Genetic Manipulation and Gene Modification Technologies in Bifidobacteria

Fukiya, Satoru; Sakanaka, Mikiyasu; Yokota, Atsushi

doi:10.1016/b978-0-12-805060-6.00015-6

Cited by 9 publications

(11 citation statements)

References 116 publications

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“…In the efforts to optimize the RBS for efficient protein, two primary considerations are taken into account. First, the flanking sequences of the RBS site influence the recruitment of the ribosomal subunits to the mRNA sequences ( Fukiya et al, 2018 ). Second, the optimal distance between the RBS site and the start codon influences the rate of protein expression ( Fukiya et al, 2018 ).…”

Section: Current Development Of Engineering Of Bifidobacteriummentioning

confidence: 99%

“…First, the flanking sequences of the RBS site influence the recruitment of the ribosomal subunits to the mRNA sequences ( Fukiya et al, 2018 ). Second, the optimal distance between the RBS site and the start codon influences the rate of protein expression ( Fukiya et al, 2018 ). Interestingly, certain studies have shown that the predominant conserved Shine-Dalgarno sequence in Bifidobacterium differs from conventional microbes where the most common of 6-mer consensus RBS in B. longum is AAGGAG as compared to the common AGGAGG ( He et al, 2012b ; Kozakai et al, 2020 ).…”

Section: Current Development Of Engineering Of Bifidobacteriummentioning

confidence: 99%

See 1 more Smart Citation

Recent Development of Probiotic Bifidobacteria for Treating Human Diseases

Chen

2021

Front. Bioeng. Biotechnol.

108

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Bifidobacterium is a non-spore-forming, Gram-positive, anaerobic probiotic actinobacterium and commonly found in the gut of infants and the uterine region of pregnant mothers. Like all probiotics, Bifidobacteria confer health benefits on the host when administered in adequate amounts, showing multifaceted probiotic effects. Examples include B. bifidum, B. breve, and B. longum, common Bifidobacterium strains employed to prevent and treat gastrointestinal disorders, including intestinal infections and cancers. Herein, we review the latest development in probiotic Bifidobacteria research, including studies on the therapeutic impact of Bifidobacterial species on human health and recent efforts in engineering Bifidobacterium. This review article would provide readers with a wholesome understanding of Bifidobacteria and its potentials to improve human health.

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Section: Current Development Of Engineering Of Bifidobacteriummentioning

confidence: 99%

Section: Current Development Of Engineering Of Bifidobacteriummentioning

confidence: 99%

Recent Development of Probiotic Bifidobacteria for Treating Human Diseases

Chen

2021

Front. Bioeng. Biotechnol.

108

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“…The extensive characterization of CRISPR-Cas systems in the human commensal Bifidobacterium performed in this analysis allowed us to elucidate all the essential elements for repurposing these endogenous systems for various applications, including genome editing and transcriptional regulation. Although transformation protocols using Escherichia coli-Bifidobacterium shuttle vectors have been established, such systems work only in limited species with low transformation efficiency [48]. The complex cell wall structure along with restriction and modification systems has made bifidobacteria notoriously recalcitrant to genome editing.…”

Section: Discussionmentioning

confidence: 99%

Comprehensive Mining and Characterization of CRISPR-Cas Systems in Bifidobacterium

et al. 2020

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The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas (CRISPR-associated cas) systems constitute the adaptive immune system in prokaryotes, which provides resistance against bacteriophages and invasive genetic elements. The landscape of applications in bacteria and eukaryotes relies on a few Cas effector proteins that have been characterized in detail. However, there is a lack of comprehensive studies on naturally occurring CRISPR-Cas systems in beneficial bacteria, such as human gut commensal Bifidobacterium species. In this study, we mined 954 publicly available Bifidobacterium genomes and identified CRIPSR-Cas systems in 57% of these strains. A total of five CRISPR-Cas subtypes were identified as follows: Type I-E, I-C, I-G, II-A, and II-C. Among the subtypes, Type I-C was the most abundant (23%). We further characterized the CRISPR RNA (crRNA), tracrRNA, and PAM sequences to provide a molecular basis for the development of new genome editing tools for a variety of applications. Moreover, we investigated the evolutionary history of certain Bifidobacterium strains through visualization of acquired spacer sequences and demonstrated how these hypervariable CRISPR regions can be used as genotyping markers. This extensive characterization will enable the repurposing of endogenous CRISPR-Cas systems in Bifidobacteria for genome engineering, transcriptional regulation, genotyping, and screening of rare variants.

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“…1-4 In contrast, the genetic tools (especially mutagenesis) to investigate and enhanced their probiotic activity are rather poorly developed, especially for bifidobacteria. 5 The traditional genome engineering methods are largely dependent on the bacterial transformation efficiency. This defect can be overcome by the conditional replicate plasmid assisted homologous recombination, such as plasmids containing a thermosensitive replication origin, 6, 7 but the latter may have a limited host range.…”

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confidence: 99%

“…10 ssDNA recombineering allows high efficiency mutagenesis in lactobacilli and lactococci independent of antibiotic selection, while it still requires high transformation efficiency (i.e. ∼≥10 5 cfu/μg DNA) and inducible expression of recombinase RecT. 11 Therefore, it might be difficult to be used in strains with low transformation efficiency.…”

mentioning

confidence: 99%

Inducible Plasmid Self-Destruction (IPSD) assisted genome engineering in lactobacilli and bifidobacteria

Zuo

Zeng

Hammarström

et al. 2019

Preprint

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Genome engineering is essential for application of synthetic biology in probiotics including lactobacilli and bifidobacteria. Several homologous recombination system-based mutagenesis tools have been developed for these bacteria but still, have many limitations in different species or strains. Here we developed a genome engineering method based on an inducible self-destruction plasmid delivering homologous DNA into bacteria. Excision of the replicon by induced recombinase facilitates selection of homologous recombination events. This new genome editing tool called Inducible Plasmid Self-Destruction (IPSD) was successfully used to perform gene knock-out and knock-in in lactobacilli and bifidobacteria. Due to its simplicity and universality, the IPSD strategy may provide a general approach for genetic engineering of various bacterial species.

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Genetic Manipulation and Gene Modification Technologies in Bifidobacteria

Cited by 9 publications

References 116 publications

Recent Development of Probiotic Bifidobacteria for Treating Human Diseases

Recent Development of Probiotic Bifidobacteria for Treating Human Diseases

Comprehensive Mining and Characterization of CRISPR-Cas Systems in Bifidobacterium

Inducible Plasmid Self-Destruction (IPSD) assisted genome engineering in lactobacilli and bifidobacteria

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