RESUMO
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. The 3.9-Mb genome uncovers its potential for understanding the nature of leaf colonization as well as antibiosis against plant pathogens.
Assuntos
Bacillus/genética , Bacillus/isolamento & purificação , Genoma Bacteriano , Folhas de Planta/microbiologia , Prunus/microbiologia , Bacillus/classificação , Regulação Bacteriana da Expressão Gênica/fisiologia , Dados de Sequência MolecularRESUMO
Thermococcus zilligii, a thermophilic anaerobe in freshwater, is useful for physiological research and biotechnological applications. Here we report the high-quality draft genome sequence of T. zilligii AN1(T). The genome contains a number of genes for an immune system and adaptation to a microbial biomass-rich environment as well as hydrogenase genes.
Assuntos
Genoma Arqueal , Fontes Termais/microbiologia , Thermococcus/genética , Regulação da Expressão Gênica em Archaea/fisiologia , Dados de Sequência Molecular , Thermococcus/isolamento & purificação , Microbiologia da ÁguaRESUMO
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. The 6.6-Mb genome, consisting of three chromosomes and a single plasmid, contains genes related to plant growth promotion or degradation of aromatic compounds.
Assuntos
Burkholderia/genética , DNA Bacteriano/química , DNA Bacteriano/genética , Genoma Bacteriano , Análise de Sequência de DNA , Antifúngicos/metabolismo , Burkholderia/isolamento & purificação , Burkholderia/metabolismo , Cromossomos Bacterianos , Endófitos/genética , Endófitos/isolamento & purificação , Endófitos/metabolismo , Genes Bacterianos , Hidrocarbonetos Aromáticos/metabolismo , Redes e Vias Metabólicas/genética , Dados de Sequência Molecular , Oryza/microbiologia , PlasmídeosRESUMO
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.
Assuntos
Escherichia coli Êntero-Hemorrágica/genética , Regulação Bacteriana da Expressão Gênica/fisiologia , Genoma Bacteriano , Síndrome Hemolítico-Urêmica/microbiologia , Colite/microbiologia , Colite/patologia , Diarreia/microbiologia , Hemorragia/microbiologia , Humanos , Dados de Sequência Molecular , PrófagosRESUMO
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. Its genome size was determined to be 5.46 Mb, and its genomic features, including genes encoding virulence factors, were analyzed.
Assuntos
Escherichia coli Êntero-Hemorrágica/genética , Genoma Bacteriano , Escherichia coli Êntero-Hemorrágica/classificação , Feminino , Gastroenteropatias/epidemiologia , Gastroenteropatias/microbiologia , Regulação Bacteriana da Expressão Gênica/fisiologia , Humanos , Dados de Sequência Molecular , República da Coreia/epidemiologiaRESUMO
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. The genome has virulence genes, many in the locus of enterocyte effacement (LEE) island, encoding a metalloprotease, the Shiga toxin, and constituents of type III secretion.
Assuntos
Genoma Bacteriano , Escherichia coli Shiga Toxigênica/genética , Colite/microbiologia , Diarreia/complicações , Diarreia/microbiologia , Surtos de Doenças , Regulação Bacteriana da Expressão Gênica/fisiologia , Alemanha/epidemiologia , Síndrome Hemolítico-Urêmica/microbiologia , Hemorragia/microbiologia , Dados de Sequência MolecularRESUMO
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. Its 4.1-Mb genome reveals a number of genes whose products are possibly involved in promotion of plant growth or antibiosis.
Assuntos
Bacillus/genética , Genoma Bacteriano , Bacillus/classificação , Regulação Bacteriana da Expressão Gênica/fisiologia , Dados de Sequência Molecular , Desenvolvimento Vegetal , Plantas/microbiologiaRESUMO
An increasing number of microbial genomes have been completely sequenced, and functional analyses of these genomic sequences are under way. To facilitate these analyses, we have developed a genome-engineering tool for determining essential genes and minimizing bacterial genomes. We made two large pools of independent transposon mutants in Escherichia coli using modified Tn5 transposons with two different selection markers and precisely mapped the chromosomal location of 800 of these transposons. By combining a mapped transposon mutation from each of the mutant pools into the same chromosome using phage P1 transduction and then excising the flanked genomic segment by Cre-mediated loxP recombination, we obtained E. coli strains in which large genomic fragments (59-117 kilobases) were deleted. Some of these individual deletions were then combined into a single "cumulative deletion strain" that lacked 287 open reading frames (313.1 kilobases) but that nevertheless exhibited normal growth under standard laboratory conditions.
Assuntos
Clonagem Molecular/métodos , Elementos de DNA Transponíveis , Escherichia coli/genética , Deleção de Genes , Engenharia Genética/métodos , Genoma Bacteriano , Transdução Genética/métodos , Bacteriófago P1/enzimologia , Linhagem Celular , Cromossomos Bacterianos , Escherichia coli/classificação , Integrases/genética , Mutagênese , Recombinação Genética , Origem de Replicação , Especificidade da Espécie , Proteínas Virais/genéticaRESUMO
In this paper, we propose an autocorrelation function (ACF) based watermarking scheme in the discrete wavelet transform (DWT) domain. Conventional ACF-based watermarking embeds a watermark in the spatial domain due to its detection mechanism.We show that the autocorrelation (AC) peaks, which play an important role in estimating the applied geometric attacks in ACF-based watermarking, can also be extracted by embedding the watermark in the DWT domain. In the proposed scheme, a periodic watermark is embedded in the DWT domain by considering the AC peak strength and noise visibility. The proposed scheme also deals efficiently with the image shift problem in the detection process by using the undecimated DWT. Experimental results show that the proposed scheme yields stronger AC peaks than the spatial domain scheme does and, as a result, shows improved robustness against combined geometric-removal.
RESUMO
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. 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, alphaproteobacteria, a species of Cytophagia, a deinococcus, and even a eukaryote diatom. They all contain the characteristic NQ motif and form a phylogenetically distinct group. Expression analysis of this rhodopsin gene in DSW-6 indicated 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.
Assuntos
Bacteriorodopsinas/genética , Flavobacterium/genética , Genoma Bacteriano , Adaptação Fisiológica/genética , Motivos de Aminoácidos , Bacteriorodopsinas/química , Sequência de Bases , Ecossistema , Flavobacterium/química , Dados de Sequência Molecular , Água do Mar , Análise de Sequência de DNARESUMO
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. Thus, accurate assignment of functionally equivalent proteins from aligned sequences remains a challenge in bioinformatics. We have developed the FEP-BH algorithm to predict functionally equivalent proteins from protein-protein pairs identified by BLAST and from protein-domain pairs predicted by HMMER. When examined against domain classes of the Pfam-A seed database, FEP-BH showed 71.53% accuracy, whereas BLAST and HMMER were 57.72% and 36.62%, respectively. We expect that the FEP-BH algorithm will be effective in predicting functionally equivalent proteins from BLAST and HMMER outputs and will also suit biologists who want to search out functionally equivalent proteins from among sequence-homologous proteins.
Assuntos
Biologia Computacional/métodos , Proteínas/genética , Proteínas/metabolismo , Algoritmos , Estrutura Terciária de Proteína , Homologia de Sequência de AminoácidosRESUMO
BACKGROUND: Elucidation of a genotype-phenotype relationship is critical to understand an organism at the whole-system level. Here, we demonstrate that comparative analyses of multi-omics data combined with a computational modeling approach provide a framework for elucidating the phenotypic characteristics of organisms whose genomes are sequenced. RESULTS: We present a comprehensive analysis of genome-wide measurements incorporating multifaceted holistic data - genome, transcriptome, proteome, and phenome - to determine the differences between Escherichia coli B and K-12 strains. A genome-scale metabolic network of E. coli B was reconstructed and used to identify genetic bases of the phenotypes unique to B compared with K-12 through in silico complementation testing. This systems analysis revealed that E. coli B is well-suited for production of recombinant proteins due to a greater capacity for amino acid biosynthesis, fewer proteases, and lack of flagella. Furthermore, E. coli B has an additional type II secretion system and a different cell wall and outer membrane composition predicted to be more favorable for protein secretion. In contrast, E. coli K-12 showed a higher expression of heat shock genes and was less susceptible to certain stress conditions. CONCLUSIONS: This integrative systems approach provides a high-resolution system-wide view and insights into why two closely related strains of E. coli, B and K-12, manifest distinct phenotypes. Therefore, systematic understanding of cellular physiology and metabolism of the strains is essential not only to determine culture conditions but also to design recombinant hosts.
Assuntos
Escherichia coli/metabolismo , Escherichia coli/classificação , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Estudos de Associação Genética , Genoma Bacteriano , Genômica , Glioxilatos/metabolismo , Redes e Vias Metabólicas , Proteoma/genética , Proteoma/metabolismo , Proteômica , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismoRESUMO
Escherichia coli K-12 and B have been the subjects of classical experiments from which much of our understanding of molecular genetics has emerged. We present here complete genome sequences of two E. coli B strains, REL606, used in a long-term evolution experiment, and BL21(DE3), widely used to express recombinant proteins. The two genomes differ in length by 72,304 bp and have 426 single base pair differences, a seemingly large difference for laboratory strains having a common ancestor within the last 67 years. Transpositions by IS1 and IS150 have occurred in both lineages. Integration of the DE3 prophage in BL21(DE3) apparently displaced a defective prophage in the lambda attachment site of B. As might have been anticipated from the many genetic and biochemical experiments comparing B and K-12 over the years, the B genomes are similar in size and organization to the genome of E. coli K-12 MG1655 and have >99% sequence identity over approximately 92% of their genomes. E. coli B and K-12 differ considerably in distribution of IS elements and in location and composition of larger mobile elements. An unexpected difference is the absence of a large cluster of flagella genes in B, due to a 41 kbp IS1-mediated deletion. Gene clusters that specify the LPS core, O antigen, and restriction enzymes differ substantially, presumably because of horizontal transfer. Comparative analysis of 32 independently isolated E. coli and Shigella genomes, both commensals and pathogenic strains, identifies a minimal set of genes in common plus many strain-specific genes that constitute a large E. coli pan-genome.
Assuntos
DNA Bacteriano/genética , Escherichia coli/genética , Genoma Bacteriano , Análise de Sequência de DNA , DNA Bacteriano/química , Sequências Repetitivas Dispersas , Dados de Sequência Molecular , Polimorfismo Genético , Prófagos/genéticaRESUMO
The Suzuki-coupling reaction of 2-(dihydroxyboryl)-3,4-dimethyl-2-cyclopenten-1-one and 2-(dihydroxyboryl)-3-methyl-2-cyclopenten-1-one with 2-bromoaniline derivatives affords cyclopentenone compounds from which cyclopentadiene compounds, 4,6-R'(2)-2-(2,5-Me2C5H3)C6H2NH2 and 4,6-R'(2)-2-(2,3,5-Me3C5H2)C6H2NH2 are prepared. After sulfonation of the -NH2 group with p-TsCl, metallation is carried out by successive addition of Ti(NMe2)4 and Me2SiCl2 affording o-phenylene-bridged Cp/sulfonamido titanium dichloride complexes, [4,6-R'(2)-2-(2,5-Me2C5H2)C6H2NSO2C6H4CH3)]TiCl2 (R'=H, ; R'=Me, ; R'=F, ) and [4,6-R'(2)-2-(2,3,5-Me3C5H)C6H2NSO2C6H4CH3)]TiCl2 (R'=H, ; R'=Me, ; R'=F, ). The molecular structures of and [2-(2,5-Me2C5H2)C6H4NSO2C6H4CH3)]Ti(NMe2)2 are determined by X-ray crystallography. The Cp(centroid)-Ti-N angle in is smaller (100.90 degrees) than that observed for the CGC (constrained-geometry catalyst), [Me2Si(eta5-Me4Cp)(NtBu)]TiCl2 (107.6 degrees) indicating a more "constrained feature" in than in the CGC. Complex shows the highest activity among the newly prepared complexes in ethylene/1-octene copolymerization but it is slightly inferior to the CGC in terms of activity, comonomer-incorporation ability, and molecular weight of the obtained polymers.
RESUMO
Bacteria form biofilms by adhering to biotic or abiotic surfaces. This phenomenon causes several problems, including a reduction in the transport of mass and heat, an increase in resistance to antibiotics, and a shortening of the lifetimes of modules in bioindustrial fermentors. To overcome these difficulties, we created a biofilm production-deficient Escherichia coli strain, BD123, by deleting genes involved in curli biosynthesis and assembly, Delta(csgG-csgC); colanic acid biosynthesis and assembly, Delta(wcaL-wza); and type I pilus biosynthesis, Delta(fimB-fimH). E. coli BD123 remained mostly in the form of planktonic cells under the conditions tested and became more sensitive to the antibiotics streptomycin and rifampin than the wild-type E. coli MG1655: the growth of BD123 was inhibited by one-fourth of the concentrations needed to inhibit MG1655. In addition, the transformation efficiency of BD123 was about 20 times higher than that of MG1655, and the production and secretion of recombinant proteins were approximately 16% and approximately 25% greater, respectively, with BD123 than with MG1655. These results indicate that the newly created biofilm production-deficient strain of E. coli displays several key properties that substantially enhance its utility in the biotechnology arena.