Towards in vivo regulon kinetics: PurR activation by 5-phosphoribosyl-a-1-pyrophosphate during purine depletion in Lactococcus lactis.

Christian Bille Jendresen, Peter Dimitrov, Laurent Gautier, Meng Lui, Jan Martinussen, Mogens Kilstrup

    Research output: Contribution to journalJournal articleResearchpeer-review

    Abstract

    Short-term adaptation to changing environments relies on regulatory elements translating shifting metabolite concentrations into a specifically optimized transcriptome. So far the focus of analyses has been divided between regulatory elements identified in vivo and kinetic studies of small molecules interacting with the regulatory elements in vitro. Here we describe how in vivo regulon
    kinetics can describe a regulon through the effects of the metabolite controlling it, exemplified by temporal purine exhaustion in Lactococcus lactis. We deduced a causal relation between the pathway precursor 5-phosphoribosyl-a-1-pyrophosphate (PRPP) and individual mRNA levels, whereby unambiguous and homogeneous relations could be obtained for PurR regulated genes, thus linking a specific regulon to a specific metabolite. As PurR activates gene expression upon binding of PRPP, the pur mRNA curves reflect the in vivo kinetics of PurR PRPP binding and activation. The method singled out the xpt-pbuX operon as kinetically distinct, which was found to be caused by a guanine riboswitch whose regulation was overlaying the PurR regulation.
    Importantly, genes could be clustered according to regulatory mechanism and long-term consequences could be distinguished from transient changes – many of which would not be seen in a long-term adaptation to a new environment. The strategy outlined here can be adapted to analyse the individual effects of members from larger metabolomes in virtually any organism, for elucidating regulatory networks in vivo.
    Original languageEnglish
    JournalMicrobiology-Sgm
    Volume160
    Issue number7
    Pages (from-to)1321-1331
    ISSN1350-0872
    DOIs
    Publication statusPublished - 2014

    Cite this

    @article{60404b036e1b43baab906c3589e883de,
    title = "Towards in vivo regulon kinetics: PurR activation by 5-phosphoribosyl-a-1-pyrophosphate during purine depletion in Lactococcus lactis.",
    abstract = "Short-term adaptation to changing environments relies on regulatory elements translating shifting metabolite concentrations into a specifically optimized transcriptome. So far the focus of analyses has been divided between regulatory elements identified in vivo and kinetic studies of small molecules interacting with the regulatory elements in vitro. Here we describe how in vivo regulonkinetics can describe a regulon through the effects of the metabolite controlling it, exemplified by temporal purine exhaustion in Lactococcus lactis. We deduced a causal relation between the pathway precursor 5-phosphoribosyl-a-1-pyrophosphate (PRPP) and individual mRNA levels, whereby unambiguous and homogeneous relations could be obtained for PurR regulated genes, thus linking a specific regulon to a specific metabolite. As PurR activates gene expression upon binding of PRPP, the pur mRNA curves reflect the in vivo kinetics of PurR PRPP binding and activation. The method singled out the xpt-pbuX operon as kinetically distinct, which was found to be caused by a guanine riboswitch whose regulation was overlaying the PurR regulation.Importantly, genes could be clustered according to regulatory mechanism and long-term consequences could be distinguished from transient changes – many of which would not be seen in a long-term adaptation to a new environment. The strategy outlined here can be adapted to analyse the individual effects of members from larger metabolomes in virtually any organism, for elucidating regulatory networks in vivo.",
    author = "Jendresen, {Christian Bille} and Peter Dimitrov and Laurent Gautier and Meng Lui and Jan Martinussen and Mogens Kilstrup",
    year = "2014",
    doi = "10.1099/mic.0.077933-0",
    language = "English",
    volume = "160",
    pages = "1321--1331",
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    Towards in vivo regulon kinetics: PurR activation by 5-phosphoribosyl-a-1-pyrophosphate during purine depletion in Lactococcus lactis. / Jendresen, Christian Bille; Dimitrov, Peter; Gautier, Laurent; Lui, Meng; Martinussen, Jan; Kilstrup, Mogens.

    In: Microbiology-Sgm, Vol. 160, No. 7, 2014, p. 1321-1331.

    Research output: Contribution to journalJournal articleResearchpeer-review

    TY - JOUR

    T1 - Towards in vivo regulon kinetics: PurR activation by 5-phosphoribosyl-a-1-pyrophosphate during purine depletion in Lactococcus lactis.

    AU - Jendresen, Christian Bille

    AU - Dimitrov, Peter

    AU - Gautier, Laurent

    AU - Lui, Meng

    AU - Martinussen, Jan

    AU - Kilstrup, Mogens

    PY - 2014

    Y1 - 2014

    N2 - Short-term adaptation to changing environments relies on regulatory elements translating shifting metabolite concentrations into a specifically optimized transcriptome. So far the focus of analyses has been divided between regulatory elements identified in vivo and kinetic studies of small molecules interacting with the regulatory elements in vitro. Here we describe how in vivo regulonkinetics can describe a regulon through the effects of the metabolite controlling it, exemplified by temporal purine exhaustion in Lactococcus lactis. We deduced a causal relation between the pathway precursor 5-phosphoribosyl-a-1-pyrophosphate (PRPP) and individual mRNA levels, whereby unambiguous and homogeneous relations could be obtained for PurR regulated genes, thus linking a specific regulon to a specific metabolite. As PurR activates gene expression upon binding of PRPP, the pur mRNA curves reflect the in vivo kinetics of PurR PRPP binding and activation. The method singled out the xpt-pbuX operon as kinetically distinct, which was found to be caused by a guanine riboswitch whose regulation was overlaying the PurR regulation.Importantly, genes could be clustered according to regulatory mechanism and long-term consequences could be distinguished from transient changes – many of which would not be seen in a long-term adaptation to a new environment. The strategy outlined here can be adapted to analyse the individual effects of members from larger metabolomes in virtually any organism, for elucidating regulatory networks in vivo.

    AB - Short-term adaptation to changing environments relies on regulatory elements translating shifting metabolite concentrations into a specifically optimized transcriptome. So far the focus of analyses has been divided between regulatory elements identified in vivo and kinetic studies of small molecules interacting with the regulatory elements in vitro. Here we describe how in vivo regulonkinetics can describe a regulon through the effects of the metabolite controlling it, exemplified by temporal purine exhaustion in Lactococcus lactis. We deduced a causal relation between the pathway precursor 5-phosphoribosyl-a-1-pyrophosphate (PRPP) and individual mRNA levels, whereby unambiguous and homogeneous relations could be obtained for PurR regulated genes, thus linking a specific regulon to a specific metabolite. As PurR activates gene expression upon binding of PRPP, the pur mRNA curves reflect the in vivo kinetics of PurR PRPP binding and activation. The method singled out the xpt-pbuX operon as kinetically distinct, which was found to be caused by a guanine riboswitch whose regulation was overlaying the PurR regulation.Importantly, genes could be clustered according to regulatory mechanism and long-term consequences could be distinguished from transient changes – many of which would not be seen in a long-term adaptation to a new environment. The strategy outlined here can be adapted to analyse the individual effects of members from larger metabolomes in virtually any organism, for elucidating regulatory networks in vivo.

    U2 - 10.1099/mic.0.077933-0

    DO - 10.1099/mic.0.077933-0

    M3 - Journal article

    VL - 160

    SP - 1321

    EP - 1331

    JO - Microbiology

    JF - Microbiology

    SN - 1350-0872

    IS - 7

    ER -