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Li S, Xu T, Meng X, Yan Y, Zhou Y, Duan L, Tang Y, Zhu L, Sun L. Ocr-mediated suppression of BrxX unveils a phage counter-defense mechanism. Nucleic Acids Res 2024:gkae608. [PMID: 38989624 DOI: 10.1093/nar/gkae608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/12/2024] Open
Abstract
The burgeoning crisis of antibiotic resistance has directed attention to bacteriophages as natural antibacterial agents capable of circumventing bacterial defenses. Central to this are the bacterial defense mechanisms, such as the BREX system, which utilizes the methyltransferase BrxX to protect against phage infection. This study presents the first in vitro characterization of BrxX from Escherichia coli, revealing its substrate-specific recognition and catalytic activity. We demonstrate that BrxX exhibits nonspecific DNA binding but selectively methylates adenine within specific motifs. Kinetic analysis indicates a potential regulation of BrxX by the concentration of its co-substrate, S-adenosylmethionine, and suggests a role for other BREX components in modulating BrxX activity. Furthermore, we elucidate the molecular mechanism by which the T7 phage protein Ocr (Overcoming classical restriction) inhibits BrxX. Despite low sequence homology between BrxX from different bacterial species, Ocr effectively suppresses BrxX's enzymatic activity through high-affinity binding. Cryo-electron microscopy and biophysical analyses reveal that Ocr, a DNA mimic, forms a stable complex with BrxX, highlighting a conserved interaction interface across diverse BrxX variants. Our findings provide insights into the strategic counteraction by phages against bacterial defense systems and offer a foundational understanding of the complex interplay between phages and their bacterial hosts, with implications for the development of phage therapy to combat antibiotic resistance.
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Affiliation(s)
- Shen Li
- Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Tianhao Xu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xinru Meng
- Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Yujuan Yan
- Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Ying Zhou
- Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Lei Duan
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yulong Tang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Li Zhu
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
- Electron Microscopy Centre of Lanzhou University, Lanzhou 730000, China
| | - Litao Sun
- Shenzhen Key Laboratory of Pathogenic Microbes and Biosafety, School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
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Bao Q, Ma X, Bo X, Pang J, Dai L, Wang H, Chen Y, Kwok LY. Transcriptomic analysis of Lacticaseibacillus paracasei Zhang in transition to the viable but non-culturable state by RNA sequencing. Front Microbiol 2023; 14:1280350. [PMID: 38188563 PMCID: PMC10768001 DOI: 10.3389/fmicb.2023.1280350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
Background Some bacteria enter the viable but non-culturable (VBNC) state to survive harsh environmental conditions and external stresses. This alters cell physiology and has implications for the food industry as some bacteria, such as lactobacilli, undergo similar changes during food processing. Methods This study aimed to investigate the transcriptomic changes of a probiotic strain, Lacticaseibacillus paracasei Zhang (L. paracasei Zhang), upon transition to the VBNC state using high throughput RNA sequencing (RNA-seq). Results Bacteria were inoculated into the de Man, Rogosa, and Sharpe medium and maintained at low temperature and pH to induce cell transition to the VBNC state. Cells were harvested for analysis at five stages of VBNC induction: 0, 3, 30, and 180 days after induction and 210 days when the cells entered the VBNC state. Our results showed that the expression of 2,617, 2,642, 2,577, 2,829, and 2,840 genes was altered at these five different stages. The function of differentially expressed genes (DEGs, compared to healthy cells collected at day 0) and their encoded pathways were analyzed by the Gene Ontology Consortium and the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. A total of 10 DEGs were identified in cells that entered the VBNC state: five continuously upregulated (LCAZH_0621, LCAZH_1986, LCAZH_2038, LCAZH_2040, and LCAZH_2174) and five continuously downregulated (LCAZH_0024, LCAZH_0210, LCAZH_0339, LCAZH_0621, and LCAZH_0754). Conclusions This study proposes a molecular model of the VBNC mechanism in L. paracasei Zhang, highlighting that changes in cell metabolism improve substrate utilization efficiency, thereby enhancing bacterial survival under adverse conditions. These data may be useful for improving the survival of probiotics in industrial food processing.
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Affiliation(s)
- Qiuhua Bao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Xuebo Ma
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaoyu Bo
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Jing Pang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Lixia Dai
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Huiying Wang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Yongfu Chen
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, China
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Wozniak CE, Hughes KT, Liou TG. Mutations in the C-terminal region of the bacteriophage exclusion protein PglX can selectively inactivate restriction in Salmonella. J Bacteriol 2023; 205:e0020723. [PMID: 37730541 PMCID: PMC10601704 DOI: 10.1128/jb.00207-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 07/24/2023] [Indexed: 09/22/2023] Open
Abstract
Salmonella enterica serovar Typhimurium strain LT2 is protected by two DNA restriction-modification systems (HsdRMS and Mod-Res) and a Type I bacteriophage exclusion (BREX) system (BrxA-L). The LB5000 strain was constructed to inactivate restriction but not methylation in all three systems and has been available for decades (L. R. Bullas and J. I. Ryu, J Bacteriol 156:471-474, 1983, https://doi.org/10.1128/jb.156.1.471-474.1983). However, this strain had been heavily mutagenized and contains hundreds of other mutations, including a few in DNA repair genes. Here, we describe the development of a strain that is only mutated for DNA restriction by the three systems and remains competent for DNA modification. We transferred mutations specific to DNA restriction from LB5000 to a wild-type LT2 background. The hsdR and res mutations affected only restriction in the wild-type background, but the brxC and pglZ mutations for the poorly understood BREX system also reduced modification. Amino acids in an unannotated conserved region of PglX in the BREX system were then randomized. Mutations were identified that specifically affected restriction at 37°C but were found to be temperature sensitive for restriction and methylation when tested at 30°C and 42°C. These mutations in PglX are consistent with a domain that communicates DNA methylation information to other BREX effector proteins. Finally, mutations generated in the specificity domain of PglX may have changed the DNA binding site recognized by the BREX system. IMPORTANCE The restriction system mutants constructed in this study will be useful for cloning DNA and transferring plasmids from other bacterial species into Salmonella. We verified which mutations in strain LB5000 resulted in loss of restriction for each restriction-modification system and the BREX system by moving these mutations to a wild-type Salmonella background. The methylase PglX was then mutagenized, which adds to our knowledge of the BREX system that is found in many bacteria but is not well understood. These PglX mutations affected restriction and methylation at different temperatures, which suggests that the C-terminal region of PglX may coordinate interactions between the methylase and other BREX system proteins.
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Affiliation(s)
| | - Kelly T. Hughes
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
| | - Theodore G. Liou
- Department of Internal Medicine, University of Utah, Salt Lake City, Utah, USA
- Center for Quantitative Biology, University of Utah, Salt Lake City, Utah, USA
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Kelly A, Went SC, Mariano G, Shaw LP, Picton DM, Duffner SJ, Coates I, Herdman-Grant R, Gordeeva J, Drobiazko A, Isaev A, Lee YJ, Luyten Y, Morgan RD, Weigele P, Severinov K, Wenner N, Hinton JCD, Blower TR. Diverse Durham collection phages demonstrate complex BREX defense responses. Appl Environ Microbiol 2023; 89:e0062323. [PMID: 37668405 PMCID: PMC10537673 DOI: 10.1128/aem.00623-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/10/2023] [Indexed: 09/06/2023] Open
Abstract
Bacteriophages (phages) outnumber bacteria ten-to-one and cause infections at a rate of 1025 per second. The ability of phages to reduce bacterial populations makes them attractive alternative antibacterials for use in combating the rise in antimicrobial resistance. This effort may be hindered due to bacterial defenses such as Bacteriophage Exclusion (BREX) that have arisen from the constant evolutionary battle between bacteria and phages. For phages to be widely accepted as therapeutics in Western medicine, more must be understood about bacteria-phage interactions and the outcomes of bacterial phage defense. Here, we present the annotated genomes of 12 novel bacteriophage species isolated from water sources in Durham, UK, during undergraduate practical classes. The collection includes diverse species from across known phylogenetic groups. Comparative analyses of two novel phages from the collection suggest they may be founding members of a new genus. Using this Durham phage collection, we determined that particular BREX defense systems were likely to confer a varied degree of resistance against an invading phage. We concluded that the number of BREX target motifs encoded in the phage genome was not proportional to the degree of susceptibility. IMPORTANCE Bacteriophages have long been the source of tools for biotechnology that are in everyday use in molecular biology research laboratories worldwide. Phages make attractive new targets for the development of novel antimicrobials. While the number of phage genome depositions has increased in recent years, the expected bacteriophage diversity remains underrepresented. Here we demonstrate how undergraduates can contribute to the identification of novel phages and that a single City in England can provide ample phage diversity and the opportunity to find novel technologies. Moreover, we demonstrate that the interactions and intricacies of the interplay between bacterial phage defense systems such as Bacteriophage Exclusion (BREX) and phages are more complex than originally thought. Further work will be required in the field before the dynamic interactions between phages and bacterial defense systems are fully understood and integrated with novel phage therapies.
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Affiliation(s)
- Abigail Kelly
- Department of Biosciences, Durham University, Durham, UK
| | - Sam C. Went
- Department of Biosciences, Durham University, Durham, UK
| | - Giuseppina Mariano
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Liam P. Shaw
- Department of Biosciences, Durham University, Durham, UK
- Department of Biology, University of Oxford, Oxford, UK
| | | | | | - Isabel Coates
- Department of Biosciences, Durham University, Durham, UK
| | | | - Julia Gordeeva
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Alena Drobiazko
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Artem Isaev
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Yan-Jiun Lee
- New England Biolabs, Ipswich, Massachusetts, USA
| | | | | | | | | | - Nicolas Wenner
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Jay C. D. Hinton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Tim R. Blower
- Department of Biosciences, Durham University, Durham, UK
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Zhao J, Zhang M, Hui W, Zhang Y, Wang J, Wang S, Kwok LY, Kong J, Zhang H, Zhang W. Roles of adenine methylation in the physiology of Lacticaseibacillus paracasei. Nat Commun 2023; 14:2635. [PMID: 37149616 PMCID: PMC10164179 DOI: 10.1038/s41467-023-38291-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 04/21/2023] [Indexed: 05/08/2023] Open
Abstract
Lacticaseibacillus paracasei is an economically important bacterial species, used in the food industry and as a probiotic. Here, we investigate the roles of N6-methyladenine (6mA) modification in L. paracasei using multi-omics and high-throughput chromosome conformation capture (Hi-C) analyses. The distribution of 6mA-modified sites varies across the genomes of 28 strains, and appears to be enriched near genes involved in carbohydrate metabolism. A pglX mutant, defective in 6mA modification, shows transcriptomic alterations but only modest changes in growth and genomic spatial organization.
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Affiliation(s)
- Jie Zhao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Meng Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Wenyan Hui
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Yue Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Jing Wang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Shaojing Wang
- Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Jian Kong
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China
| | - Wenyi Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot, 010018, China.
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot, 010018, China.
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, China.
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mobileOG-db: a Manually Curated Database of Protein Families Mediating the Life Cycle of Bacterial Mobile Genetic Elements. Appl Environ Microbiol 2022; 88:e0099122. [PMID: 36036594 PMCID: PMC9499024 DOI: 10.1128/aem.00991-22] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacterial mobile genetic elements (MGEs) encode functional modules that perform both core and accessory functions for the element, the latter of which are often only transiently associated with the element. The presence of these accessory genes, which are often close homologs to primarily immobile genes, incur high rates of false positives and, therefore, limits the usability of these databases for MGE annotation. To overcome this limitation, we analyzed 10,776,849 protein sequences derived from eight MGE databases to compile a comprehensive set of 6,140 manually curated protein families that are linked to the “life cycle” (integration/excision, replication/recombination/repair, transfer, stability/transfer/defense, and phage-specific processes) of plasmids, phages, integrative, transposable, and conjugative elements. We overlay experimental information where available to create a tiered annotation scheme of high-quality annotations and annotations inferred exclusively through bioinformatic evidence. We additionally provide an MGE-class label for each entry (e.g., plasmid or integrative element), and assign to each entry a major and minor category. The resulting database, mobileOG-db (for mobile orthologous groups), comprises over 700,000 deduplicated sequences encompassing five major mobileOG categories and more than 50 minor categories, providing a structured language and interpretable basis for an array of MGE-centered analyses. mobileOG-db can be accessed at mobileogdb.flsi.cloud.vt.edu/, where users can select, refine, and analyze custom subsets of the dynamic mobilome. IMPORTANCE The analysis of bacterial mobile genetic elements (MGEs) in genomic data is a critical step toward profiling the root causes of antibiotic resistance, phenotypic or metabolic diversity, and the evolution of bacterial genera. Existing methods for MGE annotation pose high barriers of biological and computational expertise to properly harness. To bridge this gap, we systematically analyzed 10,776,849 proteins derived from eight databases of MGEs to identify 6,140 MGE protein families that can serve as candidate hallmarks, i.e., proteins that can be used as “signatures” of MGEs to aid annotation. The resulting resource, mobileOG-db, provides a multilevel classification scheme that encompasses plasmid, phage, integrative, and transposable element protein families categorized into five major mobileOG categories and more than 50 minor categories. mobileOG-db thus provides a rich resource for simple and intuitive element annotation that can be integrated seamlessly into existing MGE detection pipelines and colocalization analyses.
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Hui W, Zhang W, Li J, Kwok LY, Zhang H, Kong J, Sun T. Functional analysis of the second methyltransferase in the bacteriophage exclusion system of Lactobacillus casei Zhang. J Dairy Sci 2022; 105:2049-2057. [PMID: 34998557 DOI: 10.3168/jds.2021-21000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/13/2021] [Indexed: 01/21/2023]
Abstract
The antiphage ability is an important feature of fermentation strains in the dairy industry. Our previous work described the bacteriophage exclusion (BREX) system in the probiotic strain, Lactobacillus casei Zhang. The function of L. casei Zhang pglX gene in mediating 5'-ACRCm6AG-3' methylation was also confirmed. This study aimed to further dissect the function of the BREX system of L. casei Zhang by inactivating its second methyltransferase gene (LCAZH_2054). The methylome of the mutant, L. casei Zhang Δ2054, was profiled by single-molecule real-time sequencing. Then, the cell morphology, growth, plasmid transformation efficiency, and stability of the wildtype and mutant were compared. The mutant did not have an observable effect in microscopic and colony morphology, but it reached a higher cell density after entering the exponential phase without obvious increase in the cell viability. The mutant had fewer 5'-ACRCm6AG-3' methylation compared with the wildtype (1835 versus 1906). Interestingly, no significant difference was observed in the transformation efficiency between the 2 strains when plasmids without cognate recognition sequence (pSec:Leiss:Nuc and pG+host9) were transformed, contrasting to transforming cells with cognate recognition sequence-containing plasmids (pMSP3535 and pTRKH2). The efficiency of transforming pMSP3535 into the LCAZH_2054 mutant was significantly lower than the wildtype, whereas an opposite trend was seen in pTRKH2 transformation. Moreover, compared with the wildtype, the mutant strain had higher capacity in retaining pMSP3535 and lower capacity in retaining pTRKH2, suggesting an unequal tolerance level to different foreign DNA. In conclusion, LCAZH_2054 was not directly responsible for 5'-ACRCm6AG-3' methylation in L. casei Zhang, but it might help regulate the function and specificity of the BREX system.
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Affiliation(s)
- Wenyan Hui
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, P. R. China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot 010018, P. R. China
| | - Wenyi Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, P. R. China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot 010018, P. R. China
| | - Jing Li
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, P. R. China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot 010018, P. R. China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, P. R. China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot 010018, P. R. China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, P. R. China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot 010018, P. R. China
| | - Jian Kong
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, P. R. China.
| | - Tiansong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, P. R. China; Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Hohhot 010018, P. R. China.
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Beck IN, Picton DM, Blower TR. Crystal structure of the BREX phage defence protein BrxA. Curr Res Struct Biol 2022; 4:211-219. [PMID: 35783086 PMCID: PMC9240713 DOI: 10.1016/j.crstbi.2022.06.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/13/2022] [Accepted: 06/01/2022] [Indexed: 11/24/2022] Open
Abstract
Bacteria are constantly challenged by bacteriophage (phage) infection and have developed multitudinous and varied resistance mechanisms. Bacteriophage Exclusion (BREX) systems protect from phage infection by generating methylation patterns at non-palindromic 6 bp sites in host bacterial DNA, to distinguish and block replication of non-self DNA. Type 1 BREX systems are comprised of six conserved core genes. Here, we present the first reported structure of a BREX core protein, BrxA from the phage defence island of Escherichia fergusonii ATCC 35469 plasmid pEFER, solved to 2.09 Å. BrxA is a monomeric protein in solution, with an all α-helical globular fold. Conservation of surface charges and structural homology modelling against known phage defence systems highlighted that BrxA contains two helix-turn-helix motifs, juxtaposed by 180°, positioned to bind opposite sides of a DNA major groove. BrxA was subsequently shown to bind dsDNA. This new understanding of BrxA structure, and first indication of BrxA biological activity, suggests a conserved mode of DNA-recognition has become widespread and implemented by diverse phage defence systems. The crystal structure of BrxA from multi-drug resistant plasmid pEFER of Escherichia fergusonii has been solved to 2.09 Å. BrxA is the first reported structure for a conserved core protein from the widespread BREX phage defence systems. BrxA contains two HTH motifs, analogous to DNA-binding domains of diverse phage defence systems, and is shown to bind dsDNA.
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Luyten Y, Hausman DE, Young JC, Doyle L, Higashi K, Ubilla-Rodriguez N, Lambert AR, Arroyo CS, Forsberg K, Morgan R, Stoddard B, Kaiser B. OUP accepted manuscript. Nucleic Acids Res 2022; 50:5171-5190. [PMID: 35511079 PMCID: PMC9122589 DOI: 10.1093/nar/gkac311] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 11/16/2022] Open
Abstract
Bacteriophage exclusion (‘BREX’) phage restriction systems are found in a wide range of bacteria. Various BREX systems encode unique combinations of proteins that usually include a site-specific methyltransferase; none appear to contain a nuclease. Here we describe the identification and characterization of a Type I BREX system from Acinetobacter and the effect of deleting each BREX ORF on growth, methylation, and restriction. We identified a previously uncharacterized gene in the BREX operon that is dispensable for methylation but involved in restriction. Biochemical and crystallographic analyses of this factor, which we term BrxR (‘BREX Regulator’), demonstrate that it forms a homodimer and specifically binds a DNA target site upstream of its transcription start site. Deletion of the BrxR gene causes cell toxicity, reduces restriction, and significantly increases the expression of BrxC. In contrast, the introduction of a premature stop codon into the BrxR gene, or a point mutation blocking its DNA binding ability, has little effect on restriction, implying that the BrxR coding sequence and BrxR protein play independent functional roles. We speculate that elements within the BrxR coding sequence are involved in cis regulation of anti-phage activity, while the BrxR protein itself plays an additional regulatory role, perhaps during horizontal transfer.
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Affiliation(s)
- Yvette A Luyten
- New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | - Deanna E Hausman
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA 98109, USA
| | - Juliana C Young
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA 98109, USA
| | - Lindsey A Doyle
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA 98109, USA
| | - Kerilyn M Higashi
- Department of Biology, Seattle University, 901 12th Avenue, Seattle, WA 98122, USA
| | - Natalia C Ubilla-Rodriguez
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA 98109, USA
| | - Abigail R Lambert
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA 98109, USA
| | - Corina S Arroyo
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA 98109, USA
| | - Kevin J Forsberg
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. North, Seattle, WA 98109, USA
| | | | - Barry L Stoddard
- To whom correspondence should be addressed. Tel: +1 206 667 4031;
| | - Brett K Kaiser
- Correspondence may also be addressed to Brett K. Kaiser. Tel: +1 206 220 8266;
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10
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Ren J, Lee HM, Shen J, Na D. Advanced biotechnology using methyltransferase and its applications in bacteria: a mini review. Biotechnol Lett 2021; 44:33-44. [PMID: 34820721 DOI: 10.1007/s10529-021-03208-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/12/2021] [Indexed: 11/26/2022]
Abstract
Since prokaryotic restriction-modification (RM) systems protect the host by cleaving foreign DNA by restriction endonucleases, it is difficult to introduce engineered plasmid DNAs into newly isolated microorganisms whose RM system is not discovered. The prokaryotes also possess methyltransferases to protect their own DNA from the endonucleases. As those methyltransferases can be utilized to methylate engineered plasmid DNAs before transformation and to enhance the stability within the cells, the study on methyltransferases in newly isolated bacteria is essential for genetic engineering. Here, we introduce the mechanism of the RM system, specifically the methyltransferases and their biotechnological applications. These biotechnological strategies could facilitate plasmid DNA-based genetic engineering in bacteria strains that strongly defend against foreign DNA.
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Affiliation(s)
- Jun Ren
- Department of Biomedical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Hyang-Mi Lee
- Department of Biomedical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - JunHao Shen
- Department of Biomedical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Dokyun Na
- Department of Biomedical Engineering, Chung-Ang University, Seoul, 06974, Republic of Korea.
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11
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Picton DM, Luyten YA, Morgan RD, Nelson A, Smith DL, Dryden DTF, Hinton JCD, Blower TR. The phage defence island of a multidrug resistant plasmid uses both BREX and type IV restriction for complementary protection from viruses. Nucleic Acids Res 2021; 49:11257-11273. [PMID: 34657954 PMCID: PMC8565348 DOI: 10.1093/nar/gkab906] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/20/2021] [Accepted: 09/23/2021] [Indexed: 01/21/2023] Open
Abstract
Bacteria have evolved a multitude of systems to prevent invasion by bacteriophages and other mobile genetic elements. Comparative genomics suggests that genes encoding bacterial defence mechanisms are often clustered in 'defence islands', providing a concerted level of protection against a wider range of attackers. However, there is a comparative paucity of information on functional interplay between multiple defence systems. Here, we have functionally characterised a defence island from a multidrug resistant plasmid of the emerging pathogen Escherichia fergusonii. Using a suite of thirty environmentally-isolated coliphages, we demonstrate multi-layered and robust phage protection provided by a plasmid-encoded defence island that expresses both a type I BREX system and the novel GmrSD-family type IV DNA modification-dependent restriction enzyme, BrxU. We present the structure of BrxU to 2.12 Å, the first structure of the GmrSD family of enzymes, and show that BrxU can utilise all common nucleotides and a wide selection of metals to cleave a range of modified DNAs. Additionally, BrxU undergoes a multi-step reaction cycle instigated by an unexpected ATP-dependent shift from an intertwined dimer to monomers. This direct evidence that bacterial defence islands can mediate complementary layers of phage protection enhances our understanding of the ever-expanding nature of phage-bacterial interactions.
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Affiliation(s)
- David M Picton
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Yvette A Luyten
- New England Biolabs, 240 County Road, Ipswich, MA 01938, USA
| | | | - Andrew Nelson
- Department of Applied Sciences, University of Northumbria, Newcastle Upon Tyne NE1 8ST, UK
| | - Darren L Smith
- Department of Applied Sciences, University of Northumbria, Newcastle Upon Tyne NE1 8ST, UK
| | - David T F Dryden
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
| | - Jay C D Hinton
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool L69 7ZB, UK
| | - Tim R Blower
- Department of Biosciences, Durham University, Stockton Road, Durham DH1 3LE, UK
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12
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Huang Z, Zhang Z, Tong J, Malakar PK, Chen L, Liu H, Pan Y, Zhao Y. Phages and their lysins: Toolkits in the battle against foodborne pathogens in the postantibiotic era. Compr Rev Food Sci Food Saf 2021; 20:3319-3343. [PMID: 33938116 DOI: 10.1111/1541-4337.12757] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 12/13/2022]
Abstract
Worldwide, foods waste caused by putrefactive organisms and diseases caused by foodborne pathogens persist as public health problems even with a plethora of modern antimicrobials. Our over reliance on antimicrobials use in agriculture, medicine, and other fields will lead to a postantibiotic era where bacterial genotypic resistance, phenotypic adaptation, and other bacterial evolutionary strategies cause antimicrobial resistance (AMR). This AMR is evidenced by the emergence of multiple drug-resistant (MDR) bacteria and pan-resistant (PDR) bacteria, which produces cross-contamination in multiple fields and poses a more serious threat to food safety. A "red queen premise" surmises that the coevolution of phages and bacteria results in an evolutionary arms race that compels phages to adapt and survive bacterial antiphage strategies. Phages and their lysins are therefore useful toolkits in the design of novel antimicrobials in food protection and foodborne pathogens control, and the modality of using phages as a targeted vector against foodborne pathogens is gaining momentum based on many encouraging research outcomes. In this review, we discuss the rationale of using phages and their lysins as weapons against spoilage organisms and foodborne pathogens, and outline the targeted conquest or dodge mechanism of phages and the development of novel phage prospects. We also highlight the implementation of phages and their lysins to control foodborne pathogens in a farm-table-hospital domain in the postantibiotic era.
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Affiliation(s)
- Zhenhua Huang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Zhaohuan Zhang
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Jinrong Tong
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Pradeep K Malakar
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Liangbiao Chen
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, 201306, China
| | - Haiquan Liu
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai, China.,Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China
| | - Yingjie Pan
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai, China.,Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China
| | - Yong Zhao
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.,Laboratory of Quality & Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture and Rural Affairs, Shanghai, China.,Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China
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