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  1. Article: Bacterial DNA Methylation and Methylomes.

    Casadesús, Josep

    Advances in experimental medicine and biology

    2016  Volume 945, Page(s) 35–61

    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 ... ...

    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.
    MeSH term(s) 5-Methylcytosine/chemistry ; 5-Methylcytosine/metabolism ; Adenine/chemistry ; Adenine/metabolism ; Adenosine/analogs & derivatives ; Adenosine/chemistry ; Adenosine/genetics ; Alphaproteobacteria/genetics ; Cell Lineage/genetics ; DNA Methylation/genetics ; DNA Replication/genetics ; Gammaproteobacteria/genetics ; Gene Expression Regulation, Bacterial/genetics ; Genome, Bacterial
    Chemical Substances 5-Methylcytosine (6R795CQT4H) ; N-methyladenosine (CLE6G00625) ; Adenine (JAC85A2161) ; Adenosine (K72T3FS567)
    Language English
    Publishing date 2016-10-25
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ISSN 2214-8019 ; 0065-2598
    ISSN (online) 2214-8019
    ISSN 0065-2598
    DOI 10.1007/978-3-319-43624-1_3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: DNA Methylation in Prokaryotes.

    Casadesús, Josep / Sánchez-Romero, María A

    Advances in experimental medicine and biology

    2022  Volume 1389, Page(s) 21–43

    Abstract: The genomes of bacteria, archaea, and phage contain small amounts of ... ...

    Abstract The genomes of bacteria, archaea, and phage contain small amounts of C
    MeSH term(s) DNA Methylation ; Prokaryotic Cells/metabolism ; DNA Modification Methylases/genetics ; Epigenomics ; Bacteria/metabolism ; DNA/metabolism ; DNA, Bacterial/genetics ; DNA, Bacterial/metabolism
    Chemical Substances DNA Modification Methylases (EC 2.1.1.-) ; DNA (9007-49-2) ; DNA, Bacterial
    Language English
    Publishing date 2022-11-09
    Publishing country United States
    Document type Journal Article
    ISSN 2214-8019 ; 0065-2598
    ISSN (online) 2214-8019
    ISSN 0065-2598
    DOI 10.1007/978-3-031-11454-0_2
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Single Cell Analysis of Bistable Expression of Pathogenicity Island 1 and the Flagellar Regulon in Salmonella enterica

    Sánchez-Romero, María Antonia / Casadesús, Josep

    Microorganisms. 2021 Jan. 20, v. 9, no. 2

    2021  

    Abstract: Bistable expression of the Salmonella enterica pathogenicity island 1 (SPI-1) and the flagellar network (Flag) has been described previously. In this study, simultaneous monitoring of OFF and ON states in SPI-1 and in the flagellar regulon reveals ... ...

    Abstract Bistable expression of the Salmonella enterica pathogenicity island 1 (SPI-1) and the flagellar network (Flag) has been described previously. In this study, simultaneous monitoring of OFF and ON states in SPI-1 and in the flagellar regulon reveals independent switching, with concomitant formation of four subpopulations: SPI-1ᴼFF FlagᴼFF, SPI-1ᴼFF Flagᴼᴺ, SPI-1ᴼᴺ FlagᴼFF, and SPI-1ᴼᴺ Flagᴼᴺ. Invasion assays upon cell sorting show that none of the four subpopulations is highly invasive, thus raising the possibility that FlagᴼFF cells might contribute to optimal invasion as previously proposed for SPI-1ᴼFF cells. Time lapse microscopy observation indicates that expression of the flagellar regulon contributes to the growth impairment previously described in SPI-1ᴼᴺ cells. As a consequence, growth resumption in SPI-1ᴼᴺ Flagᴼᴺ cells requires switching to both SPI-1ᴼFF and FlagᴼFF states.
    Keywords Salmonella enterica ; microscopy ; pathogenicity islands ; regulon
    Language English
    Dates of publication 2021-0120
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms9020210
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: Transcription-driven DNA supercoiling counteracts H-NS-mediated gene silencing in bacterial chromatin.

    Figueroa-Bossi, Nara / Fernández-Fernández, Rocío / Kerboriou, Patricia / Bouloc, Philippe / Casadesús, Josep / Sánchez-Romero, María Antonia / Bossi, Lionello

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 2787

    Abstract: In all living cells, genomic DNA is compacted through interactions with dedicated proteins and/or the formation of plectonemic coils. In bacteria, DNA compaction is achieved dynamically, coordinated with dense and constantly changing transcriptional ... ...

    Abstract In all living cells, genomic DNA is compacted through interactions with dedicated proteins and/or the formation of plectonemic coils. In bacteria, DNA compaction is achieved dynamically, coordinated with dense and constantly changing transcriptional activity. H-NS, a major bacterial nucleoid structuring protein, is of special interest due to its interplay with RNA polymerase. H-NS:DNA nucleoprotein filaments inhibit transcription initiation by RNA polymerase. However, the discovery that genes silenced by H-NS can be activated by transcription originating from neighboring regions has suggested that elongating RNA polymerases can disassemble H-NS:DNA filaments. In this study, we present evidence that transcription-induced counter-silencing does not require transcription to reach the silenced gene; rather, it exerts its effect at a distance. Counter-silencing is suppressed by introducing a DNA gyrase binding site within the intervening segment, suggesting that the long-range effect results from transcription-driven positive DNA supercoils diffusing toward the silenced gene. We propose a model wherein H-NS:DNA complexes form in vivo on negatively supercoiled DNA, with H-NS bridging the two arms of the plectoneme. Rotational diffusion of positive supercoils generated by neighboring transcription will cause the H-NS-bound negatively-supercoiled plectoneme to "unroll" disrupting the H-NS bridges and releasing H-NS.
    MeSH term(s) Chromatin/metabolism ; DNA-Binding Proteins/metabolism ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Bacteria/genetics ; DNA-Directed RNA Polymerases/genetics ; DNA-Directed RNA Polymerases/metabolism ; DNA/metabolism ; Gene Silencing ; Gene Expression Regulation, Bacterial ; DNA, Bacterial/genetics ; DNA, Bacterial/metabolism ; Transcription, Genetic
    Chemical Substances Chromatin ; DNA-Binding Proteins ; Bacterial Proteins ; DNA-Directed RNA Polymerases (EC 2.7.7.6) ; DNA (9007-49-2) ; DNA, Bacterial
    Language English
    Publishing date 2024-03-30
    Publishing country England
    Document type Journal Article
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-47114-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Waddington's Landscapes in the Bacterial World.

    Sánchez-Romero, María A / Casadesús, Josep

    Frontiers in microbiology

    2021  Volume 12, Page(s) 685080

    Abstract: Conrad Waddington's epigenetic landscape, a visual metaphor for the development of multicellular organisms, is appropriate to depict the formation of phenotypic variants of bacterial cells. Examples of bacterial differentiation that result in ... ...

    Abstract Conrad Waddington's epigenetic landscape, a visual metaphor for the development of multicellular organisms, is appropriate to depict the formation of phenotypic variants of bacterial cells. Examples of bacterial differentiation that result in morphological change have been known for decades. In addition, bacterial populations contain phenotypic cell variants that lack morphological change, and the advent of fluorescent protein technology and single-cell analysis has unveiled scores of examples. Cell-specific gene expression patterns can have a random origin or arise as a programmed event. When phenotypic cell-to-cell differences are heritable, bacterial lineages are formed. The mechanisms that transmit epigenetic states to daughter cells can have strikingly different levels of complexity, from the propagation of simple feedback loops to the formation of complex DNA methylation patterns. Game theory predicts that phenotypic heterogeneity can facilitate bacterial adaptation to hostile or unpredictable environments, serving either as a division of labor or as a bet hedging that anticipates future challenges. Experimental observation confirms the existence of both types of strategies in the bacterial world.
    Language English
    Publishing date 2021-06-04
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2021.685080
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Analysis of

    Fernández-Fernández, Rocío / López-Igual, Rocío / Casadesús, Josep / Sánchez-Romero, María Antonia

    Frontiers in cellular and infection microbiology

    2023  Volume 13, Page(s) 1146070

    Abstract: Microbial cell individuality is receiving increasing interest in the scientific community. Individual cells within clonal populations exhibit noticeable phenotypic heterogeneity. The advent of fluorescent protein technology and advances in single-cell ... ...

    Abstract Microbial cell individuality is receiving increasing interest in the scientific community. Individual cells within clonal populations exhibit noticeable phenotypic heterogeneity. The advent of fluorescent protein technology and advances in single-cell analysis has revealed phenotypic cell variant in bacterial populations. This heterogeneity is evident in a wide range of phenotypes, for example, individual cells display variable degrees of gene expression and survival under selective conditions and stresses, and can exhibit differing propensities to host interactions. Last few years, numerous cell sorting approaches have been employed for resolving the properties of bacterial subpopulations. This review provides an overview of applications of cell sorting to analyze
    MeSH term(s) Salmonella/genetics ; Phenotype ; Bacteria ; Gene Expression Profiling
    Language English
    Publishing date 2023-03-29
    Publishing country Switzerland
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 2619676-1
    ISSN 2235-2988 ; 2235-2988
    ISSN (online) 2235-2988
    ISSN 2235-2988
    DOI 10.3389/fcimb.2023.1146070
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  7. Article: Single Cell Analysis of Bistable Expression of Pathogenicity Island 1 and the Flagellar Regulon in

    Sánchez-Romero, María Antonia / Casadesús, Josep

    Microorganisms

    2021  Volume 9, Issue 2

    Abstract: Bistable expression of ... ...

    Abstract Bistable expression of the
    Language English
    Publishing date 2021-01-20
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2720891-6
    ISSN 2076-2607
    ISSN 2076-2607
    DOI 10.3390/microorganisms9020210
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  8. Article ; Online: Genome-Wide Identification and Expression Analysis of SOS Response Genes in

    Mérida-Floriano, Angela / Rowe, Will P M / Casadesús, Josep

    Cells

    2021  Volume 10, Issue 4

    Abstract: A bioinformatic search for LexA boxes, combined with transcriptomic detection of loci responsive to DNA damage, identified 48 members of the SOS regulon in the genome ... ...

    Abstract A bioinformatic search for LexA boxes, combined with transcriptomic detection of loci responsive to DNA damage, identified 48 members of the SOS regulon in the genome of
    MeSH term(s) Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Base Sequence ; Chromosomes, Bacterial/genetics ; DNA Damage/genetics ; Gene Expression Regulation, Bacterial/drug effects ; Genetic Loci ; Genome, Bacterial ; Nalidixic Acid/pharmacology ; SOS Response, Genetics/drug effects ; Salmonella typhimurium/drug effects ; Salmonella typhimurium/genetics ; Single-Cell Analysis
    Chemical Substances Bacterial Proteins ; Nalidixic Acid (3B91HWA56M)
    Language English
    Publishing date 2021-04-19
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2661518-6
    ISSN 2073-4409 ; 2073-4409
    ISSN (online) 2073-4409
    ISSN 2073-4409
    DOI 10.3390/cells10040943
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  9. Article: Epigenetic biosensors for bacteriophage detection and phage receptor discrimination

    Olivenza, David R / Casadesús, Josep / Ansaldi, Mireille

    Environmental microbiology. 2020 Aug., v. 22, no. 8

    2020  

    Abstract: Environmental monitoring of bacteria using phage‐based biosensors has been widely developed for many different species. However, there are only a few available methods to detect specific bacteriophages in raw environmental samples. In this work, we ... ...

    Abstract Environmental monitoring of bacteria using phage‐based biosensors has been widely developed for many different species. However, there are only a few available methods to detect specific bacteriophages in raw environmental samples. In this work, we developed a simple and efficient assay to rapidly monitor the phage content of a given sample. The assay is based on the bistable expression of the Salmonella enterica opvAB operon. Under regular growth conditions, opvAB is only expressed by a small fraction of the bacterial subpopulation. In the OpvABᴼᴺ subpopulation, synthesis of the OpvA and OpvB products shortens the O‐antigen and confers resistance to phages that use LPS as a receptor. As a consequence, the OpvABᴼᴺ subpopulation is selected in the presence of such phages. Using an opvAB::gfp fusion, we could monitor LPS‐binding phages in various media, including raw water samples. To enlarge our phage‐biosensor panoply, we also developed biosensors able to detect LPS, as well as protein‐binding coliphages. Moreover, the combination of these tools allowed to identify the bacterial receptor triggering phage infection. The epigenetic opvAB::gfp biosensor thus comes in different flavours to detect a wide range of bacteriophages and identify the type of receptor they recognize.
    Keywords O-antigens ; Salmonella enterica ; biosensors ; coliphages ; epigenetics ; operon ; protein binding ; virus receptors
    Language English
    Dates of publication 2020-08
    Size p. 3126-3142.
    Publishing place John Wiley & Sons, Inc.
    Document type Article
    Note NAL-AP-2-clean ; JOURNAL ARTICLE
    ZDB-ID 2020213-1
    ISSN 1462-2920 ; 1462-2912
    ISSN (online) 1462-2920
    ISSN 1462-2912
    DOI 10.1111/1462-2920.15050
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  10. Article ; Online: Adaptation of Salmonella enterica to bile: essential role of AcrAB-mediated efflux.

    Urdaneta, Verónica / Casadesús, Josep

    Environmental microbiology

    2018  Volume 20, Issue 4, Page(s) 1405–1418

    Abstract: Adaptation to bile is the ability to endure the lethal effects of bile salts after growth on sublethal concentrations. Surveys of adaptation to bile in Salmonella enterica ser. Tyhimurium reveal that active efflux is essential for adaptation while other ... ...

    Abstract Adaptation to bile is the ability to endure the lethal effects of bile salts after growth on sublethal concentrations. Surveys of adaptation to bile in Salmonella enterica ser. Tyhimurium reveal that active efflux is essential for adaptation while other bacterial functions involved in bile resistance are not. Among S. enterica mutants lacking one or more efflux systems, only strains lacking AcrAB are unable to adapt, thus revealing an essential role for AcrAB. Transcription of the acrAB operon is upregulated in the presence of a sublethal concentration of sodium deoxycholate (DOC) while other efflux loci are either weakly upregulated or irresponsive. Upregulation of acrAB transcription is strong during exponential growth, and weak in stationary cultures. Single cell analysis of ethidium bromide accumulation indicates that DOC-induced AcrAB-mediated efflux occurs in both exponential and stationary cultures. Upregulation of acrAB expression may thus be crucial at early stages of adaptation, while sustained AcrAB activity may be sufficient to confer bile resistance in nondividing cells.
    MeSH term(s) Acclimatization/physiology ; Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/metabolism ; Bile/microbiology ; Bile Acids and Salts/metabolism ; Deoxycholic Acid/metabolism ; Ethidium/metabolism ; Gene Expression Regulation, Bacterial/drug effects ; Microbial Sensitivity Tests ; Salmonella typhimurium/genetics ; Salmonella typhimurium/growth & development ; Salmonella typhimurium/physiology
    Chemical Substances Anti-Bacterial Agents ; Bacterial Proteins ; Bile Acids and Salts ; Deoxycholic Acid (005990WHZZ) ; Ethidium (EN464416SI)
    Language English
    Publishing date 2018-02-02
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2020213-1
    ISSN 1462-2920 ; 1462-2912
    ISSN (online) 1462-2920
    ISSN 1462-2912
    DOI 10.1111/1462-2920.14047
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