BREX system of<i>Escherichia coli</i>distinguishes self from non-self by methylation of a specific DNA site

Gordeeva, Julia; Morozova, Natalia; Sierro, Nicolas; Isaev, Artem; Šinkūnas, Tomas; Tsvetkova, Ksenia; Matlashov, Mikhail E.; Truncaitė, Lidija; Morgan, Richard D.; Ivanov, Nikolai V.; Siksnys, Virgis; Zeng, Lanying; Severinov, Konstantin

doi:10.1093/nar/gky1125

Cited by 84 publications

(127 citation statements)

References 39 publications

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“…Moreover, the insertion of the BREX gene cassette into Bacillus subtilis conferred bacterial resistance to phage infection, while inactivating pglX rendered the strain sensitive to phage infection (15). The pglX gene played a similar role in the BREX system of E. coli, and deleting such a gene in E. coli abolished the phage protection function (30). Thus, our results provide further evidence that L. casei Zhang pglX is an important component of the BREX system.…”

Section: Discussionsupporting

confidence: 53%

“…Our results showed that when transforming plasmids that contained pglX recognition sequences, the plasmid acquisition capacity of the mutant strain was always much higher than that of the wild-type strain, suggesting that the loss of the m6A MTase pglX led to a decreased capacity of mutants to block and/or restrict the invading plasmids. A recent study revealed that the MTase is essential for BREX function; inactivating such a gene would obliterate the activity of the BREX system (30). Moreover, the insertion of the BREX gene cassette into Bacillus subtilis conferred bacterial resistance to phage infection, while inactivating pglX rendered the strain sensitive to phage infection (15).…”

Section: Discussionmentioning

confidence: 99%

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A Novel Bacteriophage Exclusion (BREX) System Encoded by the pglX Gene in Lactobacillus casei Zhang

Hui

Zhang

Kwok

et al. 2019

Appl Environ Microbiol

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The bacteriophage exclusion (BREX) system is a novel prokaryotic defense system against bacteriophages. To our knowledge, no study has systematically characterized the function of the BREX system in lactic acid bacteria. Lactobacillus casei Zhang is a probiotic bacterium originating from koumiss. By using single-molecule real-time sequencing, we previously identified N6-methyladenine (m6A) signatures in the genome of L. casei Zhang and a putative methyltransferase (MTase), namely, pglX. This work further analyzed the genomic locus near the pglX gene and identified it as a component of the BREX system. To decipher the biological role of pglX, an L. casei Zhang pglX mutant (ΔpglX) was constructed. Interestingly, m6A methylation of the 5′-ACRCAG-3′ motif was eliminated in the ΔpglX mutant. The wild-type and mutant strains exhibited no significant difference in morphology or growth performance in de Man-Rogosa-Sharpe (MRS) medium. A significantly higher plasmid acquisition capacity was observed for the ΔpglX mutant than for the wild type if the transformed plasmids contained pglX recognition sites (i.e., 5′-ACRCAG-3′). In contrast, no significant difference was observed in plasmid transformation efficiency between the two strains when plasmids lacking pglX recognition sites were tested. Moreover, the ΔpglX mutant had a lower capacity to retain the plasmids than the wild type, suggesting a decrease in genetic stability. Since the Rebase database predicted that the L. casei PglX protein was bifunctional, as both an MTase and a restriction endonuclease, the PglX protein was heterologously expressed and purified but failed to show restriction endonuclease activity. Taken together, the results show that the L. casei Zhang pglX gene is a functional adenine MTase that belongs to the BREX system. IMPORTANCE Lactobacillus casei Zhang is a probiotic that confers beneficial effects on the host, and it is thus increasingly used in the dairy industry. The possession of an effective bacterial immune system that can defend against invasion of phages and exogenous DNA is a desirable feature for industrial bacterial strains. The bacteriophage exclusion (BREX) system is a recently described phage resistance system in prokaryotes. This work confirmed the function of the BREX system in L. casei and that the methyltransferase (pglX) is an indispensable part of the system. Overall, our study characterizes a BREX system component gene in lactic acid bacteria.

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Section: Discussionsupporting

confidence: 53%

Section: Discussionmentioning

confidence: 99%

A Novel Bacteriophage Exclusion (BREX) System Encoded by the pglX Gene in Lactobacillus casei Zhang

Hui

Zhang

Kwok

et al. 2019

Appl Environ Microbiol

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“…However, the much lower concentration of Cascade required for priming allows the persistent acquisition of new spacers from the infecting virus and the enrichment of Cascade effectors that specifically target this virus. Moreover, the host cell usually encodes additional defense systems, such as toxin-antitoxin systems which can elicit temporary cell dormancy upon infection (52), and BREX systems which can inhibit viral DNA replication (53,54). Such additional defense mechanisms will buy time for the robust and effective primed adaptation process and for the recovery of the concentration of effective Cascade complex.…”

Section: Discussionmentioning

confidence: 99%

Primed adaptation tolerates extensive structural and size variations of the CRISPR RNA guide in Haloarcula hispanica

Gong

Cheng

et al. 2019

Nucleic Acids Research

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Recent studies on CRISPR adaptation revealed that priming is a major pathway of spacer acquisition, at least for the most prevalent type I systems. Priming is guided by a CRISPR RNA which fully/partially matches the invader DNA, but the plasticity of this RNA guide has not yet been characterized. In this study, we extensively modified the two conserved handles of a priming crRNA in Haloarcula hispanica , and altered the size of its central spacer part. Interestingly, priming is insusceptible to the full deletion of 3′ handle, which seriously impaired crRNA stability and interference effects. With 3′ handle deletion, further truncation of 5′ handle revealed that its spacer-proximal 6 nucleotides could provide the least conserved sequence required for priming. Subsequent scanning mutation further identified critical nucleotides within 5′ handle. Besides, priming was also shown to tolerate a wider size variation of the spacer part, compared to interference. These data collectively illustrate the high tolerance of priming to extensive structural/size variations of the crRNA guide, which highlights the structural flexibility of the crRNA-effector ribonucleoprotein complex. The observed high priming effectiveness suggests that primed adaptation promotes clearance of the fast-replicating and ever-evolving viral DNA, by rapidly and persistently multiplexing the interference pathway.

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“…Bacteria have evolved different mechanisms such as restriction-modification systems [21,22], CRISPR-Cas immunity systems [23,24] and some poorly characterized systems like the BREX system [25,26], to protect them from foreign DNA. The annotated genome of strain RZ05 T showed that four genes (locus tags: GJ691_06025, GJ691_10275, GJ691_16545 and GJ691_17420) coding restriction-modification system associated proteins are present.…”

Section: Genome Featuresmentioning

confidence: 99%

Maribacter luteus sp. nov., a marine bacterium isolated from intertidal sand of the Yellow Sea

Liu

Zhang

Liu

et al. 2020

International Journal of Systematic and Evolutionary Microbiology

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A novel rod-shaped and Gram-stain-negative bacterium, designated strain RZ05T, was isolated from a sand sample collected from the intertidal zone of the Yellow Sea, PR China. Results of phylogenetic analysis based on 16S rRNA gene sequences revealed that strain RZ05T clusters within the genus Maribacter , a member of the family Flavobacteriaceae , and has the highest sequence similarity to Maribacter polysiphoniae KCTC 22021T (97.8 %), followed by Maribacter arenosus KCTC 52191T (97.2 %). Cells of this strain were observed to be aerobic, oxidase- and catalase-positive, motile by gliding and formed yellow colonies. Growth occurred at 7–40 °C (optimum, 30 °C), at pH 6.5–9.5 (optimum, pH 7.0) and with 0.5–6 % (optimum, 2 %) NaCl. Its polar lipid profile included phosphatidylethanolamine, two unidentified glycolipids, one unidentified aminolipid and four unidentified lipids. The major cellular fatty acids were iso-C15 : 0, iso-C15 : 1 G, iso-C17 : 0 3-OH, iso-C16 : 0 3-OH, iso-C15 : 0 3-OH, summed feature 9 (10-methyl C16 : 0/iso-C17 : 1 ω9c) and summed feature 3 (iso-C15 : 0 2-OH/C16 : 1 ω7c/C16 : 1 ω6c). The only respiratory quinone was menaquinone 6 (MK-6). The genome of strain RZ05T was 4.65 Mbp with a G+C content of 38.9 mol%. The average nucleotide identity and in silico DNA–DNA hybridization values between strain RZ05T and its most closely related type strain M. polysiphoniae KCTC 22021T were 80.3 and 26.3 %, respectively. The results of phylogenetic, phenotypic and chemotaxonomic analyses indicated that strain RZ05T represents a novel species of the genus Maribacter , for which the name Maribacter luteus sp. nov. is proposed. The type strain is RZ05T (=KCTC 62834T=MCCC 1K03617T).

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BREX system ofEscherichia colidistinguishes self from non-self by methylation of a specific DNA site

Cited by 84 publications

References 39 publications

A Novel Bacteriophage Exclusion (BREX) System Encoded by the pglX Gene in Lactobacillus casei Zhang

A Novel Bacteriophage Exclusion (BREX) System Encoded by the pglX Gene in Lactobacillus casei Zhang

Primed adaptation tolerates extensive structural and size variations of the CRISPR RNA guide in Haloarcula hispanica

Maribacter luteus sp. nov., a marine bacterium isolated from intertidal sand of the Yellow Sea

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