Transcription bubble

Last updated May 22, 2024

A transcription bubble is a molecular structure formed during DNA transcription when a limited portion of the DNA double helix is unwound. The size of a transcription bubble ranges from 12 to 14 base pairs. A transcription bubble is formed when the RNA polymerase enzyme binds to a promoter and causes two DNA strands to detach.^[1] It presents a region of unpaired DNA, where a short stretch of nucleotides are exposed on each strand of the double helix.^[1]^[2]

RNA polymerase

The bacterial RNA polymerase, a leading enzyme involved in formation of a transcription bubble, uses DNA template to guide RNA synthesis.^[2] It is present in two main forms: as a core enzyme, when it is inactive, and as a holoenzyme, when it is activated. A sigma (σ) factor is a subunit that assists the process of transcription and it stabilizes the transcription bubble when it binds to unpaired bases.^[1] These two components, RNA polymerase and sigma factor, when paired together, build RNA polymerase holoenzyme which is then in its active form and ready to bind to a promoter and initiate DNA transcription.^[3] Once it binds to the DNA, RNA polymerase turns from a closed to an open complex, forming the transcription bubble. RNA polymerase synthesizes the new RNA in the 5' to 3' direction by adding complementary bases to the 3' end of a new strand.^[3] The holoenzyme composition dissociates after transcription initiation, where the σ factor disengages the complex and the RNA polymerase, in its core form, slides along the DNA molecule.^[1]

The transcription cycle of bacterial RNA polymerase

The RNA polymerase holoenzyme binds to a promoter of an exposed DNA strand and begins to synthesize the new strand of RNA. The double helix DNA is unwound and a short nucleotide sequence is accessible on each strand.^[1] The transcription bubble is a region of unpaired bases on one of the exposed DNA strands. The starting transcription point is determined by the place where the holoenzyme binds to a promoter. The DNA is unwound and single-stranded at the start site. The DNA promoter interaction is interrupted as the RNA polymerase moves down the template DNA strand and the sigma factor is released.^[1] The σ factor is required for the initiation but not for the remaining steps of the DNA transcription. Once the σ factor dissociates from the RNA polymerase, the transcription continues. About 10 synthesized nucleotides of a new RNA strand are required for this to proceed to the elongation step. The process of transcribing during elongation is very fast. Elongation takes place until the RNA polymerase comes across a termination signal (terminator) which arrests the process and causes the release of both the DNA template and the new RNA molecule. The DNA usually encodes the termination signal.^[1]^[2]

Eukaryotic transcription

The majority of eukaryotic genes are transcribed by RNA polymerase II, proceeding in the 5' to 3' direction.^[4] In eukaryotes, specific subunits within the RNA polymerase II complex allow it to carry out multiple functions. General transcription factors help binding RNA polymerase II to DNA. Promoters are sites where RNA polymerase II binds to start transcription and, in eukaryotes, transcription starting point is positioned at +1 nucleotide.^[2] Like all RNA polymerases, it travels along the template DNA, in the 3' to 5' direction and synthesizes a new RNA strand in the 5' to 3' direction, by adding new bases to the 3' end of the new RNA.^[4] A transcription bubble occurs as a result of the double stranded DNA unwinding. After about 25 base pairs of the DNA double strand are unwound, RNA synthesis takes place within the transcription bubble region.^[4] Supercoiling is also part of this process since DNA regions in front of the RNA polymerase II are unwinding, while DNA regions behind it are rewinding, forming a double helix again.^[1]

The RNA polymerase carries out the majority of the steps during the transcription cycle, especially in maintaining the transcription bubble open for the complementary base pairing.^[2] There are some steps of the transcription cycle that require more proteins, such as the Rpb4/7 complex and the RNA polymerase attached to the elongation factor transcription factor IIS (TFIIS).^[4]

Related Research Articles

In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. DNA replication occurs in all living organisms acting as the most essential part of biological inheritance. This is essential for cell division during growth and repair of damaged tissues, while it also ensures that each of the new cells receives its own copy of the DNA. The cell possesses the distinctive property of division, which makes replication of DNA essential.

Transcription is the process of copying a segment of DNA into RNA. The segments of DNA transcribed into RNA molecules that can encode proteins produce messenger RNA (mRNA). Other segments of DNA are transcribed into RNA molecules called non-coding RNAs (ncRNAs).

<span class="mw-page-title-main">RNA polymerase</span> Enzyme that synthesizes RNA from DNA

In molecular biology, RNA polymerase, or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that catalyzes the chemical reactions that synthesize RNA from a DNA template.

A DNA polymerase is a member of a family of enzymes that catalyze the synthesis of DNA molecules from nucleoside triphosphates, the molecular precursors of DNA. These enzymes are essential for DNA replication and usually work in groups to create two identical DNA duplexes from a single original DNA duplex. During this process, DNA polymerase "reads" the existing DNA strands to create two new strands that match the existing ones. These enzymes catalyze the chemical reaction

DNA synthesis is the natural or artificial creation of deoxyribonucleic acid (DNA) molecules. DNA is a macromolecule made up of nucleotide units, which are linked by covalent bonds and hydrogen bonds, in a repeating structure. DNA synthesis occurs when these nucleotide units are joined to form DNA; this can occur artificially or naturally. Nucleotide units are made up of a nitrogenous base, pentose sugar (deoxyribose) and phosphate group. Each unit is joined when a covalent bond forms between its phosphate group and the pentose sugar of the next nucleotide, forming a sugar-phosphate backbone. DNA is a complementary, double stranded structure as specific base pairing occurs naturally when hydrogen bonds form between the nucleotide bases.

A sigma factor is a protein needed for initiation of transcription in bacteria. It is a bacterial transcription initiation factor that enables specific binding of RNA polymerase (RNAP) to gene promoters. It is homologous to archaeal transcription factor B and to eukaryotic factor TFIIB. The specific sigma factor used to initiate transcription of a given gene will vary, depending on the gene and on the environmental signals needed to initiate transcription of that gene. Selection of promoters by RNA polymerase is dependent on the sigma factor that associates with it. They are also found in plant chloroplasts as a part of the bacteria-like plastid-encoded polymerase (PEP).

When referring to DNA transcription, the coding strand is the DNA strand whose base sequence is identical to the base sequence of the RNA transcript produced. It is this strand which contains codons, while the non-coding strand contains anticodons. During transcription, RNA Pol II binds to the non-coding template strand, reads the anti-codons, and transcribes their sequence to synthesize an RNA transcript with complementary bases.

The preinitiation complex is a complex of approximately 100 proteins that is necessary for the transcription of protein-coding genes in eukaryotes and archaea. The preinitiation complex positions RNA polymerase II at gene transcription start sites, denatures the DNA, and positions the DNA in the RNA polymerase II active site for transcription.

<span class="mw-page-title-main">Primary transcript</span> RNA produced by transcription

A primary transcript is the single-stranded ribonucleic acid (RNA) product synthesized by transcription of DNA, and processed to yield various mature RNA products such as mRNAs, tRNAs, and rRNAs. The primary transcripts designated to be mRNAs are modified in preparation for translation. For example, a precursor mRNA (pre-mRNA) is a type of primary transcript that becomes a messenger RNA (mRNA) after processing.

<span class="mw-page-title-main">RNA polymerase II</span> Protein complex that transcribes DNA

RNA polymerase II is a multiprotein complex that transcribes DNA into precursors of messenger RNA (mRNA) and most small nuclear RNA (snRNA) and microRNA. It is one of the three RNAP enzymes found in the nucleus of eukaryotic cells. A 550 kDa complex of 12 subunits, RNAP II is the most studied type of RNA polymerase. A wide range of transcription factors are required for it to bind to upstream gene promoters and begin transcription.

General transcription factors (GTFs), also known as basal transcriptional factors, are a class of protein transcription factors that bind to specific sites (promoter) on DNA to activate transcription of genetic information from DNA to messenger RNA. GTFs, RNA polymerase, and the mediator constitute the basic transcriptional apparatus that first bind to the promoter, then start transcription. GTFs are also intimately involved in the process of gene regulation, and most are required for life.

In eukaryote cells, RNA polymerase III is a protein that transcribes DNA to synthesize 5S ribosomal RNA, tRNA, and other small RNAs.

The replisome is a complex molecular machine that carries out replication of DNA. The replisome first unwinds double stranded DNA into two single strands. For each of the resulting single strands, a new complementary sequence of DNA is synthesized. The total result is formation of two new double stranded DNA sequences that are exact copies of the original double stranded DNA sequence.

T7 RNA Polymerase is an RNA polymerase from the T7 bacteriophage that catalyzes the formation of RNA from DNA in the 5'→ 3' direction.

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.

Eukaryotic transcription is the elaborate process that eukaryotic cells use to copy genetic information stored in DNA into units of transportable complementary RNA replica. Gene transcription occurs in both eukaryotic and prokaryotic cells. Unlike prokaryotic RNA polymerase that initiates the transcription of all different types of RNA, RNA polymerase in eukaryotes comes in three variations, each translating a different type of gene. A eukaryotic cell has a nucleus that separates the processes of transcription and translation. Eukaryotic transcription occurs within the nucleus where DNA is packaged into nucleosomes and higher order chromatin structures. The complexity of the eukaryotic genome necessitates a great variety and complexity of gene expression control.

Transcription factor II B (TFIIB) is a general transcription factor that is involved in the formation of the RNA polymerase II preinitiation complex (PIC) and aids in stimulating transcription initiation. TFIIB is localised to the nucleus and provides a platform for PIC formation by binding and stabilising the DNA-TBP complex and by recruiting RNA polymerase II and other transcription factors. It is encoded by the TFIIB gene, and is homologous to archaeal transcription factor B and analogous to bacterial sigma factors.

RNA polymerase II holoenzyme is a form of eukaryotic RNA polymerase II that is recruited to the promoters of protein-coding genes in living cells. It consists of RNA polymerase II, a subset of general transcription factors, and regulatory proteins known as SRB proteins.

Abortive initiation, also known as abortive transcription, is an early process of genetic transcription in which RNA polymerase binds to a DNA promoter and enters into cycles of synthesis of short mRNA transcripts which are released before the transcription complex leaves the promoter. This process occurs in both eukaryotes and prokaryotes. Abortive initiation is typically studied in the T3 and T7 RNA polymerases in bacteriophages and in E. coli.

Archaeal transcription is the process in which a segment of archaeal DNA is copied into a newly synthesized strand of RNA using the sole Pol II-like RNA polymerase (RNAP). The process occurs in three main steps: initiation, elongation, and termination; and the end result is a strand of RNA that is complementary to a single strand of DNA. A number of transcription factors govern this process with homologs in both bacteria and eukaryotes, with the core machinery more similar to eukaryotic transcription.

References

1 2 3 4 5 6 7 8 Alberts, Bruce; Johnson, Alexander; Lewis, Julian; Morgan, David; Raff, Martin; Roberts, Keith; Walter, Peter (2015). Wilson, John; Hunt, Tim (eds.). Molecular Biology of the Cell (6 ed.). Garland Science. pp. 306–307. doi:10.1201/9781315735368. ISBN 9781315735368.
1 2 3 4 5 Clark, David P.; Pazdernik, Nanette J. (1 January 2016), Clark, David P.; Pazdernik, Nanette J. (eds.), "Chapter 2 - DNA, RNA, and Protein", Biotechnology (Second Edition), Academic Cell, pp. 33–61, doi:10.1016/b978-0-12-385015-7.00002-8, ISBN 9780123850157 , retrieved 30 September 2019
1 2 Lodish, Harvey F., author (April 2016). Molecular cell biology. Macmillan Learning. ISBN 9781464183393. OCLC 1003278428.{{cite book}}: |last= has generic name (help)CS1 maint: multiple names: authors list (link)
1 2 3 4 Cramer, Patrick (1 January 2004). "Structure and Function of RNA Polymerase II". Proteins in Eukaryotic Transcription. Vol. 67. Academic Press. pp. 1–42. doi:10.1016/s0065-3233(04)67001-x. ISBN 9780120342679. PMID 14969722 . Retrieved 30 September 2019.{{cite book}}: |journal= ignored (help)

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[:03-1] 1 2 3 4 5 6 7 8 Alberts, Bruce; Johnson, Alexander; Lewis, Julian; Morgan, David; Raff, Martin; Roberts, Keith; Walter, Peter (2015). Wilson, John; Hunt, Tim (eds.). Molecular Biology of the Cell (6 ed.). Garland Science. pp. 306–307. doi:10.1201/9781315735368. ISBN 9781315735368.

[:12-2] 1 2 3 4 5 Clark, David P.; Pazdernik, Nanette J. (1 January 2016), Clark, David P.; Pazdernik, Nanette J. (eds.), "Chapter 2 - DNA, RNA, and Protein", Biotechnology (Second Edition), Academic Cell, pp. 33–61, doi:10.1016/b978-0-12-385015-7.00002-8, ISBN 9780123850157 , retrieved 30 September 2019

[:2-3] 1 2 Lodish, Harvey F., author (April 2016). Molecular cell biology. Macmillan Learning. ISBN 9781464183393. OCLC 1003278428.{{cite book}}: |last= has generic name (help)CS1 maint: multiple names: authors list (link)

[:3-4] 1 2 3 4 Cramer, Patrick (1 January 2004). "Structure and Function of RNA Polymerase II". Proteins in Eukaryotic Transcription. Vol. 67. Academic Press. pp. 1–42. doi:10.1016/s0065-3233(04)67001-x. ISBN 9780120342679. PMID 14969722 . Retrieved 30 September 2019.{{cite book}}: |journal= ignored (help)

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