Draft Genome Sequence of Micromonospora sp. Strain MW-13, a Bacterial Strain with Antibacterial Properties and Plant Growth Promotion Potential Isolated from the Rhizosphere of Wheat in Iran.

Jahanshah G, Miess H, Busche T, et al. Draft Genome Sequence of Micromonospora sp. Strain MW-13, a Bacterial Strain with Antibacterial Properties and Plant Growth Promotion Potential Isolated from the Rhizosphere of Wheat in Iran. Microbiology resource announcements. 2019;8(2): e01375-18

The antimicrobial compound xantholysin defines a new group of Pseudomonas cyclic lipopeptides

The rhizosphere isolate Pseudomonas putida BW11M1 produces a mixture of cyclic lipopeptide congeners, designated xantholysins. Properties of the major compound xantholysin A, shared with several other Pseudomonas lipopeptides, include antifungal activity and toxicity to Gram-positive bacteria, a supportive role in biofilm formation, and facilitation of surface colonization through swarming. Atypical is the lipopeptide’s capacity to inhibit some Gram-negative bacteria, including several xanthomonads. The lipotetradecadepsipeptides are assembled by XtlA, XtlB and XtlC, three co-linearly operating non-ribosomal peptide synthetases (NRPSs) displaying similarity in modular architecture with the entolysin-producing enzymes of the entomopathogenic Pseudomonas entomophila L48. A shifted serine-incorporating unit in the eight-module enzyme XtlB elongating the central peptide moiety not only generates an amino acid sequence differing at several equivalent positions from entolysin, but also directs xantholysin’s macrocyclization into an octacyclic structure, distinct from the pentacyclic closure in entolysin. Relaxed fatty acid specificity during lipoinitiation by XtlA (acylation with 3-hydroxydodec-5-enoate instead of 3-hydroxydecanoate) and for incorporation of the ultimate amino acid by XtlC (valine instead of isoleucine) account for the production of the minor structural variants xantholysin C and B, respectively. Remarkably, the genetic backbones of the xantholysin and entolysin NRPS systems also bear pronounced phylogenetic similarity to those of the P. putida strains PCL1445 and RW10S2, albeit generating the seemingly structurally unrelated cyclic lipopeptides putisolvin (undecapeptide containing a cyclotetrapeptide) and WLIP (nonapeptide containing a cycloheptapeptide), respectively. This similarity includes the linked genes encoding the cognate LuxR-family regulator and tripartite export system components in addition to individual modules of the NRPS enzymes, and probably reflects a common evolutionary origin. Phylogenetic scrutiny of the modules used for selective amino acid activation by these synthetases indicates that bacteria such as pseudomonads recruit and reshuffle individual biosynthetic units and blocks thereof to engineer reorganized or novel NRPS assembly lines for diversified synthesis of lipopeptides

Human germline heterozygous gain-of-function STAT6 variants cause severe allergic disease

STAT6 (signal transducer and activator of transcription 6) is a transcription factor that plays a central role in the pathophysiology of allergic inflammation. We have identified 16 patients from 10 families spanning three continents with a profound phenotype of early-life onset allergic immune dysregulation, widespread treatment-resistant atopic dermatitis, hypereosinophilia with esosinophilic gastrointestinal disease, asthma, elevated serum IgE, IgE-mediated food allergies, and anaphylaxis. The cases were either sporadic (seven kindreds) or followed an autosomal dominant inheritance pattern (three kindreds). All patients carried monoallelic rare variants in STAT6 and functional studies established their gain-of-function (GOF) phenotype with sustained STAT6 phosphorylation, increased STAT6 target gene expression, and TH2 skewing. Precision treatment with the anti-IL-4Rα antibody, dupilumab, was highly effective improving both clinical manifestations and immunological biomarkers. This study identifies heterozygous GOF variants in STAT6 as a novel autosomal dominant allergic disorder. We anticipate that our discovery of multiple kindreds with germline STAT6 GOF variants will facilitate the recognition of more affected individuals and the full definition of this new primary atopic disorder

Secondary metabolites of Pseudomonas putida and Pseudomonas fluorescens involved in antagonistic interactions with phylogenetically related plant-associated bacteria

Secondary metabolites of Pseudomonas putida and Pseudomonas fluorescens involved in antagonistic interactions with phylogenetically related plant-associated bacteria Several species of the genus Pseudomonas produce compounds with antimicrobial activity, targeting different microorganisms. Bacteriocins are used to kill related bacteria while antibiotics mediate inhibition of bacterial or fungal growth. In this work the objective was to identify novel antibacterial activities elaborated by non-pathogenic plant-associated fluorescent Pseudomonads against related phytopathogenic bacteria, focusing on a member of the Pseudomonas syringae group (Pseudomonas savastanoi, causative agent of olive knot disease) and pathogenic Xanthomonas species. Screening of a collection of Pseudomonas rhizosphere isolates for constitutive and inducible anti-P. savastanoi activity retained two strains for further characterization. Pseudomonas fluorescens SWRI196, a wheat rhizosphere isolate from Iran, exhibits an antagonistic activity that is not restricted to Pseudomonas species but also affects other g-proteobacteria as well as alfa- and ß-proteobacteria. Mutational analysis revealed a putative type-II polyketide system, with no known equivalent in other microorganisms, to be required for this antagonism. The corresponding biosynthetic gene cluster encodes components of a divergent polyketide synthase (PKS) linked to several putative tailoring genes and is associated with an acyl-homoserine lactone-responsive quorum sensing (QS) system. In addition, the Gac/Rsm signaling cascade is required as an additional regulatory system.Pseudomonas putida RW10S2, a rice rhizosphere isolate from Sri Lanka, displays both anti-Pseudomonas and -Xanthomonas activity which was shown to be achieved through different mechanisms. Antagonism against Pseudomonas is observed only when both producer and indicator are cocultured and also requires a functional Gac/Rsm system. This target-induced killing is specifically activated by QS via the RW10S2 Pmr system, producing and responding to 3-OH-C12-homoserine lactone. The pmr genes are part of an operon with seven orfs. Both this gene cluster and the P. fluorescens SWRI196 PKS-based gene cluster, contain genes with low homology to non-Pseudomonas genes, indicative of acquisition by horizontal gene transfer from other bacteria. In both cases, this precludes a reliable prediction of the chemical nature of the compounds synthesized, and structure elucidation will be imperative to resolve the biosynthetic functions of the respective genes. Using a different strategy, P. putida RW10S2 kills some Xanthomonas species by constitutive production of the cyclic lipopeptide WLIP (white line-inducing principle). Here also, global regulation involves the GacS/Rsm system and, in addition, a cognate non-QS type of LuxR family activator controls production. WLIP biosynthesis is performed by three non-ribosomal peptide synthetases (NRPSs), encoded by the wlp genes located in two separate genomic regions that equally carry genes for an export system and the dedicated LuxR-type regulator. One of these NRPS genes (wlpC) is also involved in mounting the inducible anti-P. savastanoi activity of P. putida RW10S2 but the mechanism behind this remains to be elucidated. In addition to its function as an antibacterial compound, WLIP contributes to proper biofilm formation and swarming, suggestive of a role in competitive solid surface colonization in structured environments. By characterization of the WLIP biosynthetic genes of P. fluorescens LMG 5329, a second WLIP-producing system (Wip) was identified, being clearly distinct from that of P. putida RW10S2 (Wlp). The Wlp components are more related to those of the putisolvin and entolysin systems, whereas a strong similarity exists between the Wip and viscosin systems.status: publishe

Assessing the impact of exact reads on reducing the error rate of read mapping

Abstract Background Nowadays, according to valuable resources of high-quality genome sequences, reference-based assembly methods with high accuracy and efficiency are strongly required. Many different algorithms have been designed for mapping reads onto a genome sequence which try to enhance the accuracy of reconstructed genomes. In this problem, one of the challenges occurs when some reads are aligned to multiple locations due to repetitive regions in the genomes. Results In this paper, our goal is to decrease the error rate of rebuilt genomes by resolving multi-mapping reads. To achieve this purpose, we reduce the search space for the reads which can be aligned against the genome with mismatches, insertions or deletions to decrease the probability of incorrect read mapping. We propose a pipeline divided to three steps: ExactMapping, InExactMapping, and MergingContigs, where exact and inexact reads are aligned in two separate phases. We test our pipeline on some simulated and real data sets by applying some read mappers. The results show that the two-step mapping of reads onto the contigs generated by a mapper such as Bowtie2, BWA and Yara is effective in improving the contigs in terms of error rate. Conclusions Assessment results of our pipeline suggest that reducing the error rate of read mapping, not only can improve the genomes reconstructed by reference-based assembly in a reasonable running time, but can also have an impact on improving the genomes generated by de novo assembly. In fact, our pipeline produces genomes comparable to those of a multi-mapping reads resolution tool, namely MMR by decreasing the number of multi-mapping reads. Consequently, we introduce EIM as a post-processing step to genomes reconstructed by mappers

Biocontrol of Pseudomonas savastanoi, causative agent of olive knot disease: antagonistic potential of non-pathogenic rhizosphere isolates of fluorescent Pseudomonas

status: publishe

Draft Genome Sequence of Pseudomonas gingeri Strain LMG 5327, the Causative Agent of Ginger Blotch in Agaricus bisporus

The draft genome sequence of Pseudomonas gingeri LMG 5327 (NCPPB 3146), the causative agent of ginger blotch in Agaricus bisporus, is reported. Together with another mushroom pathogen, Pseudomonas agarici, it belongs to a distinct phylogenomic group.status: publishe

Genetic and functional characterization of cyclic lipopeptide white-line-inducing principle (WLIP) production by rice rhizosphere isolate Pseudomonas putida RW10S2

The secondary metabolite mediating the GacS-dependent growth-inhibitory effect exerted by the rice rhizosphere isolate Pseudomonas putida RW10S2 on phytopathogenic Xanthomonas species was identified as white-line-inducing principle (WLIP), a member of the viscosin group of cyclic lipononadepsipeptides. WLIP producers are commonly referred to by the taxonomically invalid name “Pseudomonas reactans,” based on their capacity to reveal the presence of a nearby colony of Pseudomonas tolaasii by inducing the formation of a visible precipitate (“white line”) in agar medium between both colonies. This phenomenon is attributed to the interaction of WLIP with a cyclic lipopeptide of a distinct structural group, the fungitoxic tolaasin, and has found application as a diagnostic tool to identify tolaasin-producing bacteria pathogenic to mushrooms. The genes encoding the WLIP nonribosomal peptide synthetases WlpA, WlpB, and WlpC were identified in two separate genomic clusters (wlpR-wlpA and wlpBC) with an operon organization similar to that of the viscosin, massetolide, and entolysin biosynthetic systems. Expression of wlpR is dependent on gacS, and the encoded regulator of the LuxR family (WlpR) activates transcription of the biosynthetic genes and the linked export genes, which is not controlled by the RW10S2 quorum-sensing system PmrR/PmrI. In addition to linking the known phenotypes of white line production and hemolytic activity of a WLIP producer with WLIP biosynthesis, additional properties of ecological relevance conferred by WLIP production were identified, namely, antagonism against Xanthomonas and involvement in swarming and biofilm formation