1
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Kato A. Development of conjugation-mediated versatile site-specific single-copy luciferase fusion system. J GEN APPL MICROBIOL 2024; 69:318-326. [PMID: 37940551 DOI: 10.2323/jgam.2023.10.001] [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] [Indexed: 11/10/2023]
Abstract
There are a number of reporter systems that are useful for gene expression analysis in bacteria. However, at least in Salmonella, a versatile and simple luciferase reporter system that can be integrated precisely behind a promoter or gene of interest on a chromosome is not currently available. The luciferase operon luxCDABE from Photorhabdus luminescens has several advantages, including brightness, wide linear range, absence in most bacteria, stability at high temperature, and no substrate addition required for the assay. Here, a conjugation-mediated site-specific single-copy luciferase fusion system is developed. A reporter plasmid containing the conditional replication origin R6Kgγ, FRT-luxCDABE, and KmR marker was designed to be incorporated into the FRT site behind the promoter or gene of interest on the chromosome in cells expressing FLP. However, when this reporter plasmid was electroporated directly into such a S. enterica strain, no colonies appeared, likely due to the low transformation efficiency of this relatively large plasmid DNA. Meanwhile, the same reporter plasmid was successfully introduced and launched as an insert of an FRT-containing conjugative transfer plasmid from a mating E. coli strain to the same recipient S. enterica strain, as well as Citrobacter koseri. RcsB-dependent inducible luminescence from the constructed wzc-luxCDABE strains was confirmed. This system is feasible for detecting very low levels of transcription, even in Gram-negative bacterial species that are relatively difficult to genetically manipulate.
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Affiliation(s)
- Akinori Kato
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University
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2
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Davies CP, Jurkiw T, Haendiges J, Reed E, Anderson N, Grasso-Kelley E, Hoffmann M, Zheng J. Changes in the genomes and methylomes of three Salmonella enterica serovars after long-term storage in ground black pepper. Front Microbiol 2022; 13:970135. [PMID: 36160197 PMCID: PMC9507087 DOI: 10.3389/fmicb.2022.970135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/16/2022] [Indexed: 11/28/2022] Open
Abstract
Low moisture foods (LMFs) have traditionally been recognized as safe for consumption, as most bacteria require higher water content to grow. However, outbreaks due to LMF foods are increasing, and the microbial pathogen Salmonella enterica is frequently implicated. S. enterica can survive in LMFs for years, but few serovars have been studied, and the mechanisms which underlie this longevity are not well understood. Here, we determine that S. enterica serovars S. Tennessee, S. Anatum, and S. Reading but not S. Oranienburg can survive in the ground black pepper for 6 years. S. Reading was not previously associated with any LMF. Using both Illumina and Pacific Biosciences sequencing technologies, we also document changes in the genomes and methylomes of the surviving serovars over this 6-year period. The three serovars acquired a small number of single nucleotide polymorphisms (SNPs) including seven substitutions (four synonymous, two non-synonymous, and one substitution in a non-coding region), and two insertion-deletions. Nine distinct N6-methyladenine (m6A) methylated motifs across the three serovars were identified including five which were previously known, Gm6ATC, CAGm6AG, BATGCm6AT, CRTm6AYN6CTC, and CCm6AN7TGAG, and four novel serovar-specific motifs, GRTm6AN8TTYG, GAm6ACN7GTA, GAA m6ACY, and CAAm6ANCC. Interestingly, the BATGCAT motif was incompletely methylated (35–64% sites across the genome methylated), suggesting a possible role in gene regulation. Furthermore, the number of methylated BATGCm6AT motifs increased after storage in ground black pepper for 6 years from 475 to 657 (S. Tennessee), 366 to 608 (S. Anatum), and 525 to 570 (S. Reading), thus warranting further study as an adaptive mechanism. This is the first long-term assessment of genomic changes in S. enterica in a low moisture environment, and the first study to examine the methylome of any bacteria over a period of years, to our knowledge. These data contribute to our understanding of S. enterica survival in LMFs, and coupled with further studies, will provide the information necessary to design effective interventions which reduce S. enterica in LMFs and maintain a healthy, safe food supply.
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Affiliation(s)
- Cary P. Davies
- Animal Biosciences and Biotechnology Laboratory, Beltsville Agricultural Research Center, NEA, U.S. Department of Agriculture, Beltsville, MD, United States
- *Correspondence: Cary P. Davies,
| | - Thomas Jurkiw
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Julie Haendiges
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Elizabeth Reed
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Nathan Anderson
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Bedford Park, IL, United States
| | - Elizabeth Grasso-Kelley
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, Bedford Park, IL, United States
| | - Maria Hoffmann
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
| | - Jie Zheng
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, United States
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3
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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]
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4
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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.
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5
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A Hidden Markov Model for predicting the methylome of the DNA adenine methyltransferase in bacterial genome. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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6
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Zaworski J, Dagva O, Kingston AW, Fomenkov A, Morgan RD, Bossi L, Raleigh EA. Genome archaeology of two laboratory Salmonella enterica enterica sv Typhimurium. G3 (BETHESDA, MD.) 2021; 11:jkab226. [PMID: 34544129 PMCID: PMC8496262 DOI: 10.1093/g3journal/jkab226] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 06/29/2021] [Indexed: 11/25/2022]
Abstract
The Salmonella research community has used strains and bacteriophages over decades, exchanging useful new isolates among laboratories for the study of cell surface antigens, metabolic pathways and restriction-modification (RM) studies. Here we present the sequences of two laboratory Salmonella strains (STK005, an isolate of LB5000; and its descendant ER3625). In the ancestry of LB5000, segments of ∼15 and ∼42 kb were introduced from Salmonella enterica sv Abony 803 into S. enterica sv Typhimurium LT2, forming strain SD14; this strain is thus a hybrid of S. enterica isolates. Strains in the SD14 lineage were used to define flagellar antigens from the 1950s to the 1970s, and to define three RM systems from the 1960s to the 1980s. LB5000 was also used as a host in phage typing systems used by epidemiologists. In the age of cheaper and easier sequencing, this resource will provide access to the sequence that underlies the extensive literature.
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Affiliation(s)
- Julie Zaworski
- Research Department, New England Biolabs, Ipswich, MA 01938-2723, USA
| | - Oyut Dagva
- Research Department, New England Biolabs, Ipswich, MA 01938-2723, USA
| | | | - Alexey Fomenkov
- Research Department, New England Biolabs, Ipswich, MA 01938-2723, USA
| | - Richard D Morgan
- Research Department, New England Biolabs, Ipswich, MA 01938-2723, USA
| | - Lionello Bossi
- CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), University Paris-Saclay, Gif-sur-Yvette 91198, France
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7
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Vaid RK, Thakur Z, Anand T, Kumar S, Tripathi BN. Comparative genome analysis of Salmonella enterica serovar Gallinarum biovars Pullorum and Gallinarum decodes strain specific genes. PLoS One 2021; 16:e0255612. [PMID: 34411120 PMCID: PMC8375982 DOI: 10.1371/journal.pone.0255612] [Citation(s) in RCA: 11] [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: 02/12/2021] [Accepted: 07/19/2021] [Indexed: 12/27/2022] Open
Abstract
Salmonella enterica serovar Gallinarum biovar Pullorum (bvP) and biovar Gallinarum (bvG) are the etiological agents of pullorum disease (PD) and fowl typhoid (FT) respectively, which cause huge economic losses to poultry industry especially in developing countries including India. Vaccination and biosecurity measures are currently being employed to control and reduce the S. Gallinarum infections. High endemicity, poor implementation of hygiene and lack of effective vaccines pose challenges in prevention and control of disease in intensively maintained poultry flocks. Comparative genome analysis unravels similarities and dissimilarities thus facilitating identification of genomic features that aids in pathogenesis, niche adaptation and in tracing of evolutionary history. The present investigation was carried out to assess the genotypic differences amongst S.enterica serovar Gallinarum strains including Indian strain S. Gallinarum Sal40 VTCCBAA614. The comparative genome analysis revealed an open pan-genome consisting of 5091 coding sequence (CDS) with 3270 CDS belonging to core-genome, 1254 CDS to dispensable genome and strain specific genes i.e. singletons ranging from 3 to 102 amongst the analyzed strains. Moreover, the investigated strains exhibited diversity in genomic features such as virulence factors, genomic islands, prophage regions, toxin-antitoxin cassettes, and acquired antimicrobial resistance genes. Core genome identified in the study can give important leads in the direction of design of rapid and reliable diagnostics, and vaccine design for effective infection control as well as eradication. Additionally, the identified genetic differences among the S. enterica serovar Gallinarum strains could be used for bacterial typing, structure based inhibitor development by future experimental investigations on the data generated.
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Affiliation(s)
- Rajesh Kumar Vaid
- Bacteriology Laboratory, National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, Haryana, India
| | - Zoozeal Thakur
- Bacteriology Laboratory, National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, Haryana, India
| | - Taruna Anand
- Bacteriology Laboratory, National Centre for Veterinary Type Cultures, ICAR-National Research Centre on Equines, Hisar, Haryana, India
| | - Sanjay Kumar
- Bacteriology Laboratory, ICAR-National Research Centre on Equines, Hisar, Haryana, India
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8
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Anton BP, Roberts RJ. Beyond Restriction Modification: Epigenomic Roles of DNA Methylation in Prokaryotes. Annu Rev Microbiol 2021; 75:129-149. [PMID: 34314594 DOI: 10.1146/annurev-micro-040521-035040] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The amount of bacterial and archaeal genome sequence and methylome data has greatly increased over the last decade, enabling new insights into the functional roles of DNA methylation in these organisms. Methyltransferases (MTases), the enzymes responsible for DNA methylation, are exchanged between prokaryotes through horizontal gene transfer and can function either as part of restriction-modification systems or in apparent isolation as single (orphan) genes. The patterns of DNA methylation they confer on the host chromosome can have significant effects on gene expression, DNA replication, and other cellular processes. Some processes require very stable patterns of methylation, resulting in conservation of persistent MTases in a particular lineage. Other processes require patterns that are more dynamic yet more predictable than what is afforded by horizontal gene transfer and gene loss, resulting in phase-variable or recombination-driven MTase alleles. In this review, we discuss what is currently known about the functions of DNA methylation in prokaryotes in light of these evolutionary patterns. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Brian P Anton
- New England Biolabs, Ipswich, Massachusetts 01938, USA; ,
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9
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Wahlig TA, Stanton E, Godfrey JJ, Stasic AJ, Wong ACL, Kaspar CW. A Single Nucleotide Polymorphism in lptG Increases Tolerance to Bile Salts, Acid, and Staining of Calcofluor-Binding Polysaccharides in Salmonella enterica Serovar Typhimurium E40. Front Microbiol 2021; 12:671453. [PMID: 34149657 PMCID: PMC8208086 DOI: 10.3389/fmicb.2021.671453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 04/12/2021] [Indexed: 11/13/2022] Open
Abstract
The outer membrane of Salmonella enterica plays an important role in combating stress encountered in the environment and hosts. The transport and insertion of lipopolysaccharides (LPS) into the outer membrane involves lipopolysaccharide transport proteins (LptA-F) and mutations in the genes encoding for these proteins are often lethal or result in the transport of atypical LPS that can alter stress tolerance in bacteria. During studies of heterogeneity in bile salts tolerance, S. enterica serovar Typhimurium E40 was segregated into bile salts tolerant and sensitive cells by screening for growth in TSB with 10% bile salts. An isolate (E40V) with a bile salts MIC >20% was selected for further characterization. Whole-genome sequencing of E40 and E40V using Illumina and PacBio SMRT technologies revealed a non-synonymous single nucleotide polymorphism (SNP) in lptG. Leucine at residue 26 in E40 was substituted with proline in E40V. In addition to growth in the presence of 10% bile salts, E40V was susceptible to novobiocin while E40 was not. Transcriptional analysis of E40 and E40V, in the absence of bile salts, revealed significantly greater (p < 0.05) levels of transcript in three genes in E40V; yjbE (encoding for an extracellular polymeric substance production protein), yciE (encoding for a putative stress response protein), and an uncharacterized gene annotated as an acid shock protein precursor (ASPP). No transcripts of genes were present at a greater level in E40 compared to E40V. Corresponding with the greater level of these transcripts, E40V had greater survival at pH 3.35 and staining of Calcofluor-binding polysaccharide (CBPS). To confirm the SNP in lptG was associated with these phenotypes, strain E40E was engineered from E40 to encode for the variant form of LptG (L26P). E40E exhibited the same differences in gene transcripts and phenotypes as E40V, including susceptibility to novobiocin, confirming the SNP was responsible for these differences.
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Affiliation(s)
- Taylor A Wahlig
- Department of Bacteriology, University of Wisconsin, Madison, WI, United States
| | - Eliot Stanton
- Department of Bacteriology, University of Wisconsin, Madison, WI, United States
| | - Jared J Godfrey
- Department of Bacteriology, University of Wisconsin, Madison, WI, United States
| | - Andrew J Stasic
- U. S. Food and Drug Administration, Center for Biologics Evaluation and Research, Washington, DC, United States
| | - Amy C L Wong
- Department of Bacteriology, University of Wisconsin, Madison, WI, United States
| | - Charles W Kaspar
- Department of Bacteriology, University of Wisconsin, Madison, WI, United States
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10
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Spadar A, Perdigão J, Phelan J, Charleston J, Modesto A, Elias R, de Sessions PF, Hibberd ML, Campino S, Duarte A, Clark TG. Methylation analysis of Klebsiella pneumoniae from Portuguese hospitals. Sci Rep 2021; 11:6491. [PMID: 33753763 PMCID: PMC7985491 DOI: 10.1038/s41598-021-85724-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 02/11/2021] [Indexed: 12/13/2022] Open
Abstract
Klebsiella pneumoniae is an important nosocomial infectious agent with a high antimicrobial resistance (AMR) burden. The application of long read sequencing technologies is providing insights into bacterial chromosomal and putative extra-chromosomal genetic elements (PEGEs) associated with AMR, but also epigenetic DNA methylation, which is thought to play a role in cleavage of foreign DNA and expression regulation. Here, we apply the PacBio sequencing platform to eight Portuguese hospital isolates, including one carbapenemase producing isolate, to identify methylation motifs. The resulting assembled chromosomes were between 5.2 and 5.5Mbp in length, and twenty-six PEGEs were found. Four of our eight samples carry blaCTX-M-15, a dominant Extended Spectrum Beta Lactamase in Europe. We identified methylation motifs that control Restriction-Modification systems, including GATC of the DNA adenine methylase (Dam), which methylates N6-methyladenine (m6A) across all our K. pneumoniae assemblies. There was a consistent lack of methylation by Dam of the GATC motif downstream of two genes: fosA, a locus associated with low level fosfomycin resistance, and tnpB transposase on IncFIB(K) plasmids. Overall, we have constructed eight high quality reference genomes of K. pneumoniae, with insights into horizontal gene transfer and methylation m6A motifs.
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Affiliation(s)
- Anton Spadar
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - João Perdigão
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - James Charleston
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Ana Modesto
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Rita Elias
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | | | - Martin L Hibberd
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | - Aida Duarte
- Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, Almada, Portugal
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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11
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Complete Annotated Genome Sequence of the Salmonella enterica Serovar Typhimurium LT7 Strain STK003, Historically Used in Gene Transfer Studies. Microbiol Resour Announc 2021; 10:10/10/e01217-20. [PMID: 33707333 PMCID: PMC7953296 DOI: 10.1128/mra.01217-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome of Salmonella enterica serovar Typhimurium LT7 comprises a chromosome and two plasmids. One plasmid is very close to pSLT of Salmonella Typhimurium LT2; the second harbors a shufflon region. Prophage content is distinct: LT7 lacks Fels-1, while Gifsy-1 and Fels-2 show island-like divergence and likely programmed inversion, respectively. The genome of Salmonella enterica serovar Typhimurium LT7 comprises a chromosome and two plasmids. One plasmid is very close to pSLT of Salmonella Typhimurium LT2; the second harbors a shufflon region. Prophage content is distinct: LT7 lacks Fels-1, while Gifsy-1 and Fels-2 show island-like divergence and likely programmed inversion, respectively.
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12
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Sui Y, Wisniewski M, Droby S, Piombo E, Wu X, Yue J. Genome Sequence, Assembly, and Characterization of the Antagonistic Yeast Candida oleophila Used as a Biocontrol Agent Against Post-harvest Diseases. Front Microbiol 2020; 11:295. [PMID: 32158440 PMCID: PMC7052047 DOI: 10.3389/fmicb.2020.00295] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 02/10/2020] [Indexed: 11/29/2022] Open
Abstract
Candida oleophila is an effective biocontrol agent used to control post-harvest diseases of fruits and vegetables. C. oleophila I-182 was the active agent used in the first-generation yeast-based commercial product, Aspire®, for post-harvest disease management. Several action modes, like competition for nutrients and space, induction of pathogenesis-related genes in host tissues, and production of extracellular lytic enzymes, have been demonstrated for the biological control activity exhibited by C. oleophila through which it inhibits post-harvest pathogens. In the present study, the whole genome of C. oleophila I-182 was sequenced using PacBio and Illumina shotgun sequencing technologies, yielding an estimated genome size of 14.73 Mb. The genome size is similar in length to that of the model yeast strain Saccharomyces cerevisiae S288c. Based on the assembled genome, protein-coding sequences were identified and annotated. The predicted genes were further assigned with gene ontology terms and clustered in special functional groups. A comparative analysis of C. oleophila proteome with the proteomes of 11 representative yeasts revealed 2 unique and 124 expanded families of proteins in C. oleophila. Availability of the genome sequence will facilitate a better understanding the properties of biocontrol yeasts at the molecular level.
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Affiliation(s)
- Yuan Sui
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, College of Forestry and Life Science, Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan, China
| | - Michael Wisniewski
- U.S. Department of Agriculture-Agricultural Research Service, Kearneysville, WV, United States
| | - Samir Droby
- Department of Postharvest Science, Agricultural Research Organization, Volcani Center, Bet Dagan, Israel
| | - Edoardo Piombo
- Department of Agricultural, Forestry and Food Sciences, University of Turin, Turin, Italy
| | - Xuehong Wu
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Junyang Yue
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
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13
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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: 102] [Impact Index Per Article: 20.4] [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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14
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Asenso J, Wang L, Du Y, Liu QH, Xu BJ, Guo MZ, Tang DQ. Advances in detection and quantification of methylcytosine and its derivatives. J Sep Sci 2018; 42:1105-1116. [PMID: 30575277 DOI: 10.1002/jssc.201801100] [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: 10/21/2018] [Revised: 11/21/2018] [Accepted: 12/16/2018] [Indexed: 11/08/2022]
Abstract
Methylation of the fifth carbon atom in cytosine is an epigenetic modification of deoxyribonucleic acid that plays important roles in numerous cellular processes and disease pathogenesis. Three additional states of cytosine, that is, 5-hydroxymethylcytosine, 5-formylcytosine and 5-carboxylcytosine, have been identified and associated with the diagnosis and/or prognosis of diseases. However, accurate measurement of those intermediates is a challenge since their global levels are relatively low. A number of innovative methods have been developed to detect and quantify these compounds in biological samples, such as blood, tissue and urine, etc. This review focuses on recent advancement in detection and quantification of four cytosine modifications, based on which, the development, diagnosis, and prognosis of diseases could be monitored through non-invasive procedures.
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Affiliation(s)
- James Asenso
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Liang Wang
- Department of Bioinformatics, School of Medical Informatics, Xuzhou Medical University, Xuzhou, P. R. China
| | - Yan Du
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Qing-Hua Liu
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Bing-Ju Xu
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Meng-Zhe Guo
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
| | - Dao-Quan Tang
- Key Laboratory of New Drug Research and Clinical Pharmacy of Jiangsu Province, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China.,Department of Pharmaceutical Analysis, School of Pharmacy, Xuzhou Medical University, Xuzhou, P. R. China
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15
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Koh C, Goh YT, Toh J, Neo SP, Ng S, Gunaratne J, Gao YG, Quake SR, Burkholder W, Goh W. Single-nucleotide-resolution sequencing of human N6-methyldeoxyadenosine reveals strand-asymmetric clusters associated with SSBP1 on the mitochondrial genome. Nucleic Acids Res 2018; 46:11659-11670. [PMID: 30412255 PMCID: PMC6294517 DOI: 10.1093/nar/gky1104] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/15/2018] [Accepted: 10/22/2018] [Indexed: 01/08/2023] Open
Abstract
N6-methyldeoxyadenosine (6mA) is a well-characterized DNA modification in prokaryotes but reports on its presence and function in mammals have been controversial. To address this issue, we established the capacity of 6mA-Crosslinking-Exonuclease-sequencing (6mACE-seq) to detect genome-wide 6mA at single-nucleotide-resolution, demonstrating this by accurately mapping 6mA in synthesized DNA and bacterial genomes. Using 6mACE-seq, we generated a human-genome-wide 6mA map that accurately reproduced known 6mA enrichment at active retrotransposons and revealed mitochondrial chromosome-wide 6mA clusters asymmetrically enriched on the heavy-strand. We identified a novel putative 6mA-binding protein in single-stranded DNA-binding protein 1 (SSBP1), a mitochondrial DNA (mtDNA) replication factor known to coat the heavy-strand, linking 6mA with the regulation of mtDNA replication. Finally, we characterized AlkB homologue 1 (ALKBH1) as a mitochondrial protein with 6mA demethylase activity and showed that its loss decreases mitochondrial oxidative phosphorylation. Our results show that 6mA clusters play a previously unappreciated role in regulating human mitochondrial function, despite 6mA being an uncommon DNA modification in the human genome.
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Affiliation(s)
- Casslynn W Q Koh
- Genome Institute of Singapore, 60 Biopolis Street, Genome, Singapore 138672, Singapore
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Yeek Teck Goh
- Genome Institute of Singapore, 60 Biopolis Street, Genome, Singapore 138672, Singapore
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Joel D W Toh
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Suat Peng Neo
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Sarah B Ng
- Genome Institute of Singapore, 60 Biopolis Street, Genome, Singapore 138672, Singapore
| | - Jayantha Gunaratne
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
| | - Yong-Gui Gao
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Stephen R Quake
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
- Department of Bioengineering and Applied Physics, Stanford University, Stanford, CA 94305, USA
| | - William F Burkholder
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
- Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
| | - Wee Siong S Goh
- Genome Institute of Singapore, 60 Biopolis Street, Genome, Singapore 138672, Singapore
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Proteos, Singapore 138673, Singapore
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16
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Binet R, Pettengill EA, Hoffmann M, Hammack TS, Monday SR. Construction of stable fluorescent laboratory control strains for several food safety relevant Enterobacteriaceae. Food Microbiol 2018; 76:553-563. [DOI: 10.1016/j.fm.2017.10.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 10/26/2017] [Accepted: 10/27/2017] [Indexed: 02/06/2023]
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17
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Nguyen SV, Harhay DM, Bono JL, Smith TPL, Fields PI, Dinsmore BA, Santovenia M, Wang R, Bosilevac JM, Harhay GP. Comparative genomics of Salmonella enterica serovar Montevideo reveals lineage-specific gene differences that may influence ecological niche association. Microb Genom 2018; 4:e000202. [PMID: 30052174 PMCID: PMC6159554 DOI: 10.1099/mgen.0.000202] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/05/2018] [Indexed: 01/01/2023] Open
Abstract
Salmonella enterica serovar Montevideo has been linked to recent foodborne illness outbreaks resulting from contamination of products such as fruits, vegetables, seeds and spices. Studies have shown that Montevideo also is frequently associated with healthy cattle and can be isolated from ground beef, yet human salmonellosis outbreaks of Montevideo associated with ground beef contamination are rare. This disparity fuelled our interest in characterizing the genomic differences between Montevideo strains isolated from healthy cattle and beef products, and those isolated from human patients and outbreak sources. To that end, we sequenced 13 Montevideo strains to completion, producing high-quality genome assemblies of isolates from human patients (n=8) or from healthy cattle at slaughter (n=5). Comparative analysis of sequence data from this study and publicly available sequences (n=72) shows that Montevideo falls into four previously established clades, differentially occupied by cattle and human strains. The results of these analyses reveal differences in metabolic islands, environmental adhesion determinants and virulence factors within each clade, and suggest explanations for the infrequent association between bovine isolates and human illnesses.
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Affiliation(s)
- Scott V. Nguyen
- UCD-Centre for Food Safety, School of Public Health, Physiotherapy and Sports Science, University College Dublin, Belfield, Dublin D04 N2E5, Ireland
| | - Dayna M. Harhay
- USDA-ARS-US Meat Animal Research Center, Clay Center, NE 68933, USA
| | - James L. Bono
- USDA-ARS-US Meat Animal Research Center, Clay Center, NE 68933, USA
| | | | - Patricia I. Fields
- Enteric Disease Laboratory Branch, Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Blake A. Dinsmore
- Enteric Disease Laboratory Branch, Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Monica Santovenia
- Enteric Disease Laboratory Branch, Division of Foodborne, Waterborne, and Environmental Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Rong Wang
- USDA-ARS-US Meat Animal Research Center, Clay Center, NE 68933, USA
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18
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Timme RE, Rand H, Sanchez Leon M, Hoffmann M, Strain E, Allard M, Roberson D, Baugher JD. GenomeTrakr proficiency testing for foodborne pathogen surveillance: an exercise from 2015. Microb Genom 2018; 4. [PMID: 29906258 PMCID: PMC6113870 DOI: 10.1099/mgen.0.000185] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Pathogen monitoring is becoming more precise as sequencing technologies become more affordable and accessible worldwide. This transition is especially apparent in the field of food safety, which has demonstrated how whole-genome sequencing (WGS) can be used on a global scale to protect public health. GenomeTrakr coordinates the WGS performed by public-health agencies and other partners by providing a public database with real-time cluster analysis for foodborne pathogen surveillance. Because WGS is being used to support enforcement decisions, it is essential to have confidence in the quality of the data being used and the downstream data analyses that guide these decisions. Routine proficiency tests, such as the one described here, have an important role in ensuring the validity of both data and procedures. In 2015, the GenomeTrakr proficiency test distributed eight isolates of common foodborne pathogens to participating laboratories, who were required to follow a specific protocol for performing WGS. Resulting sequence data were evaluated for several metrics, including proper labelling, sequence quality and new single nucleotide polymorphisms (SNPs). Illumina MiSeq sequence data collected for the same set of strains across 21 different laboratories exhibited high reproducibility, while revealing a narrow range of technical and biological variance. The numbers of SNPs reported for sequencing runs of the same isolates across multiple laboratories support the robustness of our cluster analysis pipeline in that each individual isolate cultured and resequenced multiple times in multiple places are all easily identifiable as originating from the same source.
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Affiliation(s)
- Ruth E Timme
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, USA
| | - Hugh Rand
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, USA
| | - Maria Sanchez Leon
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, USA
| | - Maria Hoffmann
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, USA
| | - Errol Strain
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, USA
| | - Marc Allard
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, USA
| | - Dwayne Roberson
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, USA
| | - Joseph D Baugher
- Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, MD, USA
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19
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Rapidly moving new bacteria to model-organism status. Curr Opin Biotechnol 2018; 51:116-122. [DOI: 10.1016/j.copbio.2017.12.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 12/11/2017] [Indexed: 11/23/2022]
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20
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Oliver A, Kay M, Cooper KK. Comparative genomics of cocci-shaped Sporosarcina strains with diverse spatial isolation. BMC Genomics 2018; 19:310. [PMID: 29716534 PMCID: PMC5930826 DOI: 10.1186/s12864-018-4635-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 03/28/2018] [Indexed: 12/31/2022] Open
Abstract
Background Cocci-shaped Sporosarcina strains are currently one of the few known cocci-shaped spore-forming bacteria, yet we know very little about the genomics. The goal of this study is to utilize comparative genomics to investigate the diversity of cocci-shaped Sporosarcina strains that differ in their geographical isolation and show different nutritional requirements. Results For this study, we sequenced 28 genomes of cocci-shaped Sporosarcina strains isolated from 13 different locations around the world. We generated the first six complete genomes and methylomes utilizing PacBio sequencing, and an additional 22 draft genomes using Illumina sequencing. Genomic analysis revealed that cocci-shaped Sporosarcina strains contained an average genome of 3.3 Mb comprised of 3222 CDS, 54 tRNAs and 6 rRNAs, while only two strains contained plasmids. The cocci-shaped Sporosarcina genome on average contained 2.3 prophages and 15.6 IS elements, while methylome analysis supported the diversity of these strains as only one of 31 methylation motifs were shared under identical growth conditions. Analysis with a 90% identity cut-off revealed 221 core genes or ~ 7% of the genome, while a 30% identity cut-off generated a pan-genome of 8610 genes. The phylogenetic relationship of the cocci-shaped Sporosarcina strains based on either core genes, accessory genes or spore-related genes consistently resulted in the 29 strains being divided into eight clades. Conclusions This study begins to unravel the phylogenetic relationship of cocci-shaped Sporosarcina strains, and the comparative genomics of these strains supports identification of several new species. Electronic supplementary material The online version of this article (10.1186/s12864-018-4635-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew Oliver
- Department of Biology, California State University Northridge, Northridge, CA, USA.,Present Address: Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA, USA
| | - Matthew Kay
- Department of Biology, California State University Northridge, Northridge, CA, USA
| | - Kerry K Cooper
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA.
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21
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Bohm K, Porwollik S, Chu W, Dover JA, Gilcrease EB, Casjens SR, McClelland M, Parent KN. Genes affecting progression of bacteriophage P22 infection in Salmonella identified by transposon and single gene deletion screens. Mol Microbiol 2018; 108:288-305. [PMID: 29470858 PMCID: PMC5912970 DOI: 10.1111/mmi.13936] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2018] [Indexed: 12/20/2022]
Abstract
Bacteriophages rely on their hosts for replication, and many host genes critically determine either viral progeny production or host success via phage resistance. A random insertion transposon library of 240,000 mutants in Salmonella enterica serovar Typhimurium was used to monitor effects of individual bacterial gene disruptions on bacteriophage P22 lytic infection. These experiments revealed candidate host genes that alter the timing of phage P22 propagation. Using a False Discovery Rate of < 0.1, mutations in 235 host genes either blocked or delayed progression of P22 lytic infection, including many genes for which this role was previously unknown. Mutations in 77 genes reduced the survival time of host DNA after infection, including mutations in genes for enterobacterial common antigen (ECA) synthesis and osmoregulated periplasmic glucan (OPG). We also screened over 2000 Salmonella single gene deletion mutants to identify genes that impacted either plaque formation or culture growth rates. The gene encoding the periplasmic membrane protein YajC was newly found to be essential for P22 infection. Targeted mutagenesis of yajC shows that an essentially full-length protein is required for function, and potassium efflux measurements demonstrated that YajC is critical for phage DNA ejection across the cytoplasmic membrane.
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Affiliation(s)
- Kaitlynne Bohm
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Steffen Porwollik
- Department of Microbiology and Molecular Genetics, University of California, School of Medicine, Irvine, California 92697, USA
| | - Weiping Chu
- Department of Microbiology and Molecular Genetics, University of California, School of Medicine, Irvine, California 92697, USA
| | - John A Dover
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Eddie B Gilcrease
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Sherwood R Casjens
- Division of Microbiology and Immunology, Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Michael McClelland
- Department of Microbiology and Molecular Genetics, University of California, School of Medicine, Irvine, California 92697, USA
| | - Kristin N Parent
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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22
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Piombo E, Sela N, Wisniewski M, Hoffmann M, Gullino ML, Allard MW, Levin E, Spadaro D, Droby S. Genome Sequence, Assembly and Characterization of Two Metschnikowia fructicola Strains Used as Biocontrol Agents of Postharvest Diseases. Front Microbiol 2018; 9:593. [PMID: 29666611 PMCID: PMC5891927 DOI: 10.3389/fmicb.2018.00593] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 03/15/2018] [Indexed: 01/08/2023] Open
Abstract
The yeast Metschnikowia fructicola was reported as an efficient biological control agent of postharvest diseases of fruits and vegetables, and it is the bases of the commercial formulated product "Shemer." Several mechanisms of action by which M. fructicola inhibits postharvest pathogens were suggested including iron-binding compounds, induction of defense signaling genes, production of fungal cell wall degrading enzymes and relatively high amounts of superoxide anions. We assembled the whole genome sequence of two strains of M. fructicola using PacBio and Illumina shotgun sequencing technologies. Using the PacBio, a high-quality draft genome consisting of 93 contigs, with an estimated genome size of approximately 26 Mb, was obtained. Comparative analysis of M. fructicola proteins with the other three available closely related genomes revealed a shared core of homologous proteins coded by 5,776 genes. Comparing the genomes of the two M. fructicola strains using a SNP calling approach resulted in the identification of 564,302 homologous SNPs with 2,004 predicted high impact mutations. The size of the genome is exceptionally high when compared with those of available closely related organisms, and the high rate of homology among M. fructicola genes points toward a recent whole-genome duplication event as the cause of this large genome. Based on the assembled genome, sequences were annotated with a gene description and gene ontology (GO term) and clustered in functional groups. Analysis of CAZymes family genes revealed 1,145 putative genes, and transcriptomic analysis of CAZyme expression levels in M. fructicola during its interaction with either grapefruit peel tissue or Penicillium digitatum revealed a high level of CAZyme gene expression when the yeast was placed in wounded fruit tissue.
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Affiliation(s)
- Edoardo Piombo
- Department of Agricultural, Forestry and Food Sciences, University of Torino, Turin, Italy
- Centre of Competence for the Innovation in the Agro-environmental Sector, University of Torino, Turin, Italy
| | - Noa Sela
- Department of Plant Pathology and Weed Research, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Michael Wisniewski
- United States Department of Agriculture – Agricultural Research Service, Kernersville, WV, United States
| | - Maria Hoffmann
- Division of Microbiology, United States Food and Drug Administration, College Park, MD, United States
| | - Maria L. Gullino
- Department of Agricultural, Forestry and Food Sciences, University of Torino, Turin, Italy
- Centre of Competence for the Innovation in the Agro-environmental Sector, University of Torino, Turin, Italy
| | - Marc W. Allard
- Division of Microbiology, United States Food and Drug Administration, College Park, MD, United States
| | - Elena Levin
- Department of Postharvest Science, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Davide Spadaro
- Department of Agricultural, Forestry and Food Sciences, University of Torino, Turin, Italy
- Centre of Competence for the Innovation in the Agro-environmental Sector, University of Torino, Turin, Italy
| | - Samir Droby
- Department of Postharvest Science, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
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23
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Abrams AJ, Trees DL. Genomic sequencing of Neisseria gonorrhoeae to respond to the urgent threat of antimicrobial-resistant gonorrhea. Pathog Dis 2017; 75:3106325. [PMID: 28387837 PMCID: PMC6956991 DOI: 10.1093/femspd/ftx041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/04/2017] [Indexed: 01/02/2023] Open
Abstract
The development of resistance of Neisseria gonorrhoeae to available first-line antibiotics, including penicillins, tetracyclines, fluoroquinolones and cephalosporins, has led to the circulation of multidrug-resistant gonorrhea at a global scale. Advancements in high-throughput whole-genome sequencing (WGS) provide useful tools that can be used to enhance gonococcal detection, treatment and management capabilities, which will ultimately aid in the control of antimicrobial resistant gonorrhea worldwide. In this minireview, we discuss the application of WGS of N. gonorrhoeae to strain typing, phylogenomic, molecular surveillance and transmission studies. We also examine the application of WGS analyses to the public health sector as well as the potential usage of WGS-based transcriptomic and epigenetic methods to identify novel gonococcal resistance mechanisms.
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Affiliation(s)
- A. Jeanine Abrams
- Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, US Department of Health and Human Services, Atlanta, GA 30333, USA
| | - David L. Trees
- Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, US Department of Health and Human Services, Atlanta, GA 30333, USA
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24
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Genome Sequence of the Thermotolerant Foodborne Pathogen Salmonella enterica Serovar Senftenberg ATCC 43845 and Phylogenetic Analysis of Loci Encoding Increased Protein Quality Control Mechanisms. mSystems 2017; 2:mSystems00190-16. [PMID: 28293682 PMCID: PMC5347186 DOI: 10.1128/msystems.00190-16] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 01/28/2017] [Indexed: 12/11/2022] Open
Abstract
Thermal interventions are commonly used in the food industry as a means of mitigating pathogen contamination in food products. Concern over heat-resistant food contaminants has recently increased, with the identification of a conserved locus shown to confer heat resistance in disparate lineages of Gram-negative bacteria. Complete sequence analysis of a historical isolate of Salmonella enterica serovar Senftenberg, used in numerous studies because of its novel heat resistance, revealed that this important strain possesses two distinct copies of this conserved thermotolerance locus, residing on a multireplicon IncHI2/IncHI2A plasmid. Phylogenetic analysis of these loci in comparison with homologs identified in various bacterial genera provides an opportunity to examine the evolution and distribution of loci conferring resistance to environmental stressors, such as heat and desiccation. Salmonella enterica subsp. enterica bacteria are important foodborne pathogens with major economic impact. Some isolates exhibit increased heat tolerance, a concern for food safety. Analysis of a finished-quality genome sequence of an isolate commonly used in heat resistance studies, S. enterica subsp. enterica serovar Senftenberg 775W (ATCC 43845), demonstrated an interesting observation that this strain contains not just one, but two horizontally acquired thermotolerance locus homologs. These two loci reside on a large 341.3-kbp plasmid that is similar to the well-studied IncHI2 R478 plasmid but lacks any antibiotic resistance genes found on R478 or other IncHI2 plasmids. As this historical Salmonella isolate has been in use since 1941, comparative analysis of the plasmid and of the thermotolerance loci contained on the plasmid will provide insight into the evolution of heat resistance loci as well as acquisition of resistance determinants in IncHI2 plasmids. IMPORTANCE Thermal interventions are commonly used in the food industry as a means of mitigating pathogen contamination in food products. Concern over heat-resistant food contaminants has recently increased, with the identification of a conserved locus shown to confer heat resistance in disparate lineages of Gram-negative bacteria. Complete sequence analysis of a historical isolate of Salmonella enterica serovar Senftenberg, used in numerous studies because of its novel heat resistance, revealed that this important strain possesses two distinct copies of this conserved thermotolerance locus, residing on a multireplicon IncHI2/IncHI2A plasmid. Phylogenetic analysis of these loci in comparison with homologs identified in various bacterial genera provides an opportunity to examine the evolution and distribution of loci conferring resistance to environmental stressors, such as heat and desiccation.
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25
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Identification of a Pseudomonas aeruginosa PAO1 DNA Methyltransferase, Its Targets, and Physiological Roles. mBio 2017; 8:mBio.02312-16. [PMID: 28223461 PMCID: PMC5358918 DOI: 10.1128/mbio.02312-16] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
DNA methylation is widespread among prokaryotes, and most DNA methylation reactions are catalyzed by adenine DNA methyltransferases, which are part of restriction-modification (R-M) systems. R-M systems are known for their role in the defense against foreign DNA; however, DNA methyltransferases also play functional roles in gene regulation. In this study, we used single-molecule real-time (SMRT) sequencing to uncover the genome-wide DNA methylation pattern in the opportunistic pathogen Pseudomonas aeruginosa PAO1. We identified a conserved sequence motif targeted by an adenine methyltransferase of a type I R-M system and quantified the presence of N6-methyladenine using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Changes in the PAO1 methylation status were dependent on growth conditions and affected P. aeruginosa pathogenicity in a Galleria mellonella infection model. Furthermore, we found that methylated motifs in promoter regions led to shifts in sense and antisense gene expression, emphasizing the role of enzymatic DNA methylation as an epigenetic control of phenotypic traits in P. aeruginosa. Since the DNA methylation enzymes are not encoded in the core genome, our findings illustrate how the acquisition of accessory genes can shape the global P. aeruginosa transcriptome and thus may facilitate adaptation to new and challenging habitats. With the introduction of advanced technologies, epigenetic regulation by DNA methyltransferases in bacteria has become a subject of intense studies. Here we identified an adenosine DNA methyltransferase in the opportunistic pathogen Pseudomonas aeruginosa PAO1, which is responsible for DNA methylation of a conserved sequence motif. The methylation level of all target sequences throughout the PAO1 genome was approximated to be in the range of 65 to 85% and was dependent on growth conditions. Inactivation of the methyltransferase revealed an attenuated-virulence phenotype in the Galleria mellonella infection model. Furthermore, differential expression of more than 90 genes was detected, including the small regulatory RNA prrF1, which contributes to a global iron-sparing response via the repression of a set of gene targets. Our finding of a methylation-dependent repression of the antisense transcript of the prrF1 small regulatory RNA significantly expands our understanding of the regulatory mechanisms underlying active DNA methylation in bacteria.
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26
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Cole J, Morris P, Dickman MJ, Dockrell DH. The therapeutic potential of epigenetic manipulation during infectious diseases. Pharmacol Ther 2016; 167:85-99. [PMID: 27519803 PMCID: PMC5109899 DOI: 10.1016/j.pharmthera.2016.07.013] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 07/20/2016] [Indexed: 12/16/2022]
Abstract
Epigenetic modifications are increasingly recognized as playing an important role in the pathogenesis of infectious diseases. They represent a critical mechanism regulating transcriptional profiles in the immune system that contributes to the cell-type and stimulus specificity of the transcriptional response. Recent data highlight how epigenetic changes impact macrophage functional responses and polarization, influencing the innate immune system through macrophage tolerance and training. In this review we will explore how post-translational modifications of histone tails influence immune function to specific infectious diseases. We will describe how these may influence outcome, highlighting examples derived from responses to acute bacterial pathogens, models of sepsis, maintenance of viral latency and HIV infection. We will discuss how emerging classes of pharmacological agents, developed for use in oncology and other settings, have been applied to models of infectious diseases and their potential to modulate key aspects of the immune response to bacterial infection and HIV therapy.
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Affiliation(s)
- Joby Cole
- Department of Infection and Immunity, University of Sheffield Medical School, UK; Sheffield Teaching Hospitals, UK; Chemical and Biologic Engineering, University of Sheffield, UK
| | - Paul Morris
- Department of Infection and Immunity, University of Sheffield Medical School, UK; Sheffield Teaching Hospitals, UK
| | - Mark J Dickman
- Chemical and Biologic Engineering, University of Sheffield, UK
| | - David H Dockrell
- Department of Infection and Immunity, University of Sheffield Medical School, UK; Sheffield Teaching Hospitals, UK.
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27
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Ee R, Lim YL, Yin WF, See-Too WS, Roberts RJ, Chan KG. Novel Methyltransferase Recognition Motif Identified in Chania multitudinisentens RB-25(T) gen. nov., sp. nov. Front Microbiol 2016; 7:1362. [PMID: 27630623 PMCID: PMC5005818 DOI: 10.3389/fmicb.2016.01362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 08/17/2016] [Indexed: 11/13/2022] Open
Affiliation(s)
- Robson Ee
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Yan-Lue Lim
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Wai-Fong Yin
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | - Wah-Seng See-Too
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
| | | | - Kok-Gan Chan
- Division of Genetics and Molecular Biology, Faculty of Science, Institute of Biological Sciences, University of Malaya Kuala Lumpur, Malaysia
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Comparative Methylome Analysis of the Occasional Ruminant Respiratory Pathogen Bibersteinia trehalosi. PLoS One 2016; 11:e0161499. [PMID: 27556252 PMCID: PMC4996451 DOI: 10.1371/journal.pone.0161499] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 08/05/2016] [Indexed: 01/31/2023] Open
Abstract
We examined and compared both the methylomes and the modification-related gene content of four sequenced strains of Bibersteinia trehalosi isolated from the nasopharyngeal tracts of Nebraska cattle with symptoms of bovine respiratory disease complex. The methylation patterns and the encoded DNA methyltransferase (MTase) gene sets were different between each strain, with the only common pattern being that of Dam (GATC). Among the observed patterns were three novel motifs attributable to Type I restriction-modification systems. In some cases the differences in methylation patterns corresponded to the gain or loss of MTase genes, or to recombination at target recognition domains that resulted in changes of enzyme specificity. However, in other cases the differences could be attributed to differential expression of the same MTase gene across strains. The most obvious regulatory mechanism responsible for these differences was slipped strand mispairing within short sequence repeat regions. The combined action of these evolutionary forces allows for alteration of different parts of the methylome at different time scales. We hypothesize that pleiotropic transcriptional modulation resulting from the observed methylomic changes may be involved with the switch between the commensal and pathogenic states of this common member of ruminant microflora.
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Weigele P, Raleigh EA. Biosynthesis and Function of Modified Bases in Bacteria and Their Viruses. Chem Rev 2016; 116:12655-12687. [PMID: 27319741 DOI: 10.1021/acs.chemrev.6b00114] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Naturally occurring modification of the canonical A, G, C, and T bases can be found in the DNA of cellular organisms and viruses from all domains of life. Bacterial viruses (bacteriophages) are a particularly rich but still underexploited source of such modified variant nucleotides. The modifications conserve the coding and base-pairing functions of DNA, but add regulatory and protective functions. In prokaryotes, modified bases appear primarily to be part of an arms race between bacteriophages (and other genomic parasites) and their hosts, although, as in eukaryotes, some modifications have been adapted to convey epigenetic information. The first half of this review catalogs the identification and diversity of DNA modifications found in bacteria and bacteriophages. What is known about the biogenesis, context, and function of these modifications are also described. The second part of the review places these DNA modifications in the context of the arms race between bacteria and bacteriophages. It focuses particularly on the defense and counter-defense strategies that turn on direct recognition of the presence of a modified base. Where modification has been shown to affect other DNA transactions, such as expression and chromosome segregation, that is summarized, with reference to recent reviews.
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Affiliation(s)
- Peter Weigele
- Chemical Biology, New England Biolabs , Ipswich, Massachusetts 01938, United States
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Complete Genome Sequence and Methylome of Salmonella enterica subsp. enterica Cerro, a Frequent Dairy Cow Serovar. GENOME ANNOUNCEMENTS 2016; 4:4/1/e01350-15. [PMID: 26823571 PMCID: PMC4732324 DOI: 10.1128/genomea.01350-15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Salmonella enterica subsp. enterica serovar Cerro is an infrequent pathogen of humans and other mammals but is frequently isolated from the hindgut of asymptomatic cattle in the United States. To further understand the genomic determinants of S. Cerro specificity for the bovine hindgut, the genome of isolate CFSAN001588 was fully sequenced and deposited in the GenBank database.
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Casadesús J. Bacterial DNA Methylation and Methylomes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 945:35-61. [PMID: 27826834 DOI: 10.1007/978-3-319-43624-1_3] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Formation of C5-methylcytosine, N4-methylcytosine, and N6-methyladenine in bacterial genomes is postreplicative and involves transfer of a methyl group from S-adenosyl-methionine to a base embedded in a specific DNA sequence context. Most bacterial DNA methyltransferases belong to restriction-modification systems; in addition, "solitary" or "orphan" DNA methyltransferases are frequently found in the genomes of bacteria and phage. Base methylation can affect the interaction of DNA-binding proteins with their cognate sites, either by a direct effect (e.g., steric hindrance) or by changes in DNA topology. In both Alphaproteobacteria and Gammaproteobacteria, the roles of DNA base methylation are especially well known for N6-methyladenine, including control of chromosome replication, nucleoid segregation, postreplicative correction of DNA mismatches, cell cycle-coupled transcription, formation of bacterial cell lineages, and regulation of bacterial virulence. Technical procedures that permit genome-wide analysis of DNA methylation are nowadays expanding our knowledge of the extent, evolution, and physiological significance of bacterial DNA methylation.
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Affiliation(s)
- Josep Casadesús
- Departamento de Genética, Universidad de Sevilla, Apartado 1095, Seville, 41080, Spain.
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Complete Genome Sequence of Enteroinvasive Escherichia coli O96:H19 Associated with a Severe Foodborne Outbreak. GENOME ANNOUNCEMENTS 2015; 3:3/4/e00883-15. [PMID: 26251502 PMCID: PMC4541276 DOI: 10.1128/genomea.00883-15] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
We present here the complete genome sequence of a strain of enteroinvasive Escherichia coli O96:H19 from a severe foodborne outbreak in a canteen in Italy in 2014. The complete genome may provide important information about the acquired pathogenicity of this strain and the transition between commensal and pathogenic E. coli.
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Complete Genome Sequence of Salmonella enterica subsp. enterica Serovar Agona 460004 2-1, Associated with a Multistate Outbreak in the United States. GENOME ANNOUNCEMENTS 2015; 3:3/4/e00690-15. [PMID: 26139714 PMCID: PMC4490842 DOI: 10.1128/genomea.00690-15] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Within the last several years, Salmonella enterica subsp. enterica serovar Agona has been among the 20 most frequently isolated serovars in clinical cases of salmonellosis. In this report, the complete genome sequence of S. Agona strain 460004 2-1 isolated from unsweetened puffed-rice cereal during a multistate outbreak in 2008 was sequenced using single-molecule real-time DNA sequencing.
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