Search

We present draft genome sequences for three strains of Xanthomonas species, each of which was associated with banana plants (Musa species) but is not closely related to the previously sequenced banana-pathogen Xanthomonas campestris pathovar musacearum. Strain NCPPB4393 had been deposited as Xanthomonas campestris pathovar musacearum but in fact falls within the species Xanthomonas sacchari. Strain NCPPB1132 is more distantly related to Xanthomonas sacchari whilst strain NCPPB 1131 grouped in a distinct species-level clade related to X. sacchari, along with strains from ginger, rice, cotton and sugarcane. These three newly sequenced strains share many genomic features with the previously sequenced Xanthomonas albilineans, for example possessing an unsual metE allele and lacking the Hrp type III secretion system. However, they are distinct from Xanthomonas albilineans in many respects, for example showing little evidence of genome reduction. They also lack the SPI-1 type III secretion system found in Xanthomonas albilineans. Unlike X. albilineans, all three strains possess a gum gene cluster. The data reported here provide the first genome-wide survey of non-Hrp Xanthomonas species other than Xanthomonas albilineans, which is an atypical member of this group. We hope that the availability of complete sequence data for this group of organisms is the first step towards understanding their interactions with plants and identifying potential virulence factors.

DNA-looping mediated by regulatory proteins is a ubiquitous mode of transcriptional control that allows interactions between genetic elements separated over long distances in DNA. In prokaryotes, one of the best-studied examples of regulatory proteins that use DNA-looping is the NtrC family of enhancer-binding proteins (EBPs), which activate transcription from sigmaN (sigma-N, sigma-54) dependent promoters. The completely sequenced genome of food-borne pathogen Salmonella enterica serovar Typhimurium LT2 contains seven novel EBPs of unknown function. Four of these EBPs have a similar domain organisation to NtrC whilst surprisingly the remaining three resemble LevR in Bacillus subtilis. Probable transcriptional targets are identified for each of the EBPs, including novel homologues of phosphotransferase system Enzyme II (EII) and several virulence-associated functions. Comparisons are made with the related enteric bacteria Salmonella Typhi, Escherichia coli and Yersinia pestis.

The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins in many Gram-negative pathogenic bacteria and its homologue in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma(54) containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. We show that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator. Interactions involving PspF and nucleotide are changed by the action of PspA. These changes and the complexes that form between PspF and PspA can explain how PspA exerts its negative effects upon transcription activated by PspF, and are of significance when considering how activities of other AAA(+) proteins might be controlled.

Sigma factor sigma(28) (sigma(F), FliA, SigD) directs RNA polymerase to transcribe the genes required for flagellar biosynthesis and chemotaxis in many bacteria, including Bacillus subtilis, Legionella pneumophila, Salmonella typhimurium, Escherichia coli, Yersinia enterolytica, Treponema maltophilum and Pseudomonas aeruginosa. Remarkably the fliA gene from the extreme thermophile Aquifex aeolicus restored motility to the E. coli mutant at relatively low temperature, albeit partially. This clearly demonstrates that A. aeolicus sigma(28) is able to direct RNA polymerase to E. coli sigma(28)-dependent promoters and take part in the complex interactions required to support transcription of the flagellar apparatus in vivo. The ability of A. aeolicus sigma(28) to function with mesophilic components shows that critical functional interactions made by these sigma factors are well conserved, and are not dependent upon high temperature. We over-produced and purified the sigma(28) protein and demonstrated binding to E. coli core RNA polymerase in vitro. In common with SigD from B. subtilis, but unlike most sigma factors, A. aeolicus sigma(28) showed DNA binding activity in vitro but there was no evidence of sequence specificity. We note that A. aeolicus sigma(28) is a good candidate for structural studies.

The special form of bacterial RNA polymerase (RNAP) containing alternative sigma factor ςN or ς54 (ςN-RNAP), initiates transcription by a mechanism quite distinct from RNAP containing the major ς70 sigma factor (35, 39, 48). Transcription initiation by ςN-RNAP requires the hydrolysis of nucleoside triphosphate, catalyzed by activator proteins bound to upstream activator sequences (enhancer elements). The mechanisms of regulation involving this form of RNAP are among the most sophisticated in bacteria (52). Since this novel form of RNAP was first recognized in enteric bacteria (25, 29, 47), ςN has been discovered in many other bacteria, including several proteobacteria, as well as in the gram-positive Bacillus subtilis (14) and in Planctomyces limnophila (36). Furthermore, ςN appears to be encoded by the genomes of the hyperthermophile Aquifex aeolicus (15), the spirochete Borrelia burgdorferi (18), and the obligate intracellular pathogens Chlamydia trachomatis (51) and Chlamydia pneumoniae (31). The ςN proteins from Klebsiella pneumoniae and Escherichia coli have been the subject of much genetic and biochemical analysis (e.g., see references 8, 20, and 23). Although considerable progress has been made towards understanding the mechanisms by which ςN performs its function, to date no high-resolution structural data are available for this system. Thermophilic homologues of mesophilic proteins have often been shown to be tractable for structural studies. For example, the crystal structures of the histidine kinase domain of CheA from Thermotoga maritima and the core RNAP from Thermus aquaticus have recently been elucidated (4, 57). The publication of the complete genome sequence (15) of A. aeolicus, a hyperthermophilic bacterium capable of growth at temperatures as high as 95°C, provides a potentially valuable resource for the study of thermostable proteins. A tRNA-binding protein has previously been purified from A. aeolicus (41), and Klenk et al. (33) have demonstrated activity and thermostability in the RNAP holoenzyme from its relative Aquifex pyrophilus. Characteristics of the hyperthermophile A. aeolicus pose important questions about the evolutionary origins and relationships of the bacteria. According to 16S ribosomal DNA (rDNA)-based phylogenies, the order Aquifecales (of which A. aeolicus is a member) represents the deepest branch of the bacterial evolutionary tree (7). Thus, it has been argued that by studying these organisms we can gain insights about the original bacterial ancestor. In particular, the hyperthermophilic nature of the deepest-branching organisms has been cited to support the hypothesis of a hyperthermophilic origin for the bacteria (1). However, several protein-based phylogenetic analyses, including that of the RNAP β and β′ subunits, have thrown into question the status of the Aquifecales as the deepest-branching group (e.g., see reference 33). Based on sequences of ς70 sigma factors, Aquifecales appears to be an early-branching member of the proteobacteria (22). In this paper we describe the heterologous overexpression and purification of the ςN and show its core RNAP-binding activity and sequence-specific DNA binding. We also purified a NifA-like protein from A. aeolicus and demonstrate activator-dependent transcription activity of a holoenzyme containing A. aeolicus ςN in vitro. We predict possible functions of the ςN-RNAP mode of transcription in A. aeolicus.

New sequencing methods have enabled the assembly of whole microbial genomes in a matter of days, greatly expanding the volume and scope of microbial sequencing efforts. This article reviews the current capabilities of the various high-throughput sequencing technologies and data analysis tools in the context of their application to microbial genomics. New sequencing methods generate data that can allow the assembly of microbial genome sequences in days. With such revolutionary advances in technology come new challenges in methodologies and informatics. In this article, we review the capabilities of high-throughput sequencing technologies and discuss the many options for getting useful information from the data.

The sigma(N) protein is an alternative sigma subunit of bacterial RNA polymerase. We investigated the role of a 12-amino-acid "tail" at the C-terminus of Klebsiella pneumoniae sigma(N), which was predicted to be largely surface-exposed and to be mostly loop (that is not alpha-helical or beta-strand). Deletion of this tail from N-terminal hexahistidine-tagged sigma(N) led to loss of sigma(N)-dependent transcription activity in vivo. We overexpressed and purified this deletion-mutant protein for in vitro characterization. The purified deleted protein showed decreased RNA polymerase core- and DNA-binding activities compared to the full-length protein and transcription activity was greatly impaired. Furthermore, evidence from circular dichroism and protease digestion experiments together suggested that deletion of the C-terminus tail resulted in a loss of conformational constraint in the protein. We discuss a possible structural role for the 12 amino acids at the C-terminus of sigma(N).

Summary: Recent developments in high-throughput sequencing technologies have generated considerable demand for tools to analyse large datasets of small RNA sequences. Here, we describe a suite of web-based tools for processing plant small RNA datasets. Our tools can be used to identify micro RNAs and their targets, compare expression levels in sRNA loci, and find putative trans-acting siRNA loci. Availability: The tools are freely available for use at http://srna-tools.cmp.uea.ac.uk Contact: vincent.moulton@cmp.uea.ac.uk

Summary: We report AtPRIMER, an application that automates the discovery of new polymorphic markers between ecotypes of Arabidopsis thaliana. On specifying two ecotypes and the genomic region of interest, the script retrieves all corresponding single nucleotide polymorphisms (SNPs) and generates CAPS and/or dCAPS PCR primer sequences. We show that AtPRIMER accurately found specific polymorphic markers for our linkage mapping project. AtPRIMER will therefore be useful for efficient marker development with high density and specificity.Availability: This PERL/CGI program is available for non-commercial users at http://www.AtPRIMER.tsl.ac.uk. The web-based version is available for public use at the same URL.Contact: adnane.nemri@tsl.ac.uk

Salicylidene acylhydrazides identified as inhibitors of virulence-mediating type III secretion systems (T3SSs) potentially target their inner membrane export apparatus. They also lead to inhibition of flagellar T3SS-mediated swimming motility in Salmonella enterica serovar. Typhimurium. We show that INP0404 and INP0405 act by reducing the number of flagella/cell. These molecules still inhibit motility of a Salmonella ΔfliH-fliI-fliJ/flhB((P28T)) strain, which lacks three soluble components of the flagellar T3S apparatus, suggesting that they are not the target of this drug family. We implemented a genetic screen to search for the inhibitors' molecular target(s) using motility assays in the ΔfliH-fliI/flhB((P28T)) background. Both mutants identified were more motile than the background strain in the absence of the drugs, although HM18 was considerably more so. HM18 was more motile than its parent strain in the presence of both drugs while DI15 was only insensitive to INP0405. HM18 was hypermotile due to hyperflagellation, whereas DI15 was not hyperflagellated. HM18 was also resistant to a growth defect induced by high concentrations of the drugs. Whole-genome resequencing of HM18 indicated two alterations within protein coding regions, including one within atpB, which encodes the inner membrane a-subunit of the F(O)F(1)-ATP synthase. Reverse genetics indicated that the alteration in atpB was responsible for all of HM18's phenotypes. Genome sequencing of DI15 uncovered a single A562P mutation within a gene encoding the flagellar inner membrane protein FlhA, the direct role of which in mediating drug insensitivity could not be confirmed. We discuss the implications of these findings in terms of T3SS export apparatus function and drug target identification.

Background Next-generation sequencing technologies allow researchers to obtain millions of sequence reads in a single experiment. One important use of the technology is the sequencing of small non-coding regulatory RNAs and the identification of the genomic locales from which they originate. Currently, there is a paucity of methods for finding small RNA generative locales. Results We describe and implement an algorithm that can determine small RNA generative locales from high-throughput sequencing data. The algorithm creates a network, or graph, of the small RNAs by creating links between them depending on their proximity on the target genome. For each of the sub-networks in the resulting graph the clustering coefficient, a measure of the interconnectedness of the subnetwork, is used to identify the generative locales. We test the algorithm over a wide range of parameters using RFAM sequences as positive controls and demonstrate that the algorithm has good sensitivity and specificity in a range of Arabidopsis and mouse small RNA sequence sets and that the locales it generates are robust to differences in the choice of parameters. Conclusions NiBLS is a fast, reliable and sensitive method for determining small RNA locales in high-throughput sequence data that is generally applicable to all classes of small RNA.

The NCD3G [for nine-cysteine domain of family 3 G-protein-coupled receptors (GPCRs)] domain is a novel protein domain that is conserved in family 3 GPCRs, including metabotropic glutamate receptors, calcium-sensing receptors, pheromone receptors and taste receptors, with the exception of GABA(B) receptors. The NCD3G domain contains nine highly conserved cysteine residues. Structural predictions suggest that NCD3G might possess four beta strands and three disulfide bridges. The structural model of NCD3G highlights the conserved residues co-segregated with certain familial diseases.

Streptomyces coelicolor is a bacterium with a vast repertoire of metabolic functions and complex systems of cellular development. Its genome sequence is rich in genes that encode regulatory proteins to control these processes in response to its changing environment. We wished to apply a recently published bioinformatic method for identifying novel regulatory sequence signals to gain new insights into regulation in S. coelicolor. The method involved production of position-specific weight matrices from alignments of over-represented words of DNA sequence. We generated 2497 weight matrices, each representing a candidate regulatory DNA sequence motif. We scanned the genome sequence of S. coelicolor against each of these matrices. A DNA sequence motif represented by one of the matrices was found preferentially in non-coding sequences immediately upstream of genes involved in polysaccharide degradation, including several that encode chitinases. This motif (TGGTCTAGACCA) was also found upstream of genes encoding components of the phosphoenolpyruvate phosphotransfer system (PTS). We hypothesise that this DNA sequence motif represents a regulatory element that is responsive to availability of carbon-sources. Other motifs of potential biological significance were found upstream of genes implicated in secondary metabolism (TTAGGTtAGgCTaACCTAA), sigma factors (TGACN19TGAC), DNA replication and repair (ttgtCAGTGN13TGGA), nucleotide conversions (CTACgcNCGTAG), and ArsR (TCAGN12TCAG). A motif found upstream of genes involved in chromosome replication (TGTCagtgcN7Tagg) was similar to a previously described motif found in UV-responsive promoters. We successfully applied a recently published in silico method to identify conserved sequence motifs in S. coelicolor that may be biologically significant as regulatory elements. Our data are broadly consistent with and further extend data from previously published studies. We invite experimental testing of our hypotheses in vitro and in vivo.

The transition metal molybdenum is essential for life. Escherichia coli imports this metal into the cell in the form of molybdate ions, which are taken up via an ABC transport system. In E. coli and other Proteobacteria molybdenum metabolism and homeostasis are regulated by the molybdate-responsive transcription factor ModE. Orthologues of ModE are widespread amongst diverse prokaryotes, but not ubiquitous. We identified probable ModE-binding sites upstream of genes implicated in molybdenum metabolism in green sulphur bacteria and methanogenic Archaea as well as in Proteobacteria. We also present evidence of horizontal transfer of nitrogen fixation genes between green sulphur bacteria and methanogenic Archaea. Whereas most of the archaeal helix-turn-helix-containing transcription factors belong to families that are Archaea-specific, ModE is unusual in that it is found in both Archaea and Bacteria. Moreover, its cognate upstream DNA recognition sequence is also conserved between Archaea and Bacteria, despite the fundamental differences in their core transcription machinery. ModE is the third example of a transcriptional regulator with a binding signal that is conserved in Bacteria and Archaea.

We wished to compare two databases based on sequence similarity: one that aims to be comprehensive in its coverage of known sequences, and one that specialises in a relatively small subset of known sequences. One of the motivations behind this study was quality control. Pfam is a comprehensive collection of alignments and hidden Markov models representing families of proteins and domains. MEROPS is a catalogue and classification of enzymes with proteolytic activity (peptidases or proteases). These secondary databases are used by researchers worldwide, yet their contents are not peer reviewed. Therefore, we hoped that a systematic comparison of the contents of Pfam and MEROPS would highlight missing members and false-positives leading to improvements in quality of both databases. An additional reason for carrying out this study was to explore the extent of consensus in the definition of a protein family. About half (89 out of 174) of the peptidase families in MEROPS overlapped single Pfam families. A further 32 MEROPS families overlapped multiple Pfam families. Where possible, new Pfam families were built to represent most of the MEROPS families that did not overlap Pfam. When comparing the numbers of sequences found in the overlap between a MEROPS family and its corresponding Pfam family, in most cases the overlap was substantial (52 pairs of MEROPS and Pfam families had an intersection size of greater than 75% of the union) but there were some differences in the sets of sequences included in the MEROPS families versus the overlapping Pfam families. A number of the discrepancies between MEROPS families and their corresponding Pfam families arose from differences in the aims and philosophies of the two databases. Examination of some of the discrepancies highlighted additional members of families, which have subsequently been added in both Pfam and MEROPS. This has led to improvements in the quality of both databases. Overall there was a great deal of consensus between the databases in definitions of a protein family.

Highlights • We generate a pilot library of 32 Z. tritici over-expression strains. • We develop a high throughput technique for in vitro phenotypic screening. • This protocol can probe both hyphal and budding Z. tritici morphologies. • A putative transcription factor impedes hyphal biosynthesis when over-expressed. • Genome wide functional analysis will enable discovery of novel virulence attributes., Targeted gene deletion has been instrumental in elucidating many aspects of Zymoseptoria tritici pathogenicity. Gene over-expression is a complementary approach that is amenable to rapid strain construction and high-throughput screening, which has not been exploited to analyze Z. tritici, largely due to a lack of available techniques. Here we exploit the Gateway® cloning technology for rapid construction of over-expression vectors and improved homologous integration efficiency of a Z. tritici Δku70 strain to build a pilot over-expression library encompassing 32 genes encoding putative DNA binding proteins, GTPases or kinases. We developed a protocol using a Rotor-HDA robot for rapid and reproducible cell pinning for high-throughput in vitro screening. This screen identified an over-expression strain that demonstrated a marked reduction in hyphal production relative to the isogenic progenitor. This study provides a protocol for rapid generation of Z. tritici over-expression libraries and a technique for functional genomic screening in this important pathogen.

Xanthomonas wilt, caused by Xanthomonas vasicola pv. musacearum (Xvm), formerly X. campestris pv. musacearum, is the most threatening and economically important disease of enset (Ensete ventricosum), the multipurpose food security crop orphan in south and southwestern Ethiopia. Xvm has also had a major impact on banana and plantain production in east Africa following its detection in Uganda in 2001 and subsequent spread. The only current effective control of this disease relies on integrated disease management strategies including minimizing field pathogen inoculum and deployment of wilt-resistant enset landraces. Identifying landraces with stable and durable Xvm resistance will greatly accelerate breeding programmes. While previous reports have identified landraces with varying degrees of tolerance to Xvm, no systematic study has collectively assessed their relative resistance. Here we undertook a detailed “common garden” analysis of 20 enset landraces previously reported to exhibit lower susceptibility to Xvm using an aggressive Xvm inoculum isolated from a disease hotspot area. Detailed longitudinal and survival analyses were applied to each landrace, using a combination of area-under-disease progress stairs, disease index and apparent infection rate to capture disease metrics as well as disease progression symptoms. Considerable variation was observed among the 20 landraces; however, none exhibited full immunity to Xvm infection. Landraces Haella,Mazia and Lemat showed the lowest susceptibility to Xvm as evidenced by reduced disease units and higher survival rates compared to the susceptible control landrace Arkiya, which exhibited the highest infection level and lowest survival rate, consistent with a high degree of susceptibility to Xvm. Thus, we have in this controlled experiment identified new material suitable for incorporation into future breeding programmes to develop Xvmresistant enset varieties.

Bacterial wilt, caused by Xanthomonas vasicola pv. musacearum (Xvm), formerly X. campestris pv. musacearum, is the most threatening and economically important disease of enset (Ensete ventricosum), the multipurpose food security crop orphan to south and southwestern Ethiopia. Xvm has also had a major impact on banana and plantain production in East Africa following its detection in Uganda in 2001 and subsequent spread. Effective control of this disease currently relies on integrated disease management (IDM) strategies including minimization of field pathogen inoculum and deployment of wilt resistant enset landraces. Identifying landraces with stable and durable Xvm resistance will greatly accelerate breeding of varieties that can be included as a component of IDM. In this study, 20 enset landraces previously reported to exhibit lower susceptibility to Xvm were grown in pots under open field conditions and inoculated with an aggressive Xvm inoculum isolated from a disease hotspot area. Longitudinal and survival analyses were applied to each landrace, based on disease units representing a combination of area-under-disease progress stairs, disease index and apparent infection rate. Considerable variation was observed among the 20 landraces; however, none exhibited full immunity to Xvm infection. Three landraces, viz. Hae’la, Mazia and Lemat (HML), showed lowest susceptibility to Xvm as evidenced by lower disease units and higher survival rates. Landraces Kuro, Gezewet, Bededet, and Alagena showed similar levels of Xvm infection as did HML, but with lower survival rates. By contrast, landrace Arkia showed the highest infection level and lowest survival rate, suggesting a high degree of susceptibility to Xvm. This study identifies new material that can be used in future breeding programmes to develop Xvm-resistant enset varieties.

It is imperative to identify highly polymorphic and tightly linked markers of a known trait for molecular marker-assisted selection. Potyvirus resistance 4 (Pvr4) locus in pepper confers resistance to three pathotypes of potato virus Y and to pepper mottle virus. We describe the use of next-generation sequencing technology to generate molecular markers tightly linked to Pvr4. Initially, comparative genomics was carried out, and a syntenic region of tomato on\ud chromosome ten was used to generate PCR-based markers and map Pvr4. Subsequently, the genomic sequence of pepper was used, and more than 5000 single-nucleotide variants (SNVs) were identified within the interval. In addition, we identified nucleotide binding site–leucine-rich repeat-type disease resistance genes within the interval. Several of these SNVs were converted to molecular markers desirable\ud for large-scale molecular breeding programmes.

Background Campylobacter jejuni and C. coli are human intestinal pathogens that are the most frequent causes of bacterial foodborne gastroenteritis in humans in the UK. In this study, we aimed to characterise the metabolic diversity of both C. jejuni and C. coli using a diverse panel of clinical strains isolated from the UK, Pakistan and Thailand, thereby representing both the developed and developing world. Our aim was to apply multi genome analysis and Biolog phenotyping to determine differences in carbon source utilisation by C. jejuni and C. coli strains. Results We have identified a core set of carbon sources (utilised by all strains tested) and a set that are differentially utilised for a diverse panel of thirteen C. jejuni and two C. coli strains. This study used multi genome analysis to show that propionic acid is utilised only by C. coli strains tested. A broader PCR screen of 16 C. coli strains and 42 C. jejuni confirmed the absence of the genes needed for propanoate metabolism. Conclusions From our analysis we have identified a phenotypic method and two genotypic methods based on propionic utilisation that might be applicable for distinguishing between C. jejuni and C. coli. Electronic supplementary material The online version of this article (doi:10.1186/s12866-014-0262-y) contains supplementary material, which is available to authorized users.

Background Pseudomonas syringae is a widespread bacterial pathogen that causes disease on a broad range of economically important plant species. Pathogenicity of P. syringae strains is dependent on the type III secretion system, which secretes a suite of up to about thirty virulence 'effector' proteins into the host cytoplasm where they subvert the eukaryotic cell physiology and disrupt host defences. P. syringae pathovar tabaci naturally causes disease on wild tobacco, the model member of the Solanaceae, a family that includes many crop species as well as on soybean. Results We used the 'next-generation' Illumina sequencing platform and the Velvet short-read assembly program to generate a 145X deep 6,077,921 nucleotide draft genome sequence for P. syringae pathovar tabaci strain 11528. From our draft assembly, we predicted 5,300 potential genes encoding proteins of at least 100 amino acids long, of which 303 (5.72%) had no significant sequence similarity to those encoded by the three previously fully sequenced P. syringae genomes. Of the core set of Hrp Outer Proteins that are conserved in three previously fully sequenced P. syringae strains, most were also conserved in strain 11528, including AvrE1, HopAH2, HopAJ2, HopAK1, HopAN1, HopI, HopJ1, HopX1, HrpK1 and HrpW1. However, the hrpZ1 gene is partially deleted and hopAF1 is completely absent in 11528. The draft genome of strain 11528 also encodes close homologues of HopO1, HopT1, HopAH1, HopR1, HopV1, HopAG1, HopAS1, HopAE1, HopAR1, HopF1, and HopW1 and a degenerate HopM1'. Using a functional screen, we confirmed that hopO1, hopT1, hopAH1, hopM1', hopAE1, hopAR1, and hopAI1' are part of the virulence-associated HrpL regulon, though the hopAI1' and hopM1' sequences were degenerate with premature stop codons. We also discovered two additional HrpL-regulated effector candidates and an HrpL-regulated distant homologue of avrPto1. Conclusion The draft genome sequence facilitates the continued development of P. syringae pathovar tabaci on wild tobacco as an attractive model system for studying bacterial disease on plants. The catalogue of effectors sheds further light on the evolution of pathogenicity and host-specificity as well as providing a set of molecular tools for the study of plant defence mechanisms. We also discovered several large genomic regions in Pta 11528 that do not share detectable nucleotide sequence similarity with previously sequenced Pseudomonas genomes. These regions may include horizontally acquired islands that possibly contribute to pathogenicity or epiphytic fitness of Pta 11528.