some of these proteins, through careful structural analyses, serendipity, and structure-guided functional screening. Some of the success stories based on structures solved at the Northeast Structural Genomics Consortium (NESG) are reported here. These include a novel methyl salicylate esterase with important role in plant innate immunity, a novel RNA methyltransferase (H. influenzae yggJ (HI0303)), a novel spermidine/spermine N-acetyltransferase (B. subtilis PaiA), a novel methyltransferase or AdoMet binding protein (A. fulgidus AF_0241), an ATP:cob(I)alamin adenosyltransferase (B. subtilis YvqK), a novel carboxysome pore (E. coli EutN), a proline racemase homolog with a disrupted active site (B. melitensis BME11586), an FMN-dependent enzyme (S. pneumoniae SP_1951), and a 12-stranded β-barrel with a novel fold (V. parahaemolyticus VPA1032).     

Characterization of Erwinia amylovora strains from Bulgaria by pulsed-field gel electrophoresis

The aim of this study was to characterize genetically Bulgarian Erwinia amylovora strains using pulsed-field gel electrophoresis (PFGE) analysis. Fifty E. amylovora strains isolated from different hosts, locations, as well as in different years were analysed by PFGE after XbaI, SpeI, and XhoI digestion of the genomic DNA. The strains were distributed into four groups according to their XbaI-generated profile. About 82% of the strains displayed a PFGE profile identical to that of type Pt2. Three strains belonged to the Central Europe Pt1 type. Two new PFGE profiles, not reported so far, were established--one for a strain isolated from Malus domestica and another for all Fragaria spp. strains. The same grouping of the strains was obtained after analysis of the SpeI digestion patterns. On the basis of PFGE profiles, after XbaI and SpeI digestion, a genetic differentiation between the strains associated with subfamily Maloideae and subfamily Rosoideae was revealed. The presence of more than one PFGE profile in the population of E. amylovora in Bulgaria suggests a multiple source of inoculum.     

Expression of lysozymes from Erwinia amylovora phages and Erwinia genomes and inhibition by a bacterial protein

Genes coding for lysozyme-inhibiting proteins (Ivy) were cloned from the chromosomes of the plant pathogens Erwinia amylovora and Erwinia pyrifoliae. The product interfered not only with activity of hen egg white lysozyme, but also with an enzyme from E. amylovora phage ΦEa1h. We have expressed lysozyme genes from the genomes of three Erwinia species in Escherichia coli. The lysozymes expressed from genes of the E. amylovora phages ΦEa104 and ΦEa116, Erwinia chromosomes and Arabidopsis thaliana were not affected by Ivy. The enzyme from bacteriophage ΦEa1h was fused at the N- or C-terminus to other peptides. Compared to the intact lysozyme, a His-tag reduced its lytic activity about 10-fold and larger fusion proteins abolished activity completely. Specific protease cleavage restored lysozyme activity of a GST-fusion. The bacteriophage-encoded lysozymes were more active than the enzymes from bacterial chromosomes. Viral lyz genes were inserted into a broad-host range vector, and transfer to E. amylovora inhibited cell growth. Inserted in the yeast Pichia pastoris, the ΦEa1h-lysozyme was secreted and also inhibited by Ivy. Here we describe expression of unrelated cloned 'silent' lyz genes from Erwinia chromosomes and a novel interference of bacterial Ivy proteins with a viral lysozyme.     

New insights in the molecular biology and physiology of Streptococcus thermophilus revealed by comparative genomics

Streptococcus thermophilus is a major dairy starter used for the manufacture of yoghurt and cheese. The access to three genome sequences, comparative genomics and multilocus sequencing analyses suggests that this species recently emerged and is still undergoing a process of regressive evolution towards a specialised bacterium for growth in milk. Notably, S. thermophilus has maintained a well-developed nitrogen metabolism whereas its sugar catabolism has been subjected to a high level of degeneracy due to a paucity of carbon sources in milk. Furthermore, while pathogenic streptococci are recognised for a high capacity to expose proteins at their cell surface in order to achieve cell adhesion or to escape the host immune system, S. thermophilus has nearly lost this unique feature as well as many virulence-related functions. Although gene decay is obvious in S. thermophilus genome evolution, numerous small genomic islands, which were probably acquired by horizontal gene transfer, comprise important industrial phenotypic traits such as polysaccharide biosynthesis, bacteriocin production, restriction-modification systems or oxygen tolerance.     

Erwinia amylovora strains from outbreaks of fire blight in Spain: phenotypic characteristics

One hundred and thirty strains of Erwinia amylovora recovered from Spanish foci of fire blight from 1995 to 2000 were characterised and compared to reference strains from different sources and origins. Their rapid identification was performed by double antibody sandwich indirect (DASI) ELISA, using specific monoclonal antibodies against E. amylovora, and molecular confirmation by PCR using primers specific to the native plasmid pEA29. The Spanish strains of E. amylovora grew on different general and selective media producing typical colonies, except one of them that was deficient in levan production, whereas none of them grew on minimal agar medium with copper sulphate and low content of asparagine. All of them were susceptible to tetracycline, streptomycin, kasugamycin and oxolinic acid. Biochemical characterisation of selected strains by API 20E system revealed a great homogeneity, with 80% of the Spanish strains showing one of the two majority API 20E profiles described for E. amylovora, and the remaining strains showing minor differences. Pathogenicity on pear fruits and hypersensitivity reaction was confirmed, but a delayed reaction was observed for two Spanish strains. This is the first characterisation of a large collection of Spanish strains of E. amylovora.     

Interference of Copper Sulphate in Growth of Erwinia amylovora

To understand the toxicity of copper salts on Erwinia amylovora, which are used in the control of fire blight, bacterial growth and cell metabolism was assayed with copper sulphate in the presence or absence of complex-forming compounds such as various amino acids or citrate. In minimal medium without amino acids copper sulphate strongly interfered with the growth of E. amylovora. A concentration of 15 μm CuSO₄ resulted in about 50% growth inhibition. In contrast to a strong effect of streptomycin, copper ions barely killed the cells when incubated in minimal medium for 1 h. The addition of 4 g asparagine per litre relieved a‘bacteriostatic’effect of copper ions and allowed growth of the bacteria at 2 mm CuSO₄. Other amino acids had a similar effect in the protection of E. amylovora against copper ions. This was in contrast to glycine betain, which was unable to suppress growth inhibition by CuSO₄. Presumably, the free ammonium groups of amino acids participated in the protective effect. The addition of citrate, exceeding the amount of copper-ions, was also protective. Bioluminescence of E. amylovora cells was expressed via a constitutive promoter from the lux-operon of Vibrio fischeri. The light emission is dependent on active cell metabolism. In a novel approach to determine the immediate response of E. amylovora after the addition of copper sulphate, the change of bioluminescence was determined. Addition of copper ions to MM3 medium strongly affected the bioluminescence, but no change in light production was noticed, when citrate or asparagine were present in addition to copper sulphate. A decrease of bioluminescence to 50% was observed for 50 μm CuSO₄ in the absence of amino acids.     

Discrimination and Detection of Erwinia amylovora and Erwinia pyrifoliae with a Single Primer Set

Erwinia amylovora and Erwinia pyrifoliae cause fire blight and black-shoot blight, respectively, in apples and pears. E. pyrifoliae is less pathogenic and has a narrower host range than that of E. amylovora. Fire blight and black-shoot blight exhibit similar symptoms, making it difficult to distinguish one bacterial disease from the other. Molecular tools that differentiate fire blight from black-shoot blight could guide in the implementation of appropriate management strategies to control both diseases. In this study, a primer set was developed to detect and distinguish E. amylovora from E. pyrifoliae by conventional polymerase chain reaction (PCR). The primers produced amplicons of different sizes that were specific to each bacterial species. PCR products from E. amylovora and E. pyrifoliae cells at concentrations of 10⁴ cfu/ml and 10⁷ cfu/ml, respectively, were amplified, which demonstrated sufficient primer detection sensitivity. This primer set provides a simple molecular tool to distinguish between two types of bacterial diseases with similar symptoms.     

First Report of Erwinia amylovora Fire Blight in Belarus

Erwinia amylovora is a phytopathogenic bacterium that causes fire blight, an economically important disease of Rosaceae . Several isolates from pears and apples with fire blight symptoms from Belarus were identified as E. amylovora . All tested isolates were yellow and mucoid on MM2Cu medium, positive in levan production and showed pathogenicity in immature pear fruits. These isolates have identical total protein patterns with E. amylovora 1/79. The PCR with specific primers for E. amylovora harpin gene also gave positive results.     

Penicillin-binding proteins from Erwinia amylovora: mutants lacking PBP2 are avirulent.

Radiolabelled penicillin G was used to examine penicillin-binding proteins (PBPs) from Erwinia amylovora (OT1). This procedure identified seven PBPs with molecular masses ranging from 22 to 83 kDa. E. amylovora PBPs were compared with those from Escherichia coli (JM101) and from two spherical, avirulent TnphoA mutants derived from OT1. Radiolabelled penicillin G bound to only six proteins from the spherical mutants which lacked a 69-kDa PBP. The spherical mutants could be complemented by the cloned E. coli pbpA-rodA operon, which restored both cell shape and virulence to apple seedlings. This suggested that the E. amylovora 69-kDa PBP is probably the functional equivalent of the E. coli PBP2 protein. Southern blot analysis using the E. coli rodA and pbpA genes as radiolabelled probes showed that TnphoA had inserted into the E. amylovora equivalent of the E. coli rodA-pbpA operon. Southern blots to chromosomal DNAs of the two spherical mutants, using the cloned hrp and dsp genes from E. amylovora as radiolabelled probes, confirmed that the TnphoA insertions were not located in the region of the E. amylovora chromosome postulated to encode known virulence factors. Both of the spherical TnphoA mutants synthesized amounts of extracellular polysaccharide equivalent to those synthesized by the wild-type strain (OT1), were resistant to lysis in distilled water and to lysozyme, and elicited the hypersensitive response on nonhost plants. These results indicate a possible role for cell shape in the virulence of this plant pathogen.     

Molecular cloning of ompRS, a regulatory locus controlling production of outer membrane proteins in Erwinia carotovora subsp. carotovora

Summary A locus, ompRS, controlling synthesis of outer membrane proteins was cloned from Erwinia carotovora subsp. carotovora (Ecc) by complementation of an Escherichia coli ompR—envZ mutant. The Ecc ompRS locus was both structurally and functionally similar to the ompR—envZ operon controlling porin gene expression in E. coli as shown by DNA hybridization and complementation of E. coli ompR and envZ mutants. Furthermore, introduction of ompRS into E. coli (ompR—envZ) strains restored the osmoregulation of the major outer membrane protein genes ompC and ompF Maxicell analysis of ompRS-carrying plasmids suggested that proteins similar in size to the E. coli ompR and envZ gene products were encoded by the Ecc ompR and ompS genes, respectively. Introduction of an ompRS transposon mutant onto the Ecc chromosome by marker exchange mutagenesis showed that ompRS is essential for production of a major outer membrane porin in Ecc. This mutational defect could be complemented by clones carrying Ecc ompRS or E. coli ompR envZ. The lack of the porin did not, however, compromise the virulence of these Ecc mutants.     

The replication-recombination connection: insights from genomics

One amazing characteristic of DNA processing enzymes is their breakneck speed. However, considering the metabolic traffic on DNA, it is not surprising that accidents that interrupt the replication process and require immediate repair occur. Recombination is an example of a repair mechanism, and as a result of accidents, the arrested or broken fork becomes the recombination substrate. Repair proteins are on hand to assist at accident sites, but responses may be sensitive to conditions and depend on the organism. Genomics has been used to identify genetic clues that indicate the occurrence of accidents and to detect sites of recombination. DNA and protein features that may affect replication and recombination are examined and discussed.