Prokaryotic Transcription - Promoter Structure and Organization

00:06:35
https://www.youtube.com/watch?v=7AlpT7azzmE

Summary

TLDRThis video discusses the process of transcription, focusing on prokaryotic organisms. Transcription is the conversion of genetic information from the DNA coding region into messenger RNA. Key concepts include the transcription start site (TSS), promoter regions, and elements like the UPE, -35, and -10 elements, each having specific roles in initiating transcription. The video explains the consensus sequences which offer an average representation of promoter sequences that aid in transcription. It highlights the importance of sigma factors, which bind to promoter elements to initiate and stabilize the transcription process. Additionally, the video explores how promoter strength is influenced by its sequence match to consensus sequences and how sequence variations can impact transcription efficacy. Finally, structural DNA features such as curvature can affect how proteins interact with the DNA, playing a critical role in the transcription process.

Takeaways

  • 🧬 Transcription converts DNA information to messenger RNA.
  • 🔍 The Transcription Start Site (TSS) marks the beginning of a coding region.
  • 📍 Promoter regions are crucial in initiating transcription.
  • 🧾 Key promoter elements include the UPE, -35, and -10 elements.
  • 🧩 Consensus sequences represent average promoter sequences.
  • 🔗 Sigma factors bind promoter elements to start transcription.
  • ⚖️ Promoter strength depends on sequence match to consensus.
  • 🔄 Promoter sequences can vary, affecting gene regulation.
  • 🚀 RNA polymerase is essential for transcription.
  • 🔅 Structural features like DNA curvature impact protein binding and transcription.

Timeline

  • 00:00:00 - 00:06:35

    The video introduces prokaryotic transcription, outlining the process by which genetic information is transferred from DNA to mRNA. Emphasizing the importance of the transcription start site (TSS), the video describes how the coding region ends at the stop site, with regions referred to as upstream and downstream. Key focus is placed on the promoter region located upstream of the TSS, which plays a crucial role in initiating transcription. The transcription process is divided into initiation, elongation, and termination phases, highlighting the significance of promoter elements in transcription initiation.

Mind Map

Video Q&A

  • What is transcription?

    Transcription is the process of converting genetic information from the DNA molecule into messenger RNA.

  • What is the role of the promoter region in transcription?

    The promoter region is involved in initiating or promoting the process of transcription.

  • What are the main steps of transcription?

    Transcription involves three main steps: initiation, elongation, and termination.

  • What is the significance of the TSS in transcription?

    The Transcription Start Site (TSS) marks the first base of the coding region where transcription begins.

  • What are the key promoter elements in prokaryotic transcription?

    Key promoter elements include the UPE element, -35 element, -10 element, and sometimes an extended -10 element or discriminator element.

  • What is a consensus sequence?

    A consensus sequence is an average representation of expected DNA sequences in promoter regions.

  • How do sigma factors interact with promoter elements?

    Sigma factors bind promoter elements to initiate transcription and stabilize RNA polymerase.

  • Why is the structure of promoter sequences important?

    The structure can influence DNA curvature, affecting how proteins like sigma factors engage with the DNA during transcription.

  • What affects the strength of a promoter?

    The strength of a promoter is determined by how closely its sequence matches the consensus sequence, affecting transcription activity.

  • How can promoter sequences vary among different genes?

    Promoter sequences can vary in sequence and structure, leading to different transcriptional regulation and activity across genes.

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  • 00:00:00
    hey welcome to the Crux in this video
  • 00:00:03
    we're going to start our discussion on
  • 00:00:05
    transcription and in particular we start
  • 00:00:08
    by looking at the procaryotic
  • 00:00:10
    transcription so transcription is the
  • 00:00:12
    process of genetic information
  • 00:00:14
    conversion or transfer from the coding
  • 00:00:17
    region of the DNA to a messenger
  • 00:00:20
    RNA in a given piece of DNA for instance
  • 00:00:23
    a gene you have the coding region which
  • 00:00:26
    contains information about the protein
  • 00:00:28
    it codes or a functional RNA it codes
  • 00:00:31
    like the ribosomal RNA and the start of
  • 00:00:34
    this coding region is usually referred
  • 00:00:36
    to as transcription start site or TSS
  • 00:00:39
    for short and the first base of the
  • 00:00:41
    coding region is called the plus one
  • 00:00:44
    position for reference to everything
  • 00:00:46
    else around it and at the end of the
  • 00:00:50
    coding region we have the stop site
  • 00:00:53
    which marks the end of the coding region
  • 00:00:56
    now from our reference set at the TSS we
  • 00:01:00
    call all things towards the end of the
  • 00:01:02
    coding region Downstream and likewise
  • 00:01:05
    all the things before the plus one site
  • 00:01:08
    are considered Upstream one important
  • 00:01:11
    piece of DNA that is located Upstream of
  • 00:01:14
    the TSS is the promoter region and
  • 00:01:17
    promoter is involved in promoting or
  • 00:01:20
    initiating the process of transcription
  • 00:01:22
    and once transcription is initiated it
  • 00:01:25
    continues along the coding region in a
  • 00:01:27
    process called elongation and then it
  • 00:01:30
    terminates at the stop signal so you
  • 00:01:33
    could divide the entire process of
  • 00:01:35
    transcription into three steps since
  • 00:01:38
    transcription is initiated via the
  • 00:01:40
    promoters we should first discuss about
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    the organization of the promoter DNA so
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    consider this doubl stranded DNA and
  • 00:01:49
    let's mark our reference at TSS which is
  • 00:01:52
    the first base of the coding region and
  • 00:01:54
    then Downstream of the plus one site you
  • 00:01:56
    have the plus two plus three and on the
  • 00:01:59
    Upstream site you have -1 and -2 sites
  • 00:02:03
    and you can continue writing this
  • 00:02:05
    notation for all bases in both
  • 00:02:07
    directions and you should note that
  • 00:02:09
    there is no site zero now in our
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    promoter region which is the Upstream of
  • 00:02:15
    the TSS we have three main promoter
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    elements the distal or the farthest is
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    the upe element Upstream promoter
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    element which is at about 58 to- 37th
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    position then we have the -35 element
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    which is located at around -35 to -30
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    position then you have the most common
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    promoter element the -10 element located
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    at the -12th to -7th
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    position it is also known that the
  • 00:02:47
    optimal spacing between the -35 and the
  • 00:02:50
    -10 element is around 17 bases sometimes
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    the- 35 element or the -10 elements are
  • 00:02:57
    not available in the promoter of some
  • 00:02:59
    genes in those cases you can find an
  • 00:03:01
    extended -10 element at the position -17
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    to
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    -14 and then there are some genes that
  • 00:03:09
    carry a discriminator promoter element
  • 00:03:12
    which is usually three bases in length
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    as you may have already read it the -10
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    element is also sometimes called the
  • 00:03:19
    pnau box or the pnau sheller
  • 00:03:22
    box in the UK carots it's homologue can
  • 00:03:26
    be thought of as the Tata box also known
  • 00:03:28
    as The Goldberg hogness box functionally
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    speaking the up element is frequently
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    contacted by the RNA polymerase which is
  • 00:03:38
    the enzyme responsible for making RNA
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    and its binding to the upe stabilizes it
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    the up is commonly found and the
  • 00:03:45
    promoter of ribosomal RNA
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    genes then the - 35 element extended -10
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    and the -10 elements are contacted by
  • 00:03:54
    the sigma factors which are responsible
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    for the transcription initiation process
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    finally the discriminator element is
  • 00:04:03
    also Bound by the sigma factors and
  • 00:04:05
    because Sigma factors are bound to the
  • 00:04:06
    RNA polymerase the discriminator element
  • 00:04:09
    helps stabilize the polymerase when
  • 00:04:12
    looking at the sequence structure of
  • 00:04:13
    each of these elements they have some
  • 00:04:14
    underlying consensus sequences for
  • 00:04:17
    instance up has a long
  • 00:04:21
    consensus the W's and n's that you see
  • 00:04:23
    in the sequence are iopac symbols check
  • 00:04:26
    out the link in the description to learn
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    about their meaning
  • 00:04:30
    the -35 has ttgaca as its consensus
  • 00:04:33
    sequence the extended -10 has trtg as
  • 00:04:37
    its consensus and the -10 element has t
  • 00:04:40
    a t a a t as its consensus and then the
  • 00:04:44
    discriminator is usually just a g
  • 00:04:46
    triplet so you should keep in mind that
  • 00:04:49
    the consensus sequence are just an
  • 00:04:50
    average representation of the sequence
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    expectation this means that just because
  • 00:04:56
    you have a consensus sequence does not
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    mean that it is always like that in all
  • 00:04:59
    genes and therefore it can change a way
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    to get consensus is to align a
  • 00:05:04
    particular portion of DNA and compute
  • 00:05:06
    the per base average in that alignment
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    and that gives you a
  • 00:05:11
    consensus to show you what I mean
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    consider the -10 element whose consensus
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    as we just said is t a t a a
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    t but that is only true because it is
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    bound by Sigma Factor D also known as
  • 00:05:25
    Sigma 70 or rpod and because Sigma D
  • 00:05:28
    Factor binds most of the genes and
  • 00:05:31
    procaryotes the consensus of ta a tat is
  • 00:05:34
    biased towards it but when you look at
  • 00:05:37
    the negative T element sequence of
  • 00:05:38
    certain Sigma H bound genes and these
  • 00:05:41
    are usually the heat shock genes you
  • 00:05:43
    find a completely different
  • 00:05:46
    consensus so there are different Sigma
  • 00:05:48
    factors involved in the promoter binding
  • 00:05:50
    and I have a link in the description if
  • 00:05:52
    you want to read more about them now
  • 00:05:55
    depending on the promoter sequence the
  • 00:05:57
    promoters can either be strong or weak
  • 00:05:59
    that is the measure of how many
  • 00:06:01
    transcript they can produce in a given
  • 00:06:03
    time the strong promoters usually match
  • 00:06:06
    their respective consensus fairly well
  • 00:06:08
    and weak ones deviate one last thing
  • 00:06:11
    about promoters you should know is that
  • 00:06:13
    their sequence composition can cause DNA
  • 00:06:15
    to form curvatures or bends this is
  • 00:06:19
    important because the proteins like
  • 00:06:20
    Sigma factors that bind them have to
  • 00:06:22
    unfold these DNA sequence and torsion or
  • 00:06:26
    bend created by these sequence helps
  • 00:06:28
    these proteins affect L do their
  • 00:06:31
    job so that is all for the introduction
  • 00:06:33
    of bacterial promoters
Tags
  • transcription
  • prokaryotic
  • promoter
  • TSS
  • consensus sequence
  • sigma factors
  • gene expression
  • DNA curvature
  • RNA polymerase
  • genetic information