Modulation of Quorum Sensing in Acylhomoserine Lactone-Producing or -Degrading Tobacco Plants Leads to Alteration of Induced Systemic Resistance Elicited by the Rhizobacterium Serratia marcescens 90-166.

Numerous root-associated bacteria (rhizobacteria) are known to elicit induced systemic resistance (ISR) in plants. Bacterial cell-density-dependent quorum sensing (QS) is thought to be important for ISR. Here, we investigated the role of QS in the ISR elicited by the rhizobacterium, Serratia marcescens strain 90-166, in tobacco.

Two volatile organic compounds trigger plant self-defense against a bacterial pathogen and a sucking insect in cucumber under open field conditions.

Systemic acquired resistance (SAR) is a plant self-defense mechanism against a broad-range of pathogens and insect pests. Among chemical SAR triggers, plant and bacterial volatiles are promising candidates for use in pest management, as these volatiles are highly effective, inexpensive, and can be employed at relatively low concentrations compared with agrochemicals. However, such volatiles have some drawbacks, including the high evaporation rate of these compounds after application in the open field, their negative effects on plant growth, and their inconsistent levels of effectiveness.

Design and development of synthetic microbial platform cells for bioenergy.

The finite reservation of fossil fuels accelerates the necessity of development of renewable energy sources. Recent advances in synthetic biology encompassing systems biology and metabolic engineering enable us to engineer and/or create tailor made microorganisms to produce alternative biofuels for the future bio-era. For the efficient transformation of biomass to bioenergy, microbial cells need to be designed and engineered to maximize the performance of cellular metabolisms for the production of biofuels during energy flow.

One shot-two pathogens blocked: exposure of Arabidopsis to hexadecane, a long chain volatile organic compound, confers induced resistance against both Pectobacterium carotovorum and Pseudomonas syringae.

Bacteria and plant derived volatile organic compounds have been reported as the chemical triggers that elicit induced resistance in plants. Previously, volatile organic compounds (VOCs), including acetoin and 2,3-butanediol, were found to be emitted from plant growth-promoting rhizobacteria (PGPR) Bacillus subtilis GB03, which had been shown to elicit ISR and plant growth promotion. More recently, we reported data that stronger induced resistance could be elicited against Pseudomonas syringae pv maculicola ES4326 in plants exposed to C13 VOC from another PGPR Paenibacillus polymyxa E681 compared with that of strain GB03.

Development of a genome-wide random mutagenesis system using proofreading-deficient DNA polymerase δ in the methylotrophic yeast Hansenula polymorpha.

The thermotolerant methylotrophic yeast Hansenula polymorpha is attracting interest as a potential strain for the production of recombinant proteins and biofuels. However, only limited numbers of genome engineering tools are currently available for H. polymorpha.

Transcriptome analysis of xylose metabolism in the thermotolerant methylotrophic yeast Hansenula polymorpha.

The thermotolerant methylotrophic yeast Hansenula polymorpha is able to grow at elevated temperature up to 48 °C as one of a few yeast strains which are naturally capable of alcoholic fermentation of xylose, a pentose sugar abundant in lignocellulosic biomass. However, the current level of ethanol production from xylose by H. polymorpha is still very low compared to those of other xylose-fermenting strains.

Chryseobacterium kwangjuense sp. nov., isolated from pepper (Capsicum annuum L.) root.

The yellow-pigmented, Gram-stain-negative, rod-shaped bacterium KJ1R5(T) was isolated from the root of a pepper plant grown in a field in Kwangju, Korea. Strain KJ1R5(T) was characterized by physiological, biochemical, and molecular genetic analyses. Phylogenetic analyses based on 16S rRNA gene sequences showed that strain KJ1R5(T) was most closely related to members of the genus Chryseobacterium, and that the strain exhibited the highest similarities with type strains of Chryseobacterium vrystaatense (97.

Genomic makeup of the marine flavobacterium Nonlabens (Donghaeana) dokdonensis and identification of a novel class of rhodopsins.

Rhodopsin-containing marine microbes such as those in the class Flavobacteriia play a pivotal role in the biogeochemical cycle of the euphotic zone (Fuhrman JA, Schwalbach MS, Stingl U. 2008. Proteorhodopsins: an array of physiological roles? Nat Rev Microbiol.

Induced resistance by a long-chain bacterial volatile: elicitation of plant systemic defense by a C13 volatile produced by Paenibacillus polymyxa.

Background: Some strains of plant growth-promoting rhizobacteria (PGPR) elicit induced systemic resistance (ISR) by emission of volatile organic compounds (VOCs) including short chain alcohols, acetoin, and 2,3-butanediol. The objective of this study was to evaluate whether species-specific VOCs from PGPR strain Paenibacillus polymyxa E681 can promote growth and induce resistance in Arabidopsis.

Methodology/principal Findings: The efficacy of induction was strain-specific, with stronger protection against Pseudomonas syringae pv.

Genome sequence of the thermotolerant yeast Kluyveromyces marxianus var. marxianus KCTC 17555.

Kluyveromyces marxianus is a thermotolerant yeast that has been explored for potential use in biotechnological applications, such as production of biofuels, single-cell proteins, enzymes, and other heterologous proteins. Here, we present the high-quality draft of the 10.9-Mb genome of K.

Genome-wide enrichment screening reveals multiple targets and resistance genes for triclosan in Escherichia coli.

Triclosan is a widely used biocide effective against different microorganisms. At bactericidal concentrations, triclosan appears to affect multiple targets, while at bacteriostatic concentrations, triclosan targets FabI. The site-specific antibiotic-like mode-of-action and a widespread use of triclosan in household products claimed to possibly induce cross-resistance to other antibiotics.

Draft genome sequence of Bacillus oceanisediminis 2691.

Bacillus oceanisediminis 2691 is an aerobic, Gram-positive, spore-forming, and moderately halophilic bacterium that was isolated from marine sediment of the Yellow Sea coast of South Korea. Here, we report the draft genome sequence of B. oceanisediminis 2691 that may have an important role in the bioremediation of marine sediment.

Draft genome sequence of Bacillus endophyticus 2102.

Bacillus endophyticus 2102 is an endospore-forming, plant growth-promoting rhizobacterium isolated from a hypersaline pond in South Korea. Here we present the draft sequence of B. endophyticus 2102, which is of interest because of its potential use in the industrial production of algaecides and bioplastics and for the treatment of industrial textile effluents.

A novel fluorescent reporter system for monitoring and identifying RNase III activity and its target RNAs.

Bacteriophage vectors for achieving single-copy gene expression linked to a colorigenic reporter assay have been used successfully for genetic screening applications. However, the limited number of cloning sites in these vectors, combined with the requirement for lac- strains and the time- and/or media-dependence of the chemical-based colorimetric reaction, have limited the range of applications for these vectors. An alternative approach using a fluorescent reporter gene such as green fluorescent protein (GFP) or GFP derivatives could overcome some of these technical issues and facilitate real-time monitoring of promoter and/or protein activity.

Probing the ArcA regulon in the rumen bacterium Mannheimia succiniciproducens by genome-wide expression profiling.

In this study, the putative target genes of the Arc two-component system of the rumen bacterium Mannheimia succiniciproducens were determined by analyzing the transcriptome of the ArcA overexpression strain and by the in silico scanning of the entire genome sequence with the position weight matrix of the ArcA binding sequence developed for Escherichia coli. The majority of 79 repressed genes were involved in energy metabolism and carbohydrate transport and metabolism, while the majority of 82 induced genes were involved in hypothetical or unknown functions. Our results suggest that the Arc system in M.

Complete genome sequence of the probiotic bacterium Bifidobacterium bifidum strain BGN4.

Bifidobacterium bifidum, a common endosymbiotic inhabitant of the human gut, is considered a prominent probiotic microorganism that may promote health. We completely decrypted the 2.2-Mb genome sequence of B.

Complete genome sequence of the endophytic bacterium Burkholderia sp. strain KJ006.

Endophytes live inside plant tissues without causing any harm and may even benefit plants. Here, we provide the high-quality genome sequence of Burkholderia sp. strain KJ006, an endophytic bacterium of rice with antifungal activity.

Draft genome sequence of the plant growth-promoting bacterium Bacillus siamensis KCTC 13613T.

Bacillus siamensis KCTC 13613(T), a novel halophilic Bacillus species isolated from a salted Thai food, produced antimicrobial compounds against plant pathogens and promoted plant growth by volatile emission. We determined the 3.8-Mb genome sequence of B.

Genome sequence of the plant growth-promoting rhizobacterium Bacillus sp. strain JS.

Volatile and nonvolatile compounds emitted from the plant growth-promoting rhizobacterium Bacillus sp. strain JS enhance the growth of tobacco and lettuce. Here, we report the high-quality genome sequence of this bacterium.

Genome sequence of the leaf-colonizing Bacterium Bacillus sp. strain 5B6, isolated from a cherry tree.

Plant growth-promoting bacteria colonize various habitats, including the phyllosphere. Here, we present the high-quality draft genome sequence of Bacillus sp. strain 5B6, which was isolated from the leaf of a cherry tree.

Genome sequence of the Shiga toxin-producing Escherichia coli strain NCCP15657.

Shiga toxin-producing Escherichia coli causes bloody diarrhea and hemolytic-uremic syndrome and serious outbreaks worldwide. Here, we report the draft genome sequence of E. coli NCCP15657 isolated from a patient.

Genome sequence of enterohemorrhagic Escherichia coli NCCP15658.

Enterohemorrhagic Escherichia coli causes severe food-borne disease in the guts of humans and animals. Here, we report the high-quality draft genome sequence of E. coli NCCP15658 isolated from a patient in the Republic of Korea.

Genome sequence of the hemolytic-uremic syndrome-causing strain Escherichia coli NCCP15647.

Enterohemorrhagic Escherichia coli (EHEC) causes a disease involving diarrhea, hemorrhagic colitis, and hemolytic-uremic syndrome (HUS). Here we present the draft genome sequence of NCCP15647, an EHEC isolate from an HUS patient. Its genome exhibits features of EHEC, such as genes for verotoxins, a type III secretion system, and prophages.

Algorithm for predicting functionally equivalent proteins from BLAST and HMMER searches.

In order to predict biologically significant attributes such as function from protein sequences, searching against large databases for homologous proteins is a common practice. In particular, BLAST and HMMER are widely used in a variety of biological fields. However, sequencehomologous proteins determined by BLAST and proteins having the same domains predicted by HMMER are not always functionally equivalent, even though their sequences are aligning with high similarity.