The Experts below are selected from a list of 225 Experts worldwide ranked by ideXlab platform
Hideo Takahashi - One of the best experts on this subject based on the ideXlab platform.
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the site specific recombination system of actinophage tg1
Fems Microbiology Letters, 2009Co-Authors: Kentaro Morita, Naoki Fusada, Mamoru Komatsu, Nobutaka Hirano, Tomoyuki Yamamoto, Haruo Ikeda, Hideo TakahashiAbstract:Actinophage TG1 forms stable Lysogens by integrating at a unique site on chromosomes of Streptomyces strains. The phage (attPTG1) and bacterial (attBTG1) attachment sites for TG1 were deduced from comparative genomic studies on the TG1-Lysogen and nonLysogen of Streptomyces avermitilis. The attBTG1 was located within the 46-bp region in the dapC gene (SAV4517) encoding the putative N-succinyldiaminopimelate aminotransferase. TG1-Lysogens of S. avermitilis, however, did not demand either lysine or diaminopimelate for growth, indicating that the dapC annotation of S. avermitilis requires reconsideration. A bioinformatic survey of DNA databases using the fasta program for the attBTG1 sequence extracted possible integration sites from varied streptomycete genomes, including Streptomyces coelicolor A3(2) and Streptomyces griseus. The gene encoding the putative TG1 integrase (intTG1) was located adjacent to the attPTG1 site. TG1 integrase deduced from the intTG1 gene was a protein of 619 amino acids having a high sequence similarity to φC31 integrase, especially at the N-terminal catalytic region. By contrast, sequence similarities at the C-terminal regions crucial for the recognition of attachment sites were moderate or low. The site-specific recombination systems based on TG1 integrase were shown to work efficiently not only in Streptomyces strains but also in heterologous Escherichia coli.
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The site‐specific recombination system of actinophage TG1
FEMS microbiology letters, 2009Co-Authors: Kentaro Morita, Naoki Fusada, Mamoru Komatsu, Nobutaka Hirano, Tomoyuki Yamamoto, Haruo Ikeda, Hideo TakahashiAbstract:Actinophage TG1 forms stable Lysogens by integrating at a unique site on chromosomes of Streptomyces strains. The phage (attPTG1) and bacterial (attBTG1) attachment sites for TG1 were deduced from comparative genomic studies on the TG1-Lysogen and nonLysogen of Streptomyces avermitilis. The attBTG1 was located within the 46-bp region in the dapC gene (SAV4517) encoding the putative N-succinyldiaminopimelate aminotransferase. TG1-Lysogens of S. avermitilis, however, did not demand either lysine or diaminopimelate for growth, indicating that the dapC annotation of S. avermitilis requires reconsideration. A bioinformatic survey of DNA databases using the fasta program for the attBTG1 sequence extracted possible integration sites from varied streptomycete genomes, including Streptomyces coelicolor A3(2) and Streptomyces griseus. The gene encoding the putative TG1 integrase (intTG1) was located adjacent to the attPTG1 site. TG1 integrase deduced from the intTG1 gene was a protein of 619 amino acids having a high sequence similarity to φC31 integrase, especially at the N-terminal catalytic region. By contrast, sequence similarities at the C-terminal regions crucial for the recognition of attachment sites were moderate or low. The site-specific recombination systems based on TG1 integrase were shown to work efficiently not only in Streptomyces strains but also in heterologous Escherichia coli.
Heather E Allison - One of the best experts on this subject based on the ideXlab platform.
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Identification of genes expressed in cultures of E. coli Lysogens carrying the Shiga toxin-encoding prophage Φ24_B
BMC Microbiology, 2012Co-Authors: Laura M Riley, Marta Veses-garcia, Jeffrey D Hillman, Martin Handfield, Alan J Mccarthy, Heather E AllisonAbstract:Background Shigatoxigenic E. coli are a global and emerging health concern. Shiga toxin, Stx, is encoded on the genome of temperate, lambdoid Stx phages. Genes essential for phage maintenance and replication are encoded on approximately 50% of the genome, while most of the remaining genes are of unknown function nor is it known if these annotated hypothetical genes are even expressed. It is hypothesized that many of the latter have been maintained due to positive selection pressure, and that some, expressed in the Lysogen host, have a role in pathogenicity. This study used Change Mediated Antigen Technology (CMAT)™ and 2D-PAGE, in combination with RT-qPCR, to identify Stx phage genes that are expressed in E. coli during the Lysogenic cycle. Results Lysogen cultures propagated for 5-6 hours produced a high cell density with a low proportion of spontaneous prophage induction events. The expression of 26 phage genes was detected in these cultures by differential 2D-PAGE of expressed proteins and CMAT. Detailed analyses of 10 of these genes revealed that three were unequivocally expressed in the Lysogen, two expressed from a known Lysogenic cycle promoter and one uncoupled from the phage regulatory network. Conclusion Propagation of a Lysogen culture in which no cells at all are undergoing spontaneous lysis is impossible. To overcome this, RT-qPCR was used to determine gene expression profiles associated with the growth phase of Lysogens. This enabled the definitive identification of three lambdoid Stx phage genes that are expressed in the Lysogen and seven that are expressed during lysis. Conservation of these genes in this phage genome, and other Stx phages where they have been identified as present, indicates their importance in the phage/Lysogen life cycle, with possible implications for the biology and pathogenicity of the bacterial host.
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Identification of genes expressed in cultures of E. coli Lysogens carrying the Shiga toxin-encoding prophage Φ24B.
BMC microbiology, 2012Co-Authors: Laura M Riley, Marta Veses-garcia, Jeffrey D Hillman, Martin Handfield, Alan J Mccarthy, Heather E AllisonAbstract:Shigatoxigenic E. coli are a global and emerging health concern. Shiga toxin, Stx, is encoded on the genome of temperate, lambdoid Stx phages. Genes essential for phage maintenance and replication are encoded on approximately 50% of the genome, while most of the remaining genes are of unknown function nor is it known if these annotated hypothetical genes are even expressed. It is hypothesized that many of the latter have been maintained due to positive selection pressure, and that some, expressed in the Lysogen host, have a role in pathogenicity. This study used Change Mediated Antigen Technology (CMAT)™ and 2D-PAGE, in combination with RT-qPCR, to identify Stx phage genes that are expressed in E. coli during the Lysogenic cycle. Lysogen cultures propagated for 5-6 hours produced a high cell density with a low proportion of spontaneous prophage induction events. The expression of 26 phage genes was detected in these cultures by differential 2D-PAGE of expressed proteins and CMAT. Detailed analyses of 10 of these genes revealed that three were unequivocally expressed in the Lysogen, two expressed from a known Lysogenic cycle promoter and one uncoupled from the phage regulatory network. Propagation of a Lysogen culture in which no cells at all are undergoing spontaneous lysis is impossible. To overcome this, RT-qPCR was used to determine gene expression profiles associated with the growth phase of Lysogens. This enabled the definitive identification of three lambdoid Stx phage genes that are expressed in the Lysogen and seven that are expressed during lysis. Conservation of these genes in this phage genome, and other Stx phages where they have been identified as present, indicates their importance in the phage/Lysogen life cycle, with possible implications for the biology and pathogenicity of the bacterial host.
Stanley C K Lau - One of the best experts on this subject based on the ideXlab platform.
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The putative functions of Lysogeny in mediating the survivorship of Escherichia coli in seawater and marine sediment.
FEMS microbiology ecology, 2017Co-Authors: Jennifer Y H Lai, Hao Zhang, Rui Zhang, Miranda Hei Yin Chiang, Clare H.i. Lun, Stanley C K LauAbstract:Escherichia coli colonizes various body parts of animal hosts as a commensal and a pathogen. It can also persist in the external environment in the absence of fecal pollution. It remains unclear how this species has evolved to adapt to such contrasting habitats. Lysogeny plays pivotal roles in the diversification of the phenotypic and ecologic characters of E. coli as a symbiont. We hypothesized that Lysogeny could also confer fitness to survival in the external environment. To test this hypothesis, we used the induced phages of an E. coli strain originating from marine sediment to infect a fecal E. coli strain to obtain an isogenic Lysogen of the latter. The three strains were tested for survivorship in microcosms of seawater, marine sediment and sediment interstitial water as well as swimming motility, glycogen accumulation, biofilm formation, substrate utilization and stress resistance. The results indicate that Lysogenic infection led to tractable changes in many of the ecophysiological attributes tested. Particularly, the Lysogen had better survivorship in the microcosms and had a substrate utilization profile resembling the sediment strain more than the wild type fecal strain. Our findings provide new insights into the understanding of how E. coli survives in the natural environment.
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draft genome sequences of three escherichia coli strains investigated for the effects of Lysogeny on niche diversification
Genome Announcements, 2014Co-Authors: Jennifer Y H Lai, Hao Zhang, Miranda H Y Chiang, Rui Zhang, Stanley C K LauAbstract:During the course of investigating the effects of Lysogeny on niche diversification of Escherichia coli, we used the temperate phages induced from one E. coli strain to infect another and created an isogenic Lysogen of the latter. The draft genome sequences of the three E. coli strains are reported herein.
Kentaro Morita - One of the best experts on this subject based on the ideXlab platform.
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the site specific recombination system of actinophage tg1
Fems Microbiology Letters, 2009Co-Authors: Kentaro Morita, Naoki Fusada, Mamoru Komatsu, Nobutaka Hirano, Tomoyuki Yamamoto, Haruo Ikeda, Hideo TakahashiAbstract:Actinophage TG1 forms stable Lysogens by integrating at a unique site on chromosomes of Streptomyces strains. The phage (attPTG1) and bacterial (attBTG1) attachment sites for TG1 were deduced from comparative genomic studies on the TG1-Lysogen and nonLysogen of Streptomyces avermitilis. The attBTG1 was located within the 46-bp region in the dapC gene (SAV4517) encoding the putative N-succinyldiaminopimelate aminotransferase. TG1-Lysogens of S. avermitilis, however, did not demand either lysine or diaminopimelate for growth, indicating that the dapC annotation of S. avermitilis requires reconsideration. A bioinformatic survey of DNA databases using the fasta program for the attBTG1 sequence extracted possible integration sites from varied streptomycete genomes, including Streptomyces coelicolor A3(2) and Streptomyces griseus. The gene encoding the putative TG1 integrase (intTG1) was located adjacent to the attPTG1 site. TG1 integrase deduced from the intTG1 gene was a protein of 619 amino acids having a high sequence similarity to φC31 integrase, especially at the N-terminal catalytic region. By contrast, sequence similarities at the C-terminal regions crucial for the recognition of attachment sites were moderate or low. The site-specific recombination systems based on TG1 integrase were shown to work efficiently not only in Streptomyces strains but also in heterologous Escherichia coli.
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The site‐specific recombination system of actinophage TG1
FEMS microbiology letters, 2009Co-Authors: Kentaro Morita, Naoki Fusada, Mamoru Komatsu, Nobutaka Hirano, Tomoyuki Yamamoto, Haruo Ikeda, Hideo TakahashiAbstract:Actinophage TG1 forms stable Lysogens by integrating at a unique site on chromosomes of Streptomyces strains. The phage (attPTG1) and bacterial (attBTG1) attachment sites for TG1 were deduced from comparative genomic studies on the TG1-Lysogen and nonLysogen of Streptomyces avermitilis. The attBTG1 was located within the 46-bp region in the dapC gene (SAV4517) encoding the putative N-succinyldiaminopimelate aminotransferase. TG1-Lysogens of S. avermitilis, however, did not demand either lysine or diaminopimelate for growth, indicating that the dapC annotation of S. avermitilis requires reconsideration. A bioinformatic survey of DNA databases using the fasta program for the attBTG1 sequence extracted possible integration sites from varied streptomycete genomes, including Streptomyces coelicolor A3(2) and Streptomyces griseus. The gene encoding the putative TG1 integrase (intTG1) was located adjacent to the attPTG1 site. TG1 integrase deduced from the intTG1 gene was a protein of 619 amino acids having a high sequence similarity to φC31 integrase, especially at the N-terminal catalytic region. By contrast, sequence similarities at the C-terminal regions crucial for the recognition of attachment sites were moderate or low. The site-specific recombination systems based on TG1 integrase were shown to work efficiently not only in Streptomyces strains but also in heterologous Escherichia coli.
Rui Zhang - One of the best experts on this subject based on the ideXlab platform.
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Viral Regulation on Bacterial Community Impacted by Lysis-Lysogeny Switch: A Microcosm Experiment in Eutrophic Coastal Waters.
Frontiers in microbiology, 2019Co-Authors: Xiaowei Chen, Yunlan Yang, Nianzhi Jiao, Rui ZhangAbstract:Marine viruses are major drivers of global biogeochemical cycles and energy fluxes, yet the importance of viral impacts on the succession and diversity of the bacterial community remains largely unexplored. Here, we explored viral life strategy and its potential effect on the bacterial community by experimental incubations of eutrophic coastal waters under Lysogen-induced and non-induced treatments. The Lysogen-induced treatment showed relatively constant viral and bacterial abundances, lytic and Lysogenic viral production throughout the experimental period, together with the progressive declines in not only the relative abundances for SAR11, Rhodobacteraceae, Altermonadaceae and SAR86 but the bacterial community diversity. Conversely, the non-induced treatment observed the marked variation in the abundances of viruses, bacteria and cells with high nucleic acid content over the time course of incubation, which was congruent with the drastic shift in lytic and Lysogenic viral production as well as the succession of bacterial community. Our results supported the hypotheses that a high level of Lysogeny would occur with the increasing density of bacteria with rapid growth rate, which may contribute to a relatively lower host community diversity, whereas the Lysogeny to lysis switching would fuel growth opportunities for less-active or initially rare bacterial taxa and generate a more diverse bacterial community. Altogether, the present study underscored the crucial regulatory role of the viral lysis-Lysogeny pattern in bacterial community dynamics, composition and diversity, highlighting the viral impact on the microbial food web and biogeochemical processes.
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The putative functions of Lysogeny in mediating the survivorship of Escherichia coli in seawater and marine sediment.
FEMS microbiology ecology, 2017Co-Authors: Jennifer Y H Lai, Hao Zhang, Rui Zhang, Miranda Hei Yin Chiang, Clare H.i. Lun, Stanley C K LauAbstract:Escherichia coli colonizes various body parts of animal hosts as a commensal and a pathogen. It can also persist in the external environment in the absence of fecal pollution. It remains unclear how this species has evolved to adapt to such contrasting habitats. Lysogeny plays pivotal roles in the diversification of the phenotypic and ecologic characters of E. coli as a symbiont. We hypothesized that Lysogeny could also confer fitness to survival in the external environment. To test this hypothesis, we used the induced phages of an E. coli strain originating from marine sediment to infect a fecal E. coli strain to obtain an isogenic Lysogen of the latter. The three strains were tested for survivorship in microcosms of seawater, marine sediment and sediment interstitial water as well as swimming motility, glycogen accumulation, biofilm formation, substrate utilization and stress resistance. The results indicate that Lysogenic infection led to tractable changes in many of the ecophysiological attributes tested. Particularly, the Lysogen had better survivorship in the microcosms and had a substrate utilization profile resembling the sediment strain more than the wild type fecal strain. Our findings provide new insights into the understanding of how E. coli survives in the natural environment.
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draft genome sequences of three escherichia coli strains investigated for the effects of Lysogeny on niche diversification
Genome Announcements, 2014Co-Authors: Jennifer Y H Lai, Hao Zhang, Miranda H Y Chiang, Rui Zhang, Stanley C K LauAbstract:During the course of investigating the effects of Lysogeny on niche diversification of Escherichia coli, we used the temperate phages induced from one E. coli strain to infect another and created an isogenic Lysogen of the latter. The draft genome sequences of the three E. coli strains are reported herein.
