1
|
Goswami S, Singer SW, Simmons BA, Awasthi D. Optimization of electroporation method and promoter evaluation for type-1 methanotroph, Methylotuvimicrobium alcaliphilum. Front Bioeng Biotechnol 2024; 12:1412410. [PMID: 38812915 PMCID: PMC11133525 DOI: 10.3389/fbioe.2024.1412410] [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: 04/04/2024] [Accepted: 04/26/2024] [Indexed: 05/31/2024] Open
Abstract
Methanotrophic bacteria are promising hosts for methane bioconversion to biochemicals or bioproducts. However, due to limitations associated with long genetic manipulation timelines and, lack of choice in genetic tools required for strain engineering, methanotrophs are currently not employed for bioconversion technologies. In this study, a rapid and reproducible electroporation protocol is developed for type 1 methanotroph, Methylotuvimicrobium alcaliphilum using common laboratory solutions, analyzing optimal electroshock voltages and post-shock cell recovery time. Successful reproducibility of the developed method was achieved when different replicative plasmids were assessed on lab adapted vs. wild-type M. alcaliphilum strains (DASS vs. DSM19304). Overall, a ∼ 3-fold decrease in time is reported with use of electroporation protocol developed here, compared to conjugation, which is the traditionally employed approach. Additionally, an inducible (3-methyl benzoate) and a constitutive (sucrose phosphate synthase) promoter is characterized for their strength in driving gene expression.
Collapse
Affiliation(s)
- Shubhasish Goswami
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Steven W. Singer
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Joint BioEnergy Institute, Emeryville, CA, United States
| | - Blake A. Simmons
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Joint BioEnergy Institute, Emeryville, CA, United States
| | - Deepika Awasthi
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Joint BioEnergy Institute, Emeryville, CA, United States
| |
Collapse
|
2
|
Bouras G, Houtak G, Wick RR, Mallawaarachchi V, Roach MJ, Papudeshi B, Judd LM, Sheppard AE, Edwards RA, Vreugde S. Hybracter: enabling scalable, automated, complete and accurate bacterial genome assemblies. Microb Genom 2024; 10:001244. [PMID: 38717808 PMCID: PMC11165638 DOI: 10.1099/mgen.0.001244] [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: 01/08/2024] [Accepted: 04/16/2024] [Indexed: 05/21/2024] Open
Abstract
Improvements in the accuracy and availability of long-read sequencing mean that complete bacterial genomes are now routinely reconstructed using hybrid (i.e. short- and long-reads) assembly approaches. Complete genomes allow a deeper understanding of bacterial evolution and genomic variation beyond single nucleotide variants. They are also crucial for identifying plasmids, which often carry medically significant antimicrobial resistance genes. However, small plasmids are often missed or misassembled by long-read assembly algorithms. Here, we present Hybracter which allows for the fast, automatic and scalable recovery of near-perfect complete bacterial genomes using a long-read first assembly approach. Hybracter can be run either as a hybrid assembler or as a long-read only assembler. We compared Hybracter to existing automated hybrid and long-read only assembly tools using a diverse panel of samples of varying levels of long-read accuracy with manually curated ground truth reference genomes. We demonstrate that Hybracter as a hybrid assembler is more accurate and faster than the existing gold standard automated hybrid assembler Unicycler. We also show that Hybracter with long-reads only is the most accurate long-read only assembler and is comparable to hybrid methods in accurately recovering small plasmids.
Collapse
Affiliation(s)
- George Bouras
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery – Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - Ghais Houtak
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery – Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
| | - Ryan R. Wick
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Vijini Mallawaarachchi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Michael J. Roach
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
- Adelaide Centre for Epigenetics and South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, Australia
| | - Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Lousie M. Judd
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Anna E. Sheppard
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Robert A. Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Sarah Vreugde
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery – Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, South Australia, Australia
| |
Collapse
|
3
|
Bouras G, Houtak G, Wick RR, Mallawaarachchi V, Roach MJ, Papudeshi B, Judd LM, Sheppard AE, Edwards RA, Vreugde S. Hybracter: Enabling Scalable, Automated, Complete and Accurate Bacterial Genome Assemblies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.12.571215. [PMID: 38168369 PMCID: PMC10760025 DOI: 10.1101/2023.12.12.571215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Improvements in the accuracy and availability of long-read sequencing mean that complete bacterial genomes are now routinely reconstructed using hybrid (i.e. short- and long-reads) assembly approaches. Complete genomes allow a deeper understanding of bacterial evolution and genomic variation beyond single nucleotide variants (SNVs). They are also crucial for identifying plasmids, which often carry medically significant antimicrobial resistance (AMR) genes. However, small plasmids are often missed or misassembled by long-read assembly algorithms. Here, we present Hybracter which allows for the fast, automatic, and scalable recovery of near-perfect complete bacterial genomes using a long-read first assembly approach. Hybracter can be run either as a hybrid assembler or as a long-read only assembler. We compared Hybracter to existing automated hybrid and long-read only assembly tools using a diverse panel of samples of varying levels of long-read accuracy with manually curated ground truth reference genomes. We demonstrate that Hybracter as a hybrid assembler is more accurate and faster than the existing gold standard automated hybrid assembler Unicycler. We also show that Hybracter with long-reads only is the most accurate long-read only assembler and is comparable to hybrid methods in accurately recovering small plasmids.
Collapse
Affiliation(s)
- George Bouras
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, South Australia, Australia
| | - Ghais Houtak
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, South Australia, Australia
| | - Ryan R. Wick
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Vijini Mallawaarachchi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Michael J. Roach
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
- Adelaide Centre for Epigenetics and South Australian Immunogenomics Cancer Institute, The University of Adelaide, Adelaide, Australia
| | - Bhavya Papudeshi
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Lousie M. Judd
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Anna E. Sheppard
- School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Robert A. Edwards
- Flinders Accelerator for Microbiome Exploration, College of Science and Engineering, Flinders University, Adelaide, Australia
| | - Sarah Vreugde
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, South Australia, Australia
| |
Collapse
|
4
|
Zhou Q, Guo W, Hu Z, Yan S, Jie J, Su H. Can methylated purine bases act as photoionization hotspots? Photochem Photobiol 2024; 100:368-379. [PMID: 37792888 DOI: 10.1111/php.13862] [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: 05/29/2023] [Revised: 09/12/2023] [Accepted: 09/12/2023] [Indexed: 10/06/2023]
Abstract
The direct photoionization of DNA canonical bases under ultraviolet radiation is difficult due to the high ionization potentials. According to previous quantum chemical calculations, methylation can have great influence on the ionization potential. Are methylated nucleobases prone to photoionization and cause DNA damage? As an important epigenetic modification in transcription, expression, and regulation of genes, it is of great biological significance to explore the effect of methylation on base photoionization from the experimental perspective. Herein, we study the photoionization behavior of methylated purines 6 mA and 6mG at 266 nm using a nanosecond transient UV-Vis spectroscopy. The hydrated electron and methylated base radicals are observed, indicating the occurrence of photoionization for both 6mG and 6 mA. We measured one-photon ionization yields to be (5.0 ± 0.2) × 10-3 and (1.4 ± 0.2) × 10-3 for 6mG and 6 mA, respectively. These are higher than those of (dA)20 and (dA20 )·(dT20 ) previously reported, indicating that methylation significantly promotes base photoionization with a stronger effect than base stacking, consistent with calculations in literature. Given that the hydrated electrons and methylated base radicals from photoionization can trigger a cascade of deleterious reactions, the methylated purine bases may act as hotspots of DNA photoionization damage of living organisms.
Collapse
Affiliation(s)
- Qian Zhou
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Wenwen Guo
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Zheng Hu
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Shuyi Yan
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Jialong Jie
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Hongmei Su
- College of Chemistry, Beijing Normal University, Beijing, China
| |
Collapse
|
5
|
Gong C, Chakraborty D, Koudelka GB. A prophage encoded ribosomal RNA methyltransferase regulates the virulence of Shiga-toxin-producing Escherichia coli (STEC). Nucleic Acids Res 2024; 52:856-871. [PMID: 38084890 PMCID: PMC10810198 DOI: 10.1093/nar/gkad1150] [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: 03/27/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 01/26/2024] Open
Abstract
Shiga toxin (Stx) released by Shiga toxin producing Escherichia coli (STEC) causes life-threatening illness. Its production and release require induction of Stx-encoding prophage resident within the STEC genome. We identified two different STEC strains, PA2 and PA8, bearing Stx-encoding prophage whose sequences primarily differ by the position of an IS629 insertion element, yet differ in their abilities to kill eukaryotic cells and whose prophages differ in their spontaneous induction frequencies. The IS629 element in ϕPA2, disrupts an ORF predicted to encode a DNA adenine methyltransferase, whereas in ϕPA8, this element lies in an intergenic region. Introducing a plasmid expressing the methyltransferase gene product into ϕPA2 bearing-strains increases both the prophage spontaneous induction frequency and virulence to those exhibited by ϕPA8 bearing-strains. However, a plasmid bearing mutations predicted to disrupt the putative active site of the methyltransferase does not complement either of these defects. When complexed with a second protein, the methyltransferase holoenzyme preferentially uses 16S rRNA as a substrate. The second subunit is responsible for directing the preferential methylation of rRNA. Together these findings reveal a previously unrecognized role for rRNA methylation in regulating induction of Stx-encoding prophage.
Collapse
Affiliation(s)
- Chen Gong
- Department of Biological Sciences University at Buffalo, Buffalo, NY 14260, USA
| | | | - Gerald B Koudelka
- Department of Biological Sciences University at Buffalo, Buffalo, NY 14260, USA
| |
Collapse
|
6
|
Xiao YL, Wu Y, Tang W. An adenine base editor variant expands context compatibility. Nat Biotechnol 2024:10.1038/s41587-023-01994-3. [PMID: 38168987 DOI: 10.1038/s41587-023-01994-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 09/15/2023] [Indexed: 01/05/2024]
Abstract
Adenine base editors (ABEs) are precise gene-editing agents that convert A:T pairs into G:C through a deoxyinosine intermediate. Existing ABEs function most effectively when the target A is in a TA context. Here we evolve the Escherichia coli transfer RNA-specific adenosine deaminase (TadA) to generate TadA8r, which extends potent deoxyadenosine deamination to RA (R = A or G) and is faster in processing GA than TadA8.20 and TadA8e, the two most active TadA variants reported so far. ABE8r, comprising TadA8r and a Streptococcus pyogenes Cas9 nickase, expands the editing window at the protospacer adjacent motif-distal end and outperforms ABE7.10, ABE8.20 and ABE8e in correcting disease-associated G:C-to-A:T transitions in the human genome, with a controlled off-target profile. We show ABE8r-mediated editing of clinically relevant sites that are poorly accessed by existing editors, including sites in PCSK9, whose disruption reduces low-density lipoprotein cholesterol, and ABCA4-p.Gly1961Glu, the most frequent mutation in Stargardt disease.
Collapse
Affiliation(s)
- Yu-Lan Xiao
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Yuan Wu
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Weixin Tang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.
| |
Collapse
|
7
|
Niault T, Czarnecki J, Lambérioux M, Mazel D, Val ME. Cell cycle-coordinated maintenance of the Vibrio bipartite genome. EcoSal Plus 2023; 11:eesp00082022. [PMID: 38277776 PMCID: PMC10729929 DOI: 10.1128/ecosalplus.esp-0008-2022] [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] [Indexed: 01/28/2024]
Abstract
To preserve the integrity of their genome, bacteria rely on several genome maintenance mechanisms that are co-ordinated with the cell cycle. All members of the Vibrio family have a bipartite genome consisting of a primary chromosome (Chr1) homologous to the single chromosome of other bacteria such as Escherichia coli and a secondary chromosome (Chr2) acquired by a common ancestor as a plasmid. In this review, we present our current understanding of genome maintenance in Vibrio cholerae, which is the best-studied model for bacteria with multi-partite genomes. After a brief overview on the diversity of Vibrio genomic architecture, we describe the specific, common, and co-ordinated mechanisms that control the replication and segregation of the two chromosomes of V. cholerae. Particular attention is given to the unique checkpoint mechanism that synchronizes Chr1 and Chr2 replication.
Collapse
Affiliation(s)
- Théophile Niault
- Bacterial Genome Plasticity Unit, CNRS UMR3525, Institut Pasteur, Université Paris Cité, Paris, France
- Collège Doctoral, Sorbonne Université, Paris, France
| | - Jakub Czarnecki
- Bacterial Genome Plasticity Unit, CNRS UMR3525, Institut Pasteur, Université Paris Cité, Paris, France
| | - Morgan Lambérioux
- Bacterial Genome Plasticity Unit, CNRS UMR3525, Institut Pasteur, Université Paris Cité, Paris, France
- Collège Doctoral, Sorbonne Université, Paris, France
| | - Didier Mazel
- Bacterial Genome Plasticity Unit, CNRS UMR3525, Institut Pasteur, Université Paris Cité, Paris, France
| | - Marie-Eve Val
- Bacterial Genome Plasticity Unit, CNRS UMR3525, Institut Pasteur, Université Paris Cité, Paris, France
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Norris V, Kayser C, Muskhelishvili G, Konto-Ghiorghi Y. The roles of nucleoid-associated proteins and topoisomerases in chromosome structure, strand segregation, and the generation of phenotypic heterogeneity in bacteria. FEMS Microbiol Rev 2023; 47:fuac049. [PMID: 36549664 DOI: 10.1093/femsre/fuac049] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/06/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
How to adapt to a changing environment is a fundamental, recurrent problem confronting cells. One solution is for cells to organize their constituents into a limited number of spatially extended, functionally relevant, macromolecular assemblies or hyperstructures, and then to segregate these hyperstructures asymmetrically into daughter cells. This asymmetric segregation becomes a particularly powerful way of generating a coherent phenotypic diversity when the segregation of certain hyperstructures is with only one of the parental DNA strands and when this pattern of segregation continues over successive generations. Candidate hyperstructures for such asymmetric segregation in prokaryotes include those containing the nucleoid-associated proteins (NAPs) and the topoisomerases. Another solution to the problem of creating a coherent phenotypic diversity is by creating a growth-environment-dependent gradient of supercoiling generated along the replication origin-to-terminus axis of the bacterial chromosome. This gradient is modulated by transcription, NAPs, and topoisomerases. Here, we focus primarily on two topoisomerases, TopoIV and DNA gyrase in Escherichia coli, on three of its NAPs (H-NS, HU, and IHF), and on the single-stranded binding protein, SSB. We propose that the combination of supercoiling-gradient-dependent and strand-segregation-dependent topoisomerase activities result in significant differences in the supercoiling of daughter chromosomes, and hence in the phenotypes of daughter cells.
Collapse
Affiliation(s)
- Vic Norris
- University of Rouen, Laboratory of Bacterial Communication and Anti-infection Strategies, EA 4312, 76821 Mont Saint Aignan, France
| | - Clara Kayser
- University of Rouen, Laboratory of Bacterial Communication and Anti-infection Strategies, EA 4312, 76821 Mont Saint Aignan, France
| | - Georgi Muskhelishvili
- Agricultural University of Georgia, School of Natural Sciences, 0159 Tbilisi, Georgia
| | - Yoan Konto-Ghiorghi
- University of Rouen, Laboratory of Bacterial Communication and Anti-infection Strategies, EA 4312, 76821 Mont Saint Aignan, France
| |
Collapse
|
10
|
Liu S, Xue R, Qin W, Yang X, Ye Q, Wu Q. Performance and transcriptome analysis of Salmonella enterica serovar Enteritidis PT 30 under persistent desiccation stress: Cultured by lawn and broth methods. Food Microbiol 2023; 115:104323. [PMID: 37567618 DOI: 10.1016/j.fm.2023.104323] [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: 02/13/2023] [Revised: 06/04/2023] [Accepted: 06/13/2023] [Indexed: 08/13/2023]
Abstract
Lawn-harvest method uses a solid medium (e.g., tryptic soy agar, TSA) to produce bacterial lawns and is widely accepted for the culture of microorganisms in microbial studies of low-moisture foods (LMFs, foods with water activity less than 0.85). It produces desiccation-tolerant cells with higher D-values in LMFs; however, little is known about the molecular mechanisms underlying bacterial resistance. Salmonella enterica Enteritidis PT 30 (S. Enteritidis), the most pertinent pathogen in LMFs, was cultured in TSA and tryptic soy broth (TSB). Cells were harvested and inoculated on filter papers to assess their performance under a relative humidity of 32 ± 2%. Transcriptome analysis of cultured cells during long-term desiccation (24, 72, and 168 h) was conducted in TruSeq PE Cluster Kit (Illumina) by paired-end methods. Lawn-cultured S. Enteritidis cells have stronger survivability (only decreased by 0.78 ± 0.12 log after 130 d of storage) and heat tolerance (higher D/β value) than those from the broth method. More desiccation genes of lawn-cultured cells were significantly upregulated from growth to long-term desiccation. Differentially expressed genes were the most enriched in the ribosome and sulfur metabolism pathways in the lawn- and broth-cultured groups. This study tracked the transcriptomic differences between two cultured groups in response to long-term desiccation stress and revealed some molecular mechanisms underlying their different suitability in microbial studies of LMFs.
Collapse
Affiliation(s)
- Shuxiang Liu
- College of Food Science, Sichuan Agricultural University, Ya'an, 625014, China; Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
| | - Ruimin Xue
- College of Food Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Wen Qin
- College of Food Science, Sichuan Agricultural University, Ya'an, 625014, China
| | - Xiaojuan Yang
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Qinghua Ye
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China
| | - Qingping Wu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, State Key Laboratory of Applied Microbiology Southern China, Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, 510070, China.
| |
Collapse
|
11
|
Vogelgsang L, Nisar A, Scharf SA, Rommerskirchen A, Belick D, Dilthey A, Henrich B. Characterisation of Type II DNA Methyltransferases of Metamycoplasma hominis. Microorganisms 2023; 11:1591. [PMID: 37375093 DOI: 10.3390/microorganisms11061591] [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: 03/27/2023] [Revised: 06/02/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
Bacterial virulence, persistence and defence are affected by epigenetic modifications, including DNA methylation. Solitary DNA methyltransferases modulate a variety of cellular processes and influence bacterial virulence; as part of a restriction-modification (RM) system, they act as a primitive immune system in methylating the own DNA, while unmethylated foreign DNA is restricted. We identified a large family of type II DNA methyltransferases in Metamycoplasma hominis, comprising six solitary methyltransferases and four RM systems. Motif-specific 5mC and 6mA methylations were identified with a tailored Tombo analysis on Nanopore reads. Selected motifs with methylation scores >0.5 fit with the gene presence of DAM1 and DAM2, DCM2, DCM3, and DCM6, but not for DCM1, whose activity was strain-dependent. The activity of DCM1 for CmCWGG and of both DAM1 and DAM2 for GmATC was proven in methylation-sensitive restriction and finally for recombinant rDCM1 and rDAM2 against a dam-, dcm-negative background. A hitherto unknown dcm8/dam3 gene fusion containing a (TA) repeat region of varying length was characterized within a single strain, suggesting the expression of DCM8/DAM3 phase variants. The combination of genetic, bioinformatics, and enzymatic approaches enabled the detection of a huge family of type II DNA MTases in M. hominis, whose involvement in virulence and defence can now be characterized in future work.
Collapse
Affiliation(s)
- Lars Vogelgsang
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty of the Heinrich-Heine-University Duesseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany
| | - Azlan Nisar
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty of the Heinrich-Heine-University Duesseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany
| | - Sebastian Alexander Scharf
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty of the Heinrich-Heine-University Duesseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany
| | - Anna Rommerskirchen
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty of the Heinrich-Heine-University Duesseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany
| | - Dana Belick
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty of the Heinrich-Heine-University Duesseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany
| | - Alexander Dilthey
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty of the Heinrich-Heine-University Duesseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany
| | - Birgit Henrich
- Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty of the Heinrich-Heine-University Duesseldorf, Universitätsstraße 1, 40225 Duesseldorf, Germany
| |
Collapse
|
12
|
D’Aquila P, De Rango F, Paparazzo E, Passarino G, Bellizzi D. Epigenetic-Based Regulation of Transcriptome in Escherichia coli Adaptive Antibiotic Resistance. Microbiol Spectr 2023; 11:e0458322. [PMID: 37184386 PMCID: PMC10269836 DOI: 10.1128/spectrum.04583-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 04/24/2023] [Indexed: 05/16/2023] Open
Abstract
Adaptive antibiotic resistance is a transient metabolic adaptation of bacteria limiting their sensitivity to low, progressively increased, concentrations of antibiotics. Unlike innate and acquired resistance, adaptive resistance is dependent on the presence of antibiotics, and it disappears when the triggering factor is removed. Low concentrations of antibiotics are largely diffused in natural environments, in the food industry or in certain body compartments of humans when used therapeutically, or in animals when used for growth promotion. However, molecular mechanisms underlying this phenomenon are still poorly characterized. Here, we present experiments suggesting that epigenetic modifications, triggered by low concentrations of ampicillin, gentamicin, and ciprofloxacin, may modulate the sensitivity of bacteria to antibiotics. The epigenetic modifications we observed were paralleled by modifications of the expression pattern of many genes, including some of those that have been found mutated in strains with permanent antibiotic resistance. As the use of low concentrations of antibiotics is spreading in different contexts, our findings may suggest new targets and strategies to avoid adaptive antibiotic resistance. This might be very important as, in the long run, this transient adaptation may increase the chance, allowing the survival and the flourishing of bacteria populations, of the onset of mutations leading to stable resistance. IMPORTANCE In this study, we characterized the modifications of epigenetic marks and of the whole transcriptome in the adaptive response of Escherichia coli cells to low concentrations of ampicillin, gentamicin, and ciprofloxacin. As the transient adaptation does increase the chance of permanent resistance, possibly allowing the survival and flourishing of bacteria populations where casual mutations providing resistance may give an immediate advantage, the importance of this study is not only in the identification of possible molecular mechanisms underlying adaptive resistance to antibiotics, but also in suggesting new strategies to avoid adaptation.
Collapse
Affiliation(s)
- Patrizia D’Aquila
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Francesco De Rango
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Ersilia Paparazzo
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| | - Dina Bellizzi
- Department of Biology, Ecology and Earth Sciences, University of Calabria, Rende, Italy
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Koppenhöfer S, Lang AS. Patterns of abundance, chromosomal localization, and domain organization among c-di-GMP-metabolizing genes revealed by comparative genomics of five alphaproteobacterial orders. BMC Genomics 2022; 23:834. [PMID: 36522693 PMCID: PMC9756655 DOI: 10.1186/s12864-022-09072-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 10/17/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) is a bacterial second messenger that affects diverse processes in different bacteria, including the cell cycle, motility, and biofilm formation. Its cellular levels are controlled by the opposing activities of two types of enzymes, with synthesis by diguanylate cyclases containing a GGDEF domain and degradation by phosphodiesterases containing either an HD-GYP or an EAL domain. These enzymes are ubiquitous in bacteria with up to 50 encoded in some genomes, the specific functions of which are mostly unknown. RESULTS We used comparative analyses to identify genomic patterns among genes encoding proteins with GGDEF, EAL, and HD-GYP domains in five orders of the class Alphaproteobacteria. GGDEF-containing sequences and GGDEF-EAL hybrids were the most abundant and had the highest diversity of co-occurring auxiliary domains while EAL and HD-GYP containing sequences were less abundant and less diverse with respect to auxiliary domains. There were striking patterns in the chromosomal localizations of the genes found in two of the orders. The Rhodobacterales' EAL-encoding genes and Rhizobiales' GGDEF-EAL-encoding genes showed opposing patterns of distribution compared to the GGDEF-encoding genes. In the Rhodobacterales, the GGDEF-encoding genes showed a tri-modal distribution with peaks mid-way between the origin (ori) and terminus (ter) of replication and at ter while the EAL-encoding genes peaked near ori. The patterns were more complex in the Rhizobiales, but the GGDEF-encoding genes were biased for localization near ter. CONCLUSIONS The observed patterns in the chromosomal localizations of these genes suggest a coupling of synthesis and hydrolysis of c-di-GMP with the cell cycle. Moreover, the higher proportions and diversities of auxiliary domains associated with GGDEF domains and GGDEF-EAL hybrids compared to EAL or HD-GYP domains could indicate that more stimuli affect synthesis compared to hydrolysis of c-di-GMP.
Collapse
Affiliation(s)
- Sonja Koppenhöfer
- grid.25055.370000 0000 9130 6822Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador Canada
| | - Andrew S. Lang
- grid.25055.370000 0000 9130 6822Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador Canada
| |
Collapse
|
15
|
Ginibre N, Legrand L, Bientz V, Ogier JC, Lanois A, Pages S, Brillard J. Diverse Roles for a Conserved DNA-Methyltransferase in the Entomopathogenic Bacterium Xenorhabdus. Int J Mol Sci 2022; 23:ijms231911981. [PMID: 36233296 PMCID: PMC9570324 DOI: 10.3390/ijms231911981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/03/2022] [Accepted: 10/04/2022] [Indexed: 11/07/2022] Open
Abstract
In bacteria, DNA-methyltransferase are responsible for DNA methylation of specific motifs in the genome. This methylation usually occurs at a very high rate. In the present study, we studied the MTases encoding genes found in the entomopathogenic bacteria Xenorhabdus. Only one persistent MTase was identified in the various species of this genus. This MTase, also broadly conserved in numerous Gram-negative bacteria, is called Dam: DNA-adenine MTase. Methylome analysis confirmed that the GATC motifs recognized by Dam were methylated at a rate of >99% in the studied strains. The observed enrichment of unmethylated motifs in putative promoter regions of the X. nematophila F1 strain suggests the possibility of epigenetic regulations. The overexpression of the Dam MTase responsible for additional motifs to be methylated was associated with impairment of two major phenotypes: motility, caused by a downregulation of flagellar genes, and hemolysis. However, our results suggest that dam overexpression did not modify the virulence properties of X. nematophila. This study increases the knowledge on the diverse roles played by MTases in bacteria.
Collapse
Affiliation(s)
- Nadège Ginibre
- DGIMI, INRAE, Université de Montpellier, 34090 Montpellier, France
| | - Ludovic Legrand
- LIPME, Université de Toulouse, INRAE, CNRS, 31320 Castanet-Tolosan, France
| | - Victoria Bientz
- DGIMI, INRAE, Université de Montpellier, 34090 Montpellier, France
| | | | - Anne Lanois
- DGIMI, INRAE, Université de Montpellier, 34090 Montpellier, France
| | - Sylvie Pages
- DGIMI, INRAE, Université de Montpellier, 34090 Montpellier, France
| | - Julien Brillard
- DGIMI, INRAE, Université de Montpellier, 34090 Montpellier, France
- Correspondence: ; Tel.: +33-467144711
| |
Collapse
|
16
|
Dimitra Papagianeli S, Lianou A, Aspridou Z, Stathas L, Koutsoumanis K. The magnitude of heterogeneity in individual-cell growth dynamics is an inherent characteristic of Salmonella enterica ser. Typhimurium strains. Food Res Int 2022; 162:111991. [DOI: 10.1016/j.foodres.2022.111991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 11/28/2022]
|
17
|
Weber K, Doellinger J, Jeffries CM, Wilharm G. Recombinant AcnB, NrdR and RibD of Acinetobacter baumannii and their potential interaction with DNA adenine methyltransferase AamA. Protein Expr Purif 2022; 199:106134. [PMID: 35787944 DOI: 10.1016/j.pep.2022.106134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/17/2022] [Accepted: 06/20/2022] [Indexed: 11/26/2022]
Abstract
In the last decades Acinetobacter baumannii developed into an increasingly challenging nosocomial pathogen. A. baumannii ATCC 17978 harbors a DNA-(adenine N6)-methyltransferase termed AamA. Previous studies revealed a low specific activity of AamA in vitro despite proven folding, which led us to speculate about possible interaction partners assisting AamA in targeting methylation sites. Here, applying a pulldown assay with subsequent mass spectrometry we identified aconitate hydratase 2 (AcnB) as possible interaction partner. In addition, we considered the putative transcriptional regulator gene nrdR (A1S_0220) and the pyrimidine deaminase/reductase gene ribD (A1S_0221) of A. baumannii strain ATCC 17978 to encode additional potential interaction partners due to their vicinity to the aamA gene (A1S_0222). Proteins were recombinantly produced in the milligram scale, purified to near homogeneity, and interactions with AamA were studied applying blue native gel electrophoreses, electrophoretic mobility shift assay, chemical cross-linking and co-immunoprecipitation. These analyses did not provide evidence of interaction between AamA and purified proteins. Solution structures of RibD, NrdR and AcnB were studied by small-angle X-ray scattering (SAXS) alone and in combination with AamA. While in the case of RibD and AcnB no evidence of an interaction with AamA was produced, addition of AamA to NrdR resulted in dissociation of long and rod-shaped polymeric NrdR structures, implying a specific but transient interaction. Moreover, we identified a molecular crowding effect possibly impeding the DNA methyltransferase activity in vivo and a sequence-independent DNA binding activity of AamA calling for continued efforts to identify the interaction network of AamA.
Collapse
Affiliation(s)
- Kristin Weber
- Robert Koch Institute, Project Group P2 (Acinetobacter baumannii - Biology of a Nosocomial Pathogen), Burgstr. 37, 38855 Wernigerode, Germany.
| | - Joerg Doellinger
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens, ZBS 6 (Proteomics and Spectroscopy); Seestr. 10, 13353, Berlin (Wedding), Germany.
| | - Cy M Jeffries
- European Molecular Biology Laboratory (EMBL), Svergun Group (Small-angle X-ray Scattering from Macromolecular Solutions), Notkestr. 85, Geb. 25a, 22607, Hamburg, Germany.
| | - Gottfried Wilharm
- Robert Koch Institute, Project Group P2 (Acinetobacter baumannii - Biology of a Nosocomial Pathogen), Burgstr. 37, 38855 Wernigerode, Germany.
| |
Collapse
|
18
|
Baudrexl M, Fida T, Berk B, Schwarz WH, Zverlov VV, Groll M, Liebl W. Biochemical and Structural Characterization of Thermostable GH159 Glycoside Hydrolases Exhibiting α-L-Arabinofuranosidase Activity. Front Mol Biosci 2022; 9:907439. [PMID: 35847984 PMCID: PMC9278983 DOI: 10.3389/fmolb.2022.907439] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Functional, biochemical, and preliminary structural properties are reported for three glycoside hydrolases of the recently described glycoside hydrolase (GH) family 159. The genes were cloned from the genomic sequences of different Caldicellulosiruptor strains. This study extends the spectrum of functions of GH159 enzymes. The only activity previously reported for GH159 was hydrolytic activity on β-galactofuranosides. Activity screening using a set of para-nitrophenyl (pNP) glycosides suggested additional arabinosidase activity on substrates with arabinosyl residues, which has not been previously reported for members of GH159. Even though the thermophilic enzymes investigated—Cs_Gaf159A, Ch_Gaf159A, and Ck_Gaf159A—cleaved pNP-α-l-arabinofuranoside, they were only weakly active on arabinogalactan, and they did not cleave arabinose from arabinan, arabinoxylan, or gum arabic. However, the enzymes were able to hydrolyze the α-1,3-linkage in different arabinoxylan-derived oligosaccharides (AXOS) with arabinosylated xylose at the non-reducing end (A3X, A2,3XX), suggesting their role in the intracellular hydrolysis of oligosaccharides. Crystallization and structural analysis of the apo form of one of the Caldicellulosiruptor enzymes, Ch_Gaf159A, enabled the elucidation of the first 3D structure of a GH159 member. This work revealed a five-bladed β-propeller structure for GH159 enzymes. The 3D structure and its substrate-binding pocket also provides an explanation at the molecular level for the observed exo-activity of the enzyme. Furthermore, the structural data enabled the prediction of the catalytic amino acids. This was supported by the complete inactivation by mutation of residues D19, D142, and E190 of Ch_Gaf159A.
Collapse
Affiliation(s)
- Melanie Baudrexl
- Chair of Microbiology, Technical University of Munich, Freising, Germany
| | - Tarik Fida
- Chair of Microbiology, Technical University of Munich, Freising, Germany
| | - Berkay Berk
- Chair of Microbiology, Technical University of Munich, Freising, Germany
| | | | - Vladimir V. Zverlov
- Chair of Microbiology, Technical University of Munich, Freising, Germany
- Institute of Molecular Genetics, Russian Academy of Science, Moscow, Russia
| | - Michael Groll
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Garching, Germany
| | - Wolfgang Liebl
- Chair of Microbiology, Technical University of Munich, Freising, Germany
- *Correspondence: Wolfgang Liebl,
| |
Collapse
|
19
|
Integration of the Salmonella Typhimurium Methylome and Transcriptome Reveals That DNA Methylation and Transcriptional Regulation Are Largely Decoupled under Virulence-Related Conditions. mBio 2022; 13:e0346421. [PMID: 35658533 PMCID: PMC9239280 DOI: 10.1128/mbio.03464-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Despite being in a golden age of bacterial epigenomics, little work has systematically examined the plasticity and functional impacts of the bacterial DNA methylome. Here, we leveraged single-molecule, real-time sequencing (SMRT-seq) to examine the m6A DNA methylome of two Salmonella enterica serovar Typhimurium strains: 14028s and a ΔmetJ mutant with derepressed methionine metabolism, grown in Luria broth or medium that simulates the intracellular environment. We found that the methylome is remarkably static: >95% of adenosine bases retain their methylation status across conditions. Integration of methylation with transcriptomic data revealed limited correlation between changes in methylation and gene expression. Further, examination of the transcriptome in ΔyhdJ bacteria lacking the m6A methylase with the most dynamic methylation pattern in our data set revealed little evidence of YhdJ-mediated gene regulation. Curiously, despite G(m6A)TC motifs being particularly resistant to change across conditions, incorporating dam mutants into our analyses revealed two examples where changes in methylation and transcription may be linked across conditions. This includes the novel finding that the ΔmetJ motility defect may be partially driven by hypermethylation of the chemotaxis gene tsr. Together, these data redefine the S. Typhimurium epigenome as a highly stable system that has rare but important roles in transcriptional regulation. Incorporating these lessons into future studies will be critical as we progress through the epigenomic era.
Collapse
|
20
|
Emiliani FE, Hsu I, McKenna A. Multiplexed Assembly and Annotation of Synthetic Biology Constructs Using Long-Read Nanopore Sequencing. ACS Synth Biol 2022; 11:2238-2246. [PMID: 35695379 PMCID: PMC9295152 DOI: 10.1021/acssynbio.2c00126] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Recombinant DNA is
a fundamental tool in biotechnology and medicine.
These DNA sequences are often built, replicated, and delivered in
the form of plasmids. Validation of these plasmid sequences is a critical
and time-consuming step, which has been dominated for the last 35
years by Sanger sequencing. As plasmid sequences grow more complex
with new DNA synthesis and cloning techniques, we need new approaches
that address the corresponding validation challenges at scale. Here
we prototype a high-throughput plasmid sequencing approach using DNA
transposition and Oxford Nanopore sequencing. Our method, Circuit-seq,
creates robust, full-length, and accurate plasmid assemblies without
prior knowledge of the underlying sequence. We demonstrate the power
of Circuit-seq across a wide range of plasmid sizes and complexities,
generating full-length, contiguous plasmid maps. We then leverage
our long-read data to characterize epigenetic marks and estimate plasmid
contamination levels. Circuit-seq scales to large numbers of samples
at a lower per-sample cost than commercial Sanger sequencing, accelerating
a key step in synthetic biology, while low equipment costs make it
practical for individual laboratories.
Collapse
Affiliation(s)
- Francesco E Emiliani
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756, United States
| | - Ian Hsu
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756, United States
| | - Aaron McKenna
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756, United States.,Norris Cotton Cancer Center, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire 03756, United States
| |
Collapse
|
21
|
Tang X, Zheng P, Li X, Wu H, Wei DQ, Liu Y, Huang G. Deep6mAPred: A CNN and Bi-LSTM-based deep learning method for predicting DNA N6-methyladenosine sites across plant species. Methods 2022; 204:142-150. [PMID: 35477057 DOI: 10.1016/j.ymeth.2022.04.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/16/2022] [Accepted: 04/20/2022] [Indexed: 12/11/2022] Open
Abstract
DNA N6-methyladenine (6mA) is a key DNA modification, which plays versatile roles in the cellular processes, including regulation of gene expression, DNA repair, and DNA replication. DNA 6mA is closely associated with many diseases in the mammals and with growth as well as development of plants. Precisely detecting DNA 6mA sites is of great importance to exploration of 6mA functions. Although many computational methods have been presented for DNA 6mA prediction, there is still a wide gap in the practical application. We presented a convolution neural network (CNN) and bi-directional long-short term memory (Bi-LSTM)-based deep learning method (Deep6mAPred) for predicting DNA 6mA sites across plant species. The Deep6mAPred stacked the CNNs and the Bi-LSTMs in a paralleling manner instead of a series-connection manner. The Deep6mAPred also employed the attention mechanism for improving the representations of sequences. The Deep6mAPred reached an accuracy of 0.9556 over the independent rice dataset, far outperforming the state-of-the-art methods. The tests across plant species showed that the Deep6mAPred is of a remarkable advantage over the state of the art methods. We developed a user-friendly web application for DNA 6mA prediction, which is freely available at http://106.13.196.152:7001/ for all the scientific researchers. The Deep6mAPred would enrich tools to predict DNA 6mA sites and speed up the exploration of DNA modification.
Collapse
Affiliation(s)
- Xingyu Tang
- School of Electrical Engineering, Shaoyang University, Shaoyang, Hunan 422000, China
| | - Peijie Zheng
- School of Electrical Engineering, Shaoyang University, Shaoyang, Hunan 422000, China
| | - Xueyong Li
- School of Electrical Engineering, Shaoyang University, Shaoyang, Hunan 422000, China
| | - Hongyan Wu
- The Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Dong-Qing Wei
- The Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; State Key Laboratory of Microbial Metabolism, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Yuewu Liu
- College of Information and Intelligence, Hunan Agricultural University, Changsha, Hunan 410081, China
| | - Guohua Huang
- School of Electrical Engineering, Shaoyang University, Shaoyang, Hunan 422000, China.
| |
Collapse
|
22
|
Lewis EB, Chen E, Culyba MJ. DNA cytosine methylation at the lexA promoter of Escherichia coli is stationary phase specific. G3 (BETHESDA, MD.) 2022; 12:6444991. [PMID: 34849799 PMCID: PMC9210283 DOI: 10.1093/g3journal/jkab409] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/18/2021] [Indexed: 01/09/2023]
Abstract
The bacterial DNA damage response pathway (SOS response) is composed of a network of genes regulated by a single transcriptional repressor, LexA. The lexA promoter, itself, contains two LexA operators, enabling negative feedback. In Escherichia coli, the downstream operator contains a conserved DNA cytosine methyltransferase (Dcm) site that is predicted to be methylated to 5-methylcytosine (5mC) specifically during stationary phase growth, suggesting a regulatory role for DNA methylation in the SOS response. To test this, we quantified 5mC at the lexA locus, and then examined the effect of LexA on Dcm activity, as well as the impact of this 5mC mark on LexA binding, lexA transcription, and SOS response induction. We found that 5mC at the lexA promoter is specific to stationary phase growth, but that it does not affect lexA expression. Our data support a model where LexA binding at the promoter inhibits Dcm activity without an effect on the SOS regulon.
Collapse
Affiliation(s)
- Elizabeth B Lewis
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Edwin Chen
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Matthew J Culyba
- Division of Infectious Diseases, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| |
Collapse
|
23
|
O’Brown ZK, Greer EL. N6-methyladenine: A Rare and Dynamic DNA Mark. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1389:177-210. [DOI: 10.1007/978-3-031-11454-0_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
24
|
Worst EG, Finkler M, Schenkelberger M, Kurt Ö, Helms V, Noireaux V, Ott A. A Methylation-Directed, Synthetic Pap Switch Based on Self-Complementary Regulatory DNA Reconstituted in an All E. coli Cell-Free Expression System. ACS Synth Biol 2021; 10:2725-2739. [PMID: 34550672 DOI: 10.1021/acssynbio.1c00326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Pyelonephritis-associated pili (pap) enable migration of the uropathogenic Escherichia coli strain (UPEC) through the urinary tract. UPEC can switch between a stable 'ON phase' where the corresponding pap genes are expressed and a stable 'OFF phase' where their transcription is repressed. Hereditary DNA methylation of either one of two GATC motives within the regulatory region stabilizes the respective phase over many generations. The underlying molecular mechanism is only partly understood. Previous investigations suggest that in vivo phase-variation stability results from cooperative action of the transcriptional regulators Lrp and PapI. Here, we use an E. coli cell-free expression system to study molecular functions of the pap regulatory region based on a specially designed, synthetic construct flanked by two reporter genes encoding fluorescent proteins for simple readout. On the basis of our observations we suggest that besides Lrp, the conformation of the self-complementary regulatory DNA plays a strong role in the regulation of phase-variation. Our work not only contributes to better understand the phase variation mechanism, but it represents a successful start for mimicking stable, hereditary, and strong expression control based on methylation. The conformation of the regulatory DNA corresponds to a Holliday junction. Gene expression must be expected to respond if opposite arms of the junction are drawn outward.
Collapse
Affiliation(s)
- Emanuel G. Worst
- Universität des Saarlandes, Center for Biophysics, Saarbrücken, 66123, Germany
| | - Marc Finkler
- Universität des Saarlandes, Center for Biophysics, Saarbrücken, 66123, Germany
| | - Marc Schenkelberger
- Universität des Saarlandes, Center for Biophysics, Saarbrücken, 66123, Germany
| | - Ömer Kurt
- Universität des Saarlandes, Center for Biophysics, Saarbrücken, 66123, Germany
| | - Volkhard Helms
- Universität des Saarlandes, Center for Bioinformatics, Saarbrücken, 66041, Germany
| | - Vincent Noireaux
- University of Minnesota, School of Physics and Astronomy, Minneapolis, Minnesota 55455, United States
| | - Albrecht Ott
- Universität des Saarlandes, Center for Biophysics, Saarbrücken, 66123, Germany
| |
Collapse
|
25
|
Wick RR, Judd LM, Cerdeira LT, Hawkey J, Méric G, Vezina B, Wyres KL, Holt KE. Trycycler: consensus long-read assemblies for bacterial genomes. Genome Biol 2021; 22:266. [PMID: 34521459 PMCID: PMC8442456 DOI: 10.1186/s13059-021-02483-z] [Citation(s) in RCA: 166] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/31/2021] [Indexed: 01/23/2023] Open
Abstract
While long-read sequencing allows for the complete assembly of bacterial genomes, long-read assemblies contain a variety of errors. Here, we present Trycycler, a tool which produces a consensus assembly from multiple input assemblies of the same genome. Benchmarking showed that Trycycler assemblies contained fewer errors than assemblies constructed with a single tool. Post-assembly polishing further reduced errors and Trycycler+polishing assemblies were the most accurate genomes in our study. As Trycycler requires manual intervention, its output is not deterministic. However, we demonstrated that multiple users converge on similar assemblies that are consistently more accurate than those produced by automated assembly tools.
Collapse
Affiliation(s)
- Ryan R Wick
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia.
| | - Louise M Judd
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Louise T Cerdeira
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Jane Hawkey
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Guillaume Méric
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
- Cambridge Baker Systems Genomics Initiative, Baker Heart & Diabetes Institute, Melbourne, VIC, 3004, Australia
| | - Ben Vezina
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Kelly L Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, WC1E 7HT, London, UK
| |
Collapse
|
26
|
McSweeney MA, Styczynski MP. Effective Use of Linear DNA in Cell-Free Expression Systems. Front Bioeng Biotechnol 2021; 9:715328. [PMID: 34354989 PMCID: PMC8329657 DOI: 10.3389/fbioe.2021.715328] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/06/2021] [Indexed: 12/27/2022] Open
Abstract
Cell-free expression systems (CFEs) are cutting-edge research tools used in the investigation of biological phenomena and the engineering of novel biotechnologies. While CFEs have many benefits over in vivo protein synthesis, one particularly significant advantage is that CFEs allow for gene expression from both plasmid DNA and linear expression templates (LETs). This is an important and impactful advantage because functional LETs can be efficiently synthesized in vitro in a few hours without transformation and cloning, thus expediting genetic circuit prototyping and allowing expression of toxic genes that would be difficult to clone through standard approaches. However, native nucleases present in the crude bacterial lysate (the basis for the most affordable form of CFEs) quickly degrade LETs and limit expression yield. Motivated by the significant benefits of using LETs in lieu of plasmid templates, numerous methods to enhance their stability in lysate-based CFEs have been developed. This review describes approaches to LET stabilization used in CFEs, summarizes the advancements that have come from using LETs with these methods, and identifies future applications and development goals that are likely to be impactful to the field. Collectively, continued improvement of LET-based expression and other linear DNA tools in CFEs will help drive scientific discovery and enable a wide range of applications, from diagnostics to synthetic biology research tools.
Collapse
Affiliation(s)
- Megan A McSweeney
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, Atlanta, GA, United States
| | - Mark P Styczynski
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, Atlanta, GA, United States
| |
Collapse
|
27
|
Tvedte ES, Gasser M, Sparklin BC, Michalski J, Hjelmen CE, Johnston JS, Zhao X, Bromley R, Tallon LJ, Sadzewicz L, Rasko DA, Dunning Hotopp JC. Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes. G3 (BETHESDA, MD.) 2021; 11:jkab083. [PMID: 33768248 PMCID: PMC8495745 DOI: 10.1093/g3journal/jkab083] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/07/2021] [Indexed: 12/14/2022]
Abstract
The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. We used whole-genome sequencing data produced by three PacBio protocols (Sequel II CLR, Sequel II HiFi, RS II) and two ONT protocols (Rapid Sequencing and Ligation Sequencing) to compare assemblies of the bacteria Escherichia coli and the fruit fly Drosophila ananassae. In both organisms tested, Sequel II assemblies had the highest consensus accuracy, even after accounting for differences in sequencing throughput. ONT and PacBio CLR had the longest reads sequenced compared to PacBio RS II and HiFi, and genome contiguity was highest when assembling these datasets. ONT Rapid Sequencing libraries had the fewest chimeric reads in addition to superior quantification of E. coli plasmids versus ligation-based libraries. The quality of assemblies can be enhanced by adopting hybrid approaches using Illumina libraries for bacterial genome assembly or polishing eukaryotic genome assemblies, and an ONT-Illumina hybrid approach would be more cost-effective for many users. Genome-wide DNA methylation could be detected using both technologies, however ONT libraries enabled the identification of a broader range of known E. coli methyltransferase recognition motifs in addition to undocumented D. ananassae motifs. The ideal choice of long read technology may depend on several factors including the question or hypothesis under examination. No single technology outperformed others in all metrics examined.
Collapse
Affiliation(s)
- Eric S Tvedte
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Mark Gasser
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Benjamin C Sparklin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Jane Michalski
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Carl E Hjelmen
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - J Spencer Johnston
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Xuechu Zhao
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Robin Bromley
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Luke J Tallon
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Lisa Sadzewicz
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - David A Rasko
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Julie C Dunning Hotopp
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| |
Collapse
|
28
|
Payelleville A, Brillard J. Novel Identification of Bacterial Epigenetic Regulations Would Benefit From a Better Exploitation of Methylomic Data. Front Microbiol 2021; 12:685670. [PMID: 34054792 PMCID: PMC8160106 DOI: 10.3389/fmicb.2021.685670] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 04/22/2021] [Indexed: 12/21/2022] Open
Abstract
DNA methylation can be part of epigenetic mechanisms, leading to cellular subpopulations with heterogeneous phenotypes. While prokaryotic phenotypic heterogeneity is of critical importance for a successful infection by several major pathogens, the exact mechanisms involved in this phenomenon remain unknown in many cases. Powerful sequencing tools have been developed to allow the detection of the DNA methylated bases at the genome level, and they have recently been extensively applied on numerous bacterial species. Some of these tools are increasingly used for metagenomics analysis but only a limited amount of the available methylomic data is currently being exploited. Because newly developed tools now allow the detection of subpopulations differing in their genome methylation patterns, it is time to emphasize future strategies based on a more extensive use of methylomic data. This will ultimately help to discover new epigenetic gene regulations involved in bacterial phenotypic heterogeneity, including during host-pathogen interactions.
Collapse
Affiliation(s)
- Amaury Payelleville
- DGIMI, INRAE, Univ. Montpellier, Montpellier, France.,Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, Gosselies, Belgium
| | | |
Collapse
|
29
|
Hughes L, Roberts W, Johnson D. The impact of DNA adenine methyltransferase knockout on the development of triclosan resistance and antibiotic cross-resistance in Escherichia coli. Access Microbiol 2021; 3:acmi000178. [PMID: 33997609 PMCID: PMC8115981 DOI: 10.1099/acmi.0.000178] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 10/27/2020] [Indexed: 11/18/2022] Open
Abstract
Background DNA adenine methyltransferase (dam) has been well documented for its role in regulation of replication, mismatch repair and transposition. Recent studies have also suggested a role for dam in protection against antibiotic stress, although this is not yet fully defined. We therefore evaluated the role of dam in the development of antibiotic resistance and triclosan-associated cross-resistance. Results A significant impact on growth rate was seen in the dam knockout compared to the parental strain. Known triclosan resistance-associated mutations in fabI were seen regardless of dam status, with an additional mutation in lrhA seen in the dam knockout. The expression of multiple antibiotic resistance-associated genes was significantly different between the parent and dam knockout post-resistance induction. Reversion rate assays showed that resistance mechanisms were stable. Conclusions dam knockout had a significant effect on growth, but its role in the development of antibiotic resistance is likely confined to those antibiotics using acrAD-containing efflux pumps.
Collapse
Affiliation(s)
- Lewis Hughes
- Biomedical Sciences, Leeds Beckett University, Leeds, UK
| | - Wayne Roberts
- Biomedical Sciences, Leeds Beckett University, Leeds, UK
| | - Donna Johnson
- Biomedical Sciences, Leeds Beckett University, Leeds, UK
- *Correspondence: Donna Johnson,
| |
Collapse
|
30
|
Conjoint expression and purification strategy for acquiring proteins with ultra-low DNA N6-methyladenine backgrounds in Escherichia coli. Biosci Rep 2021; 41:228016. [PMID: 33660764 PMCID: PMC7960888 DOI: 10.1042/bsr20203769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 11/21/2022] Open
Abstract
DNA N6-methyladenine (6mA), a kind of DNA epigenetic modification, is widespread in eukaryotes and prokaryotes. An enzyme activity study coupled with 6mA detection using ultra-high-performance liquid chromatography-quadruple mass spectrometry (UHPLC-MS/MS) is commonly applied to investigate 6mA potentially related enzymes in vitro. However, the protein expressed in a common Escherichia coli (E. coli) strain shows an extremely high 6mA background due to minute co-purified bacterial DNA, though it has been purified to remove DNA using multiple strategies. Furthermore, as occupied by DNA with abundant 6mA, the activity of 6mA-related proteins will be influenced seriously. Here, to address this issue, we for the first time construct a derivative of E. coli Rosetta (DE3) via the λRed knockout system specifically for the expression of 6mA-related enzymes. The gene dam encoding the 6mA methyltransferase (MTase) is knocked out in the newly constructed strain named LAMBS (low adenine methylation background strain). Contrasting with E. coli Rosetta (DE3), LAMBS shows an ultra-low 6mA background on the genomic DNA when analyzed by UHPLC-MS/MS. We also demonstrate an integral strategy of protein purification, coupled with the application of LAMBS. As a result, the purified protein expressed in LAMBS exhibits an ultra-low 6mA background comparing with the one expressed in E. coli Rosetta (DE3). Our integral strategy of protein expression and purification will benefit the in vitro investigation and application of 6mA-related proteins from eukaryotes, although these proteins are elusive until now.
Collapse
|
31
|
Konto-Ghiorghi Y, Norris V. Hypothesis: nucleoid-associated proteins segregate with a parental DNA strand to generate coherent phenotypic diversity. Theory Biosci 2020; 140:17-25. [PMID: 33095418 DOI: 10.1007/s12064-020-00323-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Accepted: 10/12/2020] [Indexed: 01/07/2023]
Abstract
The generation of a phenotypic diversity that is coherent across a bacterial population is a fundamental problem. We propose here that the DNA strand-specific segregation of certain nucleoid-associated proteins or NAPs results in these proteins being asymmetrically distributed to the daughter cells. We invoke a variety of mechanisms as responsible for this asymmetrical segregation including those based on differences between the leading and lagging strands, post-translational modifications, oligomerisation and association with membrane domains.
Collapse
Affiliation(s)
- Yoan Konto-Ghiorghi
- Laboratory of Microbiology Signals and Microenvironment, EA 4312, University of Rouen, 76821, Mont Saint Aignan, France
| | - Vic Norris
- Laboratory of Microbiology Signals and Microenvironment, EA 4312, University of Rouen, 76821, Mont Saint Aignan, France.
| |
Collapse
|
32
|
Fels U, Gevaert K, Van Damme P. Bacterial Genetic Engineering by Means of Recombineering for Reverse Genetics. Front Microbiol 2020; 11:548410. [PMID: 33013782 PMCID: PMC7516269 DOI: 10.3389/fmicb.2020.548410] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/14/2020] [Indexed: 12/11/2022] Open
Abstract
Serving a robust platform for reverse genetics enabling the in vivo study of gene functions primarily in enterobacteriaceae, recombineering -or recombination-mediated genetic engineering-represents a powerful and relative straightforward genetic engineering tool. Catalyzed by components of bacteriophage-encoded homologous recombination systems and only requiring short ∼40–50 base homologies, the targeted and precise introduction of modifications (e.g., deletions, knockouts, insertions and point mutations) into the chromosome and other episomal replicons is empowered. Furthermore, by its ability to make use of both double- and single-stranded linear DNA editing substrates (e.g., PCR products or oligonucleotides, respectively), lengthy subcloning of specific DNA sequences is circumvented. Further, the more recent implementation of CRISPR-associated endonucleases has allowed for more efficient screening of successful recombinants by the selective purging of non-edited cells, as well as the creation of markerless and scarless mutants. In this review we discuss various recombineering strategies to promote different types of gene modifications, how they are best applied, and their possible pitfalls.
Collapse
Affiliation(s)
- Ursula Fels
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Petra Van Damme
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| |
Collapse
|
33
|
Nye TM, van Gijtenbeek LA, Stevens AG, Schroeder JW, Randall JR, Matthews LA, Simmons LA. Methyltransferase DnmA is responsible for genome-wide N6-methyladenosine modifications at non-palindromic recognition sites in Bacillus subtilis. Nucleic Acids Res 2020; 48:5332-5348. [PMID: 32324221 PMCID: PMC7261158 DOI: 10.1093/nar/gkaa266] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/02/2020] [Accepted: 04/06/2020] [Indexed: 12/20/2022] Open
Abstract
The genomes of organisms from all three domains of life harbor endogenous base modifications in the form of DNA methylation. In bacterial genomes, methylation occurs on adenosine and cytidine residues to include N6-methyladenine (m6A), 5-methylcytosine (m5C), and N4-methylcytosine (m4C). Bacterial DNA methylation has been well characterized in the context of restriction-modification (RM) systems, where methylation regulates DNA incision by the cognate restriction endonuclease. Relative to RM systems less is known about how m6A contributes to the epigenetic regulation of cellular functions in Gram-positive bacteria. Here, we characterize site-specific m6A modifications in the non-palindromic sequence GACGmAG within the genomes of Bacillus subtilis strains. We demonstrate that the yeeA gene is a methyltransferase responsible for the presence of m6A modifications. We show that methylation from YeeA does not function to limit DNA uptake during natural transformation. Instead, we identify a subset of promoters that contain the methylation consensus sequence and show that loss of methylation within promoter regions causes a decrease in reporter expression. Further, we identify a transcriptional repressor that preferentially binds an unmethylated promoter used in the reporter assays. With these results we suggest that m6A modifications in B. subtilis function to promote gene expression.
Collapse
Affiliation(s)
- Taylor M Nye
- Department of Molecular, Cellular, and Developmental Biology University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Lieke A van Gijtenbeek
- Department of Molecular, Cellular, and Developmental Biology University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Amanda G Stevens
- Department of Molecular, Cellular, and Developmental Biology University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Jeremy W Schroeder
- Department of Molecular, Cellular, and Developmental Biology University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Justin R Randall
- Department of Molecular, Cellular, and Developmental Biology University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Lindsay A Matthews
- Department of Molecular, Cellular, and Developmental Biology University of Michigan, Ann Arbor, MI 48109-1055, USA
| | - Lyle A Simmons
- Department of Molecular, Cellular, and Developmental Biology University of Michigan, Ann Arbor, MI 48109-1055, USA
| |
Collapse
|
34
|
Xing Y, Gong R, Xu Y, Liu K, Zhou M. Codon usage bias affects α-amylase mRNA level by altering RNA stability and cytosine methylation patterns in Escherichia coli. Can J Microbiol 2020; 66:521-528. [PMID: 32259457 DOI: 10.1139/cjm-2019-0624] [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] [Indexed: 11/22/2022]
Abstract
Codon usage bias exists in almost every organism and is reported to regulate protein translation efficiency and folding. Besides translation, the preliminary role of codon usage bias on gene transcription has also been revealed in some eukaryotes such as Neurospora crassa. In this study, we took as an example the α-amylase-coding gene (amyA) and examined the role of codon usage bias in regulating gene expression in the typical prokaryote Escherichia coli. We confirmed the higher translation efficiency on codon-optimized amyA RNAs and found that the RNA level itself was also affected by codon optimization. The decreased RNA level was caused at least in part by altered mRNA stability at the post-transcriptional level. Codon optimization also altered the number of cytosine methylation sites. Examination on dcm knockouts suggested that cytosine methylation may be a minor mechanism adopted by codon bias to regulate gene RNA levels. More studies are required to verify the global effect of codon usage and to reveal its detailed mechanism on transcription.
Collapse
Affiliation(s)
- Yanzi Xing
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China.,State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Ruiqing Gong
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China.,State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Yichun Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China.,State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Kunshan Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China.,State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
| | - Mian Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China.,State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, P.R. China
| |
Collapse
|
35
|
Kotsarenko K, Vechtova P, Hammerova Z, Langova N, Malinovska L, Wimmerova M, Sterba J, Grubhoffer L. Newly identified DNA methyltransferases of Ixodes ricinus ticks. Ticks Tick Borne Dis 2020; 11:101348. [DOI: 10.1016/j.ttbdis.2019.101348] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 11/05/2019] [Accepted: 11/28/2019] [Indexed: 01/06/2023]
|
36
|
Gurbanov R, Tunçer S, Mingu S, Severcan F, Gozen AG. Methylation, sugar puckering and Z-form status of DNA from a heavy metal-acclimated freshwater Gordonia sp. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2019; 198:111580. [DOI: 10.1016/j.jphotobiol.2019.111580] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 07/07/2019] [Accepted: 07/29/2019] [Indexed: 01/27/2023]
|
37
|
Morales-Ruiz E, López-Ceballos A, Maldonado-Mendoza IE. Transformation of the rhizospheric Bacillus cereus sensu lato B25 strain using a room-temperature electrocompetent cells preparation protocol. Plasmid 2019; 105:102435. [DOI: 10.1016/j.plasmid.2019.102435] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 07/29/2019] [Accepted: 07/30/2019] [Indexed: 11/26/2022]
|
38
|
Abstract
DNA modifications are a major form of epigenetic regulation that eukaryotic cells utilize in concert with histone modifications. While much work has been done elucidating the role of 5-methylcytosine over the past several decades, only recently has it been recognized that N(6)-methyladenine (N6-mA) is present in quantifiable and biologically active levels in the DNA of eukaryotic cells. Unlike prokaryotes which utilize N6-mA to recognize "self" from "foreign" DNA, eukaryotes have been found to use N6-mA in varying ways, from regulating transposable elements to gene regulation in response to hypoxia and stress. In this review, we examine the current state of the N6-mA in research field, and the current understanding of the biochemical mechanisms which deposit and remove N6-mA from the eukaryotic genome.
Collapse
Affiliation(s)
- Myles H Alderman
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, 06520, USA
| | - Andrew Z Xiao
- Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, 06520, USA.
| |
Collapse
|
39
|
Scholz I, Lott SC, Behler J, Gärtner K, Hagemann M, Hess WR. Divergent methylation of CRISPR repeats and cas genes in a subtype I-D CRISPR-Cas-system. BMC Microbiol 2019; 19:147. [PMID: 31262257 PMCID: PMC6604393 DOI: 10.1186/s12866-019-1526-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 06/20/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The presence and activity of CRISPR-Cas defense systems is a hallmark of many prokaryotic microorganisms. Here, the distribution of sequences related to the highly iterated palindrome 1 (HIP1) element and the DNA methylation of CGATCG motifs embedded within HIP1 as a vital part of the CRISPR1 repeat sequence was analyzed in the cyanobacterium Synechocystis sp. PCC 6803. Previously suggested functions of HIP1 include organization of chromosomal structure, DNA recombination or gene regulation, all of which could be relevant in CRISPR-Cas functionality. RESULTS The CRISPR1 repeat-spacer array contains more than 50 CGATCG elements that are double-methylated (5mCG6mATCG) by the enzymes M.Ssp6803I and M.Ssp6803III. Hence, more than 200 possible methylation events cluster over a stretch of 3600 bp of double-stranded DNA. Bisulfite sequencing showed that these motifs were highly methylated at the m5CGATCG positions whereas specific motifs within the CRISPR1 cas genes were hypomethylated suggesting a lowered accessibility for the DNA methylase to these regions. Assays for conjugation and CRISPR1-mediated DNA interference revealed a 50% drop in conjugation efficiency in the mutant lacking the 5mC methylation of CGATCG motifs, while the highly efficient DNA interference activity was not affected by the lack of m5CGATCG DNA-methylation, nor was the capability to differentiate between self and non-self targets based on the protospacer adjacent motifs (PAMs) GTA and GTC versus the non-PAM AGC. A third DNA methylation mediated by M.Ssp6803II modifies the first cytosine in the motif GGCC yielding GGm4CC. We found a remarkable absence of GGCC motifs and hence the corresponding methylation over an 11 kb stretch encompassing all the cas genes involved in interference and crRNA maturation but not adaptation of the CRISPR1 system. CONCLUSIONS The lack of GGCC tetranucleotides along the CRISPR1 interference and maturation genes supports the reported hybrid character of subtype I-D CRISPR-Cas systems. We report tight and very high 5mC methylation of the CRISPR1 repeat sequences. Nevertheless, cells lacking the 5mC methylation activity were unaffected in their CRISPR1-mediated interference response but the efficiency of conjugation was reduced by 50%. These results point to an unknown role of m5CGATCG DNA-methylation marks in conjugation and DNA transformation.
Collapse
Affiliation(s)
- Ingeborg Scholz
- Faculty of Biology, Genetics an Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Steffen C. Lott
- Faculty of Biology, Genetics an Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Juliane Behler
- Faculty of Biology, Genetics an Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
| | - Katrin Gärtner
- University of Rostock, Institute of Biosciences, Plant Physiology, A.-Einstein-Str. 3, D-18059 Rostock, Germany
| | - Martin Hagemann
- University of Rostock, Institute of Biosciences, Plant Physiology, A.-Einstein-Str. 3, D-18059 Rostock, Germany
| | - Wolfgang R. Hess
- Faculty of Biology, Genetics an Experimental Bioinformatics, University of Freiburg, Schänzlestr. 1, D-79104 Freiburg, Germany
- University of Freiburg, Freiburg Institute for Advanced Studies, Albertstr. 19, D-79104 Freiburg, Germany
| |
Collapse
|
40
|
Wang R, Lou J, Li J. A mobile restriction modification system consisting of methylases on the IncA/C plasmid. Mob DNA 2019; 10:26. [PMID: 31182978 PMCID: PMC6555945 DOI: 10.1186/s13100-019-0168-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 05/31/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND IncA/C plasmids play important roles in the development and dissemination of multidrug resistance in bacteria. These plasmids carry three methylase genes, two of which show cytosine specificity. The effects of such a plasmid on the host methylome were observed by single-molecule, real-time (SMRT) and bisulfite sequencing in this work. RESULTS The results showed that the numbers of methylation sites on the host chromosomes were changed, as were the sequences recognized by MTase. The host chromosomes were completely remodified by the plasmid with a methylation pattern different from that of the host itself. When the three dcm genes were deleted, the transferability of the plasmid into other Vibrio cholerae and Escherichia coli strains was lost. During deletion of the dcm genes, except for the wild-type strains and the targeted deletion strains, 18.7%~ 38.5% of the clones lost the IncA/C plasmid and changed from erythromycin-, azithromycin- and tetracycline-resistant strains to strains that were sensitive to these antibiotics. CONCLUSIONS Methylation of the IncA/C plasmid was a new mobile restriction modification (RM) barrier against foreign DNA. By actively changing the host's methylation pattern, the plasmid crossed the barrier of the host's RM system, and this might be the simplest and most universal method by which plasmids acquire a broad host range. Elimination of plasmids by destruction of plasmid stability could be a new effective strategy to address bacterial multidrug resistance.
Collapse
Affiliation(s)
- Ruibai Wang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changbai Road 155, Changping, Beijing, 102206 People’s Republic of China
| | - Jing Lou
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changbai Road 155, Changping, Beijing, 102206 People’s Republic of China
| | - Jie Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changbai Road 155, Changping, Beijing, 102206 People’s Republic of China
| |
Collapse
|
41
|
O'Brown ZK, Boulias K, Wang J, Wang SY, O'Brown NM, Hao Z, Shibuya H, Fady PE, Shi Y, He C, Megason SG, Liu T, Greer EL. Sources of artifact in measurements of 6mA and 4mC abundance in eukaryotic genomic DNA. BMC Genomics 2019; 20:445. [PMID: 31159718 PMCID: PMC6547475 DOI: 10.1186/s12864-019-5754-6] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 04/30/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Directed DNA methylation on N6-adenine (6mA), N4-cytosine (4mC), and C5-cytosine (5mC) can potentially increase DNA coding capacity and regulate a variety of biological functions. These modifications are relatively abundant in bacteria, occurring in about a percent of all bases of most bacteria. Until recently, 5mC and its oxidized derivatives were thought to be the only directed DNA methylation events in metazoa. New and more sensitive detection techniques (ultra-high performance liquid chromatography coupled with mass spectrometry (UHPLC-ms/ms) and single molecule real-time sequencing (SMRTseq)) have suggested that 6mA and 4mC modifications could be present in a variety of metazoa. RESULTS Here, we find that both of these techniques are prone to inaccuracies, which overestimate DNA methylation concentrations in metazoan genomic DNA. Artifacts can arise from methylated bacterial DNA contamination of enzyme preparations used to digest DNA and contaminating bacterial DNA in eukaryotic DNA preparations. Moreover, DNA sonication introduces a novel modified base from 5mC that has a retention time near 4mC that can be confused with 4mC. Our analyses also suggest that SMRTseq systematically overestimates 4mC in prokaryotic and eukaryotic DNA and 6mA in DNA samples in which it is rare. Using UHPLC-ms/ms designed to minimize and subtract artifacts, we find low to undetectable levels of 4mC and 6mA in genomes of representative worms, insects, amphibians, birds, rodents and primates under normal growth conditions. We also find that mammalian cells incorporate exogenous methylated nucleosides into their genome, suggesting that a portion of 6mA modifications could derive from incorporation of nucleosides from bacteria in food or microbiota. However, gDNA samples from gnotobiotic mouse tissues found rare (0.9-3.7 ppm) 6mA modifications above background. CONCLUSIONS Altogether these data demonstrate that 6mA and 4mC are rarer in metazoa than previously reported, and highlight the importance of careful sample preparation and measurement, and need for more accurate sequencing techniques.
Collapse
Affiliation(s)
- Zach K O'Brown
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Konstantinos Boulias
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Jie Wang
- Department of Biochemistry and Biostatistics, University at Buffalo Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, 14203, USA
| | - Simon Yuan Wang
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Natasha M O'Brown
- Department of Neurobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Ziyang Hao
- Department of Chemistry and Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Hiroki Shibuya
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
- Present address: Department of Chemistry and Molecular Biology, University of Gothenburg, SE-40530, Gothenburg, Sweden
| | - Paul-Enguerrand Fady
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
| | - Yang Shi
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Chuan He
- Department of Chemistry and Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, 60637, USA
| | - Sean G Megason
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Tao Liu
- Department of Biochemistry and Biostatistics, University at Buffalo Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, 14203, USA
| | - Eric L Greer
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA, 02115, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
| |
Collapse
|
42
|
Does the Semiconservative Nature of DNA Replication Facilitate Coherent Phenotypic Diversity? J Bacteriol 2019; 201:JB.00119-19. [PMID: 30936370 DOI: 10.1128/jb.00119-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
It has been clear for over sixty years that the principal method whereby cells replicate and segregate their DNA is semiconservative. It is much less clear why it should be like this rather than, say, conservative. Recently, evidence has accumulated that supports the hypothesis that one of the functions of the cell cycle is to generate phenotypically different daughter cells, even in nondifferentiating bacteria such as Escherichia coli Evidence has also accumulated that the bacterial phenotype is determined by the functioning of extended assemblies of macromolecules termed hyperstructures. One class of these hyperstructures is attached dynamically to a DNA strand by the coupling of transcription and translation. Previously, we proposed in the strand segregation model that one set of hyperstructures accompanies one parental strand into one daughter cell while another set of hyperstructures accompanies the other parental strand into the other daughter cell. This epigenetic mechanism results in daughter cells having different phenotypes. Here, I propose that one of the reasons why semiconservative replication has been selected is because it allows the generation of a population containing cells with very different growth rates even in steady-state conditions.
Collapse
|
43
|
Wang L, Jiang S, Deng Z, Dedon PC, Chen S. DNA phosphorothioate modification-a new multi-functional epigenetic system in bacteria. FEMS Microbiol Rev 2019; 43:109-122. [PMID: 30289455 PMCID: PMC6435447 DOI: 10.1093/femsre/fuy036] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/03/2018] [Indexed: 12/20/2022] Open
Abstract
Synthetic phosphorothioate (PT) internucleotide linkages, in which a nonbridging oxygen is replaced by a sulphur atom, share similar physical and chemical properties with phosphodiesters but confer enhanced nuclease tolerance on DNA/RNA, making PTs a valuable biochemical and pharmacological tool. Interestingly, PT modification was recently found to occur naturally in bacteria in a sequence-selective and RP configuration-specific manner. This oxygen-sulphur swap is catalysed by the gene products of dndABCDE, which constitute a defence barrier with DndFGH in some bacterial strains that can distinguish and attack non-PT-modified foreign DNA, resembling DNA methylation-based restriction-modification (R-M) systems. Despite their similar defensive mechanisms, PT- and methylation-based R-M systems have evolved to target different consensus contexts in the host cell because when they share the same recognition sequences, the protective function of each can be impeded. The redox and nucleophilic properties of PT sulphur render PT modification a versatile player in the maintenance of cellular redox homeostasis, epigenetic regulation and environmental fitness. The widespread presence of dnd systems is considered a consequence of extensive horizontal gene transfer, whereas the lability of PT during oxidative stress and the susceptibility of PT to PT-dependent endonucleases provide possible explanations for the ubiquitous but sporadic distribution of PT modification in the bacterial world.
Collapse
Affiliation(s)
- Lianrong Wang
- Zhongnan Hospital, Wuhan University, 169 Donghu Road, Wuhan 430071, China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 185 Donghu Road, Wuhan 430071, China
| | - Susu Jiang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 185 Donghu Road, Wuhan 430071, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 185 Donghu Road, Wuhan 430071, China
| | - Peter C Dedon
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Masschusetts Avenue, Cambridge, Massachusetts, USA
| | - Shi Chen
- Zhongnan Hospital, Wuhan University, 169 Donghu Road, Wuhan 430071, China.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, 185 Donghu Road, Wuhan 430071, China
| |
Collapse
|
44
|
Militello KT, Reinhardt JA. An undergraduate laboratory on RNA sequencing analysis of bacterial gene expression. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 47:161-167. [PMID: 30681282 DOI: 10.1002/bmb.21212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 11/09/2018] [Accepted: 01/02/2019] [Indexed: 06/09/2023]
Abstract
Next generation sequencing has revolutionized molecular biology and has provided a mechanism for rapid DNA and RNA sequence analysis. Yet, there are few resources to introduce next generation sequencing into the undergraduate biochemistry and molecular biology curriculum. Herein, we describe the design, execution, and assessment of a four-week laboratory for junior and senior undergraduate students that focuses on bacterial gene expression changes detected by RNA sequencing (RNA-seq). In the laboratory, students analyze a bacterial RNA-seq dataset in detail and answer questions relating to the impact of DNA methylation on bacterial gene expression. In addition, students confirm key results from the RNA-seq dataset using qRT-PCR and compare their results to similar experiments in the literature. A major strength of the laboratory is the ability of students to analyze raw RNA-seq data. In addition, another strength of the laboratory is the utilization of both dry approaches (informatics and statistics) and wet approaches (RNA isolation, cDNA synthesis, and qRT-PCR) to answer bacterial gene expression questions. Assessment of the laboratory indicates that significant learning gains were achieved with respect to next generation sequencing and RNA-seq. We expect that the laboratory will be a valuable resource as is, or via modification with other datasets and projects. © 2019 International Union of Biochemistry and Molecular Biology, 47(2): 161-167, 2019.
Collapse
Affiliation(s)
- Kevin T Militello
- Biology Department, State University of New York at Geneseo, Geneseo, New York 14454
| | - Josephine A Reinhardt
- Biology Department, State University of New York at Geneseo, Geneseo, New York 14454
| |
Collapse
|
45
|
Singh A, Vancura A, Woycicki RK, Hogan DJ, Hendrick AG, Nowacki M. Determination of the presence of 5-methylcytosine in Paramecium tetraurelia. PLoS One 2018; 13:e0206667. [PMID: 30379964 PMCID: PMC6209305 DOI: 10.1371/journal.pone.0206667] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Accepted: 10/17/2018] [Indexed: 11/19/2022] Open
Abstract
5-methylcytosine DNA methylation regulates gene expression and developmental programming in a broad range of eukaryotes. However, its presence and potential roles in ciliates, complex single-celled eukaryotes with germline-somatic genome specialization via nuclear dimorphism, are largely uncharted. While canonical cytosine methyltransferases have not been discovered in published ciliate genomes, recent studies performed in the stichotrichous ciliate Oxytricha trifallax suggest de novo cytosine methylation during macronuclear development. In this study, we applied bisulfite genome sequencing, DNA mass spectrometry and antibody-based fluorescence detection to investigate the presence of DNA methylation in Paramecium tetraurelia. While the antibody-based methods suggest cytosine methylation, DNA mass spectrometry and bisulfite sequencing reveal that levels are actually below the limit of detection. Our results suggest that Paramecium does not utilize 5-methylcytosine DNA methylation as an integral part of its epigenetic arsenal.
Collapse
Affiliation(s)
- Aditi Singh
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Freiestrasse 1, Bern, Switzerland
| | - Adrienne Vancura
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, Bern, Switzerland
| | - Rafal K. Woycicki
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, Bern, Switzerland
| | - Daniel J. Hogan
- Tocagen Incorporated, San Diego, California, United States of America
| | - Alan G. Hendrick
- Storm Therapeutics Limited, Moneta Building, Babraham Research Campus, Cambridge, United Kingdom
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, Baltzerstrasse 4, Bern, Switzerland
- * E-mail:
| |
Collapse
|
46
|
Mouammine A, Collier J. The impact of DNA methylation in Alphaproteobacteria. Mol Microbiol 2018; 110:1-10. [PMID: 29995343 DOI: 10.1111/mmi.14079] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/07/2018] [Indexed: 02/02/2023]
Abstract
Alphaproteobacteria include bacteria with very different modes of life, from free-living to host-associated and pathogenic bacteria. Their genomes vary in size and organization from single circular chromosomes to multipartite genomes and are often methylated by one or more adenine or cytosine methyltransferases (MTases). These include MTases that are part of restriction/modification systems and so-called orphan MTases. The development of novel technologies accelerated the analysis of methylomes and revealed the existence of epigenetic patterns in several Alphaproteobacteria. This review describes the known functions of DNA methylation in Alphaproteobacteria and also discusses its potential drawbacks through the accidental deamination of methylated cytosines. Particular emphasis is given to the strong connection between the cell cycle-regulated orphan MTase CcrM and the complex network that controls gene expression and cell cycle progression in Alphaproteobacteria.
Collapse
Affiliation(s)
- Annabelle Mouammine
- Faculty of Biology and Medicine, Department of Fundamental Microbiology, University of Lausanne, Quartier UNIL/Sorge, Lausanne, CH 1015, Switzerland
| | - Justine Collier
- Faculty of Biology and Medicine, Department of Fundamental Microbiology, University of Lausanne, Quartier UNIL/Sorge, Lausanne, CH 1015, Switzerland
| |
Collapse
|
47
|
The SCO1731 methyltransferase modulates actinorhodin production and morphological differentiation of Streptomyces coelicolor A3(2). Sci Rep 2018; 8:13686. [PMID: 30209340 PMCID: PMC6135851 DOI: 10.1038/s41598-018-32027-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/18/2018] [Indexed: 02/07/2023] Open
Abstract
Streptomyces coelicolor is a Gram-positive microorganism often used as a model of physiological and morphological differentiation in streptomycetes, prolific producers of secondary metabolites with important biological activities. In the present study, we analysed Streptomyces coelicolor growth and differentiation in the presence of the hypo-methylating agent 5′-aza-2′-deoxycytidine (5-aza-dC) in order to investigate whether cytosine methylation has a role in differentiation. We found that cytosine demethylation caused a delay in spore germination, aerial mycelium development, sporulation, as well as a massive impairment of actinorhodin production. Thus, we searched for putative DNA methyltransferase genes in the genome and constructed a mutant of the SCO1731 gene. The analysis of the SCO1731::Tn5062 mutant strain demonstrated that inactivation of SCO1731 leads to a strong decrease of cytosine methylation and almost to the same phenotype obtained after 5-aza-dC treatment. Altogether, our data demonstrate that cytosine methylation influences morphological differentiation and actinorhodin production in S. coelicolor and expand our knowledge on this model bacterial system.
Collapse
|
48
|
Payelleville A, Legrand L, Ogier JC, Roques C, Roulet A, Bouchez O, Mouammine A, Givaudan A, Brillard J. The complete methylome of an entomopathogenic bacterium reveals the existence of loci with unmethylated Adenines. Sci Rep 2018; 8:12091. [PMID: 30108278 PMCID: PMC6092372 DOI: 10.1038/s41598-018-30620-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 08/03/2018] [Indexed: 01/01/2023] Open
Abstract
DNA methylation can serve to control diverse phenomena in eukaryotes and prokaryotes, including gene regulation leading to cell differentiation. In bacteria, DNA methylomes (i.e., methylation state of each base of the whole genome) have been described for several species, but methylome profile variation during the lifecycle has rarely been studied, and only in a few model organisms. Moreover, major phenotypic changes have been reported in several bacterial strains with a deregulated methyltransferase, but the corresponding methylome has rarely been described. Here we report the first methylome description of an entomopathogenic bacterium, Photorhabdus luminescens. Eight motifs displaying a high rate of methylation (>94%) were identified. The methylome was strikingly stable over course of growth, but also in a subpopulation responsible for a critical step in the bacterium's lifecycle: successful survival and proliferation in insects. The rare unmethylated GATC motifs were preferentially located in putative promoter regions, and most of them were methylated after Dam methyltransferase overexpression, suggesting that DNA methylation is involved in gene regulation. Our findings bring key insight into bacterial methylomes and encourage further research to decipher the role of loci protected from DNA methylation in gene regulation.
Collapse
Affiliation(s)
| | - Ludovic Legrand
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | | | - Céline Roques
- GeT-PlaGe, INRA, US 1426, Genotoul, Castanet-Tolosan, France
| | - Alain Roulet
- GeT-PlaGe, INRA, US 1426, Genotoul, Castanet-Tolosan, France
| | - Olivier Bouchez
- GeT-PlaGe, INRA, US 1426, Genotoul, Castanet-Tolosan, France
| | - Annabelle Mouammine
- DGIMI, INRA, Univ. Montpellier, Montpellier, France
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Quartier UNIL/Sorge, Lausanne, CH1015, Switzerland
| | | | | |
Collapse
|
49
|
Hofmeister BT, Schmitz RJ. Enhanced JBrowse plugins for epigenomics data visualization. BMC Bioinformatics 2018; 19:159. [PMID: 29699480 PMCID: PMC5921565 DOI: 10.1186/s12859-018-2160-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 04/19/2018] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND New sequencing techniques require new visualization strategies, as is the case for epigenomics data such as DNA base modifications, small non-coding RNAs, and histone modifications. RESULTS We present a set of plugins for the genome browser JBrowse that are targeted for epigenomics visualizations. Specifically, we have focused on visualizing DNA base modifications, small non-coding RNAs, stranded read coverage, and sequence motif density. Additionally, we present several plugins for improved user experience such as configurable, high-quality screenshots. CONCLUSIONS In visualizing epigenomics with traditional genomics data, we see these plugins improving scientific communication and leading to discoveries within the field of epigenomics.
Collapse
Affiliation(s)
| | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA.
| |
Collapse
|
50
|
Hasegawa S, Jojima T, Inui M. Efficient construction of xenogeneic genomic libraries by circumventing restriction-modification systems that restrict methylated DNA. J Microbiol Methods 2018; 146:13-15. [PMID: 29355574 DOI: 10.1016/j.mimet.2018.01.005] [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: 11/09/2017] [Revised: 01/15/2018] [Accepted: 01/15/2018] [Indexed: 10/18/2022]
Abstract
An efficient method to construct xenogeneic genomic libraries with low errors and bias by circumventing restriction-modification systems that restrict methylated DNA was developed. Un-methylated genomic DNA of Escherichia coli prepared by ϕ29 DNA polymerase was introduced to Corynebacterium glutamicum R after ligation with un-methylated vector plasmids.
Collapse
Affiliation(s)
- Satoshi Hasegawa
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa, Kyoto 619-0292, Japan
| | - Toru Jojima
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa, Kyoto 619-0292, Japan
| | - Masayuki Inui
- Research Institute of Innovative Technology for the Earth, 9-2, Kizugawadai, Kizugawa, Kyoto 619-0292, Japan; Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0101, Japan.
| |
Collapse
|