Joyce Elizabeth Loper

Oregon State University | OSU · College of Agricultural Sciences

Agrobacterium tumefaciens is unique in that it can facilitate the interkingdom transfer of DNA and genetically modify its plant host. While Agrobacterium has been coopted for use in the genetic modification of plants, it is also a major pathogen, causing crown gall disease in the nursery, orchard, and vineyard industries. Pathogenicity in Agrobacte...

Alkyne-containing natural products have been identified from plants, insects, algae, fungi, and bacteria. This class of natural products has been characterized as having a variety of biological activities. Polyynes are a subclass of acetylenic natural products that contain conjugated alkynes and are underrepresented in natural product databases due...

Alkyne containing natural products have been identified from plants, insects, algae, fungi, and bacteria. This class of natural products have been characterized as having a variety of biological activities. Polyynes are a sub-class of acetylenic natural products that contain conjugated alkynes and are underrepresented in natural product databases d...

Alkyne containing natural products have been identified from plants, insects, algae, fungi, and bacteria. This class of natural products have been characterized as having a variety of biological activities. Polyynes are a sub-class of acetylenic natural products that contain conjugated alkynes and are underrepresented in natural product databases d...

Alkyne containing natural products have identified from plants, insects, algae, fungi, and bacteria. This class of natural products have been characterized as having a variety of biological activities. Polyynes are a sub-class of acetylenic natural products that contain conjugated alkynes and are underrepresented in natural product databases due to...

Agrobacteria virulence writ large Plasmids are widespread among bacteria and are important because they spread virulence and antibiotic resistance traits, among others. They are horizontally transferred between strains and species, so it is difficult to work out their evolution and epidemiology. Agrobacteria, a diverse grouping of species that infe...

Pseudomonas putida is one of 13 major groups of Pseudomonas spp. and contains numerous species occupying diverse niches and performing many functions such as plant growth promotion and bioremediation. Here we compared a set of 19 P. putida isolates obtained from sugarcane rhizosphere or bulk soil using a population genomics approach aiming to asses...

Diabrotica virgifera virgifera LeConte, the western corn rootworm (WCR), is the most destructive pest of maize in North America, and has recently spread across central Europe. Its subterranean larval stages are hard to reach with pesticides and it has evolved resistance to conventional management practices. The application of beneficial soil organi...

Genome mining of the Gram-negative bacterium Pseudomonas fluorescens Pf0-1 showed that the strain possesses a silent NRPS-based biosynthetic gene cluster encoding a new lipopeptide; its activation required the repair of the global regulator system. In this paper, we describe the genomics-driven discovery and characterization of the associated secon...

Bulk soil and rhizosphere are soil compartments selecting different microbial communities. However, it is unknown whether this selection also can change the genome content of specific bacterial taxa, splitting a population in distinct ecotypes. To answer this question we compared the genome sequences of 53 isolates obtained from sugarcane rhizosphe...

Pseudomonas is a large and diverse genus of Gammaproteobacteria. To provide a framework for discovery of evolutionary and taxonomic relationships of these bacteria, we compared the genomes of type strains of 163 species and 3 additional subspecies of Pseudomonas, including 118 genomes sequenced herein. A maximum likelihood phylogeny of the 166 type...

Secondary metabolites are synthesized by many microorganisms and provide a fitness benefit in the presence of competitors and predators. Secondary metabolism also can be costly, as it shunts energy and intermediates from primary metabolism. In Pseudomonas spp., secondary metabolism is controlled by the GacS-GacA global regulatory system. Intriguing...

Fluorescent Pseudomonas spp. are widely studied for their beneficial activities to plants. To explore the genetic diversity of Pseudomonas spp. in tropical regions, we collected 76 isolates from a Brazilian soil. Genomes were sequenced and compared to known strains, mostly collected from temperate regions. Phylogenetic analyses classified the isola...

Many microorganisms compete for extracellular iron using strain-specific chelators known as siderophores. The ferric-siderophore complex limits local access to iron because import requires a suitable cognate receptor. Interestingly, many species carry receptors that enable "cross-feeding" on heterologous siderophores made by neighboring organisms,...

Expression of pltL::gfp by SBW25 containing pRL-gfp in response to extracts from in vitro reactions.EM-1# to −6# refers to extracts from each in vitro reaction with the components shown.DOI: http://dx.doi.org/10.7554/eLife.22835.014

Expression of pltL::gfp by SBW25 containing pMRL-gfp in response to PG and compounds with similar structures to PG.DOI: http://dx.doi.org/10.7554/eLife.22835.017

Expression of pltL::gfp by Pf-5 wild-type (WT) and its derivatives in response to PG and/or pyoluteorin.DOI: http://dx.doi.org/10.7554/eLife.22835.005

Expression of pltL::gfp and the production of pyoluteorin by Pf-5 wild-type (WT) and its derivatives in response to chlorinated phloroglucinols.DOI: http://dx.doi.org/10.7554/eLife.22835.023

Expression of pltL::gfp by SBW25 containing pL-gfp or pRL-gfp in response to chlorinated phloroglucinols.DOI: http://dx.doi.org/10.7554/eLife.22835.025

Growth of Erwinia amylovora in response to pyoluteorin and DAPG.DOI: http://dx.doi.org/10.7554/eLife.22835.030

Expression of pltL::gfp and production of pyoluteorin by the ΔpltM mutant of Pf-5 in response to chlorinated phloroglucinols.The production of MAPG and DAPG is also shown.DOI: http://dx.doi.org/10.7554/eLife.22835.019

Expression of pltL::gfp by SBW25 and Pf-5 in response to phloroglucinol (PG) and Pf-5 culture supernatants.(A) Expression of pltL::gfp by SBW25 containing pRL-gfp. (B) Expression of pltL::gfp by Pf-5 wild-type (WT) and the ΔpltM mutant that contains pL-gfp. (C) Expression of pltL::gfp by SBW25 containing pMRL-gfp.DOI: http://dx.doi.org/10.7554/eLif...

Concentration of pyoluteorin, MAPG and DAPG (µM) in cultures of Pf-5 wild-type (WT) and its derivatives.DOI: http://dx.doi.org/10.7554/eLife.22835.010

Toxicity of PG-Cl and PG-Cl2 to P. fluorescens SBW25.PG-Cl and PG-Cl2 were tested at different concentrations as indicated. 0 means methanol was added to the cultures as a control.DOI: http://dx.doi.org/10.7554/eLife.22835.021

Expression of pltL::gfp by SBW25 in response to extracts of wild-type Pf-5 cultures.Pf-5 wild-type was cultured for different times, as indicated. The culture extracts were tested by SBW25 containing pRL-gfp.DOI: http://dx.doi.org/10.7554/eLife.22835.028

Pantoea vagans strain C9-1 is an effective biological control agent for fire blight of pear and apple. C9-1 carries three circular plasmids: pPag1 (168 kb), pPag2 (166 kb), and pPag3 (530 kb). Of these, pPag3 was proposed to contribute to epiphytic fitness. We cured C9-1 of pPag2 and pPag3, individually and together, and compared phenotypes of the...

The histidine-reversible antibiotic pantocin A is produced by Pantoea vagans strain C9-1 and Pantoea agglomerans strains Eh252, EH318 and P10c and contributes significantly to efficacy of biological control of fire blight of pear and apple flowers caused by Erwinia amylovora. Antibiosis by pantocin A is observed on solidified defined media, such as...

Ten strains representing four lineages of the Pseudomonas fluorescens group (P. chlororaphis, P. corrugata, P. koreensis, and P. fluorescens subgroups) were evaluated for toxicity to the tobacco hornworm Manduca sexta and the common fruit fly Drosophila melanogaster. The three strains within the P. chlororaphis subgroup exhibited both oral and inje...

Lethality of strains in the P. fluorescens group to the tobacco hornworm, M. sexta, post-injection. Lethality of strains in the P. fluorescens group to fifth instar of the tobacco hornworm, M. sexta. Mortality was assessed at 24h (?), 48h (?), or 72h (?) following injection with ca. 5 log(CFU per larva) or water, as a control. Three experiments (A,...

All tcaA/tcdA-like gene products have the VRP1 (PF03538) domain. (DOC)

Unrooted distance-based phylogeny of toxin complex (Tc) A components. The A-component tree contains seven TcaA sequences, seven TcaB sequences, and one TcdA sequence from the ten strains within the P. fluorescens group examined in this study (shown in red font) as well as BLASTP hits with greater than 75% query coverage and 50% identity to one or m...

Unrooted distance-based phylogeny of toxin complex (Tc) B components. The B component tree contains eight TcaC sequences and one TcdB sequence from the ten strains within the P. fluorescens group examined in this study (shown in red font) as well as BLASTP hits with greater than 75% query coverage and 50% identity to one or more of these sequences....

Unrooted distance-based phylogeny of toxin complex (Tc) C components. The C-component tree contains 15 TccC sequences from the ten strains within the P. fluorescens group examined in this study (shown in red font) as well as BLASTP hits with greater than 75% query coverage and 50% identity to one or more of these sequences. The tree also includes a...

All tccC-like gene products have RhsA (COG3209) and Rhs-core (TIGR03696) domains. (DOC)

Oral toxicity of strains in the P. fluorescens group to the tobacco hornworm, M. sexta. Cumulative mortality of M. sexta was assessed by counting the number of dead larvae at 2 d (?), 4 d (?) and 6 d (?) after larvae were placed on tomato leaves supporting epiphytic populations of the specified bacterial strain. Strain Pf0-1 gacA+ (also called LK19...

Summary of experiments evaluating mortality of D. melanogaster. (DOC)

Lethality of strains in the P. fluorescens group to the tobacco hornworm, M. sexta, post-injection. Lethality of high cell densities of strains in the P. fluorescens group to fifth instar of the tobacco hornworm, M. sexta. Mortality was assessed at 24h (?), 48h (?), or 72h (?) following injection with ca. 6 log(CFU per larva) or water, as a control...

Developmental time course of D. melanogaster after ingestion of strains in the A) P. chlororaphis, B) P. koreensis or P. corrugata, or C) P. fluorescens subgroups. Second instar larvae were fed with a yeast suspension having no bacteria (black) or amended with bacterial strains. Initial population sizes of bacterial strains [log (CFU/plate)] are sh...

All tcaC/tcdB-like gene products have SpvB (PF03534) and MidN/MidC (PF12255) domains. (DOC)

Accession numbers for housekeeping genes of type strains in the Pseudomonas fluorescens group used in phylogenetic analysis. (DOC)

Pseudomonas protegens Pf-5 (formerly Pseudomonas fluorescens) is a biocontrol bacterium that produces the siderophore enantio-pyochelin under conditions of iron starvation in a process that is often accompanied by the secretion of its biosynthesis intermediates, salicylic acid and dihydroaeruginoic acid. In this study, we investigated whether sever...

Transmembrane topology predictions of the transporters of interest performed with HMMTOP version 2.0 for (A) pchH, (B) fetF and (C) PFL_3504. Visuals were generated using TMRPres2D (Spyropoulos et al., 2004). (TIF)

Optical densities depicting pyoverdine levels in supernatants derived from P. protegens strains as measured at 403 nm. Error bars represent standard deviations between three biological replicates. (TIF)

Primers for construction of complementary plasmids. (DOCX)

Primers in qRT-PCR experiments. (DOCX)

Primers for allelic exchange mutagenesis of transporter genes. (DOCX)

Primers for verification of transporter gene truncations. (DOCX)

Tests in Phenotypes microarray that showed differential respiratory kinetics between wild-type and mutant strains. (XLSX)

Confirmation of transporter gene truncations with PCR. Amplifications on gene of interests were performed using primers (A) PFL_3495-SK-F/R, (B) PFL_3503-SK-F/R and (C) PFL_3504-SK-F/R. PCR products were run on 1% TBE agarose gel. M: marker; -ve: negative control; WT: P. protegens Pf-5 wild-type; ΔpchH: P. protegens ΔpchH strain containing 1209 bp...

The profiles of Phenotype Microarray of P. protegens wild-type (WT) versus mutant strains (ΔpchH, ΔfetF and Δ3504) as tested using PM plates 09-13B (A), 14A-18C (B) and 19-20B (C). The figure depicts wells from the microarray plates (PM09-20) where red and green areas represent the respiratory kinetics for wild-type and mutant strains respectively,...

Pseudomonas protegens strain Pf-5 is a soil bacterium that was first described for its capacity to suppress plant diseases and has since been shown to be lethal to certain insects. Among these is the common fruit fly Drosophila melanogaster, a well-established model organism for studies evaluating the molecular and cellular basis of the immune resp...

The soil bacterium Pseudomonas protegens Pf-5 can colonize root and seed surfaces of many plants, protecting them from infection by plant pathogenic fungi and oomycetes. The capacity to suppress disease is attributed to Pf-5's production of a large spectrum of antibiotics, which is controlled by complex regulatory circuits operating at the transcri...

From a screen of 36 plant-associated strains of Burkholderia spp., we identified 24 strains that suppressed leaf and pseudobulb necrosis of orchid caused by B. gladioli. To gain insights into the mechanisms of disease suppression, we generated a draft genome sequence from one suppressive strain, TC3.4.2R3. The genome is an estimated 7.67 megabases...

Swarming motility is a flagella-driven multicellular behavior that allows bacteria to colonize new niches and escape competition. Here, we investigated the evolution of specific mutations in the GacS/GacA two-component regulatory system in swarming colonies of Pseudomonas protegens Pf-5. Experimental evolution assays showed that repeated rounds of...

Pseudomonas protegens strain Pf-5 is a rhizosphere bacterium that suppresses soilborne plant diseases and produces at least seven different secondary metabolites with antifungal properties. We derived site-directed mutants of Pf-5 with single and multiple mutations in biosynthesis genes for all seven antifungal metabolites: 2,4-diacetylphoroglucino...

Bacteria can be both highly communicative and highly competitive in natural habitats and antibiotics are thought to play a role in both of these processes. The soil bacterium Pseudomonas protegens Pf-5 produces a spectrum of antibiotics, two of which, pyoluteorin and 2,4-diacetylphloroglucinol (DAPG), function in intracellular and intercellular com...

Pseudomonas spp. are prolific producers of natural products from many structural classes. Here we show that the soil bacterium Pseudomonas protegens Pf-5 is capable of producing trace levels of the triazine natural product toxoflavin (1) under microaerobic conditions. We evaluated toxoflavin production by derivatives of Pf-5 having deletions in spe...

In the summer (January to March) of 2002 and 2003, leaves and pseudobulbs of Oncidium spp. grown in a commercial orchid nursery in Mogi das Cruzes, SP in southeastern Brazil presented symptoms similar to those already described in orchids infected by Burkholderia gladioli (Keith et al. 2005; Malavolta 1998). These nursery presented temperature and...

The rhizobacterium Pseudomonas fluorescens SS101 inhibits growth of oomycete and fungal pathogens, and induces resistance in plants against pathogens and insects. To unravel regulatory pathways of secondary metabolite production in SS101, we conducted a genome-wide search for sRNAs and performed transcriptomic analyses to identify genes associated...

Members of Gram-positive Actinobacteria cause economically important diseases to plants. Within the Rhodococcus genus, some members can cause growth deformities and persist as pathogens on a wide range of host plants. The current model predicts that phytopathogenic isolates require a cluster of three loci present on a linear plasmid, with the fas o...

Bacteria in the diverse P. fluorescens group include rhizosphere inhabitants known for their antifungal metabolite production and biological control of plant disease, such as Pseudomonas protegens Pf-5, and mushroom pathogens such as Pseudomonas tolaasii. Here, we report that strain Pf-5 causes brown, sunken lesions on peeled caps of the button mus...

Transcriptome analysis of Pseudomonas fluorescens SBW25 showed that 702 genes were differentially regulated in a gacS::Tn5 mutant, with 300 and 402 genes up- and downregulated respectively. Similar to the Gac regulon of other Pseudomonas species, genes involved in motility, biofilm formation, siderophore biosynthesis and oxidative stress were diffe...

Conjugative plasmids are known to facilitate the acquisition and dispersal of genes contributing to the fitness of Pseudomonas spp. Here, we report the characterization of pA506, the 57-kb conjugative plasmid of Pseudomonas fluorescens A506, a plant epiphyte used in the United States for the biological control of fire blight disease of pear and app...

Tannins are a diverse group of plant-produced, polyphenolic compounds with metal-chelating and antimicrobial properties that are prevalent in many soils. Using transcriptomics, we determined that tannic acid, a form of hydrolysable tannin, broadly affects the expression of genes involved in iron and zinc homeostases, sulfur metabolism, biofilm form...

Gene expression profiles of the biological control strain Pseudomonas protegens Pf-5 inhabiting pea seed surfaces were revealed using a whole-genome oligonucleotide microarray. We identified genes expressed by Pf-5 under the control of two global regulators (GacA and RpoS) known to influence biological control and secondary metabolism. Transcript l...

The soil bacterium Pseudomonas protegens Pf-5 (previously called P. fluorescens Pf-5) produces two siderophores, enantio-pyochelin and a compound in the large and diverse pyoverdine family. Using high-resolution mass spectroscopy, we determined the structure of the pyoverdine produced by Pf-5. In addition to producing its own siderophores, Pf-5 als...

Zinc is an important nutrient but can be lacking in some soil environments, influencing the physiology of soil-dwelling bacteria. Hence, we studied the global effect of zinc limitation on the transcriptome of the rhizosphere biocontrol strain Pseudomonas protegens Pf-5 (formerly Pseudomonas fluorescens). We observed that the expression of the putat...

We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in thre...

We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in thre...