1
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Sperfeld M, Narváez-Barragán DA, Malitsky S, Frydman V, Yuda L, Rocha J, Segev E. Algal methylated compounds shorten the lag phase of Phaeobacter inhibens bacteria. Nat Microbiol 2024; 9:2006-2021. [PMID: 38969820 PMCID: PMC11306105 DOI: 10.1038/s41564-024-01742-6] [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: 01/12/2024] [Accepted: 05/22/2024] [Indexed: 07/07/2024]
Abstract
The lag phase is key in resuming bacterial growth, but it remains underexplored particularly in environmental bacteria. Here we use transcriptomics and 13C-labelled metabolomics to show that the lag phase of the model marine bacterium Phaeobacter inhibens is shortened by methylated compounds produced by the microalgal partner, Emiliania huxleyi. Methylated compounds are abundantly produced and released by microalgae, and we show that their methyl groups can be collected by bacteria and assimilated through the methionine cycle. Our findings underscore the significance of methyl groups as a limiting factor during the lag phase and highlight the adjustability of this growth phase. In addition, we show that methylated compounds, typical of photosynthetic organisms, prompt diverse reductions in lag times in bacteria associated with algae and plants, potentially favouring early growth in some bacteria. These findings suggest ways to accelerate bacterial growth and underscore the significance of studying bacteria within an environmental context.
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Affiliation(s)
- Martin Sperfeld
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
- Institute of Microbiology, ETH, Zurich, Switzerland
| | | | - Sergey Malitsky
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Veronica Frydman
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, Israel
| | - Lilach Yuda
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Jorge Rocha
- Agricultura en Zonas Áridas, Centro de Investigaciones Biológicas del Noroeste, La Paz, Mexico
| | - Einat Segev
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
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2
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Won C, Yim SS. Emerging methylation-based approaches in microbiome engineering. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:96. [PMID: 38987811 PMCID: PMC11238421 DOI: 10.1186/s13068-024-02529-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 06/10/2024] [Indexed: 07/12/2024]
Abstract
Bacterial epigenetics, particularly through DNA methylation, exerts significant influence over various biological processes such as DNA replication, uptake, and gene regulation in bacteria. In this review, we explore recent advances in characterizing bacterial epigenomes, accompanied by emerging strategies that harness bacterial epigenetics to elucidate and engineer diverse bacterial species with precision and effectiveness. Furthermore, we delve into the potential of epigenetic modifications to steer microbial functions and influence community dynamics, offering promising opportunities for understanding and modulating microbiomes. Additionally, we investigate the extensive diversity of DNA methyltransferases and emphasize their potential utility in the context of the human microbiome. In summary, this review highlights the potential of DNA methylation as a powerful toolkit for engineering microbiomes.
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Affiliation(s)
- Changhee Won
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Sung Sun Yim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
- Graduate School of Engineering Biology, KAIST, Daejeon, Republic of Korea.
- KAIST Institute for BioCentury, KAIST, Daejeon, Republic of Korea.
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea.
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3
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Beamud B, Benz F, Bikard D. Going viral: The role of mobile genetic elements in bacterial immunity. Cell Host Microbe 2024; 32:804-819. [PMID: 38870898 DOI: 10.1016/j.chom.2024.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 05/17/2024] [Accepted: 05/20/2024] [Indexed: 06/15/2024]
Abstract
Bacteriophages and other mobile genetic elements (MGEs) pose a significant threat to bacteria, subjecting them to constant attacks. In response, bacteria have evolved a sophisticated immune system that employs diverse defensive strategies and mechanisms. Remarkably, a growing body of evidence suggests that most of these defenses are encoded by MGEs themselves. This realization challenges our traditional understanding of bacterial immunity and raises intriguing questions about the evolutionary forces at play. Our review provides a comprehensive overview of the latest findings on the main families of MGEs and the defense systems they encode. We also highlight how a vast diversity of defense systems remains to be discovered and their mechanism of mobility understood. Altogether, the composition and distribution of defense systems in bacterial genomes only makes sense in the light of the ecological and evolutionary interactions of a complex network of MGEs.
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Affiliation(s)
- Beatriz Beamud
- Institut Pasteur, Université de Paris, Synthetic Biology, 75015 Paris, France.
| | - Fabienne Benz
- Institut Pasteur, Université de Paris, Synthetic Biology, 75015 Paris, France; Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, 75015 Paris, France
| | - David Bikard
- Institut Pasteur, Université de Paris, Synthetic Biology, 75015 Paris, France.
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4
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Wang WH, Li ZR, Zhu DX, Chen JY, Zhou Y, Li CP, Shao LH, Qiu XM, Zhu M, Long HT, Chen DP, Ouyang GP, Rong ZQ, Wang ZC. Design, synthesis, antibacterial evaluation of isopropylamine linked with different substituted phenol and piperazine novel derivatives. PEST MANAGEMENT SCIENCE 2024; 80:2710-2723. [PMID: 38358029 DOI: 10.1002/ps.7986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/02/2024] [Accepted: 01/14/2024] [Indexed: 02/16/2024]
Abstract
BACKGROUND Xanthomonas oryzae pv. oryzae (Xoo) is often considered one of the most destructive bacterial pathogens causing bacterial leaf blight (BLB), resulting in significant yield and cost losses in rice. In this study, a series of novel derivatives containing the isopropanolamine moiety linked to various substituted phenols and piperazines were designed, synthesized and screened. RESULTS Antibacterial activity results showed that most compounds had good inhibitory effects on Xoo, among which compound W2 (EC50 = 2.74 μg mL-1) exhibited the most excellent inhibitory activity, and W2 also had a certain curative effect (35.89%) on rice compared to thiodiazole copper (TC) (21.57%). Scanning electron microscopy (SEM) results indicated that compound W2 could cause rupture of the Xoo cell membrane. Subsequently, proteomics and quantitative real-time polymerase chain reaction revealed that compound W2 affected the physiological processes of Xoo and may exert antibacterial activity by targeting the two-component system pathway. Interestingly, W2 upregulated Xoo's methyltransferase to impact on its pathogenicity. CONCLUSION The present study offers a promising phenolic-piperazine-sopropanolamine compound as an innovative antibacterial strategy by specifically targeting the two-component system pathway and inducing upregulation of methyltransferase to effectively impact Xoo's pathogenicity. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Wen-Hang Wang
- College of Pharmacy, Guizhou University, Guiyang, People's Republic of China
| | - Zhu-Rui Li
- College of Pharmacy, Guizhou University, Guiyang, People's Republic of China
| | - Dan-Xue Zhu
- College of Pharmacy, Guizhou University, Guiyang, People's Republic of China
| | - Jia-Yi Chen
- College of Pharmacy, Guizhou University, Guiyang, People's Republic of China
| | - Yue Zhou
- College of Pharmacy, Guizhou University, Guiyang, People's Republic of China
| | - Cheng-Peng Li
- College of Pharmacy, Guizhou University, Guiyang, People's Republic of China
| | - Li-Hui Shao
- College of Pharmacy, Guizhou University, Guiyang, People's Republic of China
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, People's Republic of China
| | - Xue-Mei Qiu
- College of Pharmacy, Guizhou University, Guiyang, People's Republic of China
| | - Mei Zhu
- College of Pharmacy, Guizhou University, Guiyang, People's Republic of China
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, People's Republic of China
| | - Hai-Tao Long
- College of Pharmacy, Guizhou University, Guiyang, People's Republic of China
- Guizhou Engineering Laboratory for Synthetic Drugs, Guizhou University, Guiyang, People's Republic of China
| | - Dan-Ping Chen
- College of Pharmacy, Guizhou University, Guiyang, People's Republic of China
- Guizhou Engineering Laboratory for Synthetic Drugs, Guizhou University, Guiyang, People's Republic of China
| | - Gui-Ping Ouyang
- College of Pharmacy, Guizhou University, Guiyang, People's Republic of China
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, People's Republic of China
| | - Zi-Qiang Rong
- Frontiers Science Center for Flexible Electronics (FSCFE), Shaanxi Institute of Flexible Electronics (SIFE) & Shaanxi Institute of Biomedical Materials and Engineering (SIBME), Northwestern Polytechnical University (NPU), Xi'an, People's Republic of China
| | - Zhen-Chao Wang
- College of Pharmacy, Guizhou University, Guiyang, People's Republic of China
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, People's Republic of China
- Guizhou Engineering Laboratory for Synthetic Drugs, Guizhou University, Guiyang, People's Republic of China
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5
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Liu J, Zhang Y, Zhou N, He J, Xu J, Cai Z, Yang L, Liu Y. Bacmethy: A novel and convenient tool for investigating bacterial DNA methylation pattern and their transcriptional regulation effects. IMETA 2024; 3:e186. [PMID: 38898993 PMCID: PMC11183182 DOI: 10.1002/imt2.186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 06/21/2024]
Abstract
DNA methylation serves as the primary mode of epigenetic regulation in prokaryotes, particularly through transcriptional regulation. With the rapid implementation of third-generation sequencing technology, we are currently experiencing a golden age of bacterial epigenomics. However, there has been a lack of comprehensive research exploring the versatility and consequential impact of bacterial DNA methylome on cellular and physiological functions. There is a critical need for a user-friendly bioinformatics tool that can effectively characterize DNA methylation modification features and predict the regulation patterns. To address this gap, the current study introduces Bacmethy, an innovative tool that utilizes SMRT-seq data and offers a range of analytical modules. First, the tool classifies methylation sites in the genome, highlighting the distinct regulations present under varying modification fractions and location enrichment. Furthermore, this tool enables us to identify regulatory region methylation and potential cis and trans interactions between methylation sites and regulatory effectors. Using benchmark data sets and our data, we show that our tool facilitates the understanding of the distinctive traits of DNA methylation modifications and predicts transcriptional regulation effects on important physiological and pathological functions. Bacmethy code is freely available, and the Docker image is downloadable. Bacmethy has been made available as a user-friendly web server interface at https://bacmethy.med.sustech.edu.cn.
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Affiliation(s)
- Ji‐Hong Liu
- Medical Research CenterSouthern University of Science and Technology HospitalShenzhenChina
- School of Medicine, Key University Laboratory of Metabolism and Health of GuangdongSouthern University of Science and TechnologyShenzhenChina
| | - Yizhou Zhang
- Medical Research CenterSouthern University of Science and Technology HospitalShenzhenChina
- School of Medicine, Key University Laboratory of Metabolism and Health of GuangdongSouthern University of Science and TechnologyShenzhenChina
| | - Ning Zhou
- Clinical LaboratorySouthern University of Science and Technology HospitalShenzhenChina
| | - Jiale He
- Medical Research CenterSouthern University of Science and Technology HospitalShenzhenChina
- School of Medicine, Key University Laboratory of Metabolism and Health of GuangdongSouthern University of Science and TechnologyShenzhenChina
| | - Jing Xu
- Medical Research CenterSouthern University of Science and Technology HospitalShenzhenChina
| | - Zhao Cai
- School of Medicine, Key University Laboratory of Metabolism and Health of GuangdongSouthern University of Science and TechnologyShenzhenChina
| | - Liang Yang
- School of Medicine, Key University Laboratory of Metabolism and Health of GuangdongSouthern University of Science and TechnologyShenzhenChina
- Shenzhen Third People's Hospital, The Second Affiliated Hospital of Southern University of Science and TechnologyNational Clinical Research Center for Infectious DiseaseShenzhenChina
| | - Yang Liu
- Medical Research CenterSouthern University of Science and Technology HospitalShenzhenChina
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6
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Passeri I, Vaccaro F, Mengoni A, Fagorzi C. Moving toward the Inclusion of Epigenomics in Bacterial Genome Evolution: Perspectives and Challenges. Int J Mol Sci 2024; 25:4425. [PMID: 38674013 PMCID: PMC11050019 DOI: 10.3390/ijms25084425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 04/05/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
The universality of DNA methylation as an epigenetic regulatory mechanism belongs to all biological kingdoms. However, while eukaryotic systems have been the primary focus of DNA methylation studies, the molecular mechanisms in prokaryotes are less known. Nevertheless, DNA methylation in prokaryotes plays a pivotal role in many cellular processes such as defense systems against exogenous DNA, cell cycle dynamics, and gene expression, including virulence. Thanks to single-molecule DNA sequencing technologies, genome-wide identification of methylated DNA is becoming feasible on a large scale, providing the possibility to investigate more deeply the presence, variability, and roles of DNA methylation. Here, we present an overview of the multifaceted roles of DNA methylation in prokaryotes and suggest research directions and tools which can enable us to better understand the contribution of DNA methylation to prokaryotic genome evolution and adaptation. In particular, we emphasize the need to understand the presence and role of transgenerational inheritance, as well as the impact of epigenomic signatures on adaptation and genome evolution. Research directions and the importance of novel computational tools are underlined.
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Affiliation(s)
| | | | - Alessio Mengoni
- Department of Biology, University of Florence, 50121 Firenze, Italy; (I.P.); (F.V.); (C.F.)
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7
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Sperfeld M, Narváez-Barragán DA, Malitsky S, Frydman V, Yuda L, Rocha J, Segev E. Reducing the Bacterial Lag Phase Through Methylated Compounds: Insights from Algal-Bacterial Interactions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.06.543872. [PMID: 38645154 PMCID: PMC11030247 DOI: 10.1101/2023.06.06.543872] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
The bacterial lag phase is a key period for resuming growth. Despite its significance, the lag phase remains underexplored, particularly in environmental bacteria. Here, we explore the lag phase of the model marine bacterium Phaeobacter inhibens when it transitions from starvation to growth with a microalgal partner. Utilizing transcriptomics and 13 C-labeled metabolomics, our study reveals that methylated compounds, which are abundantly produced by microalgae, shorten the bacterial lag phase. Our findings underscore the significance of methyl groups as a limiting factor during the lag phase and demonstrate that methyl groups can be harvested from algal compounds and assimilated through the methionine cycle. Furthermore, we show that methylated compounds, characteristic of photosynthetic organisms, induce variable reductions in lag times among bacteria associated with algae and plants. These findings highlight the adjustability of the bacterial lag phase and emphasize the importance of studying bacteria in an environmental context. One-Sentence Summary Bacteria use algal compounds as a metabolic shortcut to transition from starvation to growth.
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8
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Beavogui A, Lacroix A, Wiart N, Poulain J, Delmont TO, Paoli L, Wincker P, Oliveira PH. The defensome of complex bacterial communities. Nat Commun 2024; 15:2146. [PMID: 38459056 PMCID: PMC10924106 DOI: 10.1038/s41467-024-46489-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 02/28/2024] [Indexed: 03/10/2024] Open
Abstract
Bacteria have developed various defense mechanisms to avoid infection and killing in response to the fast evolution and turnover of viruses and other genetic parasites. Such pan-immune system (defensome) encompasses a growing number of defense lines that include well-studied innate and adaptive systems such as restriction-modification, CRISPR-Cas and abortive infection, but also newly found ones whose mechanisms are still poorly understood. While the abundance and distribution of defense systems is well-known in complete and culturable genomes, there is a void in our understanding of their diversity and richness in complex microbial communities. Here we performed a large-scale in-depth analysis of the defensomes of 7759 high-quality bacterial population genomes reconstructed from soil, marine, and human gut environments. We observed a wide variation in the frequency and nature of the defensome among large phyla, which correlated with lifestyle, genome size, habitat, and geographic background. The defensome's genetic mobility, its clustering in defense islands, and genetic variability was found to be system-specific and shaped by the bacterial environment. Hence, our results provide a detailed picture of the multiple immune barriers present in environmentally distinct bacterial communities and set the stage for subsequent identification of novel and ingenious strategies of diversification among uncultivated microbes.
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Affiliation(s)
- Angelina Beavogui
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Auriane Lacroix
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Nicolas Wiart
- Genoscope, Institut François Jacob, CEA, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
| | - Julie Poulain
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 / Tara GOsee, Paris, France
| | - Tom O Delmont
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 / Tara GOsee, Paris, France
| | - Lucas Paoli
- Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, 8093, Switzerland
- Institut Pasteur, Université Paris Cité, INSERM U1284, Molecular Diversity of Microbes lab, Paris, France
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022 / Tara GOsee, Paris, France
| | - Pedro H Oliveira
- Génomique Métabolique, Genoscope, Institut François Jacob, Commissariat à l'Energie Atomique (CEA), CNRS, Université Evry, Université Paris-Saclay, 2 Rue Gaston Crémieux, 91057, Evry, France.
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9
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Alamri A, Bin Abbas A, Al Hassan E, Almogbel Y. Development of a Prediction Model to Identify the Risk of Clostridioides difficile Infection in Hospitalized Patients Receiving at Least One Dose of Antibiotics. PHARMACY 2024; 12:37. [PMID: 38392945 PMCID: PMC10892393 DOI: 10.3390/pharmacy12010037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/30/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
OBJECTIVE This study's objective was to develop a risk-prediction model to identify hospitalized patients at risk of Clostridioides difficile infection (CDI) who had received at least one dose of systemic antibiotics in a large tertiary hospital. PATIENTS AND METHODS This was a retrospective case-control study that included patients hospitalized for more than 2 days who received antibiotic therapy during hospitalization. The study included two groups: patients diagnosed with hospital CDI and controls without hospital CDI. Cases were matched 1:3 with assigned controls by age and sex. Descriptive statistics were used to identify the study population by comparing cases with controls. Continuous variables were stated as the means and standard deviations. A multivariate analysis was built to identify the significantly associated covariates between cases and controls for CDI. RESULTS A total of 364 patients were included and distributed between the two groups. The control group included 273 patients, and the case group included 91 patients. The risk factors for CDI were investigated, with only significant risks identified and included in the risk assessment model: age older than 70 years (p = 0.034), chronic kidney disease (p = 0.043), solid organ transplantation (p = 0.021), and lymphoma or leukemia (p = 0.019). A risk score of ≥2 showed the best sensitivity, specificity, and accuracy of 78.02%, 45.42%, and 78.02, respectively, with an area under the curve of 0.6172. CONCLUSION We identified four associated risk factors in the risk-prediction model. The tool showed good discrimination that might help predict, identify, and evaluate hospitalized patients at risk of developing CDI.
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Affiliation(s)
- Abdulrahman Alamri
- Pharmaceutical Care Services, Ministry of the National Guard Health Affairs, Riyadh 11426, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
- Department of Pharmacy Practice, College of Pharmacy, King Saud bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia
| | - AlHanoof Bin Abbas
- Department of Pharmacy Practice, College of Pharmacy, Qassim University, Buraidah 51452, Saudi Arabia; (A.B.A.); (Y.A.)
| | - Ekram Al Hassan
- Department of Pathology and Laboratory Medicine, Ministry of the National Guard Health Affairs, Riyadh 11426, Saudi Arabia;
| | - Yasser Almogbel
- Department of Pharmacy Practice, College of Pharmacy, Qassim University, Buraidah 51452, Saudi Arabia; (A.B.A.); (Y.A.)
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10
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Cao L, Kong Y, Fan Y, Ni M, Tourancheau A, Ksiezarek M, Mead EA, Koo T, Gitman M, Zhang XS, Fang G. mEnrich-seq: methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome. Nat Methods 2024; 21:236-246. [PMID: 38177508 DOI: 10.1038/s41592-023-02125-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 11/08/2023] [Indexed: 01/06/2024]
Abstract
Metagenomics has enabled the comprehensive study of microbiomes. However, many applications would benefit from a method that sequences specific bacterial taxa of interest, but not most background taxa. We developed mEnrich-seq (in which 'm' stands for methylation and seq for sequencing) for enriching taxa of interest from metagenomic DNA before sequencing. The core idea is to exploit the self versus nonself differentiation by natural bacterial DNA methylation and rationally choose methylation-sensitive restriction enzymes, individually or in combination, to deplete host and background taxa while enriching targeted taxa. This idea is integrated with library preparation procedures and applied in several applications to enrich (up to 117-fold) pathogenic or beneficial bacteria from human urine and fecal samples, including species that are hard to culture or of low abundance. We assessed 4,601 bacterial strains with mapped methylomes so far and showed broad applicability of mEnrich-seq. mEnrich-seq provides microbiome researchers with a versatile and cost-effective approach for selective sequencing of diverse taxa of interest.
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Affiliation(s)
- Lei Cao
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yimeng Kong
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yu Fan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Mi Ni
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alan Tourancheau
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Magdalena Ksiezarek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edward A Mead
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tonny Koo
- Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Melissa Gitman
- Department of Pathology, Molecular and Cell-based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Xue-Song Zhang
- Center for Advanced Biotechnology and Medicine, Rutgers University, New Brunswick, NJ, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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11
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Quintana-Feliciano R, Kottur J, Ni M, Ghosh R, Salas-Estrada L, Rechkoblit O, Filizola M, Fang G, Aggarwal AK. Burkholderia cenocepacia epigenetic regulator M.BceJIV simultaneously engages two DNA recognition sequences for methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576384. [PMID: 38328099 PMCID: PMC10849533 DOI: 10.1101/2024.01.20.576384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Burkholderia cenocepacia is an opportunistic and infective bacterium containing an orphan DNA methyltransferase (M.BceJIV) with roles in regulating gene expression and motility of the bacterium. M.BceJIV recognizes a GTWWAC motif (where W can be an adenine or a thymine) and methylates the N6 of the adenine at the fifth base position (GTWWAC). Here, we present a high-resolution crystal structure of M.BceJIV/DNA/sinefungin ternary complex and allied biochemical, computational, and thermodynamic analyses. Remarkably, the structure shows not one, but two DNA substrates bound to the M.BceJIV dimer, wherein each monomer contributes to the recognition of two recognition sequences. This unexpected mode of DNA binding and methylation has not been observed previously and sets a new precedent for a DNA methyltransferase. We also show that methylation at two recognition sequences occurs independently, and that GTWWAC motifs are enriched in intergenic regions of a strain of B. cenocepacia's genome. We further computationally assess the interactions underlying the affinities of different ligands (SAM, SAH, and sinefungin) for M.BceJIV, as a step towards developing selective inhibitors for limiting B. cenocepacia infection.
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Affiliation(s)
- Richard Quintana-Feliciano
- Department of Pharmacological Sciences Icahn School of Medicine at Mount Sinai 1425 Madison Avenue New York, New York, USA
| | - Jithesh Kottur
- Department of Pharmacological Sciences Icahn School of Medicine at Mount Sinai 1425 Madison Avenue New York, New York, USA
| | - Mi Ni
- Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai 1425 Madison Avenue New York, New York, USA
| | - Rikhia Ghosh
- Department of Pharmacological Sciences Icahn School of Medicine at Mount Sinai 1425 Madison Avenue New York, New York, USA
| | - Leslie Salas-Estrada
- Department of Pharmacological Sciences Icahn School of Medicine at Mount Sinai 1425 Madison Avenue New York, New York, USA
| | - Olga Rechkoblit
- Department of Pharmacological Sciences Icahn School of Medicine at Mount Sinai 1425 Madison Avenue New York, New York, USA
| | - Marta Filizola
- Department of Pharmacological Sciences Icahn School of Medicine at Mount Sinai 1425 Madison Avenue New York, New York, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai 1425 Madison Avenue New York, New York, USA
| | - Aneel K. Aggarwal
- Department of Pharmacological Sciences Icahn School of Medicine at Mount Sinai 1425 Madison Avenue New York, New York, USA
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12
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Manzer HS, Doran KS. Complete m6A and m4C methylomes for group B streptococcal clinical isolates CJB111, A909, COH1, and NEM316. Microbiol Resour Announc 2024; 13:e0073323. [PMID: 38099685 PMCID: PMC10793328 DOI: 10.1128/mra.00733-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/17/2023] [Indexed: 01/18/2024] Open
Abstract
Group B Streptococcus (GBS) is known to colonize the female reproductive tract and causes adverse pregnancy outcomes and neonatal disease. DNA methylation is a common mechanism for both phage defense and transcriptional regulation. Here, we report the m6A and m4C methylomes of four clinical GBS isolates, CJB111, A909, COH1, and NEM316.
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Affiliation(s)
- Haider S. Manzer
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kelly S. Doran
- Department of Immunology and Microbiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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13
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Ding Y, Zhao L, Wang G, Shi Y, Guo G, Liu C, Chen Z, Coker OO, She J, Yu J. PacBio sequencing of human fecal samples uncovers the DNA methylation landscape of 22 673 gut phages. Nucleic Acids Res 2023; 51:12140-12149. [PMID: 37904586 PMCID: PMC10711547 DOI: 10.1093/nar/gkad977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 10/03/2023] [Accepted: 10/18/2023] [Indexed: 11/01/2023] Open
Abstract
Gut phages have an important impact on human health. Methylation plays key roles in DNA recognition, gene expression regulation and replication for phages. However, the DNA methylation landscape of gut phages is largely unknown. Here, with PacBio sequencing (2120×, 4785 Gb), we detected gut phage methylation landscape based on 22 673 gut phage genomes, and presented diverse methylation motifs and methylation differences in genomic elements. Moreover, the methylation rate of phages was associated with taxonomy and host, and N6-methyladenine methylation rate was higher in temperate phages than in virulent phages, suggesting an important role for methylation in phage-host interaction. In particular, 3543 (15.63%) phage genomes contained restriction-modification system, which could aid in evading clearance by the host. This study revealed the DNA methylation landscape of gut phage and its potential roles, which will advance the understanding of gut phage survival and human health.
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Affiliation(s)
- Yanqiang Ding
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Liuyang Zhao
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Guoping Wang
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yu Shi
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Gang Guo
- Center for Gut Microbiome Research, Department of Surgery, Med-X Institute, Department of High Talent, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Changan Liu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Zigui Chen
- Department of Microbiology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Olabisi Oluwabukola Coker
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Junjun She
- Center for Gut Microbiome Research, Department of Surgery, Med-X Institute, Department of High Talent, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, CUHK-Shenzhen Research Institute, The Chinese University of Hong Kong, Hong Kong SAR, China
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14
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Chen D, Yin Y, Hu Y, Cao L, Zhao C, Li B. Transposon-aided capture (TRACA) of plasmids from the human gut. Lett Appl Microbiol 2023; 76:ovad132. [PMID: 38031336 DOI: 10.1093/lambio/ovad132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/12/2023] [Accepted: 11/28/2023] [Indexed: 12/01/2023]
Abstract
The gut microbiota consists of a vast and diverse assemblage of microorganisms that play a pivotal role in maintaining host health. Nevertheless, a significant portion of the human gut microbiota remains uncultivated. Plasmids, a type of MGE, assume a critical function in the biological evolution and adaptation of bacteria to varying environments. To investigate the plasmids present within the gut microbiota community, we used the transposon-aided capture method (TRACA) to explore plasmids derived from the gut microbiota. In this study, fecal samples were collected from two healthy human volunteers and subsequently subjected to the TRACA method for plasmid isolation. Then, the complete sequence of the plasmids was obtained using the genome walking method, and sequence identity was also analyzed. A total of 15 plasmids were isolated. At last, 13 plasmids were successfully sequenced, of which 12 plasmids were highly identical to the plasmids in the National Center for Biotechnology Information (NCBI) database and were all small plasmids. Furthermore, a putative novel plasmid, named pMRPHD, was isolated, which had mobilized elements (oriT and oriV) and a potential type II restriction-modification (R-M) system encoded by DNA cytosine methyltransferase and type II restriction enzyme (Ban I), whose specific functions and applications warrant further exploration.
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Affiliation(s)
- Dan Chen
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Engineering Research Center for Research and Development of Plant Resources in Nanling Area, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, 130 Yangzitang Road, Lingling District, Yongzhou 425199, Hunan Province, China
| | - Yeshi Yin
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Engineering Research Center for Research and Development of Plant Resources in Nanling Area, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, 130 Yangzitang Road, Lingling District, Yongzhou 425199, Hunan Province, China
| | - Yunfei Hu
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Engineering Research Center for Research and Development of Plant Resources in Nanling Area, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, 130 Yangzitang Road, Lingling District, Yongzhou 425199, Hunan Province, China
| | - Linyan Cao
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Engineering Research Center for Research and Development of Plant Resources in Nanling Area, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, 130 Yangzitang Road, Lingling District, Yongzhou 425199, Hunan Province, China
| | - Changhui Zhao
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Engineering Research Center for Research and Development of Plant Resources in Nanling Area, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, 130 Yangzitang Road, Lingling District, Yongzhou 425199, Hunan Province, China
| | - Baiyuan Li
- Key Laboratory of Comprehensive Utilization of Advantage Plants Resources in Hunan South, Hunan Engineering Research Center for Research and Development of Plant Resources in Nanling Area, College of Chemistry and Bioengineering, Hunan University of Science and Engineering, 130 Yangzitang Road, Lingling District, Yongzhou 425199, Hunan Province, China
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15
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Stone CJ, Boyer GF, Behringer MG. Differential adenine methylation analysis reveals increased variability in 6mA in the absence of methyl-directed mismatch repair. mBio 2023; 14:e0128923. [PMID: 37796009 PMCID: PMC10653831 DOI: 10.1128/mbio.01289-23] [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: 05/30/2023] [Accepted: 08/22/2023] [Indexed: 10/06/2023] Open
Abstract
IMPORTANCE Methylation greatly influences the bacterial genome by guiding DNA repair and regulating pathogenic and stress-response phenotypes. But, the rate of epigenetic changes and their consequences on molecular phenotypes are underexplored. Through a detailed characterization of genome-wide adenine methylation in a commonly used laboratory strain of Escherichia coli, we reveal that mismatch repair deficient populations experience an increase in epimutations resulting in a genome-wide reduction of 6mA methylation in a manner consistent with genetic drift. Our findings highlight how methylation patterns evolve and the constraints on epigenetic evolution due to post-replicative DNA repair, contributing to a deeper understanding of bacterial genome evolution and how epimutations may introduce semi-permanent variation that can influence adaptation.
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Affiliation(s)
- Carl J. Stone
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Gwyneth F. Boyer
- Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, Arizona, USA
| | - Megan G. Behringer
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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16
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Sturm Á, Sharma H, Bodnár F, Aslam M, Kovács T, Németh Á, Hotzi B, Billes V, Sigmond T, Tátrai K, Egyed B, Téglás-Huszár B, Schlosser G, Charmpilas N, Ploumi C, Perczel A, Tavernarakis N, Vellai T. N6-Methyladenine Progressively Accumulates in Mitochondrial DNA during Aging. Int J Mol Sci 2023; 24:14858. [PMID: 37834309 PMCID: PMC10573865 DOI: 10.3390/ijms241914858] [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: 08/04/2023] [Revised: 09/26/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
N6-methyladenine (6mA) in the DNA is a conserved epigenetic mark with various cellular, physiological and developmental functions. Although the presence of 6mA was discovered a few years ago in the nuclear genome of distantly related animal taxa and just recently in mammalian mitochondrial DNA (mtDNA), accumulating evidence at present seriously questions the presence of N6-adenine methylation in these genetic systems, attributing it to methodological errors. In this paper, we present a reliable, PCR-based method to determine accurately the relative 6mA levels in the mtDNA of Caenorhabditis elegans, Drosophila melanogaster and dogs, and show that these levels gradually increase with age. Furthermore, daf-2(-)-mutant worms, which are defective for insulin/IGF-1 (insulin-like growth factor) signaling and live twice as long as the wild type, display a half rate at which 6mA progressively accumulates in the mtDNA as compared to normal values. Together, these results suggest a fundamental role for mtDNA N6-adenine methylation in aging and reveal an efficient diagnostic technique to determine age using DNA.
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Affiliation(s)
- Ádám Sturm
- Department of Genetics, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary; (H.S.); (B.E.)
- Genetics Research Group, Eötvös Loránd Research Network-Eötvös Loránd University, 1117 Budapest, Hungary
| | - Himani Sharma
- Department of Genetics, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary; (H.S.); (B.E.)
| | - Ferenc Bodnár
- Department of Genetics, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary; (H.S.); (B.E.)
| | - Maryam Aslam
- Department of Genetics, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary; (H.S.); (B.E.)
| | - Tibor Kovács
- Department of Genetics, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary; (H.S.); (B.E.)
| | - Ákos Németh
- Department of Genetics, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary; (H.S.); (B.E.)
| | - Bernadette Hotzi
- Department of Genetics, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary; (H.S.); (B.E.)
- Genetics Research Group, Eötvös Loránd Research Network-Eötvös Loránd University, 1117 Budapest, Hungary
| | - Viktor Billes
- Department of Genetics, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary; (H.S.); (B.E.)
- Genetics Research Group, Eötvös Loránd Research Network-Eötvös Loránd University, 1117 Budapest, Hungary
| | - Tímea Sigmond
- Department of Genetics, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary; (H.S.); (B.E.)
| | - Kitti Tátrai
- Department of Genetics, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary; (H.S.); (B.E.)
| | - Balázs Egyed
- Department of Genetics, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary; (H.S.); (B.E.)
| | - Blanka Téglás-Huszár
- Department of Genetics, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary; (H.S.); (B.E.)
| | - Gitta Schlosser
- Momentum Ion Mobility Mass Spectrometry Research Group, Hungarian Academy of Sciences-Eötvös Loránd University, 1117 Budapest, Hungary
| | - Nikolaos Charmpilas
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology-Hellas, P.O. Box 1385 Heraklion, Greece
| | - Christina Ploumi
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology-Hellas, P.O. Box 1385 Heraklion, Greece
| | - András Perczel
- Department of Organic Chemistry, Eötvös Loránd University, 1117 Budapest, Hungary
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology-Hellas, P.O. Box 1385 Heraklion, Greece
| | - Tibor Vellai
- Department of Genetics, Eötvös Loránd University, Pázmány Péter sétány 1/C, 1117 Budapest, Hungary; (H.S.); (B.E.)
- Genetics Research Group, Eötvös Loránd Research Network-Eötvös Loránd University, 1117 Budapest, Hungary
- Vellab Biotech Ltd., 6722 Szeged, Hungary
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17
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Anton BP, Roberts RJ. A Survey of Archaeal Restriction-Modification Systems. Microorganisms 2023; 11:2424. [PMID: 37894082 PMCID: PMC10609329 DOI: 10.3390/microorganisms11102424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 10/29/2023] Open
Abstract
When compared with bacteria, relatively little is known about the restriction-modification (RM) systems of archaea, particularly those in taxa outside of the haloarchaea. To improve our understanding of archaeal RM systems, we surveyed REBASE, the restriction enzyme database, to catalog what is known about the genes and activities present in the 519 completely sequenced archaeal genomes currently deposited there. For 49 (9.4%) of these genomes, we also have methylome data from Single-Molecule Real-Time (SMRT) sequencing that reveal the target recognition sites of the active m6A and m4C DNA methyltransferases (MTases). The gene-finding pipeline employed by REBASE is trained primarily on bacterial examples and so will look for similar genes in archaea. Nonetheless, the organizational structure and protein sequence of RM systems from archaea are highly similar to those of bacteria, with both groups acquiring systems from a shared genetic pool through horizontal gene transfer. As in bacteria, we observe numerous examples of "persistent" DNA MTases conserved within archaeal taxa at different levels. We experimentally validated two homologous members of one of the largest "persistent" MTase groups, revealing that methylation of C(m5C)WGG sites may play a key epigenetic role in Crenarchaea. Throughout the archaea, genes encoding m6A, m4C, and m5C DNA MTases, respectively, occur in approximately the ratio 4:2:1.
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18
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Li Z, Zhou X, Liao D, Liu R, Zhao X, Wang J, Zhong Q, Zeng Z, Peng Y, Tan Y, Yang Z. Comparative genomics and DNA methylation analysis of Pseudomonas aeruginosa clinical isolate PA3 by single-molecule real-time sequencing reveals new targets for antimicrobials. Front Cell Infect Microbiol 2023; 13:1180194. [PMID: 37662009 PMCID: PMC10471985 DOI: 10.3389/fcimb.2023.1180194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 07/31/2023] [Indexed: 09/05/2023] Open
Abstract
Introduction Pseudomonas aeruginosa (P.aeruginosa) is an important opportunistic pathogen with broad environmental adaptability and complex drug resistance. Single-molecule real-time (SMRT) sequencing technique has longer read-length sequences, more accuracy, and the ability to identify epigenetic DNA alterations. Methods This study applied SMRT technology to sequence a clinical strain P. aeruginosa PA3 to obtain its genome sequence and methylation modification information. Genomic, comparative, pan-genomic, and epigenetic analyses of PA3 were conducted. Results General genome annotations of PA3 were discovered, as well as information about virulence factors, regulatory proteins (RPs), secreted proteins, type II toxin-antitoxin (TA) pairs, and genomic islands. A genome-wide comparison revealed that PA3 was comparable to other P. aeruginosa strains in terms of identity, but varied in areas of horizontal gene transfer (HGT). Phylogenetic analysis showed that PA3 was closely related to P. aeruginosa 60503 and P. aeruginosa 8380. P. aeruginosa's pan-genome consists of a core genome of roughly 4,300 genes and an accessory genome of at least 5,500 genes. The results of the epigenetic analysis identified one main methylation sites, N6-methyladenosine (m6A) and 1 motif (CATNNNNNNNTCCT/AGGANNNNNNNATG). 16 meaningful methylated sites were picked. Among these, purH, phaZ, and lexA are of great significance playing an important role in the drug resistance and biological environment adaptability of PA3, and the targeting of these genes may benefit further antibacterial studies. Disucssion This study provided a detailed visualization and DNA methylation information of the PA3 genome and set a foundation for subsequent research into the molecular mechanism of DNA methyltransferase-controlled P. aeruginosa pathogenicity.
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Affiliation(s)
- Zijiao Li
- Department of Plastic and Cosmetic Surgery, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
- Cadet Brigade 4, College of Basic Medicine, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Xiang Zhou
- Department of Plastic and Cosmetic Surgery, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
- Cadet Brigade 4, College of Basic Medicine, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Danxi Liao
- Department of Plastic and Cosmetic Surgery, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Ruolan Liu
- Department of Plastic and Cosmetic Surgery, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Xia Zhao
- Department of Microbiology, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Jing Wang
- Department of Microbiology, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Qiu Zhong
- Department of Microbiology, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Zhuo Zeng
- Institute of Burn Research, State Key Laboratory of Trauma, Burns and Combined Injury, Southwest Hospital, The First Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Yizhi Peng
- Institute of Burn Research, State Key Laboratory of Trauma, Burns and Combined Injury, Southwest Hospital, The First Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Yinling Tan
- Department of Microbiology, Army Medical University, The Third Military Medical University, Chongqing, China
| | - Zichen Yang
- Department of Plastic and Cosmetic Surgery, Xinqiao Hospital, The Second Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
- Department of Microbiology, Army Medical University, The Third Military Medical University, Chongqing, China
- Institute of Burn Research, State Key Laboratory of Trauma, Burns and Combined Injury, Southwest Hospital, The First Affiliated Hospital, Army Medical University, The Third Military Medical University, Chongqing, China
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19
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Tisza MJ, Smith DDN, Clark AE, Youn JH, Khil PP, Dekker JP. Roving methyltransferases generate a mosaic epigenetic landscape and influence evolution in Bacteroides fragilis group. Nat Commun 2023; 14:4082. [PMID: 37429841 DOI: 10.1038/s41467-023-39892-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 06/29/2023] [Indexed: 07/12/2023] Open
Abstract
Three types of DNA methyl modifications have been detected in bacterial genomes, and mechanistic studies have demonstrated roles for DNA methylation in physiological functions ranging from phage defense to transcriptional control of virulence and host-pathogen interactions. Despite the ubiquity of methyltransferases and the immense variety of possible methylation patterns, epigenomic diversity remains unexplored for most bacterial species. Members of the Bacteroides fragilis group (BFG) reside in the human gastrointestinal tract as key players in symbiotic communities but also can establish anaerobic infections that are increasingly multi-drug resistant. In this work, we utilize long-read sequencing technologies to perform pangenomic (n = 383) and panepigenomic (n = 268) analysis of clinical BFG isolates cultured from infections seen at the NIH Clinical Center over four decades. Our analysis reveals that single BFG species harbor hundreds of DNA methylation motifs, with most individual motif combinations occurring uniquely in single isolates, implying immense unsampled methylation diversity within BFG epigenomes. Mining of BFG genomes identified more than 6000 methyltransferase genes, approximately 1000 of which were associated with intact prophages. Network analysis revealed substantial gene flow among disparate phage genomes, implying a role for genetic exchange between BFG phages as one of the ultimate sources driving BFG epigenome diversity.
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Affiliation(s)
- Michael J Tisza
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, LCIM, NIAID, NIH, Bethesda, MD, USA
- The Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiol, Baylor College of Medicine, Houston, TX, USA
| | - Derek D N Smith
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, LCIM, NIAID, NIH, Bethesda, MD, USA
- Environment and Climate Change Canada, Ecotoxicology and Wildlife Health Division, Wildlife Toxicology Research Section, Ottawa, ON, Canada
| | - Andrew E Clark
- National Institutes of Health Clinical Center, NIH, Bethesda, MD, USA
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jung-Ho Youn
- National Institutes of Health Clinical Center, NIH, Bethesda, MD, USA
| | - Pavel P Khil
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, LCIM, NIAID, NIH, Bethesda, MD, USA
- National Institutes of Health Clinical Center, NIH, Bethesda, MD, USA
| | - John P Dekker
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, LCIM, NIAID, NIH, Bethesda, MD, USA.
- National Institutes of Health Clinical Center, NIH, Bethesda, MD, USA.
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20
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Wang J, Zhang F, Yang W, Gao D, Yang L, Yu C, Chen C, Li X, Zhang JS. FGF1 ameliorates obesity-associated hepatic steatosis by reversing IGFBP2 hypermethylation. FASEB J 2023; 37:e22881. [PMID: 36934380 DOI: 10.1096/fj.202201950r] [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: 11/21/2022] [Revised: 02/17/2023] [Accepted: 03/06/2023] [Indexed: 03/20/2023]
Abstract
Obesity is a major contributing factor for metabolic-associated fatty liver disease (MAFLD). Fibroblast growth factor (FGF) 1 is the first paracrine FGF family member identified to exhibit promising metabolic regulatory properties capable of conferring glucose-lowering and insulin-sensitizing effect. This study explores the role and molecular underpinnings of FGF1 in obesity-associated hepatic steatosis. In a mouse high-fat diet (HFD)-induced MAFLD model, chronic treatment with recombinant FGF1(rFGF1) was found to effectively reduce the severity of insulin resistance, hyperlipidemia, and inflammation. FGF1 treatment decreased lipid accumulation in the mouse liver and palmitic acid-treated AML12 cells. These effects were associated with decreased mature form SREBF1 expression and its target genes FASN and SCD1. Interestingly, we uncovered that rFGF1 significantly induced IGFBP2 expression at both mRNA and protein levels in HFD-fed mouse livers and cultured hepatocytes treated with palmitic acid. Adeno-associated virus-mediated IGFBP2 suppression significantly diminished the therapeutic benefit of rFGF1 on MAFLD-associated phenotypes, indicating that IGFBP2 plays a crucial role in the FGF1-mediated reduction of hepatic steatosis. Further analysis revealed that rFGF1 treatment reduces the recruitment of DNA methyltransferase 3 alpha to the IGFBP2 genomic locus, leading to decreased IGFBP2 gene methylation and increased mRNA and protein expression. Collectively, our findings reveal FGF1 modulation of lipid metabolism via epigenetic regulation of IGFBP2 expression, and unravel the therapeutic potential of the FGF1-IGFBP2 axis in metabolic diseases associated with obesity.
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Affiliation(s)
- Jie Wang
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
- International Collaborative Center on Growth Factor Research, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Feng Zhang
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
| | - Weiwei Yang
- International Collaborative Center on Growth Factor Research, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Dandan Gao
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
| | - Linglong Yang
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Chenhua Yu
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Chengshui Chen
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
| | - Xiaokun Li
- International Collaborative Center on Growth Factor Research, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Jin-San Zhang
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, China
- International Collaborative Center on Growth Factor Research, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, China
- Medical Research Center, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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Epigenetic and Drug Response Modulation of Epigalocaten-In-3-Gallate in Staphylococcus aureus with Divergent Resistance Phenotypes. Antibiotics (Basel) 2023; 12:antibiotics12030519. [PMID: 36978386 PMCID: PMC10044528 DOI: 10.3390/antibiotics12030519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/23/2023] [Accepted: 03/01/2023] [Indexed: 03/08/2023] Open
Abstract
Healthcare-associated methicillin-resistant Staphylococcus aureus infections represent extremely high morbidity and mortality rates worldwide. We aimed to assess the antimicrobial potential and synergistic effect between Epigalocatenin-3-gallate (EGCG) and different antibiotics in S. aureus strains with divergent resistance phenotypes. EGCG exposure effects in epigenetic and drug resistance key modulators were also evaluated. S. aureus strains (n = 32) were isolated from infected patients in a Lisbon hospital. The identification of the S. aureus resistance phenotype was performed through automatized methods. The antibiotic synergistic assay was performed through disk diffusion according to EUCAST guidelines with co-exposure to EGCG (250, 100, 50 and 25 µg/mL). The bacteria’s molecular profile was assessed through FTIR spectroscopy. The transcriptional expression of OrfX, SpdC and WalKR was performed by using qRT-PCR. FTIR-spectroscopy analysis enabled the clear discrimination of MRSA/MSSA strains and the EGCG exposure effect in the bacteria’s molecular profiles. Divergent resistant phenotypes were associated with divergent transcriptional expression of the epigenetic modulator OrfX, particularly in MRSA strains, as well as the key drug response modulators SpdC and WalKR. These results clearly demonstrate that EGCG exposure alters the expression patterns of key epigenetic and drug response genes with associated divergent-resistant profiles, which supports its potential for antimicrobial treatment and/or therapeutic adjuvant against antibiotic-resistant microorganisms.
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Enam SU, Cherry JL, Leonard SR, Zheludev IN, Lipman DJ, Fire AZ. Restriction Endonuclease-Based Modification-Dependent Enrichment (REMoDE) of DNA for Metagenomic Sequencing. Appl Environ Microbiol 2023; 89:e0167022. [PMID: 36519847 PMCID: PMC9888230 DOI: 10.1128/aem.01670-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Metagenomic sequencing is a swift and powerful tool to ascertain the presence of an organism of interest in a sample. However, sequencing coverage of the organism of interest can be insufficient due to an inundation of reads from irrelevant organisms in the sample. Here, we report a nuclease-based approach to rapidly enrich for DNA from certain organisms, including enterobacteria, based on their differential endogenous modification patterns. We exploit the ability of taxon-specific methylated motifs to resist the action of cognate methylation-sensitive restriction endonucleases that thereby digest unwanted, unmethylated DNA. Subsequently, we use a distributive exonuclease or electrophoretic separation to deplete or exclude the digested fragments, thus enriching for undigested DNA from the organism of interest. As a proof of concept, we apply this method to enrich for the enterobacteria Escherichia coli and Salmonella enterica by 11- to 142-fold from mock metagenomic samples and validate this approach as a versatile means to enrich for genomes of interest in metagenomic samples. IMPORTANCE Pathogens that contaminate the food supply or spread through other means can cause outbreaks that bring devastating repercussions to the health of a populace. Investigations to trace the source of these outbreaks are initiated rapidly but can be drawn out due to the labored methods of pathogen isolation. Metagenomic sequencing can alleviate this hurdle but is often insufficiently sensitive. The approach and implementations detailed here provide a rapid means to enrich for many pathogens involved in foodborne outbreaks, thereby improving the utility of metagenomic sequencing as a tool in outbreak investigations. Additionally, this approach provides a means to broadly enrich for otherwise minute levels of modified DNA, which may escape unnoticed in metagenomic samples.
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Affiliation(s)
- Syed Usman Enam
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Joshua L. Cherry
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Susan R. Leonard
- Office of Applied Research and Safety Assessment, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Laurel, Maryland, USA
| | - Ivan N. Zheludev
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA
| | - David J. Lipman
- Office of the Center Director, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, Silver Spring, Maryland, USA
| | - Andrew Z. Fire
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
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23
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Schiffer CJ, Grätz C, Pfaffl MW, Vogel RF, Ehrmann MA. Characterization of the Staphylococcus xylosus methylome reveals a new variant of type I restriction modification system in staphylococci. Front Microbiol 2023; 14:946189. [PMID: 36970683 PMCID: PMC10030836 DOI: 10.3389/fmicb.2023.946189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 02/13/2023] [Indexed: 03/29/2023] Open
Abstract
Restriction modification (RM) systems are known to provide a strong barrier to the exchange of DNA between and within bacterial species. Likewise, DNA methylation is known to have an important function in bacterial epigenetics regulating essential pathways such as DNA replication and the phase variable expression of prokaryotic phenotypes. To date, research on staphylococcal DNA methylation focused mainly on the two species Staphylococcus aureus and S. epidermidis. Less is known about other members of the genus such as S. xylosus, a coagulase-negative commensal of mammalian skin. The species is commonly used as starter organism in food fermentations but is also increasingly considered to have an as yet elusive function in bovine mastitis infections. We analyzed the methylomes of 14 S. xylosus strains using single-molecular, real-time (SMRT) sequencing. Subsequent in silico sequence analysis allowed identification of the RM systems and assignment of the respective enzymes to the discovered modification patterns. Hereby the presence of type I, II, III and IV RM systems in varying numbers and combinations among the different strains was revealed, clearly distinguishing the species from what is known for other members of the genus so far. In addition, the study characterizes a newly discovered type I RM system, encoded by S. xylosus but also by a variety of other staphylococcal species, with a hitherto unknown gene arrangement that involves two specificity units instead of one (hsdRSMS). Expression of different versions of the operon in E. coli showed proper base modification only when genes encoding both hsdS subunits were present. This study provides new insights into the general understanding of the versatility and function of RM systems as well as the distribution and variations in the genus Staphylococcus.
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Affiliation(s)
- Carolin J. Schiffer
- Chair of Technical Microbiology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
- *Correspondence: Carolin J. Schiffer,
| | - Christian Grätz
- Chair of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Michael W. Pfaffl
- Chair of Animal Physiology and Immunology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Rudi F. Vogel
- Chair of Technical Microbiology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
| | - Matthias A. Ehrmann
- Chair of Technical Microbiology, TUM School of Life Sciences, Technical University of Munich, Freising, Germany
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24
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Fang JL, Gao WL, Xu WF, Lyu ZY, Ma L, Luo S, Chen XA, Mao XM, Li YQ. m4C DNA methylation regulates biosynthesis of daptomycin in Streptomyces roseosporus L30. Synth Syst Biotechnol 2022; 7:1013-1023. [PMID: 35801092 PMCID: PMC9240718 DOI: 10.1016/j.synbio.2022.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/09/2022] [Accepted: 06/09/2022] [Indexed: 11/18/2022] Open
Affiliation(s)
- Jiao-Le Fang
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, PR China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, 310058, Hangzhou, PR China
| | - Wen-Li Gao
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, PR China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, 310058, Hangzhou, PR China
| | - Wei-Feng Xu
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, PR China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, 310058, Hangzhou, PR China
| | - Zhong-Yuan Lyu
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, PR China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, 310058, Hangzhou, PR China
| | - Lie Ma
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, PR China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, 310058, Hangzhou, PR China
| | - Shuai Luo
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, 310058, Hangzhou, PR China
| | - Xin-Ai Chen
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, PR China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, 310058, Hangzhou, PR China
| | - Xu-Ming Mao
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, PR China
| | - Yong-Quan Li
- Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, PR China
- Zhejiang Provincial Key Laboratory for Microbial Biochemistry and Metabolic Engineering, 310058, Hangzhou, PR China
- Corresponding author. Institute of Pharmaceutical Biotechnology, Zhejiang University School of Medicine, Hangzhou, 310058, PR China.
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25
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Breckell GL, Silander OK. Growth condition-dependent differences in methylation imply transiently differentiated DNA methylation states in Escherichia coli. G3 (BETHESDA, MD.) 2022; 13:6858946. [PMID: 36454087 PMCID: PMC9911048 DOI: 10.1093/g3journal/jkac310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 09/14/2022] [Accepted: 09/28/2022] [Indexed: 12/05/2022]
Abstract
DNA methylation in bacteria frequently serves as a simple immune system, allowing recognition of DNA from foreign sources, such as phages or selfish genetic elements. However, DNA methylation also affects other cell phenotypes in a heritable manner (i.e. epigenetically). While there are several examples of methylation affecting transcription in an epigenetic manner in highly localized contexts, it is not well-established how frequently methylation serves a more general epigenetic function over larger genomic scales. To address this question, here we use Oxford Nanopore sequencing to profile DNA modification marks in three natural isolates of Escherichia coli. We first identify the DNA sequence motifs targeted by the methyltransferases in each strain. We then quantify the frequency of methylation at each of these motifs across the entire genome in different growth conditions. We find that motifs in specific regions of the genome consistently exhibit high or low levels of methylation. Furthermore, we show that there are replicable and consistent differences in methylated regions across different growth conditions. This suggests that during growth, E. coli transiently differentiate into distinct methylation states that depend on the growth state, raising the possibility that measuring DNA methylation alone can be used to infer bacterial growth states without additional information such as transcriptome or proteome data. These results show the utility of using Oxford Nanopore sequencing as an economic means to infer DNA methylation status. They also provide new insights into the dynamics of methylation during bacterial growth and provide evidence of differentiated cell states, a transient analog to what is observed in the differentiation of cell types in multicellular organisms.
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Affiliation(s)
- Georgia L Breckell
- Corresponding author: School of Natural and Sciences, Massey University, Auckland 0745, New Zealand. ; Corresponding author: School of Natural and Sciences, Massey University, Auckland 0745, New Zealand. Present address: Ministry for Primary Industries, Auckland 2022, New Zealand
| | - Olin K Silander
- Corresponding author: School of Natural and Sciences, Massey University, Auckland 0745, New Zealand. ; Corresponding author: School of Natural and Sciences, Massey University, Auckland 0745, New Zealand. Present address: Ministry for Primary Industries, Auckland 2022, New Zealand
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26
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Papaleo S, Alvaro A, Nodari R, Panelli S, Bitar I, Comandatore F. The red thread between methylation and mutation in bacterial antibiotic resistance: How third-generation sequencing can help to unravel this relationship. Front Microbiol 2022; 13:957901. [PMID: 36188005 PMCID: PMC9520237 DOI: 10.3389/fmicb.2022.957901] [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: 05/31/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
DNA methylation is an important mechanism involved in bacteria limiting foreign DNA acquisition, maintenance of mobile genetic elements, DNA mismatch repair, and gene expression. Changes in DNA methylation pattern are observed in bacteria under stress conditions, including exposure to antimicrobial compounds. These changes can result in transient and fast-appearing adaptive antibiotic resistance (AdR) phenotypes, e.g., strain overexpressing efflux pumps. DNA methylation can be related to DNA mutation rate, because it is involved in DNA mismatch repair systems and because methylated bases are well-known mutational hotspots. The AdR process can be the first important step in the selection of antibiotic-resistant strains, allowing the survival of the bacterial population until more efficient resistant mutants emerge. Epigenetic modifications can be investigated by third-generation sequencing platforms that allow us to simultaneously detect all the methylated bases along with the DNA sequencing. In this scenario, this sequencing technology enables the study of epigenetic modifications in link with antibiotic resistance and will help to investigate the relationship between methylation and mutation in the development of stable mechanisms of resistance.
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Affiliation(s)
- Stella Papaleo
- Romeo ed Enrica Invernizzi Pediatric Research Center, Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Alessandro Alvaro
- Romeo ed Enrica Invernizzi Pediatric Research Center, Department of Bioscience, University of Milan, Milan, Italy
| | - Riccardo Nodari
- Romeo ed Enrica Invernizzi Pediatric Research Center, Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Simona Panelli
- Romeo ed Enrica Invernizzi Pediatric Research Center, Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
| | - Ibrahim Bitar
- Department of Microbiology, Faculty of Medicine and University Hospital in Pilsen, Charles University, Pilsen, Czechia
- Biomedical Center, Faculty of Medicine, Charles University, Pilsen, Czechia
| | - Francesco Comandatore
- Romeo ed Enrica Invernizzi Pediatric Research Center, Department of Biomedical and Clinical Sciences, University of Milan, Milan, Italy
- *Correspondence: Francesco Comandatore
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27
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De Wannemaeker L, Bervoets I, De Mey M. Unlocking the bacterial domain for industrial biotechnology applications using universal parts and tools. Biotechnol Adv 2022; 60:108028. [PMID: 36031082 DOI: 10.1016/j.biotechadv.2022.108028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 11/02/2022]
Abstract
Synthetic biology can play a major role in the development of sustainable industrial biotechnology processes. However, the development of economically viable production processes is currently hampered by the limited availability of host organisms that can be engineered for a specific production process. To date, standard hosts such as Escherichia coli and Saccharomyces cerevisiae are often used as starting points for process development since parts and tools allowing their engineering are readily available. However, their suboptimal metabolic background or impaired performance at industrial scale for a desired production process, can result in increased costs associated with process development and/or disappointing production titres. Building a universal and portable gene expression system allowing genetic engineering of hosts across the bacterial domain would unlock the bacterial domain for industrial biotechnology applications in a highly standardized manner and doing so, render industrial biotechnology processes more competitive compared to the current polluting chemical processes. This review gives an overview of a selection of bacterial hosts highly interesting for industrial biotechnology based on both their metabolic and process optimization properties. Moreover, the requirements and progress made so far to enable universal, standardized, and portable gene expression across the bacterial domain is discussed.
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Affiliation(s)
- Lien De Wannemaeker
- Centre for Synthetic Biology (CSB), Ghent University, Coupure links 653, 9000 Ghent, Belgium
| | - Indra Bervoets
- Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Marjan De Mey
- Centre for Synthetic Biology (CSB), Ghent University, Coupure links 653, 9000 Ghent, Belgium.
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28
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DNA Methyltransferases: From Evolution to Clinical Applications. Int J Mol Sci 2022; 23:ijms23168994. [PMID: 36012258 PMCID: PMC9409253 DOI: 10.3390/ijms23168994] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 11/18/2022] Open
Abstract
DNA methylation is an epigenetic mark that living beings have used in different environments. The MTases family catalyzes DNA methylation. This process is conserved from archaea to eukaryotes, from fertilization to every stage of development, and from the early stages of cancer to metastasis. The family of DNMTs has been classified into DNMT1, DNMT2, and DNMT3. Each DNMT has been duplicated or deleted, having consequences on DNMT structure and cellular function, resulting in a conserved evolutionary reaction of DNA methylation. DNMTs are conserved in the five kingdoms of life: bacteria, protists, fungi, plants, and animals. The importance of DNMTs in whether methylate or not has a historical adaptation that in mammals has been discovered in complex regulatory mechanisms to develop another padlock to genomic insurance stability. The regulatory mechanisms that control DNMTs expression are involved in a diversity of cell phenotypes and are associated with pathologies transcription deregulation. This work focused on DNA methyltransferases, their biology, functions, and new inhibitory mechanisms reported. We also discuss different approaches to inhibit DNMTs, the use of non-coding RNAs and nucleoside chemical compounds in recent studies, and their importance in biological, clinical, and industry research.
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29
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Genomic and epigenetic landscapes drive CRISPR-based genome editing in Bifidobacterium. Proc Natl Acad Sci U S A 2022; 119:e2205068119. [PMID: 35857876 PMCID: PMC9335239 DOI: 10.1073/pnas.2205068119] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Bifidobacterium is a commensal bacterial genus ubiquitous in the human gastrointestinal tract, which is associated with a range of health benefits. The advent of CRISPR-based genome editing technologies provides opportunities to investigate the genetics of important bacteria and transcend the lack of genetic tools in bifidobacteria to study the basis for their health-promoting attributes. Here, we repurpose the endogenous type I-G CRISPR-Cas system and adopt an exogenous CRISPR base editor for genome engineering in B. animalis subsp. lactis, demonstrating that both genomic and epigenetic contexts drive editing outcomes across strains. We reprogrammed the endogenous type I-G system to screen for naturally occurring large deletions up to 27 kb and to generate a 500-bp deletion in tetW to abolish tetracycline resistance. A CRISPR-cytosine base editor was optimized to install C•G-to-T•A amber mutations to resensitize multiple B. lactis strains to tetracycline. Remarkably, we uncovered epigenetic patterns that are distributed unevenly among B. lactis strains, despite their genomic homogeneity, that may contribute to editing efficiency variability. Insights were also expanded to Bifidobacterium longum subsp. infantis to emphasize the broad relevance of these findings. This study highlights the need to develop individualized CRISPR-based genome engineering approaches for distinct bacterial strains and opens avenues for engineering of next generation probiotics.
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30
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Dordet-Frisoni E, Vandecasteele C, Contarin R, Sagné E, Baranowski E, Klopp C, Nouvel LX, Citti C. Impacts of Mycoplasma agalactiae restriction-modification systems on pan-epigenome dynamics and genome plasticity. Microb Genom 2022; 8. [PMID: 35576144 PMCID: PMC9465063 DOI: 10.1099/mgen.0.000829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
DNA methylations play an important role in the biology of bacteria. Often associated with restriction modification (RM) systems, they are important drivers of bacterial evolution interfering in horizontal gene transfer events by providing a defence against foreign DNA invasion or by favouring genetic transfer through production of recombinogenic DNA ends. Little is known regarding the methylome of the Mycoplasma genus, which encompasses several pathogenic species with small genomes. Here, genome-wide detection of DNA methylations was conducted using single molecule real-time (SMRT) and bisulphite sequencing in several strains of Mycoplasma agalactiae, an important ruminant pathogen and a model organism. Combined with whole-genome analysis, this allowed the identification of 19 methylated motifs associated with three orphan methyltransferases (MTases) and eight RM systems. All systems had a homolog in at least one phylogenetically distinct Mycoplasma spp. Our study also revealed that several superimposed genetic events may participate in the M. agalactiae dynamic epigenomic landscape. These included (i) DNA shuffling and frameshift mutations that affect the MTase and restriction endonuclease content of a clonal population and (ii) gene duplication, erosion, and horizontal transfer that modulate MTase and RM repertoires of the species. Some of these systems were experimentally shown to play a major role in mycoplasma conjugative, horizontal DNA transfer. While the versatility of DNA methylation may contribute to regulating essential biological functions at cell and population levels, RM systems may be key in mycoplasma genome evolution and adaptation by controlling horizontal gene transfers.
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Affiliation(s)
- Emilie Dordet-Frisoni
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France.,Present address: INTHERES, Université de Toulouse, INRAE, ENVT, Toulouse, France
| | | | | | - Eveline Sagné
- IHAP, Université de Toulouse, INRAE, ENVT, Toulouse, France
| | | | - Christophe Klopp
- INRAE, UR875 MIAT, Sigenae, BioInfo Genotoul, BioInfoMics, F-31326 Auzeville, France
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31
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Zaworski J, Dagva O, Brandt J, Baum C, Ettwiller L, Fomenkov A, Raleigh EA. Reassembling a cannon in the DNA defense arsenal: Genetics of StySA, a BREX phage exclusion system in Salmonella lab strains. PLoS Genet 2022; 18:e1009943. [PMID: 35377874 PMCID: PMC9009780 DOI: 10.1371/journal.pgen.1009943] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 04/14/2022] [Accepted: 03/01/2022] [Indexed: 11/18/2022] Open
Abstract
Understanding mechanisms that shape horizontal exchange in prokaryotes is a key problem in biology. A major limit on DNA entry is imposed by restriction-modification (RM) processes that depend on the pattern of DNA modification at host-specified sites. In classical RM, endonucleolytic DNA cleavage follows detection of unprotected sites on entering DNA. Recent investigation has uncovered BREX (BacteRiophage EXclusion) systems. These RM-like activities employ host protection by DNA modification, but immediate replication arrest occurs without evident of nuclease action on unmodified phage DNA. Here we show that the historical stySA RM locus of Salmonella enterica sv Typhimurium is a variant BREX system. A laboratory strain disabled for both the restriction and methylation activity of StySA nevertheless has wild type sequence in pglX, the modification gene homolog. Instead, flanking genes pglZ and brxC each carry multiple mutations (μ) in their C-terminal domains. We further investigate this system in situ, replacing the mutated pglZμ and brxCμ genes with the WT counterpart. PglZ-WT supports methylation in the presence of either BrxCμ or BrxC-WT but not in the presence of a deletion/insertion allele, ΔbrxC::cat. Restriction requires both BrxC-WT and PglZ-WT, implicating the BrxC C-terminus specifically in restriction activity. These results suggests that while BrxC, PglZ and PglX are principal components of the BREX modification activity, BrxL is required for restriction only. Furthermore, we show that a partial disruption of brxL disrupts transcription globally. Horizontal gene transfer is a major driver of evolution and adaptation in bacteria. Genes from outside may be beneficial or dangerous to the receiving cell. Benefits include new food sources such as sugars, or new homes by adhesion, or new resistances, as to antibiotics. Dangers are posed by bacteriophages--viruses that take over the cell machinery, multiply, and release progeny to kill sister cells. Host-dependent restriction-modification systems enable defense that distinguishes relatives from strangers: using a modification pattern (M) carried by DNA bases added by the host cell to prevent restriction (R). Sisters and cousin cells will have the same protective pattern on DNA, while DNA of foreign origin will have the wrong M pattern and be restricted (R, rejected). Typically, restriction involves nuclease digestion. Here we address the enigmatic StySA RM system, one of the earliest to be genetically characterized. It is a variant of the newly recognized defense mechanism, BREX. BREX systems also track DNA history via modification pattern, but restrict by a novel, uncharacterized mechanism. Like other BREX family systems, StySA-BREX modification requires multiple components. When StySA-BREX transcription is unbalanced, we find global disruption of gene transcription. The disruption pattern does not suggest SOS-inducing damage to DNA.
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Affiliation(s)
- Julie Zaworski
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Oyut Dagva
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Julius Brandt
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Chloé Baum
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Laurence Ettwiller
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Alexey Fomenkov
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Elisabeth A. Raleigh
- Research Department, New England Biolabs, Ipswich, Massachusetts, United States of America
- * E-mail:
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32
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DNA Methylation in Prokaryotes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:21-43. [DOI: 10.1007/978-3-031-11454-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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33
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Mohammadi MM, Bavi O. DNA sequencing: an overview of solid-state and biological nanopore-based methods. Biophys Rev 2021; 14:99-110. [PMID: 34840616 PMCID: PMC8609259 DOI: 10.1007/s12551-021-00857-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/14/2021] [Indexed: 12/23/2022] Open
Abstract
The field of sequencing is a topic of significant interest since its emergence and has become increasingly important over time. Impressive achievements have been obtained in this field, especially in relations to DNA and RNA sequencing. Since the first achievements by Sanger and colleagues in the 1950s, many sequencing techniques have been developed, while others have disappeared. DNA sequencing has undergone three generations of major evolution. Each generation has its own specifications that are mentioned briefly. Among these generations, nanopore sequencing has its own exciting characteristics that have been given more attention here. Among pioneer technologies being used by the third-generation techniques, nanopores, either biological or solid-state, have been experimentally or theoretically extensively studied. All sequencing technologies have their own advantages and disadvantages, so nanopores are not free from this general rule. It is also generally pointed out what research has been done to overcome the obstacles. In this review, biological and solid-state nanopores are elaborated on, and applications of them are also discussed briefly.
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Affiliation(s)
- Mohammad M Mohammadi
- Department of Mechanical and Aerospace Engineering, Shiraz University of Technology, Shiraz, 71557-13876 Iran
| | - Omid Bavi
- Department of Mechanical and Aerospace Engineering, Shiraz University of Technology, Shiraz, 71557-13876 Iran
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34
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VirB4- and VirD4-Like ATPases, Components of a Putative Type 4C Secretion System in Clostridioides difficile. J Bacteriol 2021; 203:e0035921. [PMID: 34424036 DOI: 10.1128/jb.00359-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The type 4 secretion system (T4SS) represents a bacterial nanomachine capable of trans-cell wall transportation of proteins and DNA and has attracted intense interest due to its roles in the pathogenesis of infectious diseases. In the current investigation, we uncovered three distinct gene clusters in Clostridioides difficile strain 630 encoding proteins structurally related to components of the VirB4/D4 type 4C secretion system from Streptococcus suis strain 05ZYH33 and located within sequences of conjugative transposons (CTn). Phylogenic analysis revealed that VirB4- and VirD4-like proteins of the CTn4 locus, on the one hand, and those of the CTn2 and CTn5 loci, on the other hand, fit into separate clades, suggesting specific roles of identified secretion system variants in the physiology of C. difficile. Our further study on VirB4- and VirD4-like products encoded by CTn4 revealed that both proteins possess Mg2+-dependent ATPase activity, form oligomers (most likely hexamers) in aqueous solutions, and rely on potassium but not sodium ions for the highest catalytic rate. VirD4 binds nonspecifically to DNA and RNA. The DNA-binding activity of VirD4 strongly decreased with the W241A variant. Mutations in the nucleotide sequences encoding presumable Walker A and Walker B motifs decreased the stability of the oligomers and significantly but not completely attenuated the enzymatic activity of VirB4. In VirD4, substitutions of amino acid residues in the peptides reminiscent of Walker structural motifs neither attenuated the enzymatic activity of the protein nor influenced the oligomerization state of the ATPase. IMPORTANCE C. difficile is a Gram-positive, anaerobic, spore-forming bacterium that causes life-threatening colitis in humans. Major virulence factors of the microorganism include the toxins TcdA, TcdB, and CDT. However, other bacterial products, including a type 4C secretion system, have been hypothesized to contribute to the pathogenesis of the infection and are considered possible virulence factors of C. difficile. In the current paper, we describe the structural organization of putative T4SS machinery in C. difficile and characterize its VirB4- and VirD4-like components. Our studies, in addition to its significance for basic science, can potentially aid the development of antivirulence drugs suitable for the treatment of C. difficile infection.
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Zhou J, Horton JR, Yu D, Ren R, Blumenthal RM, Zhang X, Cheng X. Repurposing epigenetic inhibitors to target the Clostridioides difficile-specific DNA adenine methyltransferase and sporulation regulator CamA. Epigenetics 2021; 17:970-981. [PMID: 34523387 PMCID: PMC9487755 DOI: 10.1080/15592294.2021.1976910] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Epigenetically targeted therapeutic development, particularly for SAM-dependent methylations of DNA, mRNA and histones has been proceeding rapidly for cancer treatments over the past few years. However, this approach has barely begun to be exploited for developing new antibiotics, despite an overwhelming global need to counter antimicrobial resistance. Here, we explore whether SAM analogues, some of which are in (pre)clinical studies as inhibitors of human epigenetic enzymes, can also inhibit Clostridioides difficile-specific DNA adenine methyltransferase (CamA), a sporulation regulator present in all C. difficile genomes sequenced to date, but found in almost no other bacteria. We found that SGC0946 (an inhibitor of DOT1L), JNJ-64619178 (an inhibitor of PRMT5) and SGC8158 (an inhibitor of PRMT7) inhibit CamA enzymatic activity in vitro at low micromolar concentrations. Structural investigation of the ternary complexes of CamA-DNA in the presence of SGC0946 or SGC8158 revealed conformational rearrangements of the N-terminal arm, with no apparent disturbance of the active site. This N-terminal arm and its modulation of exchanges between SAM (the methyl donor) and SAH (the reaction product) during catalysis of methyl transfer are, to date, unique to CamA. Our work presents a substantial first step in generating potent and selective inhibitors of CamA that would serve in the near term as chemical probes to investigate the cellular mechanism(s) of CamA in controlling spore formation and colonization, and eventually as therapeutic antivirulence agents useful in treating C. difficile infection.
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Affiliation(s)
- Jujun Zhou
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Dan Yu
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ren Ren
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Abstract
Epigenetic DNA methylation in bacteria has been traditionally studied in the context of antiparasitic defense and as part of the innate immune discrimination between self and nonself DNA. However, sequencing advances that allow genome-wide analysis of DNA methylation at the single-base resolution are nowadays expanding and have propelled a modern epigenomic revolution in our understanding of the extent, evolution, and physiological relevance of methylation. Indeed, as the number of mapped bacterial methylomes recently surpassed 4,000, increasing evidence supports roles for methylation in gene expression regulation, virulence, and host colonization, among others. In this paper, I summarize lessons taken from high-dimensional methylome data analyses and recent efforts that we and others are developing to leverage such findings into meaningful biological insights and overarching frameworks. Ultimately, I highlight anticipated research avenues and technological developments likely to unfold in the coming years.
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Affiliation(s)
- Pedro H. Oliveira
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Université Évry, Université Paris-Saclay, Évry, France
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Mehershahi KS, Chen SL. DNA methylation by three Type I restriction modification systems of Escherichia coli does not influence gene regulation of the host bacterium. Nucleic Acids Res 2021; 49:7375-7388. [PMID: 34181709 PMCID: PMC8287963 DOI: 10.1093/nar/gkab530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/01/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022] Open
Abstract
DNA methylation is a common epigenetic mark that influences transcriptional regulation, and therefore cellular phenotype, across all domains of life. In particular, both orphan methyltransferases and those from phasevariable restriction modification systems (RMSs) have been co-opted to regulate virulence epigenetically in many bacteria. We now show that three distinct non-phasevariable Type I RMSs in Escherichia coli have no measurable impact on gene expression, in vivo virulence, or any of 1190 in vitro growth phenotypes. We demonstrated this using both Type I RMS knockout mutants as well as heterologous installation of Type I RMSs into two E. coli strains. These data provide three clear and currently rare examples of restriction modification systems that have no impact on their host organism’s gene regulation. This leads to the possibility that other such nonregulatory methylation systems may exist, broadening our view of the potential role that RMSs may play in bacterial evolution.
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Affiliation(s)
- Kurosh S Mehershahi
- NUHS Infectious Diseases Translational Research Programme, Department of Medicine, Division of Infectious Diseases, Yong Loo Lin School of Medicine, Singapore 119228
| | - Swaine L Chen
- NUHS Infectious Diseases Translational Research Programme, Department of Medicine, Division of Infectious Diseases, Yong Loo Lin School of Medicine, Singapore 119228.,Laboratory of Bacterial Genomics, Genome Institute of Singapore, Singapore 138672
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Dorado G, Gálvez S, Rosales TE, Vásquez VF, Hernández P. Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing - Review. Biomolecules 2021; 11:1111. [PMID: 34439777 PMCID: PMC8393538 DOI: 10.3390/biom11081111] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/12/2021] [Accepted: 07/23/2021] [Indexed: 02/06/2023] Open
Abstract
Recent developments have revolutionized the study of biomolecules. Among them are molecular markers, amplification and sequencing of nucleic acids. The latter is classified into three generations. The first allows to sequence small DNA fragments. The second one increases throughput, reducing turnaround and pricing, and is therefore more convenient to sequence full genomes and transcriptomes. The third generation is currently pushing technology to its limits, being able to sequence single molecules, without previous amplification, which was previously impossible. Besides, this represents a new revolution, allowing researchers to directly sequence RNA without previous retrotranscription. These technologies are having a significant impact on different areas, such as medicine, agronomy, ecology and biotechnology. Additionally, the study of biomolecules is revealing interesting evolutionary information. That includes deciphering what makes us human, including phenomena like non-coding RNA expansion. All this is redefining the concept of gene and transcript. Basic analyses and applications are now facilitated with new genome editing tools, such as CRISPR. All these developments, in general, and nucleic-acid sequencing, in particular, are opening a new exciting era of biomolecule analyses and applications, including personalized medicine, and diagnosis and prevention of diseases for humans and other animals.
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Affiliation(s)
- Gabriel Dorado
- Dep. Bioquímica y Biología Molecular, Campus Rabanales C6-1-E17, Campus de Excelencia Internacional Agroalimentario (ceiA3), Universidad de Córdoba, 14071 Córdoba, Spain
| | - Sergio Gálvez
- Dep. Lenguajes y Ciencias de la Computación, Boulevard Louis Pasteur 35, Universidad de Málaga, 29071 Málaga, Spain;
| | - Teresa E. Rosales
- Laboratorio de Arqueobiología, Avda. Universitaria s/n, Universidad Nacional de Trujillo, 13011 Trujillo, Peru;
| | - Víctor F. Vásquez
- Centro de Investigaciones Arqueobiológicas y Paleoecológicas Andinas Arqueobios, Martínez de Companón 430-Bajo 100, Urbanización San Andres, 13088 Trujillo, Peru;
| | - Pilar Hernández
- Instituto de Agricultura Sostenible (IAS), Consejo Superior de Investigaciones Científicas (CSIC), Alameda del Obispo s/n, 14080 Córdoba, Spain;
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Anton BP, Roberts RJ. Beyond Restriction Modification: Epigenomic Roles of DNA Methylation in Prokaryotes. Annu Rev Microbiol 2021; 75:129-149. [PMID: 34314594 DOI: 10.1146/annurev-micro-040521-035040] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The amount of bacterial and archaeal genome sequence and methylome data has greatly increased over the last decade, enabling new insights into the functional roles of DNA methylation in these organisms. Methyltransferases (MTases), the enzymes responsible for DNA methylation, are exchanged between prokaryotes through horizontal gene transfer and can function either as part of restriction-modification systems or in apparent isolation as single (orphan) genes. The patterns of DNA methylation they confer on the host chromosome can have significant effects on gene expression, DNA replication, and other cellular processes. Some processes require very stable patterns of methylation, resulting in conservation of persistent MTases in a particular lineage. Other processes require patterns that are more dynamic yet more predictable than what is afforded by horizontal gene transfer and gene loss, resulting in phase-variable or recombination-driven MTase alleles. In this review, we discuss what is currently known about the functions of DNA methylation in prokaryotes in light of these evolutionary patterns. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Brian P Anton
- New England Biolabs, Ipswich, Massachusetts 01938, USA; ,
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40
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Zhou J, Horton JR, Blumenthal RM, Zhang X, Cheng X. Clostridioides difficile specific DNA adenine methyltransferase CamA squeezes and flips adenine out of DNA helix. Nat Commun 2021; 12:3436. [PMID: 34103525 PMCID: PMC8187626 DOI: 10.1038/s41467-021-23693-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 05/13/2021] [Indexed: 12/13/2022] Open
Abstract
Clostridioides difficile infections are an urgent medical problem. The newly discovered C. difficile adenine methyltransferase A (CamA) is specified by all C. difficile genomes sequenced to date (>300), but is rare among other bacteria. CamA is an orphan methyltransferase, unassociated with a restriction endonuclease. CamA-mediated methylation at CAAAAA is required for normal sporulation, biofilm formation, and intestinal colonization by C. difficile. We characterized CamA kinetic parameters, and determined its structure bound to DNA containing the recognition sequence. CamA contains an N-terminal domain for catalyzing methyl transfer, and a C-terminal DNA recognition domain. Major and minor groove DNA contacts in the recognition site involve base-specific hydrogen bonds, van der Waals contacts and the Watson-Crick pairing of a rearranged A:T base pair. These provide sufficient sequence discrimination to ensure high specificity. Finally, the surprisingly weak binding of the methyl donor S-adenosyl-L-methionine (SAM) might provide avenues for inhibiting CamA activity using SAM analogs.
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Affiliation(s)
- Jujun Zhou
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John R Horton
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Robert M Blumenthal
- Department of Medical Microbiology and Immunology, and Program in Bioinformatics, The University of Toledo College of Medicine and Life Sciences, Toledo, OH, USA
| | - Xing Zhang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Xiaodong Cheng
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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Yadav SK, Magotra A, Ghosh S, Krishnan A, Pradhan A, Kumar R, Das J, Sharma M, Jha G. Immunity proteins of dual nuclease T6SS effectors function as transcriptional repressors. EMBO Rep 2021; 22:e51857. [PMID: 33786997 PMCID: PMC8183406 DOI: 10.15252/embr.202051857] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 02/26/2021] [Accepted: 03/08/2021] [Indexed: 12/31/2022] Open
Abstract
Bacteria utilize type VI secretion system (T6SS) to deliver antibacterial toxins to target co-habiting bacteria. Here, we report that Burkholderia gladioli strain NGJ1 deploys certain T6SS effectors (TseTBg), having both DNase and RNase activities to kill target bacteria. RNase activity is prominent on NGJ1 as well as other bacterial RNA while DNase activity is pertinent to only other bacteria. The associated immunity (TsiTBg) proteins harbor non-canonical helix-turn-helix motifs and demonstrate transcriptional repression activity, similar to the antitoxins of type II toxin-antitoxin (TA) systems. Genome analysis reveals that homologs of TseTBg are either encoded as TA or T6SS effectors in diverse bacteria. Our results indicate that a new ORF (encoding a hypothetical protein) has evolved as a result of operonic fusion of TA type TseTBg homolog with certain T6SS-related genes by the action of IS3 transposable elements. This has potentially led to the conversion of a TA into T6SS effector in Burkholderia. Our study exemplifies that bacteria can recruit toxins of TA systems as T6SS weapons to diversify its arsenal to dominate during inter-bacterial competitions.
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Affiliation(s)
- Sunil Kumar Yadav
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
| | - Ankita Magotra
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
| | - Srayan Ghosh
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
| | - Aiswarya Krishnan
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
| | - Amrita Pradhan
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
| | - Rahul Kumar
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
| | - Joyati Das
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
| | - Mamta Sharma
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
| | - Gopaljee Jha
- Plant Microbe Interactions LaboratoryNational Institute of Plant Genome ResearchAruna Asaf Ali MargIndia
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12/111phiA Prophage Domestication Is Associated with Autoaggregation and Increased Ability to Produce Biofilm in Streptococcus agalactiae. Microorganisms 2021; 9:microorganisms9061112. [PMID: 34063935 PMCID: PMC8223999 DOI: 10.3390/microorganisms9061112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 01/11/2023] Open
Abstract
CC17 Streptococcus agalactiae carrying group-A prophages is increasingly responsible for neonatal infections. To investigate the impact of the genetic features of a group-A prophage, we first conducted an in silico analysis of the genome of 12/111phiA, a group-A prophage carried by a strain responsible for a bloodstream infection in a parturient. This revealed a Restriction Modification system, suggesting a prophage maintenance strategy and five ORFs of interest for the host and encoding a type II toxin antitoxin system RelB/YafQ, an endonuclease, an S-adenosylmethionine synthetase MetK, and an StrP-like adhesin. Using the WT strain cured from 12/111phiA and constructing deleted mutants for the ORFs of interest, and their complemented mutants, we demonstrated an impact of prophage features on growth characteristics, cell morphology and biofilm formation. Our findings argue in favor of 12/111phiA domestication by the host and a role of prophage features in cell autoaggregation, glycocalyx and biofilm formation. We suggest that lysogeny may promote GBS adaptation to the acid environment of the vagina, consequently colonizing and infecting neonates.
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Negri A, Werbowy O, Wons E, Dersch S, Hinrichs R, Graumann PL, Mruk I. Regulator-dependent temporal dynamics of a restriction-modification system's gene expression upon entering new host cells: single-cell and population studies. Nucleic Acids Res 2021; 49:3826-3840. [PMID: 33744971 PMCID: PMC8053105 DOI: 10.1093/nar/gkab183] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 01/05/2023] Open
Abstract
Restriction-modification (R-M) systems represent a first line of defense against invasive DNAs, such as bacteriophage DNAs, and are widespread among bacteria and archaea. By acquiring a Type II R-M system via horizontal gene transfer, the new hosts generally become more resistant to phage infection, through the action of a restriction endonuclease (REase), which cleaves DNA at or near specific sequences. A modification methyltransferase (MTase) serves to protect the host genome against its cognate REase activity. The production of R-M system components upon entering a new host cell must be finely tuned to confer protective methylation before the REase acts, to avoid host genome damage. Some type II R-M systems rely on a third component, the controller (C) protein, which is a transcription factor that regulates the production of REase and/or MTase. Previous studies have suggested C protein effects on the dynamics of expression of an R-M system during its establishment in a new host cell. Here, we directly examine these effects. By fluorescently labelling REase and MTase, we demonstrate that lack of a C protein reduces the delay of REase production, to the point of being simultaneous with, or even preceding, production of the MTase. Single molecule tracking suggests that a REase and a MTase employ different strategies for their target search within host cells, with the MTase spending much more time diffusing in proximity to the nucleoid than does the REase. This difference may partially ameliorate the toxic effects of premature REase expression.
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Affiliation(s)
- Alessandro Negri
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Olesia Werbowy
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ewa Wons
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Simon Dersch
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany.,Department of Chemistry, Philipps Universität Marburg, Hans-Meerwein-Strasse 6, 35032 Marburg, Germany
| | - Rebecca Hinrichs
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany.,Department of Chemistry, Philipps Universität Marburg, Hans-Meerwein-Strasse 6, 35032 Marburg, Germany
| | - Peter L Graumann
- SYNMIKRO, LOEWE Center for Synthetic Microbiology, Marburg, Germany.,Department of Chemistry, Philipps Universität Marburg, Hans-Meerwein-Strasse 6, 35032 Marburg, Germany
| | - Iwona Mruk
- Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
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44
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Murphy TR, Xiao R, Hamilton-Brehm SD. Hybrid genome de novo assembly with methylome analysis of the anaerobic thermophilic subsurface bacterium Thermanaerosceptrum fracticalcis strain DRI-13 T. BMC Genomics 2021; 22:209. [PMID: 33757423 PMCID: PMC7988955 DOI: 10.1186/s12864-021-07535-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND There is a dearth of sequenced and closed microbial genomes from environments that exceed > 500 m below level terrestrial surface. Coupled with even fewer cultured isolates, study and understanding of how life endures in the extreme oligotrophic subsurface environments is greatly hindered. Using a de novo hybrid assembly of Illumina and Oxford Nanopore sequences we produced a circular genome with corresponding methylome profile of the recently characterized thermophilic, anaerobic, and fumarate-respiring subsurface bacterium, Thermanaerosceptrum fracticalcis, strain DRI-13T to understand how this microorganism survives the deep subsurface. RESULTS The hybrid assembly produced a single circular genome of 3.8 Mb in length with an overall GC content of 45%. Out of the total 4022 annotated genes, 3884 are protein coding, 87 are RNA encoding genes, and the remaining 51 genes were associated with regulatory features of the genome including riboswitches and T-box leader sequences. Approximately 24% of the protein coding genes were hypothetical. Analysis of strain DRI-13T genome revealed: 1) energy conservation by bifurcation hydrogenase when growing on fumarate, 2) four novel bacterial prophages, 3) methylation profile including 76.4% N6-methyladenine and 3.81% 5-methylcytosine corresponding to novel DNA methyltransferase motifs. As well a cluster of 45 genes of unknown protein families that have enriched DNA mCpG proximal to the transcription start sites, and 4) discovery of a putative core of bacteriophage exclusion (BREX) genes surrounded by hypothetical proteins, with predicted functions as helicases, nucleases, and exonucleases. CONCLUSIONS The de novo hybrid assembly of strain DRI-13T genome has provided a more contiguous and accurate view of the subsurface bacterium T. fracticalcis, strain DRI-13T. This genome analysis reveals a physiological focus supporting syntrophy, non-homologous double stranded DNA repair, mobility/adherence/chemotaxis, unique methylome profile/recognized motifs, and a BREX defense system. The key to microbial subsurface survival may not rest on genetic diversity, but rather through specific syntrophy niches and novel methylation strategies.
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Affiliation(s)
- Trevor R Murphy
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Rui Xiao
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, IL, USA
| | - Scott D Hamilton-Brehm
- Department of Microbiology, Southern Illinois University Carbondale, Carbondale, IL, USA.
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Chen Z, Wang H. Antibiotic Toxicity Profiles of Escherichia coli Strains Lacking DNA Methyltransferases. ACS OMEGA 2021; 6:7834-7840. [PMID: 33778295 PMCID: PMC7992158 DOI: 10.1021/acsomega.1c00378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/04/2021] [Indexed: 05/05/2023]
Abstract
Antibiotic-resistant bacteria are causing more antibiotic treatment failures. Developing new antibiotics and identifying bacterial targets will help to mitigate the emergence and reduce the spread of antibiotic resistance in the environment. We investigated whether DNA methyltransferase (MTase) can be an adjunct target for improving antibiotic toxicity. We used Escherichia coli as an example. The genes encoding DNA adenine MTase and cytosine MTase, dam and dcm, respectively, were separately knocked out using the λRed system in E. coli MG1655. MG1655 and the two knockout strains were separately exposed in 96-well plates to 20 antibiotics from five classes. The EC50 values of almost all of the tested antibiotics were lower in the dam and dcm knockout lines than that of the control. Our statistical analysis showed that the variations observed in EC50 values were independent of the mechanism underlying each antibiotic's mechanistic action.
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Affiliation(s)
- Zheng Chen
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese
Academy of Sciences, Beijing 100085, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Hailin Wang
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese
Academy of Sciences, Beijing 100085, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
- Institute
of Environment and Health, Jianghan University, Wuhan 430056, China
- . Phone/Fax: +86-10-62849600
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46
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Prokaryotic DNA methylation and its functional roles. J Microbiol 2021; 59:242-248. [DOI: 10.1007/s12275-021-0674-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 12/31/2022]
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47
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Carter MQ, Pham A, Huynh S, Parker CT, Miller A, He X, Hu B, Chain PSG. DNA adenine methylase, not the PstI restriction-modification system, regulates virulence gene expression in Shiga toxin-producing Escherichia coli. Food Microbiol 2020; 96:103722. [PMID: 33494894 DOI: 10.1016/j.fm.2020.103722] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 12/15/2020] [Accepted: 12/22/2020] [Indexed: 01/20/2023]
Abstract
We previously reported a distinct methylome between the two Shiga toxin-producing Escherichia coli (STEC) O145:H28 strains linked to the 2010 U.S. lettuce-associated outbreak (RM13514) and the 2007 Belgium ice cream-associated outbreak (RM13516), respectively. This difference was thought to be attributed to a prophage encoded type II restriction-modification system (PstI R-M) in RM13514. Here, we characterized this PstI R-M system in comparison to DNA adenine methylase (Dam), a highly conserved enzyme in γ proteobacteria, by functional genomics. Deficiency in Dam led to a differential expression of over 1000 genes in RM13514, whereas deficiency in PstI R-M only impacted a few genes transcriptionally. Dam regulated genes involved in diverse functions, whereas PstI R-M regulated genes mostly encoding transporters and adhesins. Dam regulated a large number of genes located on prophages, pathogenicity islands, and plasmids, including Shiga toxin genes, type III secretion system (TTSS) genes, and enterohemolysin genes. Production of Stx2 in dam mutant was significantly higher than in RM13514, supporting a role of Dam in maintaining lysogeny of Stx2-prophage. However, following mitomycin C treatment, Stx2 in RM13514 was significantly higher than that of dam or PstI R-M deletion mutant, implying that both Dam and PstI R-M contributed to maximum Stx2 production.
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Affiliation(s)
- Michelle Qiu Carter
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA, USA.
| | - Antares Pham
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA, USA
| | - Steven Huynh
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA, USA
| | - Craig T Parker
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA, USA
| | - Avalon Miller
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Produce Safety and Microbiology Research Unit, Albany, CA, USA
| | - Xiaohua He
- U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Foodborne Toxin and Detection Research Unit, Albany, CA, USA
| | - Bin Hu
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Patrick S G Chain
- Biosecurity and Public Health Group, Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
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48
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Ren J, Lee HM, Thai TD, Na D. Identification of a cytosine methyltransferase that improves transformation efficiency in Methylomonas sp. DH-1. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:200. [PMID: 33372613 PMCID: PMC7720504 DOI: 10.1186/s13068-020-01846-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 11/30/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Industrial biofuels and other value-added products can be produced from metabolically engineered microorganisms. Methylomonas sp. DH-1 is a candidate platform for bioconversion that uses methane as a carbon source. Although several genetic engineering techniques have been developed to work with Methylomonas sp. DH-1, the genetic manipulation of plasmids remains difficult because of the restriction-modification (RM) system present in the bacteria. Therefore, the RM system in Methylomonas sp. DH-1 must be identified to improve the genetic engineering prospects of this microorganism. RESULTS We identified a DNA methylation site, TGGCCA, and its corresponding cytosine methyltransferase for the first time in Methylomonas sp. DH-1 through whole-genome bisulfite sequencing. The methyltransferase was confirmed to methylate the fourth nucleotide of TGGCCA. In general, methylated plasmids exhibited better transformation efficiency under the protection of the RM system than non-methylated plasmids did. As expected, when we transformed Methylomonas sp. DH-1 with plasmid DNA harboring the psy gene, the metabolic flux towards carotenoid increased. The methyltransferase-treated plasmid exhibited an increase in transformation efficiency of 2.5 × 103 CFU/μg (124%). The introduced gene increased the production of carotenoid by 26%. In addition, the methyltransferase-treated plasmid harboring anti-psy sRNA gene exhibited an increase in transformation efficiency by 70% as well. The production of carotenoid was decreased by 40% when the psy gene was translationally repressed by anti-psy sRNA. CONCLUSIONS Plasmid DNA methylated by the discovered cytosine methyltransferase from Methylomonas sp. DH-1 had a higher transformation efficiency than non-treated plasmid DNA. The RM system identified in this study may facilitate the plasmid-based genetic manipulation of methanotrophs.
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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
| | - Thi Duc Thai
- 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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Gaultney RA, Vincent AT, Lorioux C, Coppée JY, Sismeiro O, Varet H, Legendre R, Cockram CA, Veyrier F, Picardeau M. 4-Methylcytosine DNA modification is critical for global epigenetic regulation and virulence in the human pathogen Leptospira interrogans. Nucleic Acids Res 2020; 48:12102-12115. [PMID: 33301041 PMCID: PMC7708080 DOI: 10.1093/nar/gkaa966] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/01/2020] [Accepted: 10/13/2020] [Indexed: 12/25/2022] Open
Abstract
In bacteria, DNA methylation can be facilitated by 'orphan' DNA methyltransferases lacking cognate restriction endonucleases, but whether and how these enzymes control key cellular processes are poorly understood. The effects of a specific modification, 4-methylcytosine (4mC), are even less clear, as this epigenetic marker is unique to bacteria and archaea, whereas the bulk of epigenetic research is currently performed on eukaryotes. Here, we characterize a 4mC methyltransferase from the understudied pathogen Leptospira spp. Inactivating this enzyme resulted in complete abrogation of CTAG motif methylation, leading to genome-wide dysregulation of gene expression. Mutants exhibited growth defects, decreased adhesion to host cells, higher susceptibility to LPS-targeting antibiotics, and, importantly, were no longer virulent in an acute infection model. Further investigation resulted in the discovery of at least one gene, that of an ECF sigma factor, whose transcription was altered in the methylase mutant and, subsequently, by mutation of the CTAG motifs in the promoter of the gene. The genes that comprise the regulon of this sigma factor were, accordingly, dysregulated in the methylase mutant and in a strain overexpressing the sigma factor. Our results highlight the importance of 4mC in Leptospira physiology, and suggest the same of other understudied species.
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Affiliation(s)
| | - Antony T Vincent
- Bacterial Symbionts Evolution, INRS-Centre Armand-Frappier, Laval, Quebec, Canada
| | - Céline Lorioux
- Unité Biologie des Spirochètes, Institut Pasteur, Paris, France
| | - Jean-Yves Coppée
- Transcriptome and Epigenome Platform, Biomics, Center for Technological Resources and Research (C2RT), Institut Pasteur, Paris, France
| | - Odile Sismeiro
- Transcriptome and Epigenome Platform, Biomics, Center for Technological Resources and Research (C2RT), Institut Pasteur, Paris, France
| | - Hugo Varet
- Transcriptome and Epigenome Platform, Biomics, Center for Technological Resources and Research (C2RT), Institut Pasteur, Paris, France
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 CNRS, Institut Pasteur, Paris, France
| | - Rachel Legendre
- Transcriptome and Epigenome Platform, Biomics, Center for Technological Resources and Research (C2RT), Institut Pasteur, Paris, France
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 CNRS, Institut Pasteur, Paris, France
| | | | - Frédéric J Veyrier
- Bacterial Symbionts Evolution, INRS-Centre Armand-Frappier, Laval, Quebec, Canada
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