Bacterial transcription

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Transcription is the process of copying DNA into RNA, usually mRNA.

Bacterial transcription is the process in which a segment of bacterial DNA is copied into a newly synthesized strand of messenger RNA (mRNA) with use of the enzyme RNA polymerase. The process occurs in three main steps: initiation, elongation, and termination; and the end result is a strand of mRNA that is complementary to a single strand of DNA. Generally, the transcribed region accounts for more than one gene.[1] Transcription is carried out by RNA polymerase but its specificity is controlled by sequence-specific DNA binding proteins called transcription factors. Transcription factors work to recognize specific DNA sequences and based on the cells needs, promote or inhibit additional transcription.[2]

Overall, transcription within bacteria is a highly regulated process that is controlled by the integration of many signals at a given time. Bacteria heavily rely on transcription and translation to generate proteins that help them respond specifically to their environment.[3]

RNA polymerase[edit]

RNA polymerase is composed of a core and a holoenzyme structure. The core enzymes contains the catalytic properties of RNA poymerasel and is made up of ββ′α2ω subunits. This sequence is conserved across all bacterial species. The holoenzyme is composed of a specific component known as the sigma factor. The sigma factor functions in aiding in promoter recognition, correct placement of RNA polymerase, and beginning unwinding at the start site. After the sigma factor performs its required function, it dissociates, while the catalytic portion remains on the DNA and continues transcription.[3] Additionally, RNA polymerase contains a core Mg+ ion that assists the enzyme with its catalytic properties. RNA polymerase works by catalyzing the nucleophilic attack of 3’ OH of RNA to the alpha phosphate of a complimentary NTP molecule to create a growing strand of RNA from the template strand of DNA. Furthermore, RNA polymerase also displays exonuclease activities, meaning that if improper base pairing is detected, it can cut out the incorrect bases and replace them with the proper, correct one.[4]

Initiation[edit]

Initiation of transcription requires two sites in DNA: a promoter that forms a recognition and binding site for the RNA polymerase, and the actual start site. RNA polymerase is made up of 4 or 5 subunits, depending on which form it is in. The subunits include α, α, β, β', and σ, and each subunit plays a role in the initiation of transcription. When all 5 subunits are present in RNA polymerase, it is in its active form and referred to as the holoenzyme. When the σ subunit detaches, it is in polymerase core enzyme form (also called core polymerase).[5][1] The σ subunit of the holoenzyme recognizes promoter elements at -35 and -10 regions (consensus sequences), and transcription begins at the start site (+1). The sequence for the -10 region is TATAAT and the sequence for the -35 region is TTGACA.[1]

  • The σ subunit, also referred to as the σ-factor, binds to the -35 promotor region. At this point, the holoenzyme is referred to as the closed complex because the DNA is still double stranded (connected by hydrogen bonds).[5]
  • Once the σ-factor binds, the remaining core enzyme subunits attach to the site. The DNA unwinds and becomes single-stranded at the start site. At this point, the holoenzyme is called the open complex.[6] An open complex is created by the unwinding of the DNA at the start sequence.[4]
  • Transcription initiates and a short "abortive" nucleotide sequence is produced and released, along with the σ-factor . This signals the end of the initiation phase and the holoenzyme is now in core polymerase form.[5] Generally, this nucleotide sequence consists of about twelve base pairs and aids in contributing to the stability of RNA polymerase so it is able to continue along the strand of DNA.[4]
  • The σ-factor is needed to initiate transcription but is not needed to continue transcribing the DNA. The σ-factor dissociates from the core enzyme and elongation proceeds.[5]

The promoter region is a prime regulator of transcription. Promoter regions regulate transcription of all genes within bacteria. As a result of their involvement, the sequence of base pairs within the promoter region is significant; the more similar the promoter region is to the consensus sequence, the tighter RNA polymerase will be able to bind. This binding contributes to the stability of elongation stage of transcription and overall results in more efficient functioning. Additionally, RNA polymerase and sigma factors are in limited supply within any given bacterial cell. Consequently, sigma factor binding to the promoter is affected by these limitations. All promoter regions contain sequences that are considered non-consensus and this helps to distribute sigma factors across the entirety of the genome.[7]

Elongation[edit]

During elongation, core polymerase moves down the double stranded DNA, unwinding it and transcribing (copying) its nucleotide sequence into newly synthesized RNA. New nucleotides complementary to the DNA template strand are synthesized to the 3' end of the RNA strand.[5] The newly formed RNA strand is practically identical to the DNA coding strand, with uracil substituting thymine. Because ribonucleoside triphosphates need to attach to the OH- molecule on the 3' end of the RNA, transcription occurs in the 5' to 3' direction. The four ribonucleoside triphosphates are adenosine-5'-triphosphate (ATP), guanoside-5"-triphosphate (GTP), uridine-5'-triphosphate (UTP), cytidine-5'-triphosphate (CTP). ATP and GTP are purine nucleoside triphosphates and they more common, with ATP being the most common. UTP and CTP are pyrimidine nucleoside triphosphates which are usually rejected at the initiation site.[6]

Termination[edit]

In order for proper gene expression to occur, transcription must stop at specific sites. Two termination mechanisms are well known:

  • Intrinsic termination (also called Rho-independent termination): Specific RNA nucleotide sequences signal the RNA polymerase to stop. The sequence is commonly a palindromic sequence that causes the strand to loop which stalls the RNA polymerase.[6] Generally, this type of termination follows the same standard procedure. A pause will occur due to a polyuridine sequence that allows the formation of a hairpin loop. This hairpin loop will aid in forming a trapped complex, which will ultimately cause the dissociation of RNA polymerase from the template DNA strand and halt transcription.[4]
  • Rho-dependent termination: ρ factor (rho factor) is a terminator protein that attaches to the RNA strand. When the RNA polymerase encounters the rho factor on the RNA strand in the transcription bubble, it pulls the DNA apart from the RNA and transcription is stopped.[8] Rho factor is a protein complex that also displays helicase activities (is able to unwind the nucleic acid strands). It will bind to the DNA in cytidine rich regions and when RNA polymerase encounters it, a trapped complex will form causing the dissociation of all molecules involved and end transcription.[4]

The termination of DNA transcription in bacteria may be stopped by certain mechanisms wherein the RNA polymerase will ignore the terminator sequence until the next one is reached. This phenomenon is known as antitermination and is utilized by certain bacteriophages.[9]

References[edit]

  1. ^ a b c "Prokaryotic Transcription and Translation | Biology for Majors I". courses.lumenlearning.com. Retrieved 2019-10-06.
  2. ^ "Clemson University Libraries - Login". login.libproxy.clemson.edu. Retrieved 2019-10-13.
  3. ^ a b Browning, Douglas F.; Busby, Stephen J. W. (January 2004). "The regulation of bacterial transcription initiation". Nature Reviews Microbiology. 2 (1): 57–65. doi:10.1038/nrmicro787. ISSN 1740-1534.
  4. ^ a b c d e "Clemson University Libraries - Login". login.libproxy.clemson.edu. Retrieved 2019-10-13.
  5. ^ a b c d e Lodish, Harvey; Berk, Arnold; Zipursky, S. Lawrence; Matsudaira, Paul; Baltimore, David; Darnell, James (2000). "Bacterial Transcription Initiation". Molecular Cell Biology. 4th edition.
  6. ^ a b c "7.6C: Prokaryotic Transcription and Translation Are Coupled". Biology LibreTexts. 2017-05-17. Retrieved 2019-10-07.
  7. ^ "Clemson University Libraries - Login". login.libproxy.clemson.edu. Retrieved 2019-10-13.
  8. ^ "Stages of transcription". Khan Academy. Retrieved 2019-10-07.
  9. ^ Lewin's genes X. Lewin, Benjamin., Krebs, Jocelyn E., Kilpatrick, Stephen T., Goldstein, Elliott S., Lewin, Benjamin. (10th ed.). Sudbury, Mass.: Jones and Bartlett. 2011. ISBN 9780763766320. OCLC 456641931.CS1 maint: others (link)

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