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    BIO Genetics Transcription

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    Anonymous SVy8sOsvJD
    The document discusses key decisions in prokaryotic transcription initiation in E. coli. It summarizes that the promoter sequence defines (1) which DNA strand serves as the template and (2) where transcription starts. It then provides details on E. coli RNA polymerase structure and function, promoter elements, and mechanisms of transcription initiation and termination.

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    BIO Genetics Transcription

    Uploaded by

    Anonymous SVy8sOsvJD
    18 views14 pages
    The document discusses key decisions in prokaryotic transcription initiation in E. coli. It summarizes that the promoter sequence defines (1) which DNA strand serves as the template and (2) where transcription starts. It then provides details on E. coli RNA polymerase structure and function, promoter elements, and mechanisms of transcription initiation and termination.

    Original Description:

    E coli transcription and operons

    Original Title

    BIO genetics transcription

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    The document discusses key decisions in prokaryotic transcription initiation in E. coli. It summarizes that the promoter sequence defines (1) which DNA strand serves as the template and (2) where transcription starts. It then provides details on E. coli RNA polymerase structure and function, promoter elements, and mechanisms of transcription initiation and termination.

    Copyright:

    © All Rights Reserved
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
    18 views14 pages

    BIO Genetics Transcription

    Uploaded by

    Anonymous SVy8sOsvJD
    The document discusses key decisions in prokaryotic transcription initiation in E. coli. It summarizes that the promoter sequence defines (1) which DNA strand serves as the template and (2) where transcription starts. It then provides details on E. coli RNA polymerase structure and function, promoter elements, and mechanisms of transcription initiation and termination.

    Copyright:

    © All Rights Reserved
    Download as PPTX, PDF, TXT or read online from Scribd
    Download as pptx, pdf, or txt
    of 14

    Promoter sequence defines two key decisions

    +1 3’
    RNA AGCU
    (nontemplate strand)
    5’ AGCT coding strand
    DNA
    3’ TCGA template strand

    promoter terminator

    Which DNA strand serves as the template

    Where does transcription start

    1
    221 S16
    Prokaryotic transcription: initiation

    2
    221 S16
    E. coli RNA polymerase

    subunit stochiometry
    protein core holoenzyme elongating
    Gene function
    subunit polymerase initiation competent termination competent

    promoter
    rpoA a recognition; 2 2 2
    bind activators

    rpoB b catalytic 1 1 1

    rpoC b’ catalytic 1 1 1
    assembly of s
    rpoZ  factors 1 1 1
    promoter
    rpoD s70 specificity 1

    aabb’  aabb’ s70) aabb’

    3
    221 S16
    E. coli RNA polymerase

    cis-acting element
    A site on a DNA (or RNA) molecule that
    functions as a regulatory site – often a
    binding site for a sequence-specific binding
    protei.
    e.g., promoter

    trans-acting factor
    A diffusible regulatory molecule - often a
    protein - that binds to a specific cis-acting
    element

    e.g., RNA polymerase

    The trans-acting factor binding to its cognate cis-acting element affects only
    adjacent DNA (or RNA) sequences on the same molecule.
    4
    221 S16
    Typical prokaryotic promoter

    RNAP binding at -10 and -35 region

    Local unwinding/melting at -10 region

    5
    221 S16
    E. coli RNA polymerase – DNA interactions during initiation

    6
    221 S16 Jie Chen et al. PNAS 2010;107:12523-12528
    E. coli RNA polymerase – DNA interactions during initiation

    template strand

    sigma70
    protein domains

    closed complex open complex

    7
    221 S16 Chen et al. PNAS 2010;107:12523-12528
    E. coli promoter alignment

    Pribnow box

    consensus sequence
    a generalized base sequence
    derived from closely related sequences
    where each position in the consensus sequence
    is found in the majority of sequences at that position
    8
    221 S16
    E. coli promoter alignment

    Sequence logo

    -35 -10
    Sequence logos are a graphical technique
    for displaying a summary of a set of aligned 263 strong promoters
    sequences.
    9
    221 S16 Dekhtyar et al. (2008) BMC Bioinformatics 2008, 9:233
    E. coli RNA polymerase: promoter binding

    (sigma70 domains)
    Biochemical evidence
    Physical evidence

    17 bp

    Genetic evidence

    usually affects usually affects


    RNAP binding RNAP binding
    also can affect
    template melting 10
    221 S16
    E. coli RNA polymerase binds to
    one side of the double-helix

    -35

    -10

    17 bp

    11
    221 S16
    E. coli RNA polymerase binds to one side of the double-helix

    consensus:
    -35 -10

    +2 bp
    insertion
    mutation:

    -37 -10

    12
    221 S16 221S’14
    Prokaryotic transcription: factor-independent termination

    loop
    Two types of termination:
    • rho-independent (intrinsic)
    • rho-dependent
    Intramolecular “stem-loop”
    G:C-rich stem
    U-rich 3’-end

    13
    221 S16
    Prokaryotic transcription: factor-independent termination

    Palindrome is
    A word, phrase, number, or other
    sequence of characters which reads
    the same backward or forward.

    14
    factor-independent (intrinsic)
    221 S16

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