Type I restriction-modification system and its resistance in electroporation efficiency in Flavobacterium columnare

Li, N.; Zhang, L.Q.; Zhang, J.; Liu, Z.X.; Huang, Bei; Zhang, S.H.; Nie, Pin

doi:10.1016/j.vetmic.2012.04.045

Cited by 5 publications

(3 citation statements)

References 34 publications

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“…Therefore, a possible explanation of the enhanced transformation efficiency is the malfunctioning of the restriction and modification system. In this context, some studies used artificial type I restriction and modification negative strains to analyze the genetics of bacteria by enhancing their transformation efficiency . Thus, these studies support the idea that the isolates with the deletion incorporated exogenous plasmid more efficiently than the isolates without the deletion because of the deletion of type I restriction and modification gene.…”

Section: Discussionmentioning

confidence: 80%

Emergence of type I restriction modification system‐negative emm1 type Streptococcus pyogenes clinical isolates in Japan

Okada

Matsumoto

Zhang

et al. 2014

APMIS

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Streptococcus pyogenes emm1 type is the dominant cause of streptococcal toxic shock syndrome (STSS) in Japan and many other developed countries. Recently, the number of STSS patients in Japan was reported to be increasing. Hence, we analyzed the S. pyogenes clinical isolates detected in Japan after 2005. We found that the regions encoding the Spy1908–1910 two-component regulatory system and the adjacent type I restriction modification system were deleted in some emm1 type isolates. The isolates with the deletion were detected only in the emm1 strains that were isolated between 2010 and 2013, but not before 2010. Twenty-six of 46 (56.5%) emm1 type isolates were isolated in 2010–2013, and among these isolates, five of seven (71.4%) emm1 type STSS isolates were shown to have that deletion. PFGE and PCR analysis for the presence of several pyrogenic exotoxin-related genes suggested that the emm1 isolates with and without the deletion shared the same genetic background. The emm1 isolates with the deletion could incorporate exogenous plasmids by experimental electroporation transformation far more efficiently. These results suggested that the novel emm1 isolates have occupied a fairly large part of total emm1 isolates.

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Section: Discussionmentioning

confidence: 80%

Emergence of type I restriction modification system‐negative emm1 type Streptococcus pyogenes clinical isolates in Japan

Okada

Matsumoto

Zhang

et al. 2014

APMIS

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“…Although significant progress has been made, still many questions remain unanswered on how this pathogenic organism elicits disease, and information concerning the bacteriological events preceding disease and death is scarce. Li et al related this lack of knowledge to the absence of an efficient molecular manipulation system for F. columnare , especially a plasmid-based inframe knockout system [66], despite two recent reports on the establishment of genetic manipulation system for the bacterium [67,68]. Li et al identified the type I restriction-modification system (R-M system) in F. columnare to improve electroporation efficiency and suggested that it would be of significant interest to examine the composition and diversity of R-M systems in strains of F. columnare in order to set up a suitable genetic manipulation system for the bacterium [66].…”

Section: Pathogenesismentioning

confidence: 99%

Columnaris disease in fish: a review with emphasis on bacterium-host interactions

Declercq

Haesebrouck

Broeck

et al. 2013

Vet Res

320

250

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Flavobacterium columnare (F. columnare) is the causative agent of columnaris disease. This bacterium affects both cultured and wild freshwater fish including many susceptible commercially important fish species. F. columnare infections may result in skin lesions, fin erosion and gill necrosis, with a high degree of mortality, leading to severe economic losses. Especially in the last decade, various research groups have performed studies aimed at elucidating the pathogenesis of columnaris disease, leading to significant progress in defining the complex interactions between the organism and its host. Despite these efforts, the pathogenesis of columnaris disease hitherto largely remains unclear, compromising the further development of efficient curative and preventive measures to combat this disease. Besides elaborating on the agent and the disease it causes, this review aims to summarize these pathogenesis data emphasizing the areas meriting further investigation.

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“…The deletion–accumulation effect is most likely a result of environmental enrichment in the cyclic process. For instance, all the mutants carried a deletion of the D1 fragment and most contained the D4 fragment (Table ), both of which harbored genes ( hsd RMS, mcr A, mcr BC, and mrr , Table ) encoding the restriction–modification (R-M) system, preventing the invasion of foreign DNA elements and is a barrier to genetic manipulation in host strains. − Removing the genes encoding the R-M system greatly enhanced the transformation capacity. − Besides, many deletion events contain the IS elements or cryptic virulence genes (Supporting Information Table S7). The deletion of these genes may also facilitate the plasmid’s stability as reported, , which might promote the improvement of the transformation efficiency.…”

Section: Discussionmentioning

confidence: 99%

Reduction of the Bacterial Genome by Transposon-Mediated Random Deletion

et al. 2022

ACS Synth. Biol.

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Genome reduction is an important strategy in synthetic biology for constructing functional chassis cells or minimal genomes. However, the limited knowledge of complex gene functions and interactions makes genome reduction by rational design encounter a bottleneck. Here, we present an iterative and random genome reduction method for Escherichia coli, named "transposon-mediated random deletion (TMRD)". TMRD generates random double-strand breaks (DSBs) in the genome by combining Tn5 transposition with the CRISPR/Cas9 system and allows genomic deletions of various sizes at random positions during DSB repair through the intracellular alternative end-joining mechanism. Using E. coli MG1655 as the original strain, a pool of cells with multiple random genomic deletions were obtained after five reduction cycles. The growth rates of the obtained cells were comparable to that of MG1655, while the electroporation efficiency increased by at least 2 magnitudes. TMRD can generate a small E. coli library carrying multiple and random genomic deletions while enriching the cells with environmental fitness in the population. TMRD has the potential to be widely applied in the construction of minimal genomes or chassis cells for metabolic engineering.

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Type I restriction-modification system and its resistance in electroporation efficiency in Flavobacterium columnare

Cited by 5 publications

References 34 publications

Emergence of type I restriction modification system‐negative emm1 type Streptococcus pyogenes clinical isolates in Japan

Emergence of type I restriction modification system‐negative emm1 type Streptococcus pyogenes clinical isolates in Japan

Columnaris disease in fish: a review with emphasis on bacterium-host interactions

Reduction of the Bacterial Genome by Transposon-Mediated Random Deletion

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