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      Draft Genome Sequence of Pseudomonas putida Strain GM4FR, an Endophytic Bacterium Isolated from Festuca rubra L.

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          ABSTRACT

          Pseudomonas putida GM4FR is an endophytic bacterium isolated from aerial plant tissues of Festuca rubra L. Functional annotation of the draft genome (7.1 Mb) revealed 6,272 predicted protein-encoding genes. The genome provides insights into the biocontrol and plant growth-promoting potential of P. putida GM4FR.

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          The multiple signaling systems regulating virulence in Pseudomonas aeruginosa.

          Pol Nadal Jimenez, Gudrun Koch, Jessica Thompson … (2012)
          Cell-to-cell communication is a major process that allows bacteria to sense and coordinately react to the fluctuating conditions of the surrounding environment. In several pathogens, this process triggers the production of virulence factors and/or a switch in bacterial lifestyle that is a major determining factor in the outcome and severity of the infection. Understanding how bacteria control these signaling systems is crucial to the development of novel antimicrobial agents capable of reducing virulence while allowing the immune system of the host to clear bacterial infection, an approach likely to reduce the selective pressures for development of resistance. We provide here an up-to-date overview of the molecular basis and physiological implications of cell-to-cell signaling systems in Gram-negative bacteria, focusing on the well-studied bacterium Pseudomonas aeruginosa. All of the known cell-to-cell signaling systems in this bacterium are described, from the most-studied systems, i.e., N-acyl homoserine lactones (AHLs), the 4-quinolones, the global activator of antibiotic and cyanide synthesis (GAC), the cyclic di-GMP (c-di-GMP) and cyclic AMP (cAMP) systems, and the alarmones guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp), to less-well-studied signaling molecules, including diketopiperazines, fatty acids (diffusible signal factor [DSF]-like factors), pyoverdine, and pyocyanin. This overview clearly illustrates that bacterial communication is far more complex than initially thought and delivers a clear distinction between signals that are quorum sensing dependent and those relying on alternative factors for their production.
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            Phylogenomics and systematics in Pseudomonas

            Margarita Gomila, Arantxa Peña, Magdalena Mulet … (2015)
            The genus Pseudomonas currently contains 144 species, making it the genus of Gram-negative bacteria that contains the largest number of species. Currently, multilocus sequence analysis (MLSA) is the preferred method for establishing the phylogeny between species and genera. Four partial gene sequences of housekeeping genes (16S rRNA, gyrB, rpoB, and rpoD) were obtained from 112 complete or draft genomes of strains related to the genus Pseudomonas that were available in databases. These genes were analyzed together with the corresponding sequences of 133 Pseudomonas type strains of validly published species to assess their correct phylogenetic assignations. We confirmed that 30% of the sequenced genomes of non-type strains were not correctly assigned at the species level in the accepted taxonomy of the genus and that 20% of the strains were not identified at the species level. Most of these strains had been isolated and classified several years ago, and their taxonomic status has not been updated by modern techniques. MLSA was also compared with indices based on the analysis of whole-genome sequences that have been proposed for species delineation, such as tetranucleotide usage patterns (TETRA), average nucleotide identity (ANIm, based on MUMmer and ANIb, based on BLAST) and genome-to-genome distance (GGDC). TETRA was useful for discriminating Pseudomonas from other genera, whereas ANIb and GGDC clearly separated strains of different species. ANIb showed the strongest correlation with MLSA. The correct species classification is a prerequisite for most diversity and evolutionary studies. This work highlights the necessity for complete genomic sequences of type strains to build a phylogenomic taxonomy and that all new genome sequences submitted to databases should be correctly assigned to species to avoid taxonomic inconsistencies.
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              Molecular and functional analysis of the TOL plasmid pWWO from Pseudomonas putida and cloning of genes for the entire regulated aromatic ring meta cleavage pathway.

              F C Franklin, M Bagdasarian, M M Bagdasarian … (1981)
              The genetic organization of the Pseudomonas putida plasmid pWWO-161, which encodes enzymes for the degradation of toluene and related aromatic hydrocarbons, has been investigated by transposition mutagenesis and gene cloning. Catabolic genes were localized to two clusters, one for upper pathway (hydrocarbon leads to carboxylic acid) enzymes and the other for lower pathway (carboxylic acid leads to tricarboxylic acid cycle) enzymes, that are separated by a 14-kilobase DNA segment. The physical organization of the catabolic genes thus reflects their functional organization into two regulatory blocks. The pWWO-161 DNA fragments Sst I fragment C and fragment D were cloned in a broad host range vector to produce plasmid pKT530. This hybrid encodes toluate oxygenase and all meta cleavage pathway enzymes, and it enables P. putida mt-2 and Escherichia coli K-12 cells to grow on m-toluate as sole carbon source. The pKT530 plasmid also carries xylS (a gene whose product has been postulated to regulate expression of the lower pathway genes) and the control sequences of the pathway that interact with this product, because catechol 2,3-oxygenase synthesis is specifically induced by m-toluate in both P. putida and E. coli. Evidence is presented that suggests the promoter operator of the meta pathway gene functions less effectively with the RNA polymerase or xylS product of E. coli than with the enzyme or product of P. putida.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Genome Announc
                Journal ID (iso-abbrev): Genome Announc
                Journal ID (hwp): ga
                Journal ID (pmc): ga
                Journal ID (publisher-id): GA
                Title: Genome Announcements
                Publisher: American Society for Microbiology (1752 N St., N.W., Washington, DC )
                ISSN (Electronic): 2169-8287
                Publication date (Electronic): 30 March 2017
                Publication date Collection: March 2017
                Volume: 5
                Issue: 13
                Electronic Location Identifier: e00086-17
                Affiliations
                [a ]Agricultural Entomology, Department of Crop Sciences, Georg-August University Göttingen, Göttingen, Germany
                [b ]Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, Germany
                Author notes
                Address correspondence to Franziska Wemheuer, fwemheu@ 123456gwdg.de .
                Author information
                http://orcid.org/0000-0002-2473-6202
                Article
                Publisher ID: genomeA00086-17
                DOI: 10.1128/genomeA.00086-17
                PMC ID: 5374236
                PubMed ID: 28360162
                SO-VID: d78efcf1-8262-414b-8c02-cb175a7f242d
                Copyright © Copyright © 2017 Wemheuer et al.
                License:

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                Date received : 24 January 2017
                Date accepted : 27 January 2017
                Page count
                Figures: 0, Tables: 0, Equations: 0, References: 20, Pages: 2, Words: 1415
                Funding
                Funded by: Niedersächsisches Ministerium für Wissenschaft und Kultur
                Award Recipient : Franziska Wemheuer
                Funded by: Niedersächsisches Vorab
                Award Recipient : Franziska Wemheuer
                Categories
                Subject: Prokaryotes
                Custom metadata
                cover-date March 2017

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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