bacLIFE: a user-friendly computational workflow for genome analysis and prediction of lifestyle-associated genes in bacteria.

Bacteria have an extensive adaptive ability to live in close association with eukaryotic hosts, exhibiting detrimental, neutral or beneficial effects on host growth and health. However, the genes involved in niche adaptation are mostly unknown and their functions poorly characterized. Here, we present bacLIFE ( https://github.

GacA reduces virulence and increases competitiveness in planta in the tumorigenic olive pathogen pv. savastanoi.

GacS/GacA is a widely distributed two-component system playing an essential role as a key global regulator, although its characterization in phytopathogenic bacteria has been deeply biased, being intensively studied in pathogens of herbaceous plants but barely investigated in pathogens of woody hosts. pv. savastanoi (Psv) is characterized by inducing tumours in the stem and branches of olive trees.

Allelic variation in the indoleacetic acid-lysine synthase gene of the bacterial pathogen and its role in auxin production.

Indole-3-acetic acid (IAA) production is a pathogenicity/virulence factor in the complex, including . pathovars (pvs.) genomes contain the gene, encoding an enzyme that catalyzes the biosynthesis of the less biologically active compound 3-indole-acetyl-ϵ-L-lysine (IAA-Lys).

Multiple relaxases contribute to the horizontal transfer of the virulence plasmids from the tumorigenic bacterium pv. savastanoi NCPPB 3335.

pv. savastanoi NCPPB 3335 is the causal agent of olive knot disease and contains three virulence plasmids: pPsv48A (pA), 80 kb; pPsv48B (pB), 45 kb, and pPsv48C (pC), 42 kb. Here we show that pB contains a complete MPF (previously type IVA secretion system) and a functional origin of conjugational transfer adjacent to a relaxase of the MOB family; pC also contains a functional -MOB array, whereas pA contains an incomplete MPF (previously type IVB secretion system), but not a recognizable .

Prevalence and Specificity of Chemoreceptor Profiles in Plant-Associated Bacteria.

Chemosensory pathways are among the most abundant prokaryotic signal transduction systems, allowing bacteria to sense and respond to environmental stimuli. Signaling is typically initiated by the binding of specific molecules to the igand inding omain (LBD) of hemoeceptor proteins (CRs). Although CRs play a central role in plant-microbiome interactions such as colonization and infection, little is known about their phylogenetic and ecological specificity.

HrpL Regulon of Bacterial Pathogen of Woody Host pv. NCPPB 3335.

The species comprises a group of phytopathogenic bacteria that cause symptoms of disease in woody hosts. This is mediated by the rapid activation of a pool of virulence factors that suppress host defences and hijack the host's metabolism to the pathogen's benefit. The gene encodes an essential transcriptional regulator of virulence functions, including the type III secretion system (T3SS), in pathogenic bacteria.

Synergistic interaction between the type III secretion system of the endophytic bacterium Pantoea agglomerans DAPP-PG 734 and the virulence of the causal agent of olive knot Pseudomonas savastanoi pv. savastanoi DAPP-PG 722.

The endophytic bacterium Pantoea agglomerans DAPP-PG 734 was previously isolated from olive knots caused by infection with Pseudomonas savastanoi pv. savastanoi DAPP-PG 722. Whole-genome analysis of this P.

The Rhizobacterium AVO110 Induces the Expression of Biofilm-Related Genes in Response to Exudates.

The rhizobacterium AVO110 exhibits antagonism toward the phytopathogenic fungus . This strain efficiently colonizes hyphae and is able to feed on their exudates. Here, we report the complete genome sequence of AVO110.

pv. pv. nov., a Clonal Pathogen Causing an Emerging, Devastating Disease of the Ornamental Plant spp.

Commercial production of the ornamental plant dipladenia ( spp.) is threatened by dipladenia leaf and stem spot disease, caused by the bacterium . includes four pathovars of woody hosts differentiated by a characteristic host range in olive, oleander, ash, and broom plants.

Two Homologues of the Global Regulator Csr/Rsm Redundantly Control Phaseolotoxin Biosynthesis and Virulence in the Plant Pathogen pv. phaseolicola 1448A.

The widely conserved Csr/Rsm (carbon storage regulator/repressor of stationary-phase metabolites) post-transcriptional regulatory system controls diverse phenotypes involved in bacterial pathogenicity and virulence. Here we show that pv. phaseolicola 1448A contains seven genes, four of which are chromosomal.

Genes and , Coding for Cytokinin Biosynthesis Enzymes, Are Essential for Tumorigenesis and Growth by pv. savastanoi NCPPB 3335.

The phytopathogenic bacterium pv. savastanoi elicits aerial tumors on olive plants and is also able to synthesize large amounts of auxins and cytokinins. The auxin indoleacetic acid was shown to be required for tumorigenesis, but there is only correlational evidence suggesting a role for cytokinins.

Host Range Determinants of Pathovars of Woody Hosts Revealed by Comparative Genomics and Cross-Pathogenicity Tests.

The study of host range determinants within the complex is gaining renewed attention due to its widespread distribution in non-agricultural environments, evidence of large variability in intra-pathovar host range, and the emergence of new epidemic diseases. This requires the establishment of appropriate model pathosystems facilitating integration of phenotypic, genomic and evolutionary data. pv.

A Na /Ca exchanger of the olive pathogen Pseudomonas savastanoi pv. savastanoi is critical for its virulence.

In a number of compatible plant-bacterium interactions, a rise in apoplastic Ca levels is observed, suggesting that Ca represents an important environmental clue, as reported for bacteria infecting mammalians. We demonstrate that Ca entry in Pseudomonas savastanoi pv. savastanoi (Psav) strain DAPP-PG 722 is mediated by a Na /Ca exchanger critical for virulence.

The toxic guardians - multiple toxin-antitoxin systems provide stability, avoid deletions and maintain virulence genes of virulence plasmids.

Background: is a γ-proteobacterium causing economically relevant diseases in practically all cultivated plants. Most isolates of this pathogen contain native plasmids collectively carrying many pathogenicity and virulence genes. However, is generally an opportunistic pathogen primarily inhabiting environmental reservoirs, which could exert a low selective pressure for virulence plasmids.

Response of the Biocontrol Agent Pseudomonas pseudoalcaligenes AVO110 to Rosellinia necatrix Exudate.

The rhizobacterium AVO110, isolated by the enrichment of competitive avocado root tip colonizers, controls avocado white root rot disease caused by Here, we applied signature-tagged mutagenesis (STM) during the growth and survival of AVO110 in fungal exudate-containing medium with the goal of identifying the molecular mechanisms linked to the interaction of this bacterium with A total of 26 STM mutants outcompeted by the parental strain in fungal exudate, but not in rich medium, were selected and named rowth-ttenuated utants (GAMs). Twenty-one genes were identified as being required for this bacterial-fungal interaction, including membrane transporters, transcriptional regulators, and genes related to the metabolism of hydrocarbons, amino acids, fatty acids, and aromatic compounds. The bacterial traits identified here that are involved in the colonization of fungal hyphae include proteins involved in membrane maintenance (a dynamin-like protein and ColS) or cyclic-di-GMP signaling and chemotaxis.

Quorum Sensing in Pseudomonas savastanoi pv. savastanoi and Erwinia toletana: Role in Virulence and Interspecies Interactions in the Olive Knot.

The olive knot disease ( L.) is caused by the bacterium pv. savastanoi.

Role of Cyclic di-GMP in the Bacterial Virulence and Evasion of the Plant Immunity.

Plant pathogenic bacteria are responsible for the loss of hundreds of millions of dollars each year, impacting a wide range of economically relevant agricultural crops. The plant immune system detects conserved bacterial molecules and deploys an arsenal of effective defense measures at different levels; however, during compatible interactions, some pathogenic bacteria suppress and manipulate the host immunity and colonize and infect the plant host. Different bacteria employ similar strategies to circumvent plant innate immunity, while other tactics are specific to certain bacterial species.

Knots Untie: Molecular Determinants Involved in Knot Formation Induced by in Woody Hosts.

The study of the molecular basis of tree diseases is lately receiving a renewed attention, especially with the emerging perception that pathogens require specific pathogenicity and virulence factors to successfully colonize woody hosts. Pathosystems involving woody plants are notoriously difficult to study, although the use of model bacterial strains together with genetically homogeneous micropropagated plant material is providing a significant impetus to our understanding of the molecular determinants leading to disease. The gammaproteobacterium belongs to the intensively studied complex, and includes three pathogenic lineages causing tumorous overgrowths (knots) in diverse economically relevant trees and shrubs.

Suppression of Plant Immune Responses by the pv. NCPPB 3335 Type III Effector Tyrosine Phosphatases HopAO1 and HopAO2.

The effector repertoire of the olive pathogen pv. NCPPB 3335 includes two members of the HopAO effector family, one of the most diverse T3E families of the complex. The study described here explores the phylogeny of these dissimilar members, HopAO1 and HopAO2, among the complex and reveals their activities as immune defense suppressors.

WHOP, a Genomic Region Associated With Woody Hosts in the Pseudomonas syringae Complex Contributes to the Virulence and Fitness of Pseudomonas savastanoi pv. savastanoi in Olive Plants.

Bacteria from the Pseudomonas syringae complex belonging to phylogroups 1 and 3 (PG1 and PG3, respectively) isolated from woody hosts share a genomic region herein referred to as WHOP (from woody host and Pseudomonas spp.), which is absent in strains infecting herbaceous organs. In this work, we show that this region is also encoded in P.

The use of stable and unstable green fluorescent proteins for studies in two bacterial models: Agrobacterium tumefaciens and Xanthomonas campestris pv. campestris.

Fluorescent proteins have been used to track plant pathogens to understand their host interactions. To be useful, the transgenic pathogens must present similar behaviour than the wild-type isolates. Herein, a GFP marker was used to transform two plant pathogenic bacteria, Agrobacterium and Xanthomonas, to localize and track the bacteria during infection.

Prediction of bacterial associations with plants using a supervised machine-learning approach.

Recent scenarios of fresh produce contamination by human enteric pathogens have resulted in severe food-borne outbreaks, and a new paradigm has emerged stating that some human-associated bacteria can use plants as secondary hosts. As a consequence, there has been growing concern in the scientific community about these interactions that have not yet been elucidated. Since this is a relatively new area, there is a lack of strategies to address the problem of food-borne illnesses due to the ingestion of fruits and vegetables.

Differential modulation of plant immune responses by diverse members of the Pseudomonas savastanoi pv. savastanoi HopAF type III effector family.

The Pseudomonas savastanoi pv. savastanoi NCPPB 3335 type III secretion system (T3SS) effector repertoire includes 33 candidates, seven of which translocate into host cells and interfere with plant defences. The present study was performed to investigate the co-existence of both plasmid- and chromosomal-encoded members of the HopAF effector family, HopAF1-1 and HopAF1-2, respectively, in the genome of NCPPB 3335.

Bioinformatics Analysis of the Complete Genome Sequence of the Mango Tree Pathogen Pseudomonas syringae pv. syringae UMAF0158 Reveals Traits Relevant to Virulence and Epiphytic Lifestyle.

The genome sequence of more than 100 Pseudomonas syringae strains has been sequenced to date; however only few of them have been fully assembled, including P. syringae pv. syringae B728a.