11 research outputs found

    A mobile genetic element in Serratia marcescens, a causative agent of onion disease

    No full text
    Aim. To screen mobile genetic elements (MGE) in the bacterium which caused decay of field-grown onion bulb and to study an integron and gene cassettes associated. Methods. Polymerase chain reaction (PCR) and PCR products sequencing were used for both the bacterium and MGE identification. Terminally-labeled Restriction Fragment Length Polymorphism (TRFLP) analysis was performed for detection of any bacterium in the onion bulb tissue. Results. The bacterium, which caused field-grown onion decay, was identified by nucleotide sequence analysis of the 16S rRNA genes to be S. marcescens known as phytopathogen. However, this isolate did not respond to specific primers designed for pathogenic strains. Inoculation of onion (Allium cepa L.), Arabidopsis thaliana (L.) Heyhn, and lettuce (Lactuca sativa) seeds resulted in biomass promotion of symptomless plants. PCR revealed the presence of a class 1 integron in S. marcescens IMBG291 which represents the first isolation of this integron in phytopathogenic Serratia species. The gene cassettes harbored by the integron have been represented with the promoterless genes encoded formimino-glutamate deiminase and ascorbate-specific phosphotransferase system enzyme IIC, and with additional three senseless sequences flanked by a 59-bp element. Conclusion. S. marcescens IMBG291 exhibited plant growth promotion or pathogenicity, depending on the environmental situation, due to horizontally acquired new gene cassettes located in the integron.Мета. Перевірити наявність мобільних генетичних елементів (МГЕ) у бактерії, що яка спричиняє гниття вирощеної за польових умов цибулі, та вивчити інтегрон разом з асоційованими з ним касетами генів. Методи. Полімеразна ланцюгова реакція (ПЛР) та секвенування продуктів ПЛР використано для ідентифікації бактерії та МГЕ. Метод аналізу поліморфізму довжини термінально мічених рестрикційних фрагментів ПЛР-продуктів застосовано для визначення ізольованої бактерії у тканинах цибулин. Результати. Аналізуючи послідовності нуклеотидів гена 16S рРНК ізоляту з гнилої цибулі, зроблено висновок про те, що бактерія належить до виду S. marcescens, відомого фітопатогену. Проте цей ізолят не реагував на специфічні праймери, характерні для фітопатогенних сератій. Інокулювання цибулі (Allium cepa L.), Arabidopsis thaliana (L.) Heyhn та салату (Lactuca sativa) призвело до зростання біомаси рослин без проявів симптомів захворювання. Інтегрон першого класу виявлено за допомогою ПЛР у геномі фітопатогенної S. marcescens вперше. Касети генів, які містили інтегрон, представлені безпромоторними генами, що кодують форміміноглутаматдеіміназу та фермент IIC аскорбатфосфотрансферазної системи, а також трьома некодуючими послідовностями, фланковами 59-п. н.-елементом. Висновки. S. marcescens IMBG291 проявляє патогенні властивості або стимулює розвиток рослини залежно від екологічної ситуації, завдяки горЦель. Проверить наявность мобильных генетических элементов (МГЭ) у бактерии, вызывающей гниль выращенного в полевых условиях лука, и изучеить интегрон вместе с ассоциированными с ним кассетами генов. Методы. Полимеразная цепная реакция (ПЦР) и секвенирование продуктов ПЦР использовали для идентификации бактерии и МГЭ. Метод анализа полиморфизма длины терминально-меченних рестрикционных фрагментов ПЦР-продуктов применен для определения изолированой бактерии в тканях луковиц. Результаты. Анализируя последовности нуклеотидов гена 16S рРНК изолята с гнилого лука, сделано вывод о том, что бактерия принадлежит к виду S. marcescens, известного фитопатогена. Однако этот изолят не реагировал на специфеские праймеры, характерные для фитопатогенных сератий. Инокулирование лука (Allium cepa L.), Arabidopsis thaliana (L.) Heyhn и салата (Lactuca sativa) приводило к возрастанию биомассы растений без проявления симптомов болезни. Интегрон первого класса выявлен с помощью ПЦР в геноме фитопатогенной S. marcescens впервые. Кассеты генов интегрона представлены беспромоторными генами, кодирующими формиминоглутамат деиминазу и фермент IIC аскорбатфосфотрансферазной системы, а также тремя некодирующими последовностями, фланкированными 59-п. н.-элементом. Выводы. S. marcescens IMBG291 проявляет патогенные свойства или стимулирует развитие растения в зависимости от экологической ситуации, благодаря горизонтально приобретенным генным кассетам, расположенным на интегроне

    SeqWord Gene Island Sniffer: A program to study the lateral genetic exchange among bacteria

    No full text
    SeqWord Gene Island Sniffer, a new program for the identification of mobile genetic elements in sequences of bacterial chromosomes is presented. This program is based on the analysis of oligonucleotide usage variations in DNA sequences. 3,518 mobile genetic elements were identified in 637 bacterial genomes and further analyzed by sequence similarity and the functionality of encoded proteins. The results of this study are stored in an open database (http://anjie.bi.up.ac.za/geidb/geidbhome. php). The developed computer program and the database provide the information valuable for further investigation of the distribution of mobile genetic elements and virulence factors among bacteria. The program is available for download at www.bi.up.ac.za/SeqWord/sniffer/index.html.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

    Cultural linguistics and language for special purposes: cognitive, ethnolinguistic and linguocultural approaches

    No full text
    The article considers the cognitive, ethnolinguistic, linguocultural approaches to the analysis of Languages for Special Purposes (LSP) serving communication in the professional sphere. The authors present the summary description of the conducted scientific research, aiming to define the main differences between general national language and the LSP as well as to reveal features of the adequacy of the translation and equivalence of the translation

    Diversity of microbes associated with the marine sponge, Haliclona simulans, isolated from Irish waters and identification of polyketide synthase genes from the sponge metagenome

    No full text
    Samples of the sponge Haliclona simulans were collected from Irish waters and subjected to a culture-independent analysis to determine the microbial, polyketide synthase (PKS) and non-ribosomal peptide synthase (NRPS) diversity. 16S rRNA gene libraries were prepared from total sponge, bacterial enriched sponge and seawater samples. Eight phyla from the Bacteria were detected in the sponge by phylogenetic analyses of the 16S rRNA gene libraries. The most abundant phylum in the total sponge library was the Proteobacteria (86%), with the majority of these clones being from the -Proteobacteria (77%); two groups of clones were dominant and together made up 69% of the total. Both of these groups were related to other sponge-derived microbes and comprised novel genera. Within the other bacterial phyla groups of clones representing novel candidate genera within the phyla Verrucomicrobia and Lentisphaerae were also found. Selective enrichment of the bacterial component of the sponge prior to 16S rRNA gene analysis resulted in a 16S rRNA gene library dominated by a novel genus of δ-Proteobacteria, most closely related to the Bdellovibrio. The potential for the sponge microbiota to produce secondary metabolites was also analysed by polymerase chain reaction amplification of PKS and NRPS genes. While no NRPS sequences were isolated seven ketosynthase (KS) sequences were obtained from the sponge metagenome. Analyses of these clones revealed a diverse collection of PKS sequences which were most closely affiliated with PKS from members of the Cyanobacteria, Myxobacteria and Dinoflagellata

    Pressure adaptation is linked to thermal adaptation in salt-saturated marine habitats

    No full text
    The present study provides a deeper view of protein functionality as a function of temperature, salt and pressure in deep-sea habitats. A set of eight different enzymes from five distinct deep-sea (3040�4908�m depth), moderately warm (14.0�16.5°C) biotopes, characterized by a wide range of salinities (39�348 practical salinity units), were investigated for this purpose. An enzyme from a �superficial� marine hydrothermal habitat (65°C) was isolated and characterized for comparative purposes. We report here the first experimental evidence suggesting that in salt-saturated deep-sea habitats, the adaptation to high pressure is linked to high thermal resistance (P value�=�0.0036). Salinity might therefore increase the temperature window for enzyme activity, and possibly microbial growth, in deep-sea habitats. As an example, Lake Medee, the largest hypersaline deep-sea anoxic lake of the Eastern Mediterranean Sea, where the water temperature is never higher than 16°C, was shown to contain halopiezophilic-like enzymes that are most active at 70°C and with denaturing temperatures of 71.4°C. The determination of the crystal structures of five proteins revealed unknown molecular mechanisms involved in protein adaptation to poly-extremes as well as distinct active site architectures and substrate preferences relative to other structurally characterized enzymes
    corecore