8 public questions tagged with this topic.
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
Prokaryotes have a single RNA polymerase, unlike eukaryotes which have multiple types of RNA polymerases.
Ref: NCERT Class 12 Biology Chapter 5: Molecular Basis of Inheritance Transcription - Mechanism and RNA Polymerase
Rifampicin, an ansamycin antibiotic used against tuberculosis, binds within a deep pocket of the RNA polymerase beta subunit encoded by rpoB gene, lined by residues of rifampicin resistance determining region. Located about twelve angstroms from active site magnesium, it does not block NTP binding but physically obstructs path of growing RNA chain longer than two to three nucleotides, acting as steric block. Binding creates highly stable drug-enzyme complex with nanomolar affinity. Eukaryotic polymerases II, I, III lack this pocket and remain insensitive. Mutations in RRDR cause clinical resistance.
Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 9: Rifampicin targets beta subunit; Nature Struct Biol, Rifampicin inhibition mechanism
Sigma70 comprises domains sigma1.1 through sigma4 connected by linkers. Region 3.2, approximately amino acids 510-520 forming acidic loop between domains sigma2 and sigma4, threads through RNA polymerase active site cleft into RNA exit channel. It acts as a molecular mimic of nascent RNA, positioning initiating nucleotides and stabilizing abortive initiation complexes while preventing extension beyond five to six nucleotides. When RNA grows longer, it collides sterically with this loop, necessitating ejection. Removal of 3.2 linker clears exit path and permits promoter clearance and transition to stable elongation.
Ref: Berg et al., Biochemistry, 9th ed., Chapter 28: Sigma region 3.2 as RNA mimic; PNAS 2013 Structure of sigma70 holoenzyme
Sigma70, encoded by rpoD, is the primary housekeeping sigma factor of Escherichia coli and most Gram-negative bacteria active during exponential growth. It directs RNA polymerase to the majority of promoters driving essential genes for central metabolism, ribosome synthesis, and cell envelope production, recognizing consensus -35 TTGACA and -10 TATAAT sequences. Housekeeping activity ensures continuous expression of vegetative functions. Under stress or developmental change, alternative sigma factors such as sigma32 for heat shock, sigma38 for general stress, sigma28 for flagella, and sigma54 for nitrogen assimilation displace sigma70.
Ref: Lodish et al., Molecular Cell Biology, 9th ed., Chapter 9: Prokaryotic transcription and housekeeping sigma70 function
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
NusG represents conserved transcription factor homologous to eukaryotic Spt5, bridging transcription and translation machineries in bacteria. N-terminal NG domain binds clamp helices of RNA polymerase increasing elongation processivity, while C-terminal KOW domain interacts with ribosomal protein NusE/S10 linking lead ribosome to polymerase during coupled transcription-translation. This physical tether prevents Rho from accessing nascent RNA, suppresses premature termination, and maintains reading frame coupling. NusG also influences DNA repair through interaction with UvrD. Thus primary described function remains coupling transcription apparatus with ribosomal translation ensuring mRNA surveillance and efficient gene expression coordination.
Ref: Alberts Chapter 6: NusG couples transcription with translation coupling mechanism; Nature 2020 Structure NusG bridging RNAP-ribosome; Lodish Chapter 8 Coupling
NusA is essential elongation factor universally conserved associating with RNA polymerase via interaction with β-flap tip helix and α-CTD as well as nascent RNA exit channel. It increases dwell time at pause sites, enhances formation terminal hairpin structures, and stimulates Rho-independent and Rho-dependent termination by stabilizing paused elongation complex and promoting RNA folding kinetics favoring terminator over antiterminator conformations. NusA also modulates attenuation in trp and his operons and interacts with λ N antitermination complex. Rather than initiating transcription or melting promoter, primary functional impact lies in pausing and termination stimulation regulating transcriptional polarity.
Ref: Alberts Chapter 6: NusA stimulates termination and pausing function; Lodish Chapter 8: NusA antitermination regulation mechanism; Nature NusA-RNAP complex
