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Kwak M.-J.,Yonsei University | Kwak M.-J.,Korea Research Institute of Bioscience and Biotechnology | Kwak M.-J.,Korean University of Science and Technology | Jeong H.,Korea Research Institute of Bioscience and Biotechnology | And 8 more authors.
PLoS ONE | Year: 2014

Pink-pigmented facultative methylotrophs in the Rhizobiales are widespread in the environment, and many Methylobacterium species associated with plants produce plant growth-promoting substances. To gain insights into the life style at the phyllosphere and the genetic bases of plant growth promotion, we determined and analyzed the complete genome sequence of Methylobacterium oryzae CBMB20T, a strain isolated from rice stem. The genome consists of a 6.29-Mb chromosome and four plasmids, designated as pMOCI to pMOC4. Among the 6,274 coding sequences in the chromosome, the bacterium has, besides most of the genes for the central metabolism, all of the essential genes for the assimilation and dissimilation of methanol that are either located in methylotrophy islands or dispersed. M. oryzae is equipped with several kinds of genes for adaptation to plant surfaces such as defense against UV radiation, oxidative stress, desiccation, or nutrient deficiency, as well as high proportion of genes related to motility and signaling. Moreover, it has an array of genes involved in metabolic pathways that may contribute to promotion of plant growth; they include auxin biosynthesis, cytokine biosynthesis, vitamin B12biosynthesis, urea metabolism, biosorption of heavy metals or decrease of metal toxicity, pyrroloquinoline quinone biosynthesis, 1 -aminocyclopropane-1 -carboxylate deamination, phosphate solubilization, and thiosulfate oxidation. Through the genome analysis of M. oryzae, we provide information on the full gene complement of M. oryzae that resides in the aerial parts of plants and enhances plant growth. The plant-associated lifestyle of M. oryzae pertaining to methylotrophy and plant growth promotion, and its potential as a candidate for a bioinoculant targeted to the phyllosphere and focused on phytostimulation are illuminated. © 2014 Kwak et al.

Dai J.,Auburn University | Yoon S.H.,Korea Research Institute of Bioscience and Biotechnology | Sim H.Y.,Auburn University | Oh T.K.,Korea Research Institute of Bioscience and Biotechnology | And 5 more authors.
15th International Conference on Miniaturized Systems for Chemistry and Life Sciences 2011, MicroTAS 2011 | Year: 2011

We have developed a microfluidic reactor array enabling systematic assessment of bacterial cells in a batch culture condition. This system enables creating a series of different growth conditions by preserving different growth factors inside nanoliter reactors and cultivating bacterial cells inside the reactors. From a single on-chip experiment, we determined the effects of carbon sources on bacterial phenotypes, i.e. the pattern of growth curves with Escherichia coli K-12. We demonstrated the systematic assessment of inhibition effect of antibiotics on the growth of Pseudomonas aeruginosa. The present system could be used for systematic phenotypic study of different types of bacterial cells.

Kim J.F.,Korea Research Institute of Bioscience and Biotechnology | Kim J.F.,Korean University of Science and Technology | Kim J.F.,Korea Advanced Institute of Science and Technology | Jeong H.,Korea Research Institute of Bioscience and Biotechnology | And 16 more authors.
Journal of Bacteriology | Year: 2010

Paenibacillus polymyxa E681, a spore-forming, low-G+C, Gram-positive bacterium isolated from the rhizosphere of winter barley grown in South Korea, has great potential for agricultural applications due to its ability to promote plant growth and suppress plant diseases. Here we present the complete genome sequence of P. polymyxa E681. Its 5.4-Mb genome encodes functions specialized to the plant-associated lifestyle and characteristics that are beneficial to plants, such as the production of a plant growth hormone, antibiotics, and hydrolytic enzymes. Copyright © 2010, American Society for Microbiology. All Rights Reserved.

Park S.-Y.,Korea Research Institute of Bioscience and Biotechnology | Choi S.-K.,Korea Research Institute of Bioscience and Biotechnology | Choi S.-K.,Korean University of Science and Technology | Kim J.,Korea Research Institute of Bioscience and Biotechnology | And 5 more authors.
Applied and Environmental Microbiology | Year: 2012

In our previous study, Bacillus subtilis strain BSK3S, containing a polymyxin biosynthetic gene cluster from Paenibacillus polymyxa, could produce polymyxin only in the presence of exogenously added L-2,4-diaminobutyric acid (Dab). The dependence of polymyxin production on exogenous Dab was removed by introducing an ectB gene encoding the diaminobutyrate synthase of P. polymyxa into BSK3S (resulting in strain BSK4). We found, by observing the complete inhibition of polymyxin synthesis when the spo0A gene was knocked out (strain BSK4-0A), that Spo0A is indispensable for the production of polymyxin. Interestingly, the abrB-spo0A double-knockout mutant, BSK4-0A-rB, and the single abrB mutant, BSK4-rB, showed 1.7- and 2.3-fold increases, respectively, in polymyxin production over that of BSK4. These results coincided with the transcription levels of pmxA in the strains observed by quantitative real-time PCR (qRT-PCR). The AbrB protein was shown to bind directly to the upstream region of pmxA, indicating that AbrB directly inhibits the transcription of polymyxin biosynthetic genes. The BSK4-rB strain, producing high levels of polymyxin, will be useful for the development and production of novel polymyxin derivatives. © 2012, American Society for Microbiology.

Kwon S.-K.,Korea Research Institute of Bioscience and Biotechnology | Kwon S.-K.,Korean University of Science and Technology | Kim B.K.,Yonsei University | Song J.Y.,Yonsei University | And 8 more authors.
Genome Biology and Evolution | Year: 2013

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 RevMicrobiol. 6:488-494). Deciphering the genome information of flavobacteria and accessing the diversity and ecological impact of microbial rhodopsins are important in understanding and preserving the global ecosystems. The genome sequence of the orange-pigmented marine flavobacterium Nonlabens dokdonensis (basonym: Donghaeana dokdonensis) DSW-6 was determined. As a marine photoheterotroph, DSW-6 has written in its genome physiological features that allow survival in the oligotrophic environments. The sequence analysis also uncovered a gene encoding an unexpected type of microbial rhodopsin containing a unique motif in addition to a proteorhodopsin gene and a number of photolyase or cryptochrome genes. Homologs of the novel rhodopsin gene were found in other flavobacteria, alphaproteo bacteria, a species of Cytophagia, a deinococcus, and even a eukaryote diatom. They all contain the characteristic NQ motif and forma phylogenetically distinct group. Expression analysis of this rhodopsin gene inDSW-6indicated that it is induced at high NaCl concentrations, as well as in the presence of light and the absence of nutrients. Genomic and metagenomic surveys demonstrate the diversity of the NQ rhodopsins in nature and the prevalent occurrence of the encoding genes among microbial communities inhabiting hypersaline niches, suggesting its involvement in sodium metabolism and the sodium-Adapted lifestyle. © The Author(s) 2013.

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