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Christi K, Hudson J, Egan S. Current approaches to genetic modification of marine bacteria and considerations for improved transformation efficiency. Microbiol Res 2024; 284:127729. [PMID: 38663232 DOI: 10.1016/j.micres.2024.127729] [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: 10/18/2023] [Revised: 02/25/2024] [Accepted: 04/15/2024] [Indexed: 05/26/2024]
Abstract
Marine bacteria play vital roles in symbiosis, biogeochemical cycles and produce novel bioactive compounds and enzymes of interest for the pharmaceutical, biofuel and biotechnology industries. At present, investigations into marine bacterial functions and their products are primarily based on phenotypic observations, -omic type approaches and heterologous gene expression. To advance our understanding of marine bacteria and harness their full potential for industry application, it is critical that we have the appropriate tools and resources to genetically manipulate them in situ. However, current genetic tools that are largely designed for model organisms such as E. coli, produce low transformation efficiencies or have no transfer ability in marine bacteria. To improve genetic manipulation applications for marine bacteria, we need to improve transformation methods such as conjugation and electroporation in addition to identifying more marine broad host range plasmids. In this review, we aim to outline the reported methods of transformation for marine bacteria and discuss the considerations for each approach in the context of improving efficiency. In addition, we further discuss marine plasmids and future research areas including CRISPR tools and their potential applications for marine bacteria.
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Affiliation(s)
- Katrina Christi
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, Australia
| | - Jennifer Hudson
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, Australia
| | - Suhelen Egan
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, Australia.
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2
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Tripathi AK, Saxena P, Thakur P, Rauniyar S, Samanta D, Gopalakrishnan V, Singh RN, Sani RK. Transcriptomics and Functional Analysis of Copper Stress Response in the Sulfate-Reducing Bacterium Desulfovibrio alaskensis G20. Int J Mol Sci 2022; 23:1396. [PMID: 35163324 PMCID: PMC8836040 DOI: 10.3390/ijms23031396] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 01/27/2023] Open
Abstract
Copper (Cu) is an essential micronutrient required as a co-factor in the catalytic center of many enzymes. However, excess Cu can generate pleiotropic effects in the microbial cell. In addition, leaching of Cu from pipelines results in elevated Cu concentration in the environment, which is of public health concern. Sulfate-reducing bacteria (SRB) have been demonstrated to grow in toxic levels of Cu. However, reports on Cu toxicity towards SRB have primarily focused on the degree of toxicity and subsequent elimination. Here, Cu(II) stress-related effects on a model SRB, Desulfovibrio alaskensis G20, is reported. Cu(II) stress effects were assessed as alterations in the transcriptome through RNA-Seq at varying Cu(II) concentrations (5 µM and 15 µM). In the pairwise comparison of control vs. 5 µM Cu(II), 61.43% of genes were downregulated, and 38.57% were upregulated. In control vs. 15 µM Cu(II), 49.51% of genes were downregulated, and 50.5% were upregulated. The results indicated that the expression of inorganic ion transporters and translation machinery was massively modulated. Moreover, changes in the expression of critical biological processes such as DNA transcription and signal transduction were observed at high Cu(II) concentrations. These results will help us better understand the Cu(II) stress-response mechanism and provide avenues for future research.
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Affiliation(s)
- Abhilash Kumar Tripathi
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (A.K.T.); (P.S.); (P.T.); (S.R.); (D.S.); (V.G.); (R.N.S.)
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Priya Saxena
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (A.K.T.); (P.S.); (P.T.); (S.R.); (D.S.); (V.G.); (R.N.S.)
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Payal Thakur
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (A.K.T.); (P.S.); (P.T.); (S.R.); (D.S.); (V.G.); (R.N.S.)
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Shailabh Rauniyar
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (A.K.T.); (P.S.); (P.T.); (S.R.); (D.S.); (V.G.); (R.N.S.)
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Dipayan Samanta
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (A.K.T.); (P.S.); (P.T.); (S.R.); (D.S.); (V.G.); (R.N.S.)
- BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Vinoj Gopalakrishnan
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (A.K.T.); (P.S.); (P.T.); (S.R.); (D.S.); (V.G.); (R.N.S.)
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Ram Nageena Singh
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (A.K.T.); (P.S.); (P.T.); (S.R.); (D.S.); (V.G.); (R.N.S.)
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
| | - Rajesh Kumar Sani
- Department of Chemical and Biological Engineering, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA; (A.K.T.); (P.S.); (P.T.); (S.R.); (D.S.); (V.G.); (R.N.S.)
- 2-Dimensional Materials for Biofilm Engineering, Science and Technology, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
- Data Driven Material Discovery Center for Bioengineering Innovation, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
- BuG ReMeDEE Consortium, South Dakota School of Mines and Technology, Rapid City, SD 57701, USA
- Composite and Nanocomposite Advanced Manufacturing Centre—Biomaterials, Rapid City, SD 57701, USA
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3
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Gaultney RA, Vincent AT, Lorioux C, Coppée JY, Sismeiro O, Varet H, Legendre R, Cockram CA, Veyrier F, Picardeau M. 4-Methylcytosine DNA modification is critical for global epigenetic regulation and virulence in the human pathogen Leptospira interrogans. Nucleic Acids Res 2020; 48:12102-12115. [PMID: 33301041 PMCID: PMC7708080 DOI: 10.1093/nar/gkaa966] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 10/01/2020] [Accepted: 10/13/2020] [Indexed: 12/25/2022] Open
Abstract
In bacteria, DNA methylation can be facilitated by 'orphan' DNA methyltransferases lacking cognate restriction endonucleases, but whether and how these enzymes control key cellular processes are poorly understood. The effects of a specific modification, 4-methylcytosine (4mC), are even less clear, as this epigenetic marker is unique to bacteria and archaea, whereas the bulk of epigenetic research is currently performed on eukaryotes. Here, we characterize a 4mC methyltransferase from the understudied pathogen Leptospira spp. Inactivating this enzyme resulted in complete abrogation of CTAG motif methylation, leading to genome-wide dysregulation of gene expression. Mutants exhibited growth defects, decreased adhesion to host cells, higher susceptibility to LPS-targeting antibiotics, and, importantly, were no longer virulent in an acute infection model. Further investigation resulted in the discovery of at least one gene, that of an ECF sigma factor, whose transcription was altered in the methylase mutant and, subsequently, by mutation of the CTAG motifs in the promoter of the gene. The genes that comprise the regulon of this sigma factor were, accordingly, dysregulated in the methylase mutant and in a strain overexpressing the sigma factor. Our results highlight the importance of 4mC in Leptospira physiology, and suggest the same of other understudied species.
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Affiliation(s)
| | - Antony T Vincent
- Bacterial Symbionts Evolution, INRS-Centre Armand-Frappier, Laval, Quebec, Canada
| | - Céline Lorioux
- Unité Biologie des Spirochètes, Institut Pasteur, Paris, France
| | - Jean-Yves Coppée
- Transcriptome and Epigenome Platform, Biomics, Center for Technological Resources and Research (C2RT), Institut Pasteur, Paris, France
| | - Odile Sismeiro
- Transcriptome and Epigenome Platform, Biomics, Center for Technological Resources and Research (C2RT), Institut Pasteur, Paris, France
| | - Hugo Varet
- Transcriptome and Epigenome Platform, Biomics, Center for Technological Resources and Research (C2RT), Institut Pasteur, Paris, France
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 CNRS, Institut Pasteur, Paris, France
| | - Rachel Legendre
- Transcriptome and Epigenome Platform, Biomics, Center for Technological Resources and Research (C2RT), Institut Pasteur, Paris, France
- Bioinformatics and Biostatistics Hub, Department of Computational Biology, USR 3756 CNRS, Institut Pasteur, Paris, France
| | | | - Frédéric J Veyrier
- Bacterial Symbionts Evolution, INRS-Centre Armand-Frappier, Laval, Quebec, Canada
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Luo H, Gao F. DoriC 10.0: an updated database of replication origins in prokaryotic genomes including chromosomes and plasmids. Nucleic Acids Res 2020; 47:D74-D77. [PMID: 30364951 PMCID: PMC6323995 DOI: 10.1093/nar/gky1014] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 10/11/2018] [Indexed: 12/11/2022] Open
Abstract
DoriC, a database of replication origins, was initially created to present the bacterial oriCs predicted by Ori-Finder or determined by experiments in 2007. DoriC 5.0, an updated database of oriC regions in both bacterial and archaeal genomes, was published in the 2013 Nucleic Acids Research database issue. Now, the latest release DoriC 10, a large-scale update of replication origins in prokaryotic genomes including chromosomes and plasmids, has been presented with a completely redesigned user interface, which is freely available at http://tubic.org/doric/ and http://tubic.tju.edu.cn/doric/. In the current release, the database of DoriC has made significant improvements compared with version 5.0 as follows: (i) inclusion of oriCs on more bacterial chromosomes increased from 1633 to 7580; (ii) inclusion of oriCs on more archaeal chromosomes increased from 86 to 226; (iii) inclusion of 1209 plasmid replication origins retrieved from NCBI annotations or predicted by in silico analysis; (iv) inclusion of more replication origin elements on bacterial chromosomes including DnaA-trio motifs. Now, DoriC becomes the most complete and scalable database of replication origins in prokaryotic genomes, and facilitates the studies in large-scale oriC data mining, strand-biased analyses and replication origin predictions.
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Affiliation(s)
- Hao Luo
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
| | - Feng Gao
- Department of Physics, School of Science, Tianjin University, Tianjin 300072, China.,Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China.,SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin 300072, China
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5
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Liu G, Jiang YM, Liu YC, Han LL, Feng H. A novel DNA methylation motif identified in Bacillus pumilus BA06 and possible roles in the regulation of gene expression. Appl Microbiol Biotechnol 2020; 104:3445-3457. [PMID: 32088759 DOI: 10.1007/s00253-020-10475-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/21/2020] [Accepted: 02/14/2020] [Indexed: 01/26/2023]
Abstract
Single-molecule real-time (SMRT) sequencing can be used to identify a wide variety of chemical modifications of the genome, such as methylation. Here, we applied this approach to identify N6-methyl-adenine (m6A) and N4-methyl-cytosine (m4C) modification in the genome of Bacillus pumilus BA06. A typical methylation recognition motif of the type I restriction-modification system (R-M), 5'-TCm6AN8TTGG-3'/3'-AGTN8m6AACC-5', was identified. We confirmed that this motif was a new type I methylation site using REBASE analysis and that it was recognized by a type I R-M system, Bpu6ORFCP, according to methylation sensitivity assays in vivo and vitro. Furthermore, we found that deletion of the R-M system Bpu6ORFCP induced transcriptional changes in many genes and led to increased gene expression in pathways related to ABC transporters, sulfur metabolism, ribosomes, cysteine and methionine metabolism and starch and sucrose metabolism, suggesting that the R-M system in B. pumilus BA06 has other significant biological functions beyond protecting the B. pumilus BA06 genome from foreign DNA.
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Affiliation(s)
- Gang Liu
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education; Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, Sichuan, People's Republic of China
| | - Yang-Mei Jiang
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education; Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, Sichuan, People's Republic of China
| | - Yong-Cheng Liu
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education; Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, Sichuan, People's Republic of China
| | - Lin-Li Han
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education; Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, Sichuan, People's Republic of China
| | - Hong Feng
- Key Laboratory of Bio-resources and Eco-environment, Ministry of Education; Sichuan Key Laboratory of Molecular Biology and Biotechnology, College of Life Sciences, Sichuan University, Chengdu, 610064, Sichuan, People's Republic of China.
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6
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Prevalence of hypermutator isolates of Achromobacter spp. from cystic fibrosis patients. Int J Med Microbiol 2020; 310:151393. [PMID: 31969255 DOI: 10.1016/j.ijmm.2020.151393] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 10/30/2019] [Accepted: 12/04/2019] [Indexed: 01/26/2023] Open
Abstract
Bacteria colonising the lungs of cystic fibrosis (CF) patients encounter high selective pressures. Hypermutation facilitates adaptation to fluctuating environments, and hypermutator strains are frequently isolated from CF patients. We investigated the prevalence of hypermutator isolates of Achromobacter spp. among patients affiliated with the CF Centre in Aarhus, Denmark. By exposure to rifampicin, the mutation frequency was determined for 90 isolates of Achromobacter spp. cultured from 42 CF patients; 20 infections were categorised as chronic, 22 as intermittent. The genetic mechanisms of hypermutation were examined by comparing DNA repair gene sequences from hypermutator and normomutator isolates. Achromobacter spp. cultured from 11 patients were categorised as hypermutators, and this phenotype was exclusively associated with chronic infections. Isolates of the Danish epidemic strain (DES) of Achromobacter ruhlandii cultured from patients from both Danish CF centres showed elevated mutation frequencies. The hypermutator state of Achromobacter spp. was most commonly associated with nonsynonymous mutations in the DNA mismatch repair gene mutS; a single clone had developed a substitution in the S-adenosyl-L-methionine-dependent methyltransferase putatively involved in DNA repair mechanisms, but not previously linked to the hypermutator phenotype. Hypermutation is prevalent among clinical isolates of Achromobacter spp. and could be a key determinant for the extraordinary adaptation and persistence of DES.
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Deng C, Naler LB, Lu C. Microfluidic epigenomic mapping technologies for precision medicine. LAB ON A CHIP 2019; 19:2630-2650. [PMID: 31338502 PMCID: PMC6697104 DOI: 10.1039/c9lc00407f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Epigenomic mapping of tissue samples generates critical insights into genome-wide regulations of gene activities and expressions during normal development and disease processes. Epigenomic profiling using a low number of cells produced by patient and mouse samples presents new challenges to biotechnologists. In this review, we first discuss the rationale and premise behind profiling epigenomes for precision medicine. We then examine the existing literature on applying microfluidics to facilitate low-input and high-throughput epigenomic profiling, with emphasis on technologies enabling interfacing with next-generation sequencing. We detail assays on studies of histone modifications, DNA methylation, 3D chromatin structures and non-coding RNAs. Finally, we discuss what the future may hold in terms of method development and translational potential.
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Affiliation(s)
- Chengyu Deng
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA.
| | - Lynette B Naler
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA.
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech, Blacksburg, Virginia 24061, USA.
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Shi Z. Methylome and Metabolome Analyses Reveal Adaptive Mechanisms in Geobacter sulfurreducens Grown on Different Terminal Electron Acceptors. J Proteome Res 2019; 18:1494-1502. [DOI: 10.1021/acs.jproteome.8b00763] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Zhenhua Shi
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
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9
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Beaulaurier J, Schadt EE, Fang G. Deciphering bacterial epigenomes using modern sequencing technologies. Nat Rev Genet 2019; 20:157-172. [PMID: 30546107 PMCID: PMC6555402 DOI: 10.1038/s41576-018-0081-3] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Prokaryotic DNA contains three types of methylation: N6-methyladenine, N4-methylcytosine and 5-methylcytosine. The lack of tools to analyse the frequency and distribution of methylated residues in bacterial genomes has prevented a full understanding of their functions. Now, advances in DNA sequencing technology, including single-molecule, real-time sequencing and nanopore-based sequencing, have provided new opportunities for systematic detection of all three forms of methylated DNA at a genome-wide scale and offer unprecedented opportunities for achieving a more complete understanding of bacterial epigenomes. Indeed, as the number of mapped bacterial methylomes approaches 2,000, increasing evidence supports roles for methylation in regulation of gene expression, virulence and pathogen-host interactions.
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Affiliation(s)
- John Beaulaurier
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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10
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Corts AD, Thomason LC, Gill RT, Gralnick JA. A new recombineering system for precise genome-editing in Shewanella oneidensis strain MR-1 using single-stranded oligonucleotides. Sci Rep 2019; 9:39. [PMID: 30631105 PMCID: PMC6328582 DOI: 10.1038/s41598-018-37025-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/27/2018] [Indexed: 11/09/2022] Open
Abstract
Shewanella oneidensis MR-1 is an invaluable host for the discovery and engineering of pathways important for bioremediation of toxic and radioactive metals and understanding extracellular electron transfer. However, genetic manipulation is challenging due to the lack of genetic tools. Previously, the only reliable method used for introducing DNA into Shewanella spp. at high efficiency was bacterial conjugation, enabling transposon mutagenesis and targeted knockouts using suicide vectors for gene disruptions. Here, we describe development of a robust and simple electroporation method in S. oneidensis that allows an efficiency of ~4.0 x 106 transformants/µg DNA. High transformation efficiency is maintained when cells are frozen for long term storage. In addition, we report a new prophage-mediated genome engineering (recombineering) system using a λ Red Beta homolog from Shewanella sp. W3-18-1. By targeting two different chromosomal alleles, we demonstrate its application for precise genome editing using single strand DNA oligonucleotides and show that an efficiency of ~5% recombinants among total cells can be obtained. This is the first effective and simple strategy for recombination with markerless mutations in S. oneidensis. Continued development of this recombinant technology will advance high-throughput and genome modification efforts to engineer and investigate S. oneidensis and other environmental bacteria.
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Affiliation(s)
- Anna D Corts
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, MN, 55108, USA
| | - Lynn C Thomason
- RNA Biology Laboratory, Basic Science Program, Leidos Biomedical Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Ryan T Gill
- Department of Chemical and Biological Engineering, University of Colorado-Boulder, Boulder, CO, 80303, USA
| | - Jeffrey A Gralnick
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, MN, 55108, USA.
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A Type I Restriction-Modification System Associated with Enterococcus faecium Subspecies Separation. Appl Environ Microbiol 2019; 85:AEM.02174-18. [PMID: 30389763 PMCID: PMC6328761 DOI: 10.1128/aem.02174-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/26/2018] [Indexed: 01/16/2023] Open
Abstract
The gastrointestinal colonizer Enterococcus faecium is a leading cause of hospital-acquired infections. Multidrug-resistant (MDR) E. faecium isolates are particularly concerning for infection treatment. Previous comparative genomic studies revealed that subspecies referred to as clade A and clade B exist within E. faecium MDR E. faecium isolates belong to clade A, while clade B consists of drug-susceptible fecal commensal E. faecium isolates. Isolates from clade A are further grouped into two subclades, clades A1 and A2. In general, clade A1 isolates are hospital-epidemic isolates, whereas clade A2 isolates are isolates from animals and sporadic human infections. Such phylogenetic separation indicates that reduced gene exchange occurs between the clades. We hypothesize that endogenous barriers to gene exchange exist between E. faecium clades. Restriction-modification (R-M) systems are such barriers in other microbes. We utilized a bioinformatics analysis coupled with second-generation and third-generation deep-sequencing platforms to characterize the methylomes of two representative E. faecium strains, one from clade A1 and one from clade B. We identified a type I R-M system that is clade A1 specific, is active for DNA methylation, and significantly reduces the transformability of clade A1 E. faecium Based on our results, we conclude that R-M systems act as barriers to horizontal gene exchange in E. faecium and propose that R-M systems contribute to E. faecium subspecies separation.IMPORTANCE Enterococcus faecium is a leading cause of hospital-acquired infections around the world. Rising antibiotic resistance in certain E. faecium lineages leaves fewer treatment options. The overarching aim of this work was to determine whether restriction-modification (R-M) systems contribute to the structure of the E. faecium species, wherein hospital-epidemic and non-hospital-epidemic isolates have distinct evolutionary histories and highly resolved clade structures. R-M provides bacteria with a type of innate immunity to horizontal gene transfer (HGT). We identified a type I R-M system that is enriched in the hospital-epidemic clade and determined that it is active for DNA modification activity and significantly impacts HGT. Overall, this work is important because it provides a mechanism for the observed clade structure of E. faecium as well as a mechanism for facilitated gene exchange among hospital-epidemic E. faecium isolates.
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Charubin K, Bennett RK, Fast AG, Papoutsakis ET. Engineering Clostridium organisms as microbial cell-factories: challenges & opportunities. Metab Eng 2018; 50:173-191. [DOI: 10.1016/j.ymben.2018.07.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/18/2018] [Accepted: 07/19/2018] [Indexed: 11/25/2022]
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13
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Chen See JR, Ulrich N, Nwanosike H, McLimans CJ, Tokarev V, Wright JR, Campa MF, Grant CJ, Hazen TC, Niles JM, Ressler D, Lamendella R. Bacterial Biomarkers of Marcellus Shale Activity in Pennsylvania. Front Microbiol 2018; 9:1697. [PMID: 30116227 PMCID: PMC6083035 DOI: 10.3389/fmicb.2018.01697] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 07/09/2018] [Indexed: 01/24/2023] Open
Abstract
Unconventional oil and gas (UOG) extraction, also known as hydraulic fracturing, is becoming more prevalent with the increasing use and demand for natural gas; however, the full extent of its environmental impacts is still unknown. Here we measured physicochemical properties and bacterial community composition of sediment samples taken from twenty-eight streams within the Marcellus shale formation in northeastern Pennsylvania differentially impacted by hydraulic fracturing activities. Fourteen of the streams were classified as UOG+, and thirteen were classified as UOG- based on the presence of UOG extraction in their respective watersheds. One stream was located in a watershed that previously had UOG extraction activities but was recently abandoned. We utilized high-throughput sequencing of the 16S rRNA gene to infer differences in sediment aquatic bacterial community structure between UOG+ and UOG- streams, as well as correlate bacterial community structure to physicochemical water parameters. Although overall alpha and beta diversity differences were not observed, there were a plethora of significantly enriched operational taxonomic units (OTUs) within UOG+ and UOG- samples. Our biomarker analysis revealed many of the bacterial taxa enriched in UOG+ streams can live in saline conditions, such as Rubrobacteraceae. In addition, several bacterial taxa capable of hydrocarbon degradation were also enriched in UOG+ samples, including Oceanospirillaceae. Methanotrophic taxa, such as Methylococcales, were significantly enriched as well. Several taxa that were identified as enriched in these samples were enriched in samples taken from different streams in 2014; moreover, partial least squares discriminant analysis (PLS-DA) revealed clustering between streams from the different studies based on the presence of hydraulic fracturing along the second axis. This study revealed significant differences between bacterial assemblages within stream sediments of UOG+ and UOG- streams and identified several potential biomarkers for evaluating and monitoring the response of autochthonous bacterial communities to potential hydraulic fracturing impacts.
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Affiliation(s)
- Jeremy R Chen See
- Department of Biology, Juniata College, Huntingdon, PA, United States
| | - Nikea Ulrich
- Department of Biology, Juniata College, Huntingdon, PA, United States
| | | | | | - Vasily Tokarev
- Department of Biology, Juniata College, Huntingdon, PA, United States
| | - Justin R Wright
- Department of Biology, Juniata College, Huntingdon, PA, United States
| | - Maria F Campa
- The Bredesen Center, The University of Tennessee, Knoxville, Knoxville, TN, United States
| | | | - Terry C Hazen
- The Bredesen Center, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Department of Civil and Environmental Engineering, The University of Tennessee, Knoxville, Knoxville, TN, United States.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jonathan M Niles
- Freshwater Research Initiative, Susquehanna University, Selinsgrove, PA, United States
| | - Daniel Ressler
- Department of Earth and Environmental Sciences, Susquehanna University, Selinsgrove, PA, United States
| | - Regina Lamendella
- Department of Biology, Juniata College, Huntingdon, PA, United States
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14
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Luo H, Quan CL, Peng C, Gao F. Recent development of Ori-Finder system and DoriC database for microbial replication origins. Brief Bioinform 2018; 20:1114-1124. [DOI: 10.1093/bib/bbx174] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/04/2017] [Indexed: 01/28/2023] Open
Abstract
Abstract
DNA replication begins at replication origins in all three domains of life. Identification and characterization of replication origins are important not only in providing insights into the structure and function of the replication origins but also in understanding the regulatory mechanisms of the initiation step in DNA replication. The Z-curve method has been used in the identification of replication origins in archaeal genomes successfully since 2002. Furthermore, the Web servers of Ori-Finder and Ori-Finder 2 have been developed to predict replication origins in both bacterial and archaeal genomes based on the Z-curve method, and the replication origins with manual curation have been collected into an online database, DoriC. Ori-Finder system and DoriC database are currently used in the research field of DNA replication origins in prokaryotes, including: (i) identification of oriC regions in bacterial and archaeal genomes; (ii) discovery and analysis of the conserved sequences within oriC regions; and (iii) strand-biased analysis of bacterial genomes.
Up to now, more and more predicted results by Ori-Finder system were supported by subsequent experiments, and Ori-Finder system has been used to identify the replication origins in > 100 newly sequenced prokaryotes in their genome reports. In addition, the data in DoriC database have been widely used in the large-scale analyses of replication origins and strand bias in prokaryotic genomes. Here, we review the development of Ori-Finder system and DoriC database as well as their applications. Some future directions and aspects for extending the application of Ori-Finder and DoriC are also presented.
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Zhong C, Han M, Yu S, Yang P, Li H, Ning K. Pan-genome analyses of 24 Shewanella strains re-emphasize the diversification of their functions yet evolutionary dynamics of metal-reducing pathway. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:193. [PMID: 30026808 PMCID: PMC6048853 DOI: 10.1186/s13068-018-1201-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 07/10/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Shewanella strains are important dissimilatory metal-reducing bacteria which are widely distributed in diverse habitats. Despite efforts to genomically characterize Shewanella, knowledge of the molecular components, functional information and evolutionary patterns remain lacking, especially for their compatibility in the metal-reducing pathway. The increasing number of genome sequences of Shewanella strains offers a basis for pan-genome studies. RESULTS A comparative pan-genome analysis was conducted to study genomic diversity and evolutionary relationships among 24 Shewanella strains. Results revealed an open pan-genome of 13,406 non-redundant genes and a core-genome of 1878 non-redundant genes. Selective pressure acted on the invariant members of core genome, in which purifying selection drove evolution in the housekeeping mechanisms. Shewanella strains exhibited extensive genome variability, with high levels of gene gain and loss during the evolution, which affected variable gene sets and facilitated the rapid evolution. Additionally, genes related to metal reduction were diversely distributed in Shewanella strains and evolved under purifying selection, which highlighted the basic conserved functionality and specificity of respiratory systems. CONCLUSIONS The diversity of genes present in the accessory and specific genomes of Shewanella strains indicates that each strain uses different strategies to adapt to diverse environments. Horizontal gene transfer is an important evolutionary force in shaping Shewanella genomes. Purifying selection plays an important role in the stability of the core-genome and also drives evolution in mtr-omc cluster of different Shewanella strains.
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Affiliation(s)
- Chaofang Zhong
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074 Hubei China
| | - Maozhen Han
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074 Hubei China
| | - Shaojun Yu
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074 Hubei China
| | - Pengshuo Yang
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074 Hubei China
| | - Hongjun Li
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074 Hubei China
| | - Kang Ning
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074 Hubei China
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16
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Gilbert KM, Blossom SJ, Reisfeld B, Erickson SW, Vyas K, Maher M, Broadfoot B, West K, Bai S, Cooney CA, Bhattacharyya S. Trichloroethylene-induced alterations in DNA methylation were enriched in polycomb protein binding sites in effector/memory CD4 + T cells. ENVIRONMENTAL EPIGENETICS 2017; 3:dvx013. [PMID: 29129997 PMCID: PMC5676456 DOI: 10.1093/eep/dvx013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 06/30/2017] [Accepted: 07/03/2017] [Indexed: 06/07/2023]
Abstract
Exposure to industrial solvent and water pollutant trichloroethylene (TCE) can promote autoimmunity, and expand effector/memory (CD62L) CD4+ T cells. In order to better understand etiology reduced representation bisulfite sequencing was used to study how a 40-week exposure to TCE in drinking water altered methylation of ∼337 770 CpG sites across the entire genome of effector/memory CD4+ T cells from MRL+/+ mice. Regardless of TCE exposure, 62% of CpG sites in autosomal chromosomes were hypomethylated (0-15% methylation), and 25% were hypermethylated (85-100% methylation). In contrast, only 6% of the CpGs on the X chromosome were hypomethylated, and 51% had mid-range methylation levels. In terms of TCE impact, TCE altered (≥ 10%) the methylation of 233 CpG sites in effector/memory CD4+ T cells. Approximately 31.7% of these differentially methylated sites occurred in regions known to bind one or more Polycomb group (PcG) proteins, namely Ezh2, Suz12, Mtf2 or Jarid2. In comparison, only 23.3% of CpG sites not differentially methylated by TCE were found in PcG protein binding regions. Transcriptomics revealed that TCE altered the expression of ∼560 genes in the same effector/memory CD4+ T cells. At least 80% of the immune genes altered by TCE had binding sites for PcG proteins flanking their transcription start site, or were regulated by other transcription factors that were in turn ordered by PcG proteins at their own transcription start site. Thus, PcG proteins, and the differential methylation of their binding sites, may represent a new mechanism by which TCE could alter the function of effector/memory CD4+ T cells.
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Affiliation(s)
- Kathleen M. Gilbert
- Arkansas Children’s Research Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
| | - Sarah J. Blossom
- Arkansas Children’s Research Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
| | - Brad Reisfeld
- Colorado State University, Fort Collins, CO 80523, USA
| | - Stephen W. Erickson
- Arkansas Children’s Research Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
| | - Kanan Vyas
- Arkansas Children’s Research Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
| | - Mary Maher
- Arkansas Children’s Research Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
| | - Brannon Broadfoot
- Arkansas Children’s Research Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
| | - Kirk West
- Arkansas Children’s Research Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
| | - Shasha Bai
- Arkansas Children’s Research Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
| | - Craig A. Cooney
- Central Arkansas Veterans Healthcare System, Little Rock, AR 72205, USA
| | - Sudeepa Bhattacharyya
- Arkansas Children’s Research Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
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17
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Hu J, Raikhel V, Gopalakrishnan K, Fernandez-Hernandez H, Lambertini L, Manservisi F, Falcioni L, Bua L, Belpoggi F, L Teitelbaum S, Chen J. Effect of postnatal low-dose exposure to environmental chemicals on the gut microbiome in a rodent model. MICROBIOME 2016; 4:26. [PMID: 27301250 PMCID: PMC4906585 DOI: 10.1186/s40168-016-0173-2] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 05/31/2016] [Indexed: 05/20/2023]
Abstract
BACKGROUND This proof-of-principle study examines whether postnatal, low-dose exposure to environmental chemicals modifies the composition of gut microbiome. Three chemicals that are widely used in personal care products-diethyl phthalate (DEP), methylparaben (MPB), triclosan (TCS)-and their mixture (MIX) were administered at doses comparable to human exposure to Sprague-Dawley rats from birth through adulthood. Fecal samples were collected at two time points: postnatal day (PND) 62 (adolescence) and PND 181 (adulthood). The gut microbiome was profiled by 16S ribosomal RNA gene sequencing, taxonomically assigned and assessed for diversity. RESULTS Metagenomic profiling revealed that the low-dose chemical exposure resulted in significant changes in the overall bacterial composition, but in adolescent rats only. Specifically, the individual taxon relative abundance for Bacteroidetes (Prevotella) was increased while the relative abundance of Firmicutes (Bacilli) was reduced in all treated rats compared to controls. Increased abundance was observed for Elusimicrobia in DEP and MPB groups, Betaproteobacteria in MPB and MIX groups, and Deltaproteobacteria in TCS group. Surprisingly, these differences diminished by adulthood (PND 181) despite continuous exposure, suggesting that exposure to the environmental chemicals produced a more profound effect on the gut microbiome in adolescents. We also observed a small but consistent reduction in the bodyweight of exposed rats in adolescence, especially with DEP and MPB treatment (p < 0.05), which is consistent with our findings of a reduced Firmicutes/Bacteroidetes ratio at PND 62 in exposed rats. CONCLUSIONS This study provides initial evidence that postnatal exposure to commonly used environmental chemicals at doses comparable to human exposure is capable of modifying the gut microbiota in adolescent rats; whether these changes lead to downstream health effects requires further investigation.
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Affiliation(s)
- Jianzhong Hu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Vincent Raikhel
- Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kalpana Gopalakrishnan
- Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Luca Lambertini
- Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fabiana Manservisi
- Cesare Maltoni Cancer Research Centre, Ramazzini Institute, Bentivoglio, Bologna, Italy
| | - Laura Falcioni
- Cesare Maltoni Cancer Research Centre, Ramazzini Institute, Bentivoglio, Bologna, Italy
| | - Luciano Bua
- Cesare Maltoni Cancer Research Centre, Ramazzini Institute, Bentivoglio, Bologna, Italy
| | - Fiorella Belpoggi
- Cesare Maltoni Cancer Research Centre, Ramazzini Institute, Bentivoglio, Bologna, Italy
| | - Susan L Teitelbaum
- Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jia Chen
- Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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18
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Adaptive engineering of a hyperthermophilic archaeon on CO and discovering the underlying mechanism by multi-omics analysis. Sci Rep 2016; 6:22896. [PMID: 26975345 PMCID: PMC4791640 DOI: 10.1038/srep22896] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/23/2016] [Indexed: 01/03/2023] Open
Abstract
The hyperthermophilic archaeon Thermococcus onnurineus NA1 can grow and produce H2 on carbon monoxide (CO) and its H2 production rates have been improved through metabolic engineering. In this study, we applied adaptive evolution to enhance H2 productivity. After over 150 serial transfers onto CO medium, cell density, CO consumption rate and H2 production rate increased. The underlying mechanism for those physiological changes could be explained by using multi-omics approaches including genomic, transcriptomic and epigenomic analyses. A putative transcriptional regulator was newly identified to regulate the expression levels of genes related to CO oxidation. Transcriptome analysis revealed significant changes in the transcript levels of genes belonging to the categories of transcription, translation and energy metabolism. Our study presents the first genome-scale methylation pattern of hyperthermophilic archaea. Adaptive evolution led to highly enhanced H2 productivity at high CO flow rates using synthesis gas produced from coal gasification.
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19
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Blow MJ, Clark TA, Daum CG, Deutschbauer AM, Fomenkov A, Fries R, Froula J, Kang DD, Malmstrom RR, Morgan RD, Posfai J, Singh K, Visel A, Wetmore K, Zhao Z, Rubin EM, Korlach J, Pennacchio LA, Roberts RJ. The Epigenomic Landscape of Prokaryotes. PLoS Genet 2016; 12:e1005854. [PMID: 26870957 PMCID: PMC4752239 DOI: 10.1371/journal.pgen.1005854] [Citation(s) in RCA: 220] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 01/19/2016] [Indexed: 11/18/2022] Open
Abstract
DNA methylation acts in concert with restriction enzymes to protect the integrity of prokaryotic genomes. Studies in a limited number of organisms suggest that methylation also contributes to prokaryotic genome regulation, but the prevalence and properties of such non-restriction-associated methylation systems remain poorly understood. Here, we used single molecule, real-time sequencing to map DNA modifications including m6A, m4C, and m5C across the genomes of 230 diverse bacterial and archaeal species. We observed DNA methylation in nearly all (93%) organisms examined, and identified a total of 834 distinct reproducibly methylated motifs. This data enabled annotation of the DNA binding specificities of 620 DNA Methyltransferases (MTases), doubling known specificities for previously hard to study Type I, IIG and III MTases, and revealing their extraordinary diversity. Strikingly, 48% of organisms harbor active Type II MTases with no apparent cognate restriction enzyme. These active ‘orphan’ MTases are present in diverse bacterial and archaeal phyla and show motif specificities and methylation patterns consistent with functions in gene regulation and DNA replication. Our results reveal the pervasive presence of DNA methylation throughout the prokaryotic kingdoms, as well as the diversity of sequence specificities and potential functions of DNA methylation systems. DNA methylation is a chemical modification of DNA present in many prokaryotic genomes. The best-known role of DNA methylation is as a component of restriction-modification systems. In these systems, restriction enzymes target foreign DNA for cleavage, while DNA methylation protects the host genome from destruction. Studies in a handful of organisms show that DNA methylation may also act independently of restriction systems and function in genome regulation. However, a lack of technologies has limited the study of DNA methylation to a small number of organisms, and the broader patterns and functions of DNA methylation remain unknown. Here we use SMRT-sequencing to determine the genome wide DNA methylation patterns of more than 200 diverse bacteria and archaea. We show that DNA methylation is pervasive and present in more than 90% of studied organisms. Analysis of this data enabled annotation of the specific DNA binding sites of more than 600 restriction systems, revealing their extraordinary diversity. Strikingly, we observed widespread DNA methylation in the absence of restriction systems. Analyses of these patterns reveal that they are conserved through evolution, and likely function in genome regulation. Thus DNA methylation may play a far wider function in prokaryotic genome biology than was previously supposed.
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Affiliation(s)
- Matthew J. Blow
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
- * E-mail: (MJB); (RJR)
| | - Tyson A. Clark
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Chris G. Daum
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Adam M. Deutschbauer
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Alexey Fomenkov
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Roxanne Fries
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Jeff Froula
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Dongwan D. Kang
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Rex R. Malmstrom
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Richard D. Morgan
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Janos Posfai
- New England Biolabs, Ipswich, Massachusetts, United States of America
| | - Kanwar Singh
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Axel Visel
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Kelly Wetmore
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Zhiying Zhao
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Edward M. Rubin
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Jonas Korlach
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Len A. Pennacchio
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America
| | - Richard J. Roberts
- New England Biolabs, Ipswich, Massachusetts, United States of America
- * E-mail: (MJB); (RJR)
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20
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DNA Methylation Assessed by SMRT Sequencing Is Linked to Mutations in Neisseria meningitidis Isolates. PLoS One 2015; 10:e0144612. [PMID: 26656597 PMCID: PMC4676702 DOI: 10.1371/journal.pone.0144612] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 11/20/2015] [Indexed: 11/20/2022] Open
Abstract
The Gram-negative bacterium Neisseria meningitidis features extensive genetic variability. To present, proposed virulence genotypes are also detected in isolates from asymptomatic carriers, indicating more complex mechanisms underlying variable colonization modes of N. meningitidis. We applied the Single Molecule, Real-Time (SMRT) sequencing method from Pacific Biosciences to assess the genome-wide DNA modification profiles of two genetically related N. meningitidis strains, both of serogroup A. The resulting DNA methylomes revealed clear divergences, represented by the detection of shared and of strain-specific DNA methylation target motifs. The positional distribution of these methylated target sites within the genomic sequences displayed clear biases, which suggest a functional role of DNA methylation related to the regulation of genes. DNA methylation in N. meningitidis has a likely underestimated potential for variability, as evidenced by a careful analysis of the ORF status of a panel of confirmed and predicted DNA methyltransferase genes in an extended collection of N. meningitidis strains of serogroup A. Based on high coverage short sequence reads, we find phase variability as a major contributor to the variability in DNA methylation. Taking into account the phase variable loci, the inferred functional status of DNA methyltransferase genes matched the observed methylation profiles. Towards an elucidation of presently incompletely characterized functional consequences of DNA methylation in N. meningitidis, we reveal a prominent colocalization of methylated bases with Single Nucleotide Polymorphisms (SNPs) detected within our genomic sequence collection. As a novel observation we report increased mutability also at 6mA methylated nucleotides, complementing mutational hotspots previously described at 5mC methylated nucleotides. These findings suggest a more diverse role of DNA methylation and Restriction-Modification (RM) systems in the evolution of prokaryotic genomes.
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21
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Kanaly RA, Micheletto R, Matsuda T, Utsuno Y, Ozeki Y, Hamamura N. Application of DNA adductomics to soil bacterium Sphingobium sp. strain KK22. Microbiologyopen 2015; 4:841-56. [PMID: 26305056 PMCID: PMC4618615 DOI: 10.1002/mbo3.283] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 07/16/2015] [Accepted: 07/21/2015] [Indexed: 12/21/2022] Open
Abstract
Toward the development of ecotoxicology methods to investigate microbial markers of impacts of hydrocarbon processing activities, DNA adductomic analyses were conducted on a sphingomonad soil bacterium. From growing cells that were exposed or unexposed to acrolein, a commonly used biocide in hydraulic fracturing processes, DNA was extracted, digested to 2'-deoxynucleosides and analyzed by liquid chromatography-positive ionization electrospray-tandem mass spectrometry in selected reaction monitoring mode transmitting the [M + H](+) > [M + H - 116](+) transition over 100 transitions. Overall data shown as DNA adductome maps revealed numerous putative DNA adducts under both conditions with some occurring specifically for each condition. Adductomic analyses of triplicate samples indicated that elevated levels of some targeted putative adducts occurred in exposed cells. Two exposure-specific adducts were identified in exposed cells as 3-(2'-deoxyribosyl)-5,6,7,8-tetrahydro-6-hydroxy-(and 8-hydroxy-)pyrimido[1,2-a]- purine-(3H)-one (6- and 8-hydroxy-PdG) following synthesis of authentic standards of these compounds and subsequent analyses. A time course experiment showed that 6- and 8-hydroxy-PdG were detected in bacterial DNA within 30 min of acrolein exposure but were not detected in unexposed cells. This work demonstrated the first application of DNA adductomics to examine DNA damage in a bacterium and sets a foundation for future work.
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Affiliation(s)
- Robert A Kanaly
- Department of Life and Environmental System Science, Graduate School of Nanobiosciences, Yokohama City University, Kanagawa, Yokohama, 236-0027, Japan
| | - Ruggero Micheletto
- Department of Nanosystem Science, Graduate School of Nanobiosciences, Yokohama City University, Kanagawa, Yokohama, 236-0027, Japan
| | - Tomonari Matsuda
- Research Center for Environmental Quality Management, Kyoto University, Otsu, Shiga, 520-0811, Japan
| | - Youko Utsuno
- Department of Life and Environmental System Science, Graduate School of Nanobiosciences, Yokohama City University, Kanagawa, Yokohama, 236-0027, Japan
| | - Yasuhiro Ozeki
- Department of Life and Environmental System Science, Graduate School of Nanobiosciences, Yokohama City University, Kanagawa, Yokohama, 236-0027, Japan
| | - Natsuko Hamamura
- Center for Marine Environmental Studies, Ehime University, Matsuyama, 790-8577, Japan.,Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka, 812-8581, Japan
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22
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Beaulaurier J, Zhang XS, Zhu S, Sebra R, Rosenbluh C, Deikus G, Shen N, Munera D, Waldor MK, Chess A, Blaser MJ, Schadt EE, Fang G. Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes. Nat Commun 2015; 6:7438. [PMID: 26074426 PMCID: PMC4490391 DOI: 10.1038/ncomms8438] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 05/08/2015] [Indexed: 12/22/2022] Open
Abstract
Beyond its role in host defense, bacterial DNA methylation also plays important roles in the regulation of gene expression, virulence and antibiotic resistance. Bacterial cells in a clonal population can generate epigenetic heterogeneity to increase population-level phenotypic plasticity. Single molecule, real-time (SMRT) sequencing enables the detection of N6-methyladenine and N4-methylcytosine, two major types of DNA modifications comprising the bacterial methylome. However, existing SMRT sequencing-based methods for studying bacterial methylomes rely on a population-level consensus that lacks the single-cell resolution required to observe epigenetic heterogeneity. Here, we present SMALR (single-molecule modification analysis of long reads), a novel framework for single molecule-level detection and phasing of DNA methylation. Using seven bacterial strains, we show that SMALR yields significantly improved resolution and reveals distinct types of epigenetic heterogeneity. SMALR is a powerful new tool that enables de novo detection of epigenetic heterogeneity and empowers investigation of its functions in bacterial populations. Bacterial DNA methylation is involved in many processes, from host defense to antibiotic resistance, however current methods for examining methylated genomes lack single-cell resolution. Here Beaulaurier et al. present Single Molecule Modification Analysis of Long Reads, a new tool for de novo detection of epigenetic heterogeneity.
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Affiliation(s)
- John Beaulaurier
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Xue-Song Zhang
- Department of Medicine, New York University School of Medicine, New York 10016, USA
| | - Shijia Zhu
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Chaggai Rosenbluh
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Nan Shen
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Diana Munera
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, and the Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA
| | - Matthew K Waldor
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, and the Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA
| | - Andrew Chess
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Martin J Blaser
- Department of Medicine, New York University School of Medicine, New York 10016, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences and Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York 10029, USA
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23
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Pirone-Davies C, Hoffmann M, Roberts RJ, Muruvanda T, Timme RE, Strain E, Luo Y, Payne J, Luong K, Song Y, Tsai YC, Boitano M, Clark TA, Korlach J, Evans PS, Allard MW. Genome-wide methylation patterns in Salmonella enterica Subsp. enterica Serovars. PLoS One 2015; 10:e0123639. [PMID: 25860355 PMCID: PMC4393132 DOI: 10.1371/journal.pone.0123639] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/20/2015] [Indexed: 11/19/2022] Open
Abstract
The methylation of DNA bases plays an important role in numerous biological processes including development, gene expression, and DNA replication. Salmonella is an important foodborne pathogen, and methylation in Salmonella is implicated in virulence. Using single molecule real-time (SMRT) DNA-sequencing, we sequenced and assembled the complete genomes of eleven Salmonella enterica isolates from nine different serovars, and analysed the whole-genome methylation patterns of each genome. We describe 16 distinct N6-methyladenine (m6A) methylated motifs, one N4-methylcytosine (m4C) motif, and one combined m6A-m4C motif. Eight of these motifs are novel, i.e., they have not been previously described. We also identified the methyltransferases (MTases) associated with 13 of the motifs. Some motifs are conserved across all Salmonella serovars tested, while others were found only in a subset of serovars. Eight of the nine serovars contained a unique methylated motif that was not found in any other serovar (most of these motifs were part of Type I restriction modification systems), indicating the high diversity of methylation patterns present in Salmonella.
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Affiliation(s)
- Cary Pirone-Davies
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
- * E-mail:
| | - Maria Hoffmann
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | | | - Tim Muruvanda
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Ruth E. Timme
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Errol Strain
- Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Yan Luo
- Office of Analytics and Outreach, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Justin Payne
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Khai Luong
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Yi Song
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Yu-Chih Tsai
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Matthew Boitano
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Tyson A. Clark
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Jonas Korlach
- Pacific Biosciences, Menlo Park, California, United States of America
| | - Peter S. Evans
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
| | - Marc W. Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland, United States of America
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24
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Genome Modification in Enterococcus faecalis OG1RF Assessed by Bisulfite Sequencing and Single-Molecule Real-Time Sequencing. J Bacteriol 2015; 197:1939-51. [PMID: 25825433 DOI: 10.1128/jb.00130-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 03/23/2015] [Indexed: 12/25/2022] Open
Abstract
UNLABELLED Enterococcus faecalis is a Gram-positive bacterium that natively colonizes the human gastrointestinal tract and opportunistically causes life-threatening infections. Multidrug-resistant (MDR) E. faecalis strains have emerged, reducing treatment options for these infections. MDR E. faecalis strains have large genomes containing mobile genetic elements (MGEs) that harbor genes for antibiotic resistance and virulence determinants. Bacteria commonly possess genome defense mechanisms to block MGE acquisition, and we hypothesize that these mechanisms have been compromised in MDR E. faecalis. In restriction-modification (R-M) defense, the bacterial genome is methylated at cytosine (C) or adenine (A) residues by a methyltransferase (MTase), such that nonself DNA can be distinguished from self DNA. A cognate restriction endonuclease digests improperly modified nonself DNA. Little is known about R-M in E. faecalis. Here, we use genome resequencing to identify DNA modifications occurring in the oral isolate OG1RF. OG1RF has one of the smallest E. faecalis genomes sequenced to date and possesses few MGEs. Single-molecule real-time (SMRT) and bisulfite sequencing revealed that OG1RF has global 5-methylcytosine (m5C) methylation at 5'-GCWGC-3' motifs. A type II R-M system confers the m5C modification, and disruption of this system impacts OG1RF electrotransformability and conjugative transfer of an antibiotic resistance plasmid. A second DNA MTase was poorly expressed under laboratory conditions but conferred global N(4)-methylcytosine (m4C) methylation at 5'-CCGG-3' motifs when expressed in Escherichia coli. Based on our results, we conclude that R-M can act as a barrier to MGE acquisition and likely influences antibiotic resistance gene dissemination in the E. faecalis species. IMPORTANCE The horizontal transfer of antibiotic resistance genes among bacteria is a critical public health concern. Enterococcus faecalis is an opportunistic pathogen that causes life-threatening infections in humans. Multidrug resistance acquired by horizontal gene transfer limits treatment options for these infections. In this study, we used innovative DNA sequencing methodologies to investigate how a model strain of E. faecalis discriminates its own DNA from foreign DNA, i.e., self versus nonself discrimination. We also assess the role of an E. faecalis genome modification system in modulating conjugative transfer of an antibiotic resistance plasmid. These results are significant because they demonstrate that differential genome modification impacts horizontal gene transfer frequencies in E. faecalis.
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25
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Mou KT, Muppirala UK, Severin AJ, Clark TA, Boitano M, Plummer PJ. A comparative analysis of methylome profiles of Campylobacter jejuni sheep abortion isolate and gastroenteric strains using PacBio data. Front Microbiol 2015; 5:782. [PMID: 25642218 PMCID: PMC4294202 DOI: 10.3389/fmicb.2014.00782] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 12/20/2014] [Indexed: 12/13/2022] Open
Abstract
Campylobacter jejuni is a leading cause of human gastrointestinal disease and small ruminant abortions in the United States. The recent emergence of a highly virulent, tetracycline-resistant C. jejuni subsp. jejuni sheep abortion clone (clone SA) in the United States, and that strain's association with human disease, has resulted in a heightened awareness of the zoonotic potential of this organism. Pacific Biosciences' Single Molecule, Real-Time sequencing technology was used to explore the variation in the genome-wide methylation patterns of the abortifacient clone SA (IA3902) and phenotypically distinct gastrointestinal-specific C. jejuni strains (NCTC 11168 and 81-176). Several notable differences were discovered that distinguished the methylome of IA3902 from that of 11168 and 81-176: identification of motifs novel to IA3902, genome-specific hypo- and hypermethylated regions, strain level variability in genes methylated, and differences in the types of methylation motifs present in each strain. These observations suggest a possible role of methylation in the contrasting disease presentations of these three C. jejuni strains. In addition, the methylation profiles between IA3902 and a luxS mutant were explored to determine if variations in methylation patterns could be identified that might explain the role of LuxS-dependent methyl recycling in IA3902 abortifacient potential.
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Affiliation(s)
- Kathy T Mou
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University Ames, IA, USA
| | - Usha K Muppirala
- Genome Informatics Facility, Office of Biotechnology, Iowa State University Ames, IA, USA
| | - Andrew J Severin
- Genome Informatics Facility, Office of Biotechnology, Iowa State University Ames, IA, USA
| | | | | | - Paul J Plummer
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University Ames, IA, USA
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26
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Kim KE, Peluso P, Babayan P, Yeadon PJ, Yu C, Fisher WW, Chin CS, Rapicavoli NA, Rank DR, Li J, Catcheside DEA, Celniker SE, Phillippy AM, Bergman CM, Landolin JM. Long-read, whole-genome shotgun sequence data for five model organisms. Sci Data 2014; 1:140045. [PMID: 25977796 PMCID: PMC4365909 DOI: 10.1038/sdata.2014.45] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 10/03/2014] [Indexed: 12/22/2022] Open
Abstract
Single molecule, real-time (SMRT) sequencing from Pacific Biosciences is increasingly used in many areas of biological research including de novo genome assembly, structural-variant identification, haplotype phasing, mRNA isoform discovery, and base-modification analyses. High-quality, public datasets of SMRT sequences can spur development of analytic tools that can accommodate unique characteristics of SMRT data (long read lengths, lack of GC or amplification bias, and a random error profile leading to high consensus accuracy). In this paper, we describe eight high-coverage SMRT sequence datasets from five organisms (Escherichia coli, Saccharomyces cerevisiae, Neurospora crassa, Arabidopsis thaliana, and Drosophila melanogaster) that have been publicly released to the general scientific community (NCBI Sequence Read Archive ID SRP040522). Data were generated using two sequencing chemistries (P4C2 and P5C3) on the PacBio RS II instrument. The datasets reported here can be used without restriction by the research community to generate whole-genome assemblies, test new algorithms, investigate genome structure and evolution, and identify base modifications in some of the most widely-studied model systems in biological research.
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Affiliation(s)
- Kristi E Kim
- Pacific Biosciences of California Inc., 1380 Willow Road, Menlo Park, California 94025, USA
| | - Paul Peluso
- Pacific Biosciences of California Inc., 1380 Willow Road, Menlo Park, California 94025, USA
| | - Primo Babayan
- Pacific Biosciences of California Inc., 1380 Willow Road, Menlo Park, California 94025, USA
| | - P. Jane Yeadon
- Flinders University, School of Biological Sciences, PO Box 2100, Adelaide, South Australia 5001, Australia
| | - Charles Yu
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - William W Fisher
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Chen-Shan Chin
- Pacific Biosciences of California Inc., 1380 Willow Road, Menlo Park, California 94025, USA
| | - Nicole A Rapicavoli
- Pacific Biosciences of California Inc., 1380 Willow Road, Menlo Park, California 94025, USA
| | - David R Rank
- Pacific Biosciences of California Inc., 1380 Willow Road, Menlo Park, California 94025, USA
| | - Joachim Li
- Department of Microbiology and Immunology, UCSF, San Francisco, California 94158, USA
| | - David E. A Catcheside
- Flinders University, School of Biological Sciences, PO Box 2100, Adelaide, South Australia 5001, Australia
| | - Susan E Celniker
- Department of Genome Dynamics, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - Adam M Phillippy
- National Biodefense Analysis and Countermeasures Center, 110 Thomas Johnson Drive, Frederick, Maryland 21702, USA
| | - Casey M Bergman
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Jane M Landolin
- Pacific Biosciences of California Inc., 1380 Willow Road, Menlo Park, California 94025, USA
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27
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Murphy J, Klumpp J, Mahony J, O'Connell-Motherway M, Nauta A, van Sinderen D. Methyltransferases acquired by lactococcal 936-type phage provide protection against restriction endonuclease activity. BMC Genomics 2014; 15:831. [PMID: 25269955 PMCID: PMC4190342 DOI: 10.1186/1471-2164-15-831] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 09/24/2014] [Indexed: 02/07/2023] Open
Abstract
Background So-called 936-type phages are among the most frequently isolated phages in dairy facilities utilising Lactococcus lactis starter cultures. Despite extensive efforts to control phage proliferation and decades of research, these phages continue to negatively impact cheese production in terms of the final product quality and consequently, monetary return. Results Whole genome sequencing and in silico analysis of three 936-type phage genomes identified several putative (orphan) methyltransferase (MTase)-encoding genes located within the packaging and replication regions of the genome. Utilising SMRT sequencing, methylome analysis was performed on all three phages, allowing the identification of adenine modifications consistent with N-6 methyladenine sequence methylation, which in some cases could be attributed to these phage-encoded MTases. Heterologous gene expression revealed that M.Phi145I/M.Phi93I and M.Phi93DAM, encoded by genes located within the packaging module, provide protection against the restriction enzymes HphI and DpnII, respectively, representing the first functional MTases identified in members of 936-type phages. Conclusions SMRT sequencing technology enabled the identification of the target motifs of MTases encoded by the genomes of three lytic 936-type phages and these MTases represent the first functional MTases identified in this species of phage. The presence of these MTase-encoding genes on 936-type phage genomes is assumed to represent an adaptive response to circumvent host encoded restriction-modification systems thereby increasing the fitness of the phages in a dynamic dairy environment. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-831) contains supplementary material, which is available to authorized users.
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28
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Lyu Y, Zheng W, Zheng T, Tian Y. Biodegradation of polycyclic aromatic hydrocarbons by Novosphingobium pentaromativorans US6-1. PLoS One 2014; 9:e101438. [PMID: 25007154 PMCID: PMC4090153 DOI: 10.1371/journal.pone.0101438] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 06/05/2014] [Indexed: 11/18/2022] Open
Abstract
Novosphingobium pentaromativorans US6-1, a marine bacterium isolated from muddy sediments of Ulsan Bay, Republic of Korea, was previously shown to be capable of degrading multiple polycyclic aromatic hydrocarbons (PAHs). In order to gain insight into the characteristics of PAHs degradation, a proteome analysis of N. pentaromativorans US6-1 exposed to phenanthrene, pyrene, and benzo[a]pyrene was conducted. Several enzymes associated with PAHs degradation were identified, including 4-hydroxybenzoate 3-monooxygenase, salicylaldehyde dehydrogenase, and PAH ring-hydroxylating dioxygenase alpha subunit. Reverse transcription and real-time quantitative PCR was used to compare RHDα and 4-hydroxybenzoate 3-monooxygenase gene expression, and showed that the genes involved in the production of these two enzymes were upregulated to varying degrees after exposing the bacterium to PAHs. These results suggested that N. pentaromativorans US6-1 degraded PAHs via the metabolic route initiated by ring-hydroxylating dioxygenase, and further degradation occurred via the o-phthalate pathway or salicylate pathway. Both pathways subsequently entered the tricarboxylic acid (TCA) cycle, and were mineralized to CO2.
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Affiliation(s)
- Yihua Lyu
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Wei Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Tianling Zheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| | - Yun Tian
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, Xiamen University, Xiamen, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
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29
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Chen P, Jeannotte R, Weimer BC. Exploring bacterial epigenomics in the next-generation sequencing era: a new approach for an emerging frontier. Trends Microbiol 2014; 22:292-300. [PMID: 24725482 DOI: 10.1016/j.tim.2014.03.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Revised: 03/13/2014] [Accepted: 03/13/2014] [Indexed: 02/08/2023]
Abstract
Epigenetics has an important role for the success of foodborne pathogen persistence in diverse host niches. Substantial challenges exist in determining DNA methylation to situation-specific phenotypic traits. DNA modification, mediated by restriction-modification systems, functions as an immune response against antagonistic external DNA, and bacteriophage-acquired methyltransferases (MTase) and orphan MTases - those lacking the cognate restriction endonuclease - facilitate evolution of new phenotypes via gene expression modulation via DNA and RNA modifications, including methylation and phosphorothioation. Recent establishment of large-scale genome sequencing projects will result in a significant increase in genome availability that will lead to new demands for data analysis including new predictive bioinformatics approaches that can be verified with traditional scientific rigor. Sequencing technologies that detect modification coupled with mass spectrometry to discover new adducts is a powerful tactic to study bacterial epigenetics, which is poised to make novel and far-reaching discoveries that link biological significance and the bacterial epigenome.
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Affiliation(s)
- Poyin Chen
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA; Universidad de Tarapacá, Avenida General Velásquez N°1775, Arica, Chile
| | - Richard Jeannotte
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA; Universidad de Tarapacá, Avenida General Velásquez N°1775, Arica, Chile; Facultad de Ciencias, Universidad de Tarapacá, Arica, Chile
| | - Bart C Weimer
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA; Universidad de Tarapacá, Avenida General Velásquez N°1775, Arica, Chile.
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