9 public questions tagged with this topic.
Transcription is the first step in gene expression, producing pre-mRNA, which undergoes processing before translation.
Ref: NCERT Class 12 Biology Chapter 5: Molecular Basis of Inheritance Post-Transcriptional Modifications - Capping Splicing Polyadenylation
The sigma (Ï) factor helps RNA polymerase recognize and bind to the promoter during transcription initiation in bacteria.
Ref: NCERT Class 12 Biology Chapter 5: Molecular Basis of Inheritance Transcription - Mechanism and RNA Polymerase
The sigma (Ï) factor of prokaryotic RNA polymerase recognizes the promoter and facilitates transcription initiation.
Ref: NCERT Class 12 Biology Chapter 5: Molecular Basis of Inheritance Transcription - Mechanism and RNA Polymerase
Phosphorylation of CTD heptad serine five by TFIIH CDK7 occurs early during transcription, peaking within fifty base pairs downstream of promoter. Serine5-phosphorylated CTD serves as landing pad for capping enzyme complex containing RNA triphosphatase, guanylyltransferase, N7-methyltransferase activities, stimulating cotranscriptional cap addition when transcript reaches twenty to thirty nucleotides. Marker also recruits early spliceosome components and H3K4 methyltransferase Set1 complex via interaction with Paf1 elongation complex. Phosphatases Ssu72 and Rtr1 later dephosphorylate serine five as serine two phosphorylation rises during elongation progression toward gene end.
Ref: Alberts et al., Molecular Biology of the Cell, 7th ed., Chapter 6: Ser5-P associated with initiation and promoter escape; PLoS Biology CTD phosphorylation dynamics
In bacteria, sigma factor combines with core RNA polymerase to form holoenzyme that recognizes -10 and -35 promoter motifs and unwinds DNA. During early elongation, the sigma 3.2 linker remains lodged inside the RNA exit channel, obstructing growth beyond a few nucleotides. Once transcript reaches 9 to 11 nucleotides, steric clash ejects region 3.2, disrupts sigma-DNA and sigma-core contacts, and triggers conformational change to processive elongation complex. Sigma is released after promoter escape, recycles to new core enzymes, while NusA, NusG and other regulators bind elongating polymerase.
Ref: Alberts et al., Molecular Biology of the Cell, 7th ed., Chapter 6: Bacterial transcription initiation, sigma cycle and promoter escape
UP element is AT-rich sequence located approximately -40 to -60 upstream of transcription start site, found in strong rRNA and tRNA promoters. Crystallographic studies show C-terminal domain of α subunit, α-CTD connected via flexible linker, contains helix-hairpin motif binding minor groove of UP element AT tracts, providing additional anchoring energy independent of sigma -10 and -35 contacts. Interaction can enhance transcription up to thirty fold. β, σ70, β', ω subunits do not directly contact UP. Presence explains why some promoters lacking perfect consensus still strong due to extra α-CTD mediated recruitment of polymerase holoenzyme.
Ref: Ross et al. Science 1993 UP element α-CTD interaction; Alberts Chapter 6: UP recognized by α-CTD domain structure
Promoter anatomy reveals two conserved hexamers spaced seventeen base pairs apart. Upstream hexamer centered around -35 position consensus sequence TTGACA contacted by sigma70 region 4 helix-turn-helix domain. Downstream Pribnow box at -10 consensus TATAAT recognized by region 2. Spacer length crucial for simultaneous contact of both elements due to helical phasing. TTGACA sequence unambiguously defines -35 element, distinguishing it from -10, UP element recognized by α-CTD, or GC-rich eukaryotic SP1 site GGGCGG. Promoter strength correlates with closeness to TTGACA consensus for -35 interaction optimizing closed complex formation.
Ref: Alberts Chapter 6: -35 consensus TTGACA bacterial promoters; Watson Molecular Biology Gene Promoter table -35 element sequence
Bacterial promoters contain 6-base AT-rich element centered near -10 relative to transcription start site, originally described by Pribnow examining phage T7 and E. coli promoters. Sequence TATAAT facilitates duplex melting due to low stability and is specifically recognized by sigma70 region 2 for open complex formation. Eukaryotic TATA box termed Hogness box located -30 recognized by TBP, distinct in position and factor. -35 element consensus TTGACA, UP element AT-rich upstream, none termed Pribnow. Therefore -10 promoter element specifically designated Pribnow box in prokaryotic literature referencing initiator melting element.
Ref: Berg Biochemistry Section 28.2: -10 element Pribnow box nomenclature; Pribnow 1975 PNAS TATAAT sequence; Watson Chapter 13 Promoter elements naming
Sigma factor constitutes dissociable specificity subunit converting promoter-non-specific core polymerase into holoenzyme able to recognize -10 and -35 promoter elements and initiate transcription at defined sites. During initiation, sigma domains 2-4 contact DNA, facilitate melting, and stabilize open complex. After RNA chain reaches about ten nucleotides, sigma releases from core, reducing affinity for promoter and allowing transition to elongation. Core continues elongation independently. Housekeeping sigma70 used exponentially, alternative sigmas redirect polymerase to stress promoters. Therefore sigma primarily governs initiation step, not elongation, termination, or proofreading functions which are core or accessory factor mediated.
Ref: Lodish Chapter 8: Sigma factor required mainly for initiation promoter recognition; Alberts Chapter 6 Sigma cycle release
