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  1. Article ; Online: Hfq protein and GcvB small RNA tailoring of

    Carrier, Marie-Claude / Lalaouna, David / Massé, Eric

    RNA biology

    2023  Volume 20, Issue 1, Page(s) 59–76

    Abstract: Traffic of molecules across the bacterial membrane mainly relies on porins and transporters, whose expression must adapt to environmental conditions. To ensure bacterial fitness, synthesis and assembly of functional porins and transporters are regulated ... ...

    Abstract Traffic of molecules across the bacterial membrane mainly relies on porins and transporters, whose expression must adapt to environmental conditions. To ensure bacterial fitness, synthesis and assembly of functional porins and transporters are regulated through a plethora of mechanisms. Among them, small regulatory RNAs (sRNAs) are known to be powerful post-transcriptional regulators. In
    MeSH term(s) RNA, Messenger ; Escherichia coli ; 5' Untranslated Regions ; ATP-Binding Cassette Transporters ; Membrane Transport Proteins ; RNA, Small Untranslated ; Escherichia coli Proteins ; Host Factor 1 Protein
    Chemical Substances RNA, Messenger ; 5' Untranslated Regions ; ATP-Binding Cassette Transporters ; Membrane Transport Proteins ; RNA, Small Untranslated ; Hfq protein, E coli ; Escherichia coli Proteins ; Host Factor 1 Protein
    Language English
    Publishing date 2023-03-01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2159587-2
    ISSN 1555-8584 ; 1555-8584
    ISSN (online) 1555-8584
    ISSN 1555-8584
    DOI 10.1080/15476286.2023.2179582
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Assembling the Current Pieces: The Puzzle of RNA-Mediated Regulation in

    Barrientos, Laura / Mercier, Noémie / Lalaouna, David / Caldelari, Isabelle

    Frontiers in microbiology

    2021  Volume 12, Page(s) 706690

    Abstract: The success of the major opportunistic ... ...

    Abstract The success of the major opportunistic human
    Language English
    Publishing date 2021-07-21
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2021.706690
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: RNA Sequencing Unveils Very Small RNAs With Potential Regulatory Functions in Bacteria.

    Diallo, Idrissa / Ho, Jeffrey / Lalaouna, David / Massé, Eric / Provost, Patrick

    Frontiers in molecular biosciences

    2022  Volume 9, Page(s) 914991

    Abstract: RNA sequencing (RNA-seq) is the gold standard for the discovery of small non-coding RNAs. Following a long-standing approach, reads shorter than 16 nucleotides (nt) are removed from the small RNA sequencing libraries or datasets. The serendipitous ... ...

    Abstract RNA sequencing (RNA-seq) is the gold standard for the discovery of small non-coding RNAs. Following a long-standing approach, reads shorter than 16 nucleotides (nt) are removed from the small RNA sequencing libraries or datasets. The serendipitous discovery of an eukaryotic 12 nt-long RNA species capable of modulating the microRNA from which they derive prompted us to challenge this dogma and, by expanding the window of RNA sizes down to 8 nt, to confirm the existence of functional very small RNAs (vsRNAs <16 nt). Here we report the detailed profiling of vsRNAs in
    Language English
    Publishing date 2022-06-03
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2814330-9
    ISSN 2296-889X
    ISSN 2296-889X
    DOI 10.3389/fmolb.2022.914991
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  4. Article ; Online: Burning the Candle at Both Ends: Have Exoribonucleases Driven Divergence of Regulatory RNA Mechanisms in Bacteria?

    Mediati, Daniel G / Lalaouna, David / Tree, Jai J

    mBio

    2021  Volume 12, Issue 4, Page(s) e0104121

    Abstract: Regulatory RNAs have emerged as ubiquitous gene regulators in all bacterial species studied to date. The combination of sequence-specific RNA interactions and malleable RNA structure has allowed regulatory RNA to adopt different mechanisms of gene ... ...

    Abstract Regulatory RNAs have emerged as ubiquitous gene regulators in all bacterial species studied to date. The combination of sequence-specific RNA interactions and malleable RNA structure has allowed regulatory RNA to adopt different mechanisms of gene regulation in a diversity of genetic backgrounds. In the model
    MeSH term(s) Bacteria/classification ; Bacteria/genetics ; Exoribonucleases/genetics ; Exoribonucleases/metabolism ; Gammaproteobacteria/genetics ; Gene Expression Regulation, Bacterial ; Gram-Positive Bacteria/genetics ; RNA Stability ; RNA, Bacterial/genetics ; RNA, Bacterial/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism
    Chemical Substances RNA, Bacterial ; RNA, Messenger ; Exoribonucleases (EC 3.1.-)
    Language English
    Publishing date 2021-08-10
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2557172-2
    ISSN 2150-7511 ; 2161-2129
    ISSN (online) 2150-7511
    ISSN 2161-2129
    DOI 10.1128/mBio.01041-21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Phytobeneficial traits of rhizobacteria under the control of multiple molecular dialogues.

    Laveilhé, Arnaud / Fochesato, Sylvain / Lalaouna, David / Heulin, Thierry / Achouak, Wafa

    Microbial biotechnology

    2022  Volume 15, Issue 7, Page(s) 2083–2096

    Abstract: Pseudomonads play crucial roles in plant growth promotion and control of plant diseases. However, under natural conditions, other microorganisms competing for the same nutrient resources in the rhizosphere may exert negative control over their ... ...

    Abstract Pseudomonads play crucial roles in plant growth promotion and control of plant diseases. However, under natural conditions, other microorganisms competing for the same nutrient resources in the rhizosphere may exert negative control over their phytobeneficial characteristics. We assessed the expression of phytobeneficial genes involved in biocontrol, biostimulation and iron regulation such as, phlD, hcnA, acdS, and iron-small regulatory RNAs prrF1 and prrF2 in Pseudomonas brassicacearum co-cultivated with three phytopathogenic fungi, and two rhizobacteria in the presence or absence of Brassica napus, and in relation to iron availability. We found that the antifungal activity of P. brassicacearum depends mostly on the production of DAPG and not on HCN whose production is suppressed by fungi. We have also shown that the two-competing bacterial strains modulate the plant growth promotion activity of P. brassicacearum by modifying the expression of phlD, hcnA and acdS according to iron availability. Overall, it allows us to better understand the complexity of the multiple molecular dialogues that take place underground between microorganisms and between plants and its rhizosphere microbiota and to show that synergy in favour of phytobeneficial gene expression may exist between different bacterial species.
    MeSH term(s) Alphaproteobacteria ; Bacteria/genetics ; Fungi ; Iron ; Plant Diseases/microbiology ; Plant Diseases/prevention & control ; Rhizosphere ; Soil Microbiology
    Chemical Substances Iron (E1UOL152H7)
    Language English
    Publishing date 2022-05-03
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2406063-X
    ISSN 1751-7915 ; 1751-7915
    ISSN (online) 1751-7915
    ISSN 1751-7915
    DOI 10.1111/1751-7915.14023
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Navigation through the twists and turns of RNA sequencing technologies: Application to bacterial regulatory RNAs.

    Desgranges, Emma / Caldelari, Isabelle / Marzi, Stefano / Lalaouna, David

    Biochimica et biophysica acta. Gene regulatory mechanisms

    2020  Volume 1863, Issue 3, Page(s) 194506

    Abstract: Discovered in the 1980s, small regulatory RNAs (sRNAs) are now considered key actors in virtually all aspects of bacterial physiology and virulence. Together with transcriptional and translational regulatory proteins, they integrate and often are hubs of ...

    Abstract Discovered in the 1980s, small regulatory RNAs (sRNAs) are now considered key actors in virtually all aspects of bacterial physiology and virulence. Together with transcriptional and translational regulatory proteins, they integrate and often are hubs of complex regulatory networks, responsible for bacterial response/adaptation to various perceived stimuli. The recent development of powerful RNA sequencing technologies has facilitated the identification and characterization of sRNAs (length, structure and expression conditions) and their RNA targets in several bacteria. Nevertheless, it could be very difficult for non-experts to understand the advantages and drawbacks related to each offered option and, consequently, to make an informed choice. Therefore, the main goal of this review is to provide a guide to navigate through the twists and turns of high-throughput RNA sequencing technologies, with a specific focus on those applied to the study of sRNAs. This article is part of a Special Issue entitled: RNA and gene control in bacteria edited by Dr. M. Guillier and F. Repoila.
    MeSH term(s) Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; Nucleic Acid Conformation ; RNA, Bacterial/chemistry ; RNA, Bacterial/metabolism ; RNA, Small Untranslated/chemistry ; RNA, Small Untranslated/metabolism ; Sequence Analysis, RNA
    Chemical Substances RNA, Bacterial ; RNA, Small Untranslated
    Language English
    Publishing date 2020-02-14
    Publishing country Netherlands
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2918786-2
    ISSN 1876-4320 ; 1874-9399
    ISSN (online) 1876-4320
    ISSN 1874-9399
    DOI 10.1016/j.bbagrm.2020.194506
    Database MEDical Literature Analysis and Retrieval System OnLINE

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 7156: Show issues Location:
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  7. Article ; Online: Battle for Metals: Regulatory RNAs at the Front Line.

    Charbonnier, Mathilde / González-Espinoza, Gabriela / Kehl-Fie, Thomas E / Lalaouna, David

    Frontiers in cellular and infection microbiology

    2022  Volume 12, Page(s) 952948

    Abstract: Metal such as iron, zinc, manganese, and nickel are essential elements for bacteria. These nutrients are required in crucial structural and catalytic roles in biological processes, including precursor biosynthesis, DNA replication, transcription, ... ...

    Abstract Metal such as iron, zinc, manganese, and nickel are essential elements for bacteria. These nutrients are required in crucial structural and catalytic roles in biological processes, including precursor biosynthesis, DNA replication, transcription, respiration, and oxidative stress responses. While essential, in excess these nutrients can also be toxic. The immune system leverages both of these facets, to limit bacterial proliferation and combat invaders. Metal binding immune proteins reduce the bioavailability of metals at the infection sites starving intruders, while immune cells intoxicate pathogens by providing metals in excess leading to enzyme mismetallation and/or reactive oxygen species generation. In this dynamic metal environment, maintaining metal homeostasis is a critical process that must be precisely coordinated. To achieve this, bacteria utilize diverse metal uptake and efflux systems controlled by metalloregulatory proteins. Recently, small regulatory RNAs (sRNAs) have been revealed to be critical post-transcriptional regulators, working in conjunction with transcription factors to promote rapid adaptation and to fine-tune bacterial adaptation to metal abundance. In this mini review, we discuss the expanding role for sRNAs in iron homeostasis, but also in orchestrating adaptation to the availability of other metals like manganese and nickel. Furthermore, we describe the sRNA-mediated interdependency between metal homeostasis and oxidative stress responses, and how regulatory networks controlled by sRNAs contribute to survival and virulence.
    MeSH term(s) Bacteria ; Gene Expression Regulation, Bacterial ; Ions/metabolism ; Iron/metabolism ; Manganese/metabolism ; Metals/metabolism ; Nickel/metabolism ; Transcription Factors/metabolism ; Virulence
    Chemical Substances Ions ; Metals ; Transcription Factors ; Manganese (42Z2K6ZL8P) ; Nickel (7OV03QG267) ; Iron (E1UOL152H7)
    Language English
    Publishing date 2022-07-05
    Publishing country Switzerland
    Document type Journal Article ; Review ; Research Support, N.I.H., Extramural ; 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.2022.952948
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  8. Article ; Online: Cut in translation: ribosome-dependent mRNA decay.

    Lalaouna, David / Massé, Eric

    The EMBO journal

    2017  Volume 36, Issue 9, Page(s) 1120–1122

    Abstract: Transcription and translation are two complex mechanisms that are tightly coupled in prokaryotic cells. Even before the completion of transcription, ribosomes attach to the nascent mRNA and initiate protein synthesis. Remarkably, recent publications have ...

    Abstract Transcription and translation are two complex mechanisms that are tightly coupled in prokaryotic cells. Even before the completion of transcription, ribosomes attach to the nascent mRNA and initiate protein synthesis. Remarkably, recent publications have indicated an association between translation and decay of certain mRNAs. In this issue of
    MeSH term(s) Bacillus subtilis/genetics ; Protein Biosynthesis ; RNA Stability ; RNA, Messenger/genetics ; Ribosomes/genetics
    Chemical Substances RNA, Messenger
    Language English
    Publishing date 2017--02
    Publishing country England
    Document type Journal Article ; Comment
    ZDB-ID 586044-1
    ISSN 1460-2075 ; 0261-4189
    ISSN (online) 1460-2075
    ISSN 0261-4189
    DOI 10.15252/embj.201797019
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 1808: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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    Zs.MG 100: Show issues

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  9. Article ; Online: RNA Sequencing Unveils Very Small RNAs With Potential Regulatory Functions in Bacteria

    Idrissa Diallo / Jeffrey Ho / David Lalaouna / Eric Massé / Patrick Provost

    Frontiers in Molecular Biosciences, Vol

    2022  Volume 9

    Abstract: RNA sequencing (RNA-seq) is the gold standard for the discovery of small non-coding RNAs. Following a long-standing approach, reads shorter than 16 nucleotides (nt) are removed from the small RNA sequencing libraries or datasets. The serendipitous ... ...

    Abstract RNA sequencing (RNA-seq) is the gold standard for the discovery of small non-coding RNAs. Following a long-standing approach, reads shorter than 16 nucleotides (nt) are removed from the small RNA sequencing libraries or datasets. The serendipitous discovery of an eukaryotic 12 nt-long RNA species capable of modulating the microRNA from which they derive prompted us to challenge this dogma and, by expanding the window of RNA sizes down to 8 nt, to confirm the existence of functional very small RNAs (vsRNAs <16 nt). Here we report the detailed profiling of vsRNAs in Escherichia coli, E. coli-derived outer membrane vesicles (OMVs) and five other bacterial strains (Pseudomonas aeruginosa PA7, P. aeruginosa PAO1, Salmonella enterica serovar Typhimurium 14028S, Legionella pneumophila JR32 Philadelphia-1 and Staphylococcus aureus HG001). vsRNAs of 8–15 nt in length [RNAs (8-15 nt)] were found to be more abundant than RNAs of 16–30 nt in length [RNAs (16–30 nt)]. vsRNA biotypes were distinct and varied within and across bacterial species and accounted for one third of reads identified in the 8–30 nt window. The tRNA-derived fragments (tRFs) have appeared as a major biotype among the vsRNAs, notably Ile-tRF and Ala-tRF, and were selectively loaded in OMVs. tRF-derived vsRNAs appear to be thermodynamically stable with at least 2 G-C basepairs and stem-loop structure. The analyzed tRF-derived vsRNAs are predicted to target several human host mRNAs with diverse functions. Bacterial vsRNAs and OMV-derived vsRNAs could be novel players likely modulating the intricate relationship between pathogens and their hosts.
    Keywords RNA sequencing ; bacteria ; E. coli ; outer membrane vesicle (OMV) ; very small RNA (vsRNA) ; tRNA fragment (tRF) ; Biology (General) ; QH301-705.5
    Language English
    Publishing date 2022-06-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: The 3' UTR of vigR is required for virulence in Staphylococcus aureus and has expanded through STAR sequence repeat insertions.

    Mediati, Daniel G / Dan, William / Lalaouna, David / Dinh, Hue / Pokhrel, Alaska / Rowell, Keiran N / Michie, Katharine A / Stinear, Timothy P / Cain, Amy K / Tree, Jai J

    Cell reports

    2024  Volume 43, Issue 4, Page(s) 114082

    Abstract: Infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are alarmingly common, and treatment is confined to last-line antibiotics. Vancomycin is the treatment of choice for MRSA bacteremia, and treatment failure is often associated with ... ...

    Abstract Infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are alarmingly common, and treatment is confined to last-line antibiotics. Vancomycin is the treatment of choice for MRSA bacteremia, and treatment failure is often associated with vancomycin-intermediate S. aureus isolates. The regulatory 3' UTR of the vigR mRNA contributes to vancomycin tolerance and upregulates the autolysin IsaA. Using MS2-affinity purification coupled with RNA sequencing, we find that the vigR 3' UTR also regulates dapE, a succinyl-diaminopimelate desuccinylase required for lysine and peptidoglycan synthesis, suggesting a broader role in controlling cell wall metabolism and vancomycin tolerance. Deletion of the 3' UTR increased virulence, while the isaA mutant is completely attenuated in a wax moth larvae model. Sequence and structural analyses of vigR indicated that the 3' UTR has expanded through the acquisition of Staphylococcus aureus repeat insertions that contribute sequence for the isaA interaction seed and may functionalize the 3' UTR.
    MeSH term(s) Virulence/genetics ; 3' Untranslated Regions/genetics ; Staphylococcus aureus/genetics ; Staphylococcus aureus/pathogenicity ; Staphylococcus aureus/drug effects ; Animals ; Staphylococcal Infections/microbiology ; Staphylococcal Infections/drug therapy ; Bacterial Proteins/genetics ; Bacterial Proteins/metabolism ; Methicillin-Resistant Staphylococcus aureus/genetics ; Methicillin-Resistant Staphylococcus aureus/pathogenicity ; Methicillin-Resistant Staphylococcus aureus/drug effects ; Gene Expression Regulation, Bacterial ; Moths/microbiology ; Vancomycin/pharmacology ; Anti-Bacterial Agents/pharmacology ; Base Sequence
    Chemical Substances 3' Untranslated Regions ; Bacterial Proteins ; Vancomycin (6Q205EH1VU) ; Anti-Bacterial Agents
    Language English
    Publishing date 2024-04-06
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2649101-1
    ISSN 2211-1247 ; 2211-1247
    ISSN (online) 2211-1247
    ISSN 2211-1247
    DOI 10.1016/j.celrep.2024.114082
    Database MEDical Literature Analysis and Retrieval System OnLINE

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